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Sample GSM1321563

Query DataSets for GSM1321563

Status

Public on Feb 05, 2014

Title

Cont-T24-A

Sample type

SRA

Source name

Whole liver_sham_biliary_fistula_24h

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

Sham biliary fistula, partial hepatectomy 24 h after sham, collect liver 24 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