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Sample GSM5416616 Query DataSets for GSM5416616
Status Public on Dec 20, 2021
Title Heart.RNA.Prdm16cKO1
Sample type SRA
 
Source name Mouse heart
Organism Mus musculus
Characteristics genetic manipulation: Prdm16 conditional knockout
strain: C57BL/6
tissue: whole heart
Extracted molecule total RNA
Extraction protocol E13.5 embryonic hearts or isolated ventricles were homogenized in TRIzol (Invitrogen) and total RNA was isolated according to the manufacturer’s instructions. The concentration and quality of purified RNA was assessed by TapeStation (Agilent). RNA integrity numbers (RIN) were in the range of 6.1 to 10. Libraries were sequenced with an Illumina HiSeq 4000 sequencer to a sequeencing depth of 20-70 million reads per sample.
cDNA libraries were prepared using an Illumina TruSeq stranded mRNA kit according to manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Sequencing reads were mapped to GENCODE mouse transcripts reference (release M22, GRCm38.p6)
Transcription levels were quantified using salmon (version: 1.2.1, parameters: -l A --validateMappings --seqBias --gcBias).
Gene expression levels were generated using tximport (version: 1.10.1) and differential expression analysis was carried out using DEseq2 (version: 1.22.2) in R.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and reads count for each sample
 
Submission date Jul 03, 2021
Last update date Dec 20, 2021
Contact name Ju Chen
E-mail(s) juchen@health.ucsd.edu
Organization name University of California San Diego
Street address 9500 Gilman Drive 0613
City La Jolla
State/province California
ZIP/Postal code 92122
Country USA
 
Platform ID GPL21103
Series (2)
GSE179386 PRDM16 Functions as A Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle (bulk RNA-seq)
GSE179393 PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle
Relations
BioSample SAMN20054470
SRA SRX11346557

Supplementary file Size Download File type/resource
GSM5416616_Heart.RNA.Prdm16cKO1.vM22.sf.gz 2.0 Mb (ftp)(http) SF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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