|
| Status |
Public on May 23, 2023 |
| Title |
P1_B07_S19, HCT116, Uninfected, plexWell |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
treatment: Uninfected
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspensions were prepared and sorted on a BD FACS Aria IIU into 96 well PCR plates that were prepared with lysis buffer according to seqWell plexWell Rapid Single Cell method (user guide v20210402) and containing ERCC spike-in mix (Invitrogen # 4456740) at a dilution of 1:1E7. Following deposition of single cells into prepared plates, they were snap-frozen and stored at -80C until further processing.
Single cell cDNA and libraries were generated for each sorted sample according to seqWell plexWell Rapid Single Cell user guide. Multiplexed libraries containing indexed single cell RNA-Seq libraries were sequenced on the either the NextSeq 2000 or NovaSeq 6000 with a target read depth of 2 million reads per cell using the following read parameters: Read 1 61bp, Index 1 8bp, Index 2 8bp, Read 2 61bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
P1_B07_S19
plexWell
|
| Data processing |
Raw sequencing data was demultiplexed into individual sample fastq sets using bcl2fastq v2.20.0.
Raw FASTQ files were trimmed using fastp v0.20.1 with the arguments “--unqualified_percent_limit 40 --cut_tail --low_complexity_filter --trim_poly_x”. The trimmed FASTQ files were aligned to the reference human genome (GRCh38 gencode release 34) and any applicable spike-in sequences using STAR63 2.7.6a_patch_2020-11-16 with the arguments “--soloType SmartSeq --soloUMIdedup Exact --soloStrand Unstranded --outSAMunmapped Within”. For analysis, we used the previously described workflow “Lun 416B cell line (Smart-seq2)” from “Orchestrating Single-Cell Analysis with Bioconductor” to specifically handle ERCC spike-in sequences. Quality filtering was performed using the quickPerCellQC function from scuttle (version 1.8.0)
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 |
SAMN35015909 |
| SRA |
SRX20273561 |
