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Sample GSM7312273 Query DataSets for GSM7312273
Status Public on May 23, 2023
Title P1_B03_S15, 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_B03_S15
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 SAMN35015911
SRA SRX20273559

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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