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Sample GSM8136444 Query DataSets for GSM8136444
Status Public on Dec 03, 2024
Title Tcf21-MCM baseline; scRNA-seq
Sample type SRA
 
Source name Heart
Organism Mus musculus
Characteristics tissue: Heart
cell type: Interstitial cells
genotype: Tcf21-MerCreMer
treatment: Tamoxifen
Extracted molecule total RNA
Extraction protocol Single cells were obtained by flow cytometry of live nucleated cells from cardiac tissue digests.
Single-cell droplet libraries were generated according to manufacturers’ instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual index), PN-1000268, 10X Genomics; user guide CG000315). Samples had a greater than 70% viability. About 16,000 cells were loaded to recover 10,000 cells. Briefly, gel emulsion beads (GEM) were generated by combining gel beads, master mix containing the cells and partitioning oil and loaded onto a Chromium Next GEM Chip G at a low dilution. Poly-adenylated mRNA from the cell lysate contained in every GEM was reverse transcribed to cDNA adding an Illumina R1 primer sequence, unique molecular identifier (UMI) and the 10X barcode. The barcoded first-strand cDNA was then purified with MyoOne Silane DynaBeads (20000048, 10x Genomics) and amplified using 14 PCR cycles. The full-length barcoded cDNA was then enzymatically fragmented and size selected using SPRIselect (B23317, Beckman Coulter) and adaptor ligated. The cDNA was then amplified for library construction adding an Illumina R2 primer sequence, paired-end constructs with the P5 and P7 sequences used for Illumina amplification and sample indexes were added.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x genomics
Data processing Raw sequencing reads were processed on Cell ranger 5.0.1 from 10X Genomics. Reads were demultiplexed and aligned to the mm10 mouse genome.
Assembly: mm10
Supplementary files format and content: tab seperated value files and matrix files
 
Submission date Mar 08, 2024
Last update date Dec 03, 2024
Contact name Jeffery D Molkentin
E-mail(s) jeff.molkentin@cchmc.org
Organization name Cincinnati Children’s Hospital Medical Center
Department Molecular Cardiovascular Biology
Lab Molkentin
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL24247
Series (1)
GSE261150 Transcription factor 21 regulates cardiac myofibroblast formation and fibrosis [scRNA-Seq]
Relations
BioSample SAMN40305997
SRA SRX23880746

Supplementary file Size Download File type/resource
GSM8136444_control_baseline_barcodes.tsv.gz 45.6 Kb (ftp)(http) TSV
GSM8136444_control_baseline_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM8136444_control_baseline_matrix.mtx.gz 72.1 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA

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