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Sample GSM7312259 Query DataSets for GSM7312259
Status Public on May 23, 2023
Title P1-SCAF2962_2_HK, HCT116, THP1 and Jurkat T, Heat Killed, 10x genomics 3' v3
Sample type SRA
 
Source name HCT116, THP1 and Jurkat T
Organism Homo sapiens
Characteristics cell line: HCT116, THP1 and Jurkat T
treatment: Heat Killed
Extracted molecule polyA RNA
Extraction protocol Single cell suspensions were prepared, and concentration and viability measured on an automated dual-fluorescence cell counter with acridine orange and propidium iodide stain (Luna Fx7, Logos Biosystems).
Single cell partitioning and RNA-Seq library preparation was performed using 10X genomics 3’ v3.1 chemistry (user guide CG000204) according to vendor recommendations. Sample viability was above 80% for all conditions. 6,000-8,000 cells were targeted to be captured for each sample. Libraries were sequenced on the NovaSeq 6000 with a target depth of 50,000 reads per cell using read parameters recommended by 10x Genomics user guides.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description P1-SCAF2962_2_HK
10x genomics 3' v3
Data processing Reads from multiplexed sequencing runs were demultiplexed using cellranger mkfastq v7.0.0 (10x Genomics).
Raw FASTQ files were aligned to the reference human genome (GRCh38 gencode release 34) using CellRanger v5.0.1. The annotated polyA and template sequence oligonucleotide (TSO) sequences were trimmed, the unmapped reads were converted to the FASTQ file format trimmed and filtered using FASTP v0.20.1 with the arguments “--unqualified_percent_limit 40 --cut_tail --low_complexity_filter --trim_poly_x” before being converted to BAM files. For quality filtering, we removed genes found in fewer than 3 cells and remove cells with fewer than 3,000 gene features or greater than 15% of reads mapping to mitochondrial genes.
Assembly: GRCh38 gencode release 34
Supplementary files format and content: Tab-separated values files and matrix files and h5 matrix files
 
Submission date May 09, 2023
Last update date May 23, 2023
Contact name Welles Robinson
E-mail(s) wir963@gmail.com
Organization name National Institutes of Health
Department National Cancer Institute
Lab Cancer Data Science Laboratory
Street address 9000 Rockville Pike
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platform ID GPL24676
Series (1)
GSE232107 scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations
Relations
BioSample SAMN35015925
SRA SRX20273497

Supplementary file Size Download File type/resource
GSM7312259_P1-SCAF2962_2_HK_raw_feature_bc_matrix.h5 89.4 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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