|
| Status |
Public on Jun 03, 2015 |
| Title |
Peril_RNA-seq_JR718 |
| Sample type |
SRA |
| |
|
| Source name |
Peril_RNA-seq_KO_E14.5
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: lincRNA knockout (KO)
litternumber_id: linc-Sox2_L43-4
lncrna previous name: linc-Sox2
Sex: male
timepoint: E14.5
litter: linc-Sox2_L43
tissue: whole brain
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
E14.5 whole brains were harvested and homogenized in TRIzol. Adult brains were harvested immediately after euthanasia, snap frozen in liquid nitrogen, and stored at -80C. These brains were pulverized in liquid nitrogen and homogenized in TRIzol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Casava 1.8.2 was used to call bases
Reads were aligned to mm10 using tophat2 (--no-coverage-search --max-multihits 10 -p 8)
Bams were quantified using cuffquant and a modified verson of the GENCODE M2 transcriptome (--no-update-check -p 8)
Differential analysis was performed using cuffdiff2 (-p 8)
Genome_build: mm10
processed data files format and content: the DiffTable output from cummeRbund, or essentially a tab-delimited file with all of the expression values and differential expression test statistics as called by cuffdiff for each gene in the transcriptome for each wt-v-ko comparison.
|
| |
|
| Submission date |
Sep 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Abbie Groff |
| E-mail(s) |
agroff@fas.harvard.edu
|
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology;
|
| Lab |
John Rinn
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE61716 |
Transcriptional perturbations by long noncoding RNAs with distinct spatio-temporal expression in the mammalian brain |
|
| Relations |
| BioSample |
SAMN03077710 |
| SRA |
SRX709084 |
