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Sample GSM3213876 Query DataSets for GSM3213876
Status Public on Jun 25, 2021
Title C37 M10 Tg+ rep2 Cardiomyocyte
Sample type SRA
Source name Cardiomyocyte
Organism Mus musculus
Characteristics genotype: Bag3-P209L Tg+
replicate: rep2
Extracted molecule total RNA
Extraction protocol Cardiomyocytes and cardiac fibroblasts were isolated from hearts of 16-month Bag3-P209L Tg+ and age matched Bag3-WT mice. Total RNA was extracted from isolated cardiomyocytes and cardiac fibroblasts using an RNEASY kit (Qiagen).
mRNA was enriched using oligo(dT) beads and randomly fragmented by adding fragmentation buffer. cDNA was then synthesized using an (Illumina) RNA library construction kit. Completed libraries, containing unique Illumina adaptors, were then pooled and fed into HiSeq/MiSeq sequencers. Following initial sequencing, cardiomyocyte samples underwent an additional second round of sequencing to increase the total data output.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Sample 6
Data processing Kallisto (v0.44.0) count abundance over GENCODE ‘comprehensive gene annotation’ (Release M18) with 50x bootstrap
tximport (v1.6.0) read count input
DESeq2 (v1.18.1) read count normalzation and differential expression analysis
R (v3.4.4) for all other analyses
genome build: GRCm38.p6
processed data files format and content: TSV, raw and normalized counts
Submission date Jun 25, 2018
Last update date Jun 25, 2021
Contact name Monte S Willis
Phone (317) 278-2674
Organization name University of Indiana School of Medicine
Street address 635 Barnhill Street Drive
City Indianapolis
ZIP/Postal code IN 46202
Country USA
Platform ID GPL24247
Series (1)
GSE116200 Bag3-P209L RNA Seq Project
BioSample SAMN09478950
SRA SRX4290496

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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