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| Status |
Public on Mar 08, 2017 |
| Title |
tbi2 (RNA-seq) |
| Sample type |
SRA |
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| Source name |
rat hippocampus
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: hippocampus
treatment: TBI by fluid percussion injury (FPI)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of RNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent Technologies, CA, USA) and Qubit RNA assay (Life Technologies, NY, USA).
The RNA-Seq libraries were prepared followed the standard Illumina protocol (http://support.illumina.com/sequencing/documentation.ilmn). Briefly, about 1,000 ng total RNA was first enriched for mRNA by poly-A selection, then fragmented, and reverse transcribed using random hexamer-primers to generate first-strand cDNA. Second-strand cDNA was then generated using RNase H and DNA polymerase. Fragments of 200-400 bp in size were next enriched through PCR and multiplex barcodes were also added. Sequencing was performed on HiSeq 2500 (Illumina Inc, CA, USA). Data quality check was done on Sequencing Analysis Viewer and demultiplexing was performed with CASAVA 1.8.2 (Illumina Inc, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
replicate 1
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| Data processing |
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the rat genome (UCSC assembly 5.0) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample
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| Submission date |
Jan 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xia Yang |
| E-mail(s) |
[email protected]
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| Organization name |
UCLA
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| Department |
IBP
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| Street address |
2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE64978 |
Gene expression profile for male SD Rats with and without traumatic brain injury (TBI) by RNA-Seq |
| GSE64986 |
Gene expression and DNA methylation profiles for male SD Rats with and without traumatic brain injury |
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| Relations |
| BioSample |
SAMN03284602 |
| SRA |
SRX843447 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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