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Sample GSM1200051 Query DataSets for GSM1200051
Status Public on Jun 05, 2014
Title RAT_6%_1
Sample type SRA
 
Source name brain
Organism Rattus norvegicus
Characteristics oxygen concentration: 6%
Treatment protocol total RNA is extracted by TRIzol Reagent
Growth protocol Total RNAs were isolated from the brain of female BMRs under various oxygen concentrations (3%, 6%, 10%, 14%, and 21%) for 6 hours. We also got RNAs from the brain of rats under 6%, 10%, 14%, and 21% oxygen conditions.
Extracted molecule total RNA
Extraction protocol For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sequenced reads were generated from Rattus norvegicus
Data processing Used Spalax galili genome and Rattus norvegicus genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.3.1 with default parameters except -I 50000 --solexa1.3-quals
Genome_build: Spalax_galili_v1 and rat Ensembl release 64
Supplementary_files_format_and_content: bedGraph file, and the format is: scaffold or contig ID, start, end, transcrptome depth
 
Submission date Aug 02, 2013
Last update date May 15, 2019
Contact name CNSA CNGB
Organization name BGI
Street address BGI
City shenzhen
ZIP/Postal code 518083
Country China
 
Platform ID GPL14844
Series (1)
GSE49485 Hypoxia transcriptome sequencing of blind mole rat (BMR, Spalax galili) and rat (Rattus norvegicus)
Relations
BioSample SAMN02302588
SRA SRX331510

Supplementary file Size Download File type/resource
GSM1200051_rat_6O2_1.bedGraph.gz 68.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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