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Sample GSM1321568 Query DataSets for GSM1321568
Status Public on Feb 05, 2014
Title BF-T0-A
Sample type SRA
 
Source name Whole liver_biliary_fistula_bile_infusion_0h
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley
Sex: Male
Extracted molecule total RNA
Extraction protocol Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Biliary fistula, bile acid infusion, partial hepatectomy 24 h after surgery, collect liver 0 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4
Data processing Sample libraries are diluted and applied to an Illumina paired end flow cell at a concentration appropriate to generate about 180 million reads per lane. All libraries are prepared with indexing barcodes to permit multiplex runs. 100 cycle single read sequencing will be used to generate base call files. Illumina’s CASAVA package will be used to assemble the reads into standard fastq formatted data.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Each RPKM data column (ex: "Cont-T0-A") was made from (1) raw data from one rat sample, and (2) raw data from combined RNA from 3 rats. Thus, two RNA sequencing runs per condition per timepoint were done; this data included 4 biological samples (1 in the first sample, and 3 in the second sample). Two RPKM file were made for each condition 4 biological samples (1 in the first sample, and 3 in the second sample). Two RPKM file were made for each condition and timepoint, then these were combined to make one RPKM file.
Genome_build: rn4
Supplementary_files_format_and_content: Text file include RPKM values
 
Submission date Feb 04, 2014
Last update date May 15, 2019
Contact name Willscott Edward Naugler
E-mail(s) nauglers@ohsu.edu
Phone 503-713-3069
Organization name Oregon Health & Science University
Department Med/GI&Hepatology
Street address 3181 SW Sam Jackson Park Blvd
City Portland
State/province OR
ZIP/Postal code 97239
Country USA
 
Platform ID GPL14844
Series (1)
GSE54673 Bile acid flux is necessary for normal liver regeneration
Relations
BioSample SAMN02617810
SRA SRX463219

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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