|
| Status |
Public on Nov 15, 2019 |
| Title |
5d4 |
| Sample type |
SRA |
| |
|
| Source name |
Oligodendrocyte Precursor Cells
|
| Organism |
Mus musculus |
| Characteristics |
condition: white matter stroke
age: Day 5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse brain LCM samples had cDNA ampified by Nugen RNAseq Ovation kit
RNA libraries were prepared for sequencing using Illumina TruSeq with Nugen Library to be prepared for multiplex Hiseq runs from the provided samples. 100 bp two-paired end, 3 samples to be run per lane. Barcode information is listed in each sample fastq read id and one unique tag is used per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 10
|
| Data processing |
Basecalls and demultiplexing was performed using CASAVA version 1.8.3 for samples labeled 7-10 and OLB version 1.9.4 for samples labeled 1-6
RNA-seq reads were aligned to the mm9 genome assembly using STAR version 2.1.4a with the default parameters: STAR --genomeDir mm9.fasta --readFilesIn $end1 $end2 --runThreadN 8
Uniquely aligned reads were quantified against the Refseq annotation mm9.gtf using HTSeq with the following parameters: htseq-count -m intersection-nonempty -s 'no' - mm9.gtf
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file including RPKM abundance measurements for each Sample
|
| |
|
| Submission date |
Dec 31, 2013 |
| Last update date |
Nov 15, 2019 |
| Contact name |
Giovanni Coppola |
| E-mail(s) |
gcoppola@ucla.edu
|
| Phone |
310-794-4172
|
| Organization name |
UCLA
|
| Department |
Psychiatry and Neurology
|
| Lab |
Neurogenetics
|
| Street address |
1524 Gonda, 695 Charles Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE53737 |
Oligodendrocyte Progenitor Cell Transcriptome in White Matter Stroke |
|
| Relations |
| BioSample |
SAMN02566399 |
| SRA |
SRX403600 |
