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Sample GSM5639808 Query DataSets for GSM5639808
Status Public on Oct 22, 2021
Title Lin28_SN_cK_N
Sample type SRA
 
Source name Lin28_SN_cK_N
Organism Mus musculus
Characteristics cell type: Lin28-/cKit-
Extracted molecule polyA RNA
Extraction protocol Briefly, heart samples were mechanically minced into 1-mm3 pieces and digested in collagenase II (150 U mg/mL, Worthington, LS004174) followed by brief low-speed (850 rpm for 2 minutes) centrifugation to remove cardiomyocytes and tissue debris.Lin28S+/- cardiac interstitial cells were obtained by FACS sorting with Lin28 antibody and concurrent cell surface expression of Lin28/cKit
The Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (PN- 1000268), Chromium Single Cell 3' Chip G kit v2 (PN-1000120) and Dual Index Kit TT Set A, (PN-1000215) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V3.1 User Guide.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The raw data was processed with the Cell Ranger pipeline (10X Genomics; version 3.0.1). Reads were aligned to the 10x mouse genome mm10.
Preparations derived from Lin28 cell surface sorting yielded 7086 barcoded cells for analysis, from which 4334 corresponded to Lin28S-, and 2752 corresponded to Lin28S+(874 Lin28S+/cKit-, 1878 Lin28S+/cKit+). Final removal of unwanted sources of variation and batch effect corrections was performed using Seurat R Package (v4.0.2)
Sequenced reads were aligned to the human reference genome mm-10
Genome_build: mm-10
Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode
 
Submission date Oct 19, 2021
Last update date Oct 22, 2021
Contact name Oscar E Echeagaray
E-mail(s) oscar.echeagaray@gmail.com
Organization name San Diego State University
Department Biology
Lab Sussman Lab
Street address 5500 Campanile Drive
City San Diego
State/province CA
ZIP/Postal code 92182
Country USA
 
Platform ID GPL24247
Series (1)
GSE186176 Surface Lin28A Expression Consistent With Cellular Stress Parallels Indicators of Senescence
Relations
BioSample SAMN22416408
SRA SRX12694120

Supplementary file Size Download File type/resource
GSM5639808_Lin28_SN_cK_N.txt.gz 83.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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