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Sample GSM4650372 Query DataSets for GSM4650372
Status Public on Dec 10, 2020
Title YTS cell replicate 4
Sample type SRA
 
Source name total RNA
Organism Homo sapiens
Characteristics strain: YTS
Treatment protocol N/A
Growth protocol NK cells were isolated by negative selection using the RosetteSep Enrichment Mixture following the recommended protocol (Stem Cell Tech) with the following minor changes: LRS filters were drained into a sterile 50-ml tube, and the contents were diluted to 30 ml using PBS with 2% IgG-depleted FBS. The cell suspension was then split into 2 × 15-ml aliquots, and each was mixed with 750 μl of the negative selection mixture. After a 20-min incubation, the steps mentioned in the protocol were followed. Contaminating erythrocytes were then removed by incubating the cells with erythrocyte lysis buffer (155 mM ammonium chloride, 12 mM sodium bicarbonate, and 0.1 mM EDTA, pH 7.4) for 10 min at room temperature. HEK293F, NK92 and YTS cells were grown in a pure culture and separated from the culture medium prior to RNA isolation.
Extracted molecule total RNA
Extraction protocol QuantSeq 3’ mRNA-Seq library kit (Lexogen, Vienna, Austria)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Read mapping to human ribosomal RNA reference: rRNA sequence filtering against human NCBI rRNA accessions, Bowtie2 ver. 2.3.4.1
Read mapping to hg38: Reads not mapped to rRNA were aligned to human genome using STAR ver. 2.7.1a
Raw count extraction: Raw counts extracted from STAR alignment BAM files using HTSEQ v0.9.1
Manual matrix count filtering: Summation of row counts in raw matrix ≥ 50 counts
Count matrix normalization, DESeq2
Genome_build: UCSC (Dec. 2013 GRCh/38hg38)
Supplementary_files_format_and_content: Tab-delimited txt file, raw count matrix
Supplementary_files_format_and_content: Tab-delimited txt file, manually filtered count matrix. Input count matrix for RNA-Seq
 
Submission date Jul 02, 2020
Last update date Dec 10, 2020
Contact name Adam W. Barb
E-mail(s) abarb@uga.edu
Organization name University of Georgia
Department Biochemistry and Molecular Biology
Lab B302A
Street address 180 E. Green Street
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platform ID GPL18573
Series (1)
GSE153738 Gene expression differences among human natural killer cells and recombinant expression hosts
Relations
BioSample SAMN15430258
SRA SRX8658394

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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