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Status |
Public on Mar 04, 2019 |
Title |
ILC2_D6_S13 |
Sample type |
SRA |
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Source name |
Group 2 innate lymphoid cells (ILC2)
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Organism |
Homo sapiens |
Characteristics |
condition: ILC2 donor: D6
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Treatment protocol |
N/A (the cells were isolated ex vivo, without treatment
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Growth protocol |
N/A (the cells were isolated ex vivo, without culture)
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Extracted molecule |
total RNA |
Extraction protocol |
The three ILC subsets were isolated using flow cytometry. In brief, CD3, CD14 and CD19 cells were MACS (Miltenyi Biotec, Bergisch Gladbach, Germany) depleted and then sorted using a FACS Aria flow cytometer (BD Bioscience, Allschwil, Switzerland). Staining procedure for sorting should be also included here. In brief, lymphocytes were initially gated based on FSC and SSC, and then dead cells were excluded using a Fixable Viability Dye (eBioscience, Frankfurt, Germany). We then gated on the linage-CD127+ viable lymphocytes population, of which the CD161mid/+ cells were the main ILC containing population. The three ILC subsets were finally distinguished based on their differential expression of c-kit, CRTH2 and NKp44. The sorted ILC populations (from N = 6 individuals) were immediately re-sorted (2-round sorting) into 96-w plate, 1000 cells per well or as close as possible. RNA libraries were prepared for sequencing using Clontech SMARTer - Low Input Mammalian kit.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
Basecalls performed with bcl2fastq-1.8.4 Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence RNA-Seq reads were aligned to Ensembl GRCh38.p10 genome assembly using STAR 2.5.4b Counts were generated by featureCounts of Rsubread 1.28.1 Genome_build: GRCh38.p10
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Submission date |
Apr 02, 2018 |
Last update date |
Mar 04, 2019 |
Contact name |
Ge Tan |
E-mail(s) |
ge_tan@outlook.com
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Organization name |
University of Zurich
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Department |
Functional Genomics Center Zurich
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Street address |
Winterthurerstrasse 190
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City |
Zurich |
ZIP/Postal code |
8057 |
Country |
Switzerland |
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Platform ID |
GPL16791 |
Series (1) |
GSE112591 |
Gene expression signatures of innate lymphoid cells from human blood |
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Relations |
BioSample |
SAMN08832109 |
SRA |
SRX3872505 |
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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