References.csv

"CSHP-2008-Estecio-pdb.prot4974.txt","1","<!>DMSO (see note at Step 10)"," -PAh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","2","<R>LowC dNTP mix (10X)"," -PRh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","2","<R>MCA reaction buffer (10X)"," -PRh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","2","<R>MCAM wash solution 1"," -PRh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","2","<R>SSC (20X)"," -PRh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","2","<!>Phenol:chloroform (1.5:1 [v/v]; pH 9.0)"," -PAh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","2","<R>Prehybridization solution for MCAM"," -PRh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","2","<R>React2 buffer (10X)"," -PRh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","2","<R>TE buffer (pH 8.0)"," -PRh(Appendix)"
"CSHP-2008-Estecio-pdb.prot4974.txt","3","This method was adapted from an original protocol by Toyota et al. (1999)."," -PXh(Toyota et al 1999)"
"CSHP-2008-Estecio-pdb.prot4974.txt","4","Combine PCR products of replicate samples and purify them using the QIAquick PCR Purification kit according to the manufacturer’s recommendation"," -MBh(QIAquick PCR Purification kit Mfr. recomm)"
"CSHP-2008-Estecio-pdb.prot4974.txt","6","The use of methylation-sensitive enzymes with frequent cutting sites, for example, HpaII/MspI (Hatada et al. 2006), results in a high genome fraction for amplification."," -PCh(Hatada et al. 2006)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","1","These platforms can be used for a variety of studies, including ChIP-Seq (Barski et al. 2007; Johnson et al. 2007; Mikkelsen et al. 2007; Robertson et al. 2007)"," -PSh(ChIP-Seq (Barski et al. 2007; Johnson et al. 2007; Mikkelsen et al. 2007; Robertson et al. 2007))"
"CSHP-2009-Cuddapah-prd.prot5237.txt","1","nucleosome position profiling (Schones et al. 2008)"," -PSh(Schones et al 2008)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","1","transcriptome profiling (RNA-Seq) (Mortazavi et al. 2008; Nagalakshmi et al. 2008)"," -PSh(Mortazavi et al 2008 and Nagalakshmi et al 2008)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","1","DNA methylation studies (Cokus et al. 2008)"," -PSh(Cokus et al 2008)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","1","SNP genotyping"," -LS"
"CSHP-2009-Cuddapah-prd.prot5237.txt","1","Use of this protocol to analyze histone modification patterns is described in Barski et al. (2007) and Wang et al. (2008)."," -PSh(Barki et al 2007 and Wang et al 2008)."
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<R>LiCl buffer for ChIP"," -PRh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<R>MNase digestion buffer for ChIP"," -PRh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<R>MNase stop buffer for ChIP"," -PRh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<!>Phenol:chloroform (1:1)"," -PAh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<R>Phosphate-buffered saline (PBS) (1X)"," -PRh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<R>Protease inhibitor cocktail for ChIP (1000X)"," -PRh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<!>Proteinase K (20 mg/mL) (Roche Diagnostics)"," -PAh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<R>RIPA buffer for ChIP"," -PRh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<!>SDS (sodium dodecyl sulfate) (10%)"," -PAh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","2","<!>Triton X-100"," -PAh(Appendix)"
"CSHP-2009-Cuddapah-prd.prot5237.txt","7","The DNA can be used for cluster generation using Illumina flow cells and sequencing-by-synthesis on an Illumina Genome Analyzer, following manufacturer’s instructions."," -MBh(Illumina Genome Analyzer Mfr. Instr)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","1","chromosome conformation capture (3C) (Dekker et al. 2002)"," -PXh(Dekker et al 2002)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<!>5-Bromo-4-chloro-3-indoyl-β-D-galactopyranoside (X-gal; 25 mg/mL in DMF [dimethylformamide])"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>Bead eluting buffer"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>Cellular lysis solution"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>ChIP diluent"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<!>DNA gel stain (SYBR Safe, 10,000X concentrate in DMSO [dimethylsulfoxide]; Invitrogen)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<!>Formaldehyde solution (≥36.5%; Sigma-Aldrich 33220)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>Immune complex wash buffers (high-salt and low-salt) Prepare the high-salt and low-salt versions of this buffer separately"," -PRmh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<!>Isopropyl-β-D-thiogalactopyranoside (IPTG; 200 mg/mL)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>LB agar"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>LB-ampicillin agar plates"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>Alternatively, LB-kanamycin agar plates can be used (see Step 48)."," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>LB (Luria-Bertani) liquid medium"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<R>Ligation buffer (10X)"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<!>Phenol:chloroform:isoamyl alcohol, UltraPure (25:24:1 v/v/v; Invitrogen)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","2","<!>Proteinase K (10 mg/mL in TE buffer, pH 8.0; Invitrogen)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<!>RNase A, DNase-free (10 mg/mL; Sigma R6513)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<R><!>SDS (Sodium dodecyl sulfate; 20% w/v; Fisher BP166)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<R><!>SDS (Sodium dodecyl sulfate; 20% w/v; Fisher BP166)"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<R>Sodium acetate (3 M, pH 5.2; Fisher BP333)"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<R>TE buffer (pH 8.0)"," -PRh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<!>Triton X-100 (20% v/v; VWR)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<!>Trypsin (1X; Invitrogen 25300)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<!>Liquid nitrogen (optional; see Step 11)"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","3","<!>UV light"," -PAh(Appendix)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","7","Using standard cloning protocols, clone the 3C-ChIP products (from Step 44) into a vector that has enzyme overhangs similar to those generated in the 3C assay. This step typically involves cloning an “IgG/no antibody 3C-ChIP product” and “Plus antibody 3C-ChIP prod- uct,” in addition to regular cloning controls."," -LBm"
"CSHP-2009-Tiwari-pdb.prot5168.txt","7","Purify the plasmids using the PureLink HQ 96 Mini Plasmid DNA Purification Kit according to the manufacturer’s instructions."," -MBh(PureLink HQ 96 Mini Plasmid DNA Purification Kit Mfr. Instr)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","7",". Screen the purified plasmids (from Step 52) by digestion with the same restriction enzyme used for Step 16, using standard restriction digestion protocols."," -LB"
"CSHP-2009-Tiwari-pdb.prot5168.txt","7","hould be validated by performing independent 3C assays (Tolhuis et al. 2002)"," -PSh(Tolhuis et al 2002)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","7","The primers for this purpose are designed exactly as described by Splinter et al. (2004)"," -PXh(Splinter et al 2004)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","7","perform ChIP assays (Tiwari et al. 2008)"," -PSh(Tiwari et al 2008)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","8","Following immunopre- cipitation with the antibody of interest, the samples can be subjected to 4C analysis (Zhao et al. 2006)"," -PSh(Zhao et al 2006)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","8","reverse-cross-linked, purified, digested with a four-cutter enzyme of choice, and processed further for either 3C-chip (Simonis et al. 2006)"," -PSh(Simonis et al 2006)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","8","or the ACT assay (Ling et al. 2006)."," -PSh(2006)"
"CSHP-2009-Tiwari-pdb.prot5168.txt","8","following the amplification criteria used in the original 3C assay, subsequent to the reversal of cross-linking and purification (Dekker et al. 2002)."," -PSh(Dekker et al 2002)"
"CSHP-2010-Liu-pdb.prot5491.txt","1","<!>Denaturation solution (0.2 N NaOH)"," -PAh(Appendix)"
"CSHP-2010-Liu-pdb.prot5491.txt","1","<!>Isopropanol"," -PAh(Appendix)"
"CSHP-2010-Liu-pdb.prot5491.txt","2","<R>RQPS annealing buffer"," -PRh(Appendix)"
"CSHP-2010-Liu-pdb.prot5491.txt","2","<R>RQPS binding buffer"," -PRh(Appendix)"
"CSHP-2010-Liu-pdb.prot5491.txt","2","<R>TE buffer for RQPS"," -PRh(Appendix)"
"CSHP-2010-Liu-pdb.prot5491.txt","2","<R>Tissue lysis buffer"," -PRh(Appendix)"
"CSHP-2010-Liu-pdb.prot5491.txt","5","Purify the final PCR product with a PCR purification kit (e.g.,QIAquick PCR Purification Kit) according to the manufacturer’s instructions."," -EB"
"CSHP-2010-Liu-pdb.prot5491.txt","5","Clone the purified PCR product into a TA vector according to the manufacturer’s instructions."," -EB"
"CSHP-2010-Liu-pdb.prot5491.txt","6","use the following method described by Laird et al. (1991)."," -PXh(Laird et al 1991)"
"CSHP-2010-Liu-pdb.prot5491.txt","9","the power of such a screening method is further enhanced when it is combined with the simple pyro- screening enrichment protocol, another pyrosequencing-based innovation we have developed (Liu et al. 2009)."," -PSh(Liu et al 2009)"
"CSHP-2010-Putnam-pdb.prot5492.txt","1","<R><!>5-FOA Can agar plate media"," -PRh(Appendix)"
"CSHP-2010-Putnam-pdb.prot5492.txt","1","<R><!>5-FOA Can agar plate media"," -PAh(Appendix)"
"CSHP-2010-Putnam-pdb.prot5492.txt","1","<R>YPD media"," -PRh(Appendix)"
"CSHP-2010-Putnam-pdb.prot5492.txt","3","Determine the 95% confidence intervals for the median (see, e.g., http://www.math.unb.ca/ ~knight/utility/MedInt95.htm)."," -PBh(http://www.math.unb.ca/~knight/utility/MedInt95.htm)"
"CSHP-2010-Putnam-pdb.prot5492.txt","5","Several modified versions of the assay have since been developed, including those with a CAN1/URA3 cassette placed at a number of different chromosomal locations (RDKY6677, RDKY6678) (Putnam et al. 2009)"," -PCh(Putnam et al 2009)"
"CSHP-2010-Putnam-pdb.prot5492.txt","5","as well as other variant GCR assays using the loss of URA3 and HIS3 markers on chromosome III (Myung et al. 2001b) or loss of CAN1, URA3, and ADE2 on chromosome XV (Hackett et al. 2001)."," -PCh(Hackett et al 2001)"
"CSHP-2010-Song-pdb.prot5384.txt","1","This DNase-seq protocol was derived from methodologies originally described by Boyle et al. (2008)."," -PXh(Boyle et al 2008)"
"CSHP-2010-Song-pdb.prot5384.txt","1","<R>B&W buffer (2X)"," -PRh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","1","<!>Chloroform (J.T. Baker)"," -PAh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<R>DNA polymerase buffer"," -PRh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<R>EDTA (50 mM, pH 8.0)"," -PRh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<!>Ethidium bromide (10 mg/mL)"," -PAh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<!>IGEPAL CA-630 (Sigma)"," -PAh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<R>LIDS buffer"," -PRh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<!>NaOH (0.15 M)"," -PAh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<R>NEB buffer 2 for washes (1X)"," -PRh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<!>Phenol (Invitrogen)"," -PAh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<!>Phenol:chloroform:isoamyl alcohol (25:24:1; Invitrogen)"," -PAh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<R>RSB buffer (prechilled)"," -PRh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<!>S-Adenosylmethionine (SAM) (500 μM; New England Biolabs)"," -PAh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<R>TBE buffer (0.5X) Where 1X TBE is called for, double the concentrations in the 0.5X TBE."," -PRmh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<R>TE buffer (1X, pH 8.0)"," -PRh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<R>Tris-Cl (10 mM, pH 8.0)"," -PRh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","2","<!>Trypan blue (GIBCO/Invitrogen)"," -PAh(Appendix)"
"CSHP-2010-Song-pdb.prot5384.txt","11","Follow-up studies, such as chromatin immunoprecipitation and/or functional assays, are needed to determine the precise function and activity associated with each regulatory region."," -LS"
"CSHP-2010-Viggiani-pdb.prot5385.txt","1","<R>Blocking DNA (50X)"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","1","<R>BrdU (100X)"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>EDTA (10 mM)"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>Elution buffer for genomic DNA"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>Immunoprecipitation (IP) buffer for genomic DNA, prechilled on ice"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>Lysis buffer for genomic DNA"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>PBS for genomic DNA (10X)"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<!>Phenol:chloroform:isoamyl alcohol (25:24:1; PCI) Store at 4°C."," -PAh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<!>Sodium azide can be added as a preservative to the slurry at 0.01% (w/v). This protocol works well with magnetic protein G beads (Dynabeads Protein G; Invitrogen)"," -PAmh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<!>RNase A (DNase-free, 20 mg/mL; Sigma) Store at -20°C."," -PAh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","The analysis described in this procedure must be conducted on yeast cells that have been engineered to assimilate BrdU from the growth medium and incorporate it into DNA. This can be accomplished in yeast by overexpressing herpes simplex virus thymidine kinase to phosphorylate nucleosides (Lengronne et al. 2001)"," -PRh(Lengronne et al 2001)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","and is made more efficient with the combined expression of an equilibrative nucleoside transporter to facilitate efficient uptake of extracellular nucleosides (or their analogs) (Vernis et al. 2003; Viggiani and Aparicio 2006)."," -PAh(Vernis et al 2003; Viggiani and Aparicio 2006)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<!>Sodium azide"," -PAh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>SSC (3X), prechilled to 4oC"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>TE (pH 7.6)"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>Tris-buffered saline (TBS) for yeast, prechilled on ice"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<R>Yeast extract-peptone-dextrose growth medium (YEPD) or other medium"," -PRh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<!>Dry ice/ethanol bath (optional; see Step 7)"," -PAh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","2","<!>Alternatively, liquid nitrogen can be used to freeze the cells."," -PAh(Appendix)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","5","Purify the samples using a QIAquick PCR Purification Kit according to the manufacturer’s instructions."," -MBh(QIAquick PCR Purification kit mfr instr)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","6","Purify the eluate using a MinElute PCR Purification Kit according to the manufacturer’s protocol with the following modifications: i. Perform two washes with PE Buffer. ii. Elute with 11 μL of 0.2X EB prewarmed to ~50°C"," -MBmh(MinElute PCR Purification Kit Mfr. Instr.)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","6","Use the GenomePlex Complete WGA Kit to separately amplify 10 ng of IP and 10 ng of reference DNA according to the manufacturer’s protocol."," -MBh(GenomePlex Complete WGA Kit Mfr. Protocol)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","6","After the amplification reaction, purify the DNA samples using a QIAquick PCR Purification Kit according to the manufacturer’s instructions."," -MBh(QIAquick PCR Purification Kit Mfr. Instr)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","6","Use the NimbleGen Dual-Color DNA Labeling Kit (or similar) to label the IP DNA with Cy5 and
reference DNA with Cy3 according to the manufacturer’s instructions.
The Klenow extension reaction in this step further amplifies the DNA samples. This amplification is dependent on several factors, including the Cy-conjugated random 9-mer primer concentration and the amount of Klenow used. We have found that hybridizations can be performed using less labeled DNA"," -MBmh(NimbleGen Dual-Color DNA Labeling Kit Mfr. Instr)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","7","Purify the labeled DNA using a MinElute PCR Purification Kit according to the manufacturer’s protocol. Elute with 10 μL of 10 mM EDTA. The volume used to dissolve the labeled DNA can be adjusted depending on the anticipated amount of DNA produced in the labeling reaction."," -MBmh(MinElute PCR Purification Kit Mfr. Instr)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","7","Follow the array manufacturer’s guidelines."," -EB  [Note: this feels like this is an alternative course rather than ""branch here and come back"".  We don't have a code for that, but maybe it counts as B]"
"CSHP-2010-Viggiani-pdb.prot5385.txt","7","Adapted from the protocols supplied by NimbleGen,"," -MX"
"CSHP-2010-Viggiani-pdb.prot5385.txt","7","For other array configurations or platforms, hybridization supplies and protocols included by the microarray manufacturer should be used."," -EB"
"CSHP-2010-Viggiani-pdb.prot5385.txt","8","Wash and dry the slides using the protocol, solutions, slide racks, and wash chambers found in the NimbleGen Wash Buffer Kit and the NimbleGen Array Processing Accessories Kit."," -MBh(NimbleGen Wash Buffer Kit and NimbleGen Array Processing Accessories Kit Mfr. Protocol)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","8","For other array platforms, perform washes as directed by the microarray supplier."," -EB"
"CSHP-2010-Viggiani-pdb.prot5385.txt","8","Scan slides according to the description in the NimbleGen Array’s User’s Guide."," -MBh(NimbleGen Array's User's Guide)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","8","open the scanned image files and create a pair report, as described in the User’s Guide."," -MBh(NimbleGen Array's User's Guide)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","9","immobilizing immunoprecipitated DNA onto nylon membranes (e.g., using a slot-blotter) and probing the membranes with anti-BrdU antibody (Viggiani and Aparicio 2006)."," -PSh(Viggiani and Aparicio 2006)"
"CSHP-2010-Viggiani-pdb.prot5385.txt","9","If necessary, reamplify the samples according to the WGA kit protocol to achieve a higher DNA yield."," -MSh(WGA kit protocol)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","96","Instead of the cap-trapper method (Carninci et al. 1996, 1997)"," -PCh(Carnici et al 1996,1997)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","96","method based on the reverse transcription of the cap of the messenger RNA (mRNA) to enrich for 5 ends (Chenchik et al. 1998)"," -PXh(Chenchik et al 1998)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","96","as well as a semisuppressive polymerase chain reaction (PCR) approach (Plessy et al. 2010)"," -PXh(Plessy et al 2010)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","96","has been comprehensively revised (Table 1) and simpli- fied from the original (Plessy et al. 2010)"," -PXh(Plessy et al 2010)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","96","For samples where ~50 μg of RNA is available, the original CAGE method (Kodzius et al. 2006) might be preferable"," -PCh(Kodzius et al 2006)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","97","CAGE libraries can be used for different types of analyses (Carninci 2010), e.g., promoter discov- ery (particularly when the available transcript annotation for a tissue or a species is rudimentary), dif- ferential expression analysis (Valen et al. 2009)"," -PSh(Valen et al 2009)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","97","inference of transcription-factor binding sites (Vitezic et al. 2010), or gene networks (Suzuki et al. 2009)."," -PSh(Suzuki et al 2009)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","97","Libraries prepared with the nanoCAGE protocol can be paired-end sequenced as CAGEscan libraries (Plessy et al. 2010)"," -PSh(Plessy et al 2010)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","97","<!>Acetic acid"," -PAh(Appendix)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","97","<!>DTT (Dithiothreitol; 0.1 M)"," -PAh(Appendix)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","97","<R>EDTA (0.5 M, pH 8.0)"," -PRh(Appendix)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","97","<R><!>Ethidium bromide (10 mg/mL)"," -PRh(Appendix)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","97","<R><!>Ethidium bromide (10 mg/mL)"," -PRh(Appendix)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","98","<R>Sorbitol/trehalose stock solution"," -PRh(Appendix)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","99","<!>UV (ultraviolet) light source"," -PAh(Appendix)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","102","Use an Agencourt RNAClean XP kit according to the manufacturer’s instructions;"," -MBh(Agencourt RNAClean XP kit Mfr. Instr)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","103","Perform quantitative real-time PCR using a StepOnePlus system according to the manufacturer’s instructions, with the following conditions:"," -MBmh(StepOnePlus system mfr. instr)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","104","Use an Agencourt AMPure XP kit according to the manufacturer’s instructions;"," -MBh(Agencourt AMPure XP kit Mfr. Instr)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","105","Determine the concentration of the purified cDNAs in triplicate using a NanoDrop spectropho- tometer according to the manufacturer’s instructions."," -MBh(NanoDrop Spectrophotometer Mfr. Instr)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","105","Use an Agencourt AMPure XP kit according to the manufacturer’s instructions;"," -MBh(Agencourt AMPure XP kit Mfr. Instr)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","106","Determine the concentration of the purified libraries in triplicate using a NanoDrop spectropho- tometer according to the manufacturer’s instructions"," -MBh(NanoDrop spectrophotometer Mfr. Instr)"
"CSHP-2011-Salimullah-pdb.prot5559.txt","106","Analyze 1 μL each of the diluted samples using a High Sensitivity DNA Reagent Kit according to the manufacturer’s instructions."," -MBh(High Sensitivity DNA Reagent Kit Mfr. Instr)"
"CSHP-2015-Cotney-pdb.prot084848.txt","1","It is essential that you consult the appropriate Material Safety Data Sheets and your institution’s Environmental Health and Safety Office for proper handling of equipment and hazardous materials used in this protocol."," -EA"
"CSHP-2015-Cotney-pdb.prot084848.txt","2","Bead binding buffer <R>"," -PRh(Appendix)"
"CSHP-2015-Cotney-pdb.prot084848.txt","2","Cell lysis buffer for ChIP-Seq <R>"," -PRh(Appendix)"
"CSHP-2015-Cotney-pdb.prot084848.txt","2","ChIP-Seq dilution buffer <R>"," -PRh(Appendix)"
"CSHP-2015-Cotney-pdb.prot084848.txt","2","ChIP-Seq elution buffer <R>"," -PRh(Appendix)"
"CSHP-2015-Cotney-pdb.prot084848.txt","2","ChIP-Seq nuclear lysis buffer (see Step 24) <R>"," -PRh(Appendix)"
"CSHP-2015-Cotney-pdb.prot084848.txt","2","ChIP-Seq wash buffer <R>"," -PRh(Appendix)"
"CSHP-2015-Cotney-pdb.prot084848.txt","2","TAE <R>"," -PRh(Appendix)"
"CSHP-2015-Cotney-pdb.prot084848.txt","2","TE buffer for ChIP-Seq <R>"," -PRh(Appendix)"
"CSHP-2015-Cotney-pdb.prot084848.txt","5","Prepare a 1× Pico- Green stock and follow the manufacturer’s instructions for setting up a standard curve on the NanoDrop instrument."," -MBh(NanoDrop 3300 Fluorospectrometer Mfr. Instr)"
"CSHP-2015-Cotney-pdb.prot084848.txt","6","FollowtheQIAquickPCRPurificationKitinstructions"," -MBh(QIAquick PCR Purification Kit Mfr. Instr)"
"CSHP-2015-Cotney-pdb.prot084848.txt","6","A good reference for performing qPCR is Bustin et al. (2009)."," -PAh(Bustin et al. 2009)"
"CSHP-2015-Cotney-pdb.prot084848.txt","7","Follow the manufacturer’s instructions for preparing libraries with a kit."," -EB"
"CSHP-2015-Cullen-pdb.prot085076.txt","1","It is essential that you consult the appropriate Material Safety Data Sheets and your institution’s Environmental Health and Safety Office for proper handling of equipment and hazardous materials used in this protocol."," -EA"
"CSHP-2015-Cullen-pdb.prot085076.txt","1","YEPD agar plates with varying agar concentrations (e.g., 0.3%, 2%, and 4%) <R> Do not invert 0.3% agar plates."," -PRmh(Appendix)"
"CSHP-2015-Cullen-pdb.prot085076.txt","2","It also allows assessment of invasive growth by the plate- washing assay (see The Plate-Washing Assay: A Simple Test for Filamentous Growth in Budding Yeast [Cullen 2015])"," -PSh(Cullen 2015)"
"CSHP-2015-Cullen-pdb.prot085076.txt","2","Measure the mat areas by photographing the plates and analyzing the photos with ImageJ software (http://imagej.nih.gov; Schneider et al. 2012)."," -PBh(Schneider et al 2012)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","This protocol was adapted from “Techniques for Visualizing Gene Products, Cells, Tissues, and Organ Systems,” Chapter 16,"," -PXh(Nagy et al 2003)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","This protocol was adapted from Dent et al. (1989) and LeMotte et al. (1989)"," -PXh(Dent et al 1989, LeMotte et al 1989)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","The following related protocols are also available in CSH Protocols:"," -PIh(many other related protocols)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","<R><!>BABB"," -PRh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","<R><!>BABB"," -PAh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","<R><!>DAB-NiCl2"," -PRh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","<R><!>DAB-NiCl2"," -PAh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","<!>DMSO"," -PAh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","1","<!>30% hydrogen peroxide (H2O2)"," -PAh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","2","<!>Methanol"," -PAh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","2","<!>4% paraformaldehyde, prepared in PBS"," -PAh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","2","see CSH Protocols article Fixation of Mouse Embryos and Tissues)"," -PIh(Fixation of Mouse Embroys and Tissues)"
"CSHP-2008-Joyner-pdb.prot4820.txt","2","<R>PBS (phosphate buffered saline)"," -PRh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","2","<R>PBTX, prepared fresh before use"," -PRh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","2","<R>PBSMT The brand of skim milk used in the PBSMT is important. Carnation gives consistently good results, whereas other brands (e.g., Kroger) do not."," -PRmh(Appendix)"
"CSHP-2008-Joyner-pdb.prot4820.txt","2","See CSH Protocols article Handling Mouse Blastocysts for Fixation."," -PIh(Handling Mouse Blastocysts for Fixation)"
"CSHP-2008-Joyner-pdb.prot4820.txt","4","Embed, section, and mount the embryos (for details, see CSH Protocols articles Embedding Mouse Embryos and Tissues in Wax and Sectioning Mouse Embryos)."," -PBh(Embedding Mouse Embryos and Tissues in Wax)"
"CSHP-2008-Joyner-pdb.prot4820.txt","4","Embed, section, and mount the embryos (for details, see CSH Protocols articles Embedding Mouse Embryos and Tissues in Wax and Sectioning Mouse Embryos)."," -PBh(Sectioning Mouse Embryos)"
"CSHP-2008-Misquitta-pdb.prot4918.txt","1","This protocol was adapted from “Targeted Disruption of Gene Function in Drosophila by RNA Interference,” Chapter 19"," -PXh(“Targeted Disruption of Gene Function in Drosophila by RNA Interference,” Chapter 19)"
"CSHP-2008-Misquitta-pdb.prot4918.txt","1","The double-stranded RNA needed for RNAi is prepared as in Preparation of Double-Stranded RNA for Drosophila RNA Interference (RNAi)."," -PRh(Preparation of Double-Stranded RNA for Drosophila RNA Interference (RNAi).)"
"CSHP-2008-Misquitta-pdb.prot4918.txt","1","see Collection of Drosophila Embryos for RNA Interference (RNAi)"," -PRh(Preparation of Double-Stranded RNA for Drosophila RNA Interference (RNAi).)"
"CSHP-2008-Misquitta-pdb.prot4918.txt","1","Drosophila RNA Interference (RNAi) Using a Gal-4 Inducible Transgene Vector (Misquitta et al. 2008)"," -PSh(Misquitta et al 2008)"
"CSHP-2008-Misquitta-pdb.prot4918.txt","1","basic methods for injection of embryos and the analysis of gene expres- sion in Drosophila embryos. If not, details for these procedures can be found elsewhere; see Ashburner (1989a,b);"," -PIh(Ashburner 1989a,b)"
"CSHP-2008-Misquitta-pdb.prot4918.txt","1","for microinjection procedures, see Kiehart et al. (2000)."," -PIh(Kiehart et al 2000)"
"CSHP-2008-Misquitta-pdb.prot4918.txt","2","Follow the manufacturer’s instructions for pulling the needles."," -MBh(Fredreck Haer and Co. Glass Capillaries Mfr. Instr)"
"CSHP-2008-Misquitta-pdb.prot4918.txt","2","If using a different model injector, calibrate the injector according to the manufacturer’s instructions."," -EB"
"CSHP-2008-Misquitta-pdb.prot4918.txt","3","Fix the embryos and stain them using standard protocols; see Ashburner (1989a,b)."," -PBh(Ashburner 1989a,b)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","This protocol was adapted from “Detection and Analysis of Mouse Genome Alterations and Specific Sequences,” Chapter 12,"," -PXh(“Detection and Analysis of Mouse Genome Alterations and Specific Sequences,” Chapter 12)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","Several methods for disaggregation of cells are described by Cronmiller and Mintz (1978)"," -PRh(cronmiller and mintz 1978)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","Additional variations on the methods for karyotyping and banding embryonal carcinomal cells are found in McBurney and Rogers (1982) and Robertson et al. (1983)."," -PCh(McBurney and Rogers (1982) and Robertson et al. (1983). )"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","For guidance in trypsinization, see Trypsinization of Cells Grown in Monolayer (Darlington 2006)."," -PIh(Darlington 2006)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","<R>Carnoy’s fixative (freshly prepared and kept at room temperature)"," -PRh(Appendix)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","<!>Ethanol, absolute:HCl, concentrated solution (1:1)"," -PAh(Appendix)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","<!>Ethanol, absolute:diethyl ether solution (1:1)"," -PAh(Appendix)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","<!>Giemsa stain (dilute 1:20 with H2O) (Sigma)"," -PAh(Appendix)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","<R>SSC (20X)"," -PRh(Appendix)"
"CSHP-2008-Nagy-pdb.prot4706.txt","1","<!>Trypsin (0.025% [w/v]) in 0.85% (w/v) NaCl"," -PAh(Appendix)"
"CSHP-2008-Nagy-pdb.prot4706.txt","2","For guidance in trypsinization, see Trypsinization of Cells Grown in Monolayer (Darlington 2006)."," -PIh(Darlington 2006)"
"CSHP-2008-Zhang-pdb.prot5014.txt","1","<R>Basic solution"," -PRh(Appendix)"
"CSHP-2008-Zhang-pdb.prot5014.txt","1","<R>Bath solution for K+ current recordings"," -PRh(Appendix)"
"CSHP-2008-Zhang-pdb.prot5014.txt","1","<R>Enzyme solution 1"," -PRh(Appendix)"
"CSHP-2008-Zhang-pdb.prot5014.txt","1","<R>Enzyme solution 2"," -PRh(Appendix)"
"CSHP-2008-Zhang-pdb.prot5014.txt","1","<R>MS medium (0.5X)"," -PRh(Appendix)"
"CSHP-2008-Zhang-pdb.prot5014.txt","1","<R>Pipette solution for K+ current recordings"," -PRh(Appendix)"
"CSHP-2008-Zhang-pdb.prot5014.txt","6","This method of patch clamping Arabidopsis guard cell protoplasts was adapted from one used for iso- lation and patch clamping of Vicia faba guard cell protoplasts (Schroeder et al. 1984; Assmann et al. 1985; Kruse et al. 1989);"," -PXh(Schroeder et al 1984, Assmann et al 1985; Kruse et al 1989)"
"CSHP-2008-Zhang-pdb.prot5014.txt","6","Pei et al. (1997) describe an alternative method to isolate Arabidopsis guard cell protoplasts suitable for patch clamping."," -PCh(Pei et al 1997)"
"CSHP-2008-Zhang-pdb.prot5014.txt","6","Another two-step pro- tocol for large-scale isolation of Arabidopsis guard cell protoplasts has also been described (Leonhardt et al. 2004)."," -PCh(Leonhardt et al 2004)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","1","Protocols for Low-Magnification Live Imaging of Xenopus Embryos for Cell and Developmental Biology (Wallingford 2010a) and Preparation of Fixed Xenopus Embryos for Confocal Imaging (Wallingford 2010b)"," -PCh(Wallingford 2010a)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","1","Protocols for Low-Magnification Live Imaging of Xenopus Embryos for Cell and Developmental Biology (Wallingford 2010a) and Preparation of Fixed Xenopus Embryos for Confocal Imaging (Wallingford 2010b)"," -PCh(wallingford 2010b)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","1","as are details on performing knockdown or misexpression studies in Xenopus embryos (Guille 1999; Sive et al. 2000)"," -PCh(Guille 1999; Sive et al 2000)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","1","Imaging can also be performed simultaneously with measurement of the forces generated by moving tissues during development (Zhou et al. 2009)."," -PAh(Zhou et al 2009)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","2","<R>Marc’s modified Ringer’s (MMR) (1X)"," -PRh(Appendix)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","2","<!>Tricaine (0.15%) (optional; see Step 5)"," -PAh(Appendix)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","3","Mounting for this application is described in Low-Magnification Live Imaging of Xenopus Embryos for Cell and Developmental Biology (Wallingford 2010a)."," -PIh(Wallingford 2010a)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","3","Golgi structures can be localized with GalT-RFP (Nichols et al. 2001)"," -PCh(Nichols et al 2001)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","3","and apical exocytic vesicles are highlighted using memGFP (Hayes et al. 2007)."," -PCh(Hayes et al 2007)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","4","Alternatively, mosaic expression can also be achieved by injection of plasmid DNA (Vize et al. 1991)."," -PBh(Vize et al 1991)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","5","For imaging cleared embryos, see Preparation of Fixed Xenopus Embryos for Confocal Imaging (Wallingford 2010b)."," -PCh(Wallingford 2010b)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","7","Tissue-level mosaics can be made by sequential injections at the four- and eight-cell stages (Kieserman et al. 2008)."," -PBh(Kieserman et al 2008)"
"CSHP-2010-Kieserman-pdb.prot5427.txt","7","Cell-level mosaics can be generated by sequential injections at the four- cell and the 16- or 32-cell stages (Gray et al. 2009)."," -PBh(Gray et al 2009)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","1","This protocol was adapted from methods originally developed in the work of Messer (1977), Gallo et al. (1982), Thangnipon et al. (1983), D’Mello et al. (1993) and Dudek et al. (1997)."," -PXh(Messer (1977), Gallo et al. (1982), Thangnipon et al. (1983), D’Mello et al. (1993) and Dudek et al. (1997).)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","1","<R><!>AraC (Cytosine-1-β-D-arabinofuranoside) solution"," -PAh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","1","<R><!>AraC (Cytosine-1-β-D-arabinofuranoside) solution"," -PRh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","1","<R>Culture medium for granule neurons"," -PRh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","1","<R>DNase (2 mg/mL) (0.5-mL aliquot for trituration; see Step 10)"," -PRh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","1","<R>HHGN dissection solution"," -PRh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","1","<R>Poly-L-ornithine-coated plates (of desired size, depending on experiments to be performed; see Step 15)"," -PRh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","2","<!>Trypan blue"," -PAh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","2","<R><!>Trypsin-DNase solution"," -PRh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","2","<R><!>Trypsin-DNase solution"," -PAh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","2","<!>CO2 chamber"," -PAh(Appendix)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","6","Although recent improvements in culture techniques may increase the survival and differentiation of Purkinje neurons in mixed cerebellar cultures (Furuya et al. 1998; Ito-Ishida et al. 2008),"," -PCh(Furuya et al 1998; Ito-Ishida et al 2008)"
"CSHP-2008-Bilimoria-pdb.prot5107.txt","6","Purifying Purkinje neurons can require Percoll sedimenta- tion and immunopanning technologies (Baptista et al. 1994),"," -PCh(Baptista et al 1994)"
"CSHP-2009-Eilers-pdb.prot5201.txt","1","This protocol assumes familiarity with the standard procedures of whole-cell patch-clamp recordings (see, e.g., Marty and Neher 1995)"," -PIh(Marty and Neher 1995)"
"CSHP-2009-Eilers-pdb.prot5201.txt","1","A protocol for Preparation of Rodent Hippocampal Slice Cultures (Fuller and Dailey 2007) is available."," -PRh(Fuller and Dailey 2007)"
"CSHP-2009-Eilers-pdb.prot5201.txt","1","<R>Pipette solution for current-clamp recordings"," -PRh(Appendix)"
"CSHP-2009-Eilers-pdb.prot5201.txt","1","<R>Pipette solution for voltage-clamp recordings can be used as an alternative (see Step 1)."," -PRh(Appendix)"
"CSHP-2009-Eilers-pdb.prot5201.txt","1","<R>Standard external saline"," -PRh(Appendix)"
"CSHP-2009-Eilers-pdb.prot5201.txt","3","Perform seal formation and establish the whole-cell configuration as per standard electrophysio- logical recordings"," -LB"
"CSHP-2010-Allen-pdb.prot5453.txt","1","<!>CO2 or ice (see Step 1)"," -PAh(Appendix)"
"CSHP-2010-Allen-pdb.prot5453.txt","1","<R>GFS saline or 3 M KCl (see Step 8)"," -PRh(Appendix)"
"CSHP-2010-Daul-pdb.prot5460.txt","1","When examining mutants that affect the development of Drosophila larval brains, it may be useful to employ other labeling methods, such as those described in EdU (5-Ethynyl-2-Deoxyuridine) Labeling of Drosophila Mitotic Neuroblasts (Daul et al. 2010a) and Multicolor Fluorescence RNA In Situ Hybridization of Drosophila Brain Tissue (Daul et al. 2010b)"," -PCh(Daul et al 2010a, 2010b)"
"CSHP-2010-Daul-pdb.prot5460.txt","1","<R>Block solution (D)"," -PRh(Appendix)"
"CSHP-2010-Daul-pdb.prot5460.txt","1","<R>Fix solution"," -PRh(Appendix)"
"CSHP-2010-Daul-pdb.prot5460.txt","1","<R>PBSBTX"," -PRh(Appendix)"
"CSHP-2010-Daul-pdb.prot5460.txt","1","<R>PBSTX"," -PRh(Appendix)"
"CSHP-2010-Granstedt-pdb.prot5410.txt","2","<!>Isoflurane"," -PAh(Appendix)"
"CSHP-2010-Granstedt-pdb.prot5410.txt","2","<R>Mammalian Ringer’s solution (prewarmed)"," -PRh(Appendix)"
"CSHP-2010-Granstedt-pdb.prot5410.txt","2","<!>Mice   If another species is used, surgical conditions and drug dosages should be optimized for that species."," -PAmh(Appendix)"
"CSHP-2010-Granstedt-pdb.prot5410.txt","2","<!>PRV369 inoculum (1010 plaque-forming units [pfu]/mL)"," -PAh(Appendix)"
"CSHP-2010-Granstedt-pdb.prot5410.txt","2","The procedure must be performed under Biosafety Level 2 conditions."," -PAh(Biosafety Level 2 conditions)"