|
| Status |
Public on Feb 02, 2015 |
| Title |
Wild-type_E_3 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Wild type miR-17-92 locus
developmental stage: E9.5 (20-22 somites)
tissue: whole embryo (- heart and tail bud)
|
| Treatment protocol |
Embryonic tail buds (corresponding to samples 1-24) and hearts (samples (25-48) were microdissected and collected in 1ml of TRIZOL. The remaining embryo was also collected in 1ml TRIZOL (samples 49-72).
|
| Growth protocol |
MiR-17~92 mutant animals were subjected to timed-mating. At E9.5, females were euthanized and embryos were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were homogenized in TRIZOL and RNA extracted according to manufacturer's instructions.
Libraries were prepared using the TruSeq SBS Kit v3 kit according to Illumina protocol and sequenced as 50 bp long single reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 51
RA3
|
| Data processing |
Reads were filtered for pass filter flag.
Filtered reads were aligned to mm9 using STAR v. 2.3.0 with the following flag: --outFilterMatchNmin 5.
Bam files were generated using samtools 0.1.14.
Counts were calculated with featureCounts (subread-1.4.2) using GTF file Mus_musculus.NCBIM37.66.gtf (ENSEMBL).
Genome_build: mm9
Supplementary_files_format_and_content: Text (tab-delimited) table, rows are ENSEMBL gene ids, columns are 71 samples.
|
| |
|
| Submission date |
Dec 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrea Ventura |
| E-mail(s) |
venturaa@mskcc.org
|
| Phone |
6468883068
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Cancer Biology & Genetics Program
|
| Lab |
Ventura
|
| Street address |
408 East 69th, ZRC-1201
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE63813 |
RNA sequencing of allelic series of miR-17~92 mutant embryos. |
|
| Relations |
| BioSample |
SAMN03251926 |
| SRA |
SRX794303 |
