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Sample GSM6139169 Query DataSets for GSM6139169
Status Public on Sep 19, 2022
Title WI-38, etoposide treated, scRNA-seq
Sample type SRA
 
Source name WI-38
Organism Homo sapiens
Characteristics cell line: WI-38
cell type: fibroblasts
treatment: etoposide
Extracted molecule polyA RNA
Extraction protocol Etoposide-treated WI38 cells were trypsinized, washed and resuspended in PBS, and subjected to single-cell GEM (Gel Bead-Emulsion) generation with Chromium Controller (10x Genomics)
scRNA-seq library was performed according to the manufacter’s instructions (10x Genomics Chromium Next Gem Single Cell 3' Regent Kits v3 protocol, 10x Genomics). In brief, single cell suspension was loaded into a Chromium Next GEM Chip G (10x Genomics), and GEMs were generated using the Chromium Single Cell Controller (10x Genomics). We used 11 and 13 cycles for cDNA amplification and Sample Index PCR (Single Index Kit T Set A, 10x Genomics), respectively
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing Cell Ranger software version 6.0.0 was used for demultiplexing, barcoded processing, sequence alignment, and for generating matrix files
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
 
Submission date May 13, 2022
Last update date Sep 19, 2022
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL24676
Series (2)
GSE202950 A BDNF-TrkB autocrine loop enhances senescent cell viability [scRNA-seq]
GSE202951 A BDNF-TrkB autocrine loop enhances senescent cell viability
Relations
BioSample SAMN28232726
SRA SRX15255136

Supplementary file Size Download File type/resource
GSM6139169_barcodes.tsv.gz 10.3 Kb (ftp)(http) TSV
GSM6139169_features.tsv.gz 297.6 Kb (ftp)(http) TSV
GSM6139169_matrix.mtx.gz 27.5 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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