|
| Status |
Public on May 23, 2023 |
| Title |
P1-SCAF2963_3_Live, HCT116, THP1 and Jurkat T, Infected, 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: Infected
|
| 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-SCAF2963_3_Live
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 |
SAMN35015924 |
| SRA |
SRX20273498 |
