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Sample GSM1328573 Query DataSets for GSM1328573
Status Public on Feb 14, 2014
Title SEQC_Kdn_F_021_1
Sample type SRA
 
Source name Kidney
Organism Rattus norvegicus
Characteristics strain: Fisher 344
tissue: Kidney
Sex: F
developmental stage (week): 21
Growth protocol Male and female (unsynchronized) Fisher 344 rats obtained from NCTR's animal breeding colony were fed the NIH-31 diet (ad libitum) and housed under AAALAC- approved conditions with a 12-hr light/dark cycle (0600 - 1800). Rats were housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of ~50%. Animals were sacrificed at 2, 5, 6, 8, 15, 21, 52, 78 and 104 weeks-of-age. Rats were treated according to the NCTR Institutional Animal Care and Use Committee guidelines.
Extracted molecule total RNA
Extraction protocol Each whole organ was individually ground (mortar and pestle, under continuous liquid N2 chilling) into a fine powder prior to RNA extraction, with the exception of liver, spleen, and gastrocnemius muscle for which approximately 100 mg was ground. Ground organ tissue was stored at -80ºC. Total RNA was extracted from approximately 30 mg of ground tissue by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including treatment with DNase.
RNA libraries were prepared for sequencing using an rRNA depletion protocol using the Ribo-Zero Nonmagnetic Kit (Epicentre) coupled with the Illumina TruSeq RNA-Seq library protocol using TruSeq RNA Sample Preparation Kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn4 whole genome using TopHat v2.0.4 with default parameters
Alignment results were then processed using Cufflinks v2.0.2 for gene and transcript quantification with default parameters. For samples with 2~3 technical replicates, average FPKM (Fragment Per Kilobase per Million mapped reads) values were used.
Genome_build: rn4
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
 
Submission date Feb 14, 2014
Last update date May 15, 2019
Contact name Leming Shi
E-mail(s) lemingshi@fudan.edu.cn
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL14844
Series (2)
GSE47792 SEQC Project
GSE53960 A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages
Relations
BioSample SAMN02642762
SRA SRX471472

Supplementary file Size Download File type/resource
GSM1328573_SEQC_Kdn_F_021_1.txt.gz 268.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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