|
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.
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|
|
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
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|
|
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 |