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| Status |
Public on Oct 15, 2020 |
| Title |
NK ctrl rep 3 |
| Sample type |
SRA |
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| Source name |
cord blood CD34+ derived NK cells
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| Organism |
Homo sapiens |
| Characteristics |
transduced with: LZRS-IRES-eGFP
markers: eGFP+CD45+CD11a+CD56+CD94+
cell type: natural killer cell
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| Growth protocol |
sorted CD34+Lin-eGFP+ stem cells were allowed to differentiate during 21 days under NK/ILC3 culture conditions as described by Cichocki and Miller, Methods Mol Biol. 2010;612:15-26
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy micro kit (Qiagen, Hilden, Germany)
50 ng of RNA was used to perform an Illumina sequencing library preparation using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to manufacturer's protocol. Libraries were quantified by qPCR, according to Illumina's protocol 'Sequencing Library qPCR Quantification protocol guide', version February 2011. A High sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US) was used to control the library's size distribution and quality. Sequencing was performed on a high throughput Illumina NextSeq 500 flow cell generating 75 bp single reads.
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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 |
Reads were trimmed using cutadapt version 1.11 to remove the “QuantSEQ FWD” adaptor sequence
The trimmed reads were mapped against the Homo sapiens GRCh38.90 reference genome using STAR version 2.5.3a.
The RSEM software version 1.2.31 was used to generated the count tables.
Genome_build: Homo sapiens GRCh38.90
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample
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| Submission date |
Oct 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wouter Van Loocke |
| E-mail(s) |
wouter.vanloocke@ugent.be
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| Organization name |
Ghent University
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| Department |
Biomolecular Medicine
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| Street address |
C. Heymanslaan 10
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| City |
Ghent |
| State/province |
East Flanders |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE105021 |
The transcription factor ETS1 is a master regulator of human NK cell differentiation [RNA-seq] |
| GSE124104 |
The transcription factor ETS1 is a master regulator of human NK cell differentiation |
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| Relations |
| BioSample |
SAMN07789059 |
| SRA |
SRX3287566 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2815731_17.genes.results.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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