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Sample GSM6149629 Query DataSets for GSM6149629
Status Public on Jun 07, 2023
Title CD56dim, controller, rep9
Sample type SRA
 
Source name blood
Organism Homo sapiens
Characteristics tissue: blood
cell type: CD56dim NK cells
treatment: HIV positive spontaneous controller
Growth protocol CD56hi, CD56dim, CD56negNK cells and ILCs were sorted from the PBMCs of HIV-1 negative people, HIV-1+ viremic people, HIV-1+ people under ART, and HIV-1+ spontaneous controllers.
Extracted molecule polyA RNA
Extraction protocol The RNA of sorted cells were extracted with Trizol.
The mRNA library was constructed by CEL-Seq2 method.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing cutadapt v2.9 was used to trim and move the first 6 bases (UMIs) of the reads to the read header; demultiplex fastq files based on the inline sample barcodes to generate per-sample fastq files and remove adapter sequences.
Star v2.6.1 was used to align reads to human genome hg38 assembly.
UMI-tools v1.1.2 was used to deduplicate PCR duplicates based on the UMI sequences.
Deduplicated bam files were converted to fastq using samtools v1.9.
Kalliso v0.46.0 was used to quantify gene expression from deduplicated fastq files.
Assembly: hg38
Supplementary files format and content: Tab separated values and matrix file.
 
Submission date May 13, 2022
Last update date Jun 07, 2023
Contact name Jeremy Luban
Organization name UMass Medical School
Street address 373 Plantation Street Biotech 2, Suite 319
City Worcester
State/province Massachusetts
ZIP/Postal code 01605
Country USA
 
Platform ID GPL24676
Series (1)
GSE203002 Clarification of human blood ILC subtype interrelatedness and discovery of amphiregulin production by human NK cells shed light on HIV-1 pathogenesis
Relations
BioSample SAMN28293245
SRA SRX15271047

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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