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Sample GSM1558012 Query DataSets for GSM1558012
Status Public on Feb 02, 2015
Title Delta_17_E_2
Sample type SRA
 
Source name embryo
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: miR-17 and miR-20a deleted
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 56
RC2
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 SAMN03251946
SRA SRX794308

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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