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Status |
Public on Oct 22, 2021 |
Title |
Lin28_SP_cK_P |
Sample type |
SRA |
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Source name |
Lin28_SP_cK_P
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Organism |
Mus musculus |
Characteristics |
cell type: Lin28+/cKit+
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Oct 19, 2021 |
Last update date |
Oct 22, 2021 |
Contact name |
Oscar E Echeagaray |
E-mail(s) |
oscar.echeagaray@gmail.com
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Organization name |
San Diego State University
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Department |
Biology
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Lab |
Sussman Lab
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Street address |
5500 Campanile Drive
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City |
San Diego |
State/province |
CA |
ZIP/Postal code |
92182 |
Country |
USA |
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Platform ID |
GPL24247 |
Series (1) |
GSE186176 |
Surface Lin28A Expression Consistent With Cellular Stress Parallels Indicators of Senescence |
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Relations |
BioSample |
SAMN22416410 |
SRA |
SRX12694119 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5639810_Lin28_SP_cK_P.txt.gz |
19.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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