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| Status |
Public on Dec 10, 2020 |
| Title |
NK92 cell replicate 1 |
| Sample type |
SRA |
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| Source name |
total RNA
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| Organism |
Homo sapiens |
| Characteristics |
strain: NK92
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| Treatment protocol |
N/A
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| 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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
QuantSeq 3’ mRNA-Seq library kit (Lexogen, Vienna, Austria)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Jul 02, 2020 |
| Last update date |
Dec 10, 2020 |
| Contact name |
Adam W. Barb |
| E-mail(s) |
abarb@uga.edu
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| Organization name |
University of Georgia
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| Department |
Biochemistry and Molecular Biology
|
| Lab |
B302A
|
| Street address |
180 E. Green Street
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE153738 |
Gene expression differences among human natural killer cells and recombinant expression hosts |
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| Relations |
| BioSample |
SAMN15430268 |
| SRA |
SRX8658384 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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