|
| Status |
Public on Jan 16, 2017 |
| Title |
sample bi43638, brain region #3, population:A |
| Sample type |
SRA |
| |
|
| Source name |
mouse brain cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/Bl6
tissue: brain
brain region: Brainstem
cell type: astrocyte
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA‑Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
brain region #3, population:A
|
| Data processing |
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.
|
| |
|
| Submission date |
Sep 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chad Creighton |
| E-mail(s) |
[email protected]
|
| Organization name |
Baylor College of Medicine
|
| Department |
Biostatistics, Ducan Cancer Center
|
| Street address |
One Baylor Plaza, Mail Stop: BCM305
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE72826 |
Gene expression profiling of cell subpopulations from different regions of the mouse brain |
|
| Relations |
| BioSample |
SAMN04043932 |
| SRA |
SRX1212512 |
