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| Status |
Public on Jun 05, 2014 |
| Title |
RAT_10% |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Rattus norvegicus |
| Characteristics |
oxygen concentration: 10%
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| Treatment protocol |
total RNA is extracted by TRIzol Reagent
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sequenced reads were generated from Rattus norvegicus
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| 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
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| Submission date |
Aug 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
CNSA CNGB |
| Organization name |
BGI
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| Street address |
BGI
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| City |
shenzhen |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE49485 |
Hypoxia transcriptome sequencing of blind mole rat (BMR, Spalax galili) and rat (Rattus norvegicus) |
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| Relations |
| BioSample |
SAMN02302585 |
| SRA |
SRX331509 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1200050_rat_10O2.bedGraph.gz |
127.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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