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Sample GSM3666018 Query DataSets for GSM3666018
Status Public on Nov 21, 2019
Title Sample 23_exvivo_PNT_S2_gd
Sample type SRA
Source name exvivo_PNT
Organism Homo sapiens
Characteristics age: 4 months
tissue/cell type source: Thymus
cell type: gamma delta thymocytes
cell subset: nonVg9Vd2
Growth protocol Only for samples 1-12: Isolated HSPC (CD34+ cells) were seeded in a 6-well culture plate (5x105 cells/well) containing a monolayer of OP9DL1 cells in MEMα (Minimum Essential Medium α) supplemented with 20% fetal bovine serum, 1% NEAA, 1% Glutamine, 1% Pen/Strep in the presence of 10 ng/ml IL-7,10 ng/ml Flt3L and 5 ng/ml SCF. Every 4-5 days cells were harvested by vigorous pipetting and transferred in a new 6-well plate (between 5x105-1x106 cells/well). This in vitro system allow the generation of T cells. After ca. 30 days in co-culture with OP9DL1 cells, HPSC-derived γẟ T cells were stained and sorted on a FACS Aria III cell sorter, snap frozen in liquid nitrogen and stored at -80 °C for later RNA extraction.
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy Plus Micro kit according to manufacturer’s instructions
Library was obtained using the Ovation Solo RNA-Seq System (NuGen) following manufacturer's instruction
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description processed data file: CPM_FT_PNT.csv
Data processing Approximately 30 million paired-end reads (2x101 bases) /sample were collected on a NovaSeq 6000 (Illumina)
Paired-end reads with variable trimming (minimum size 36 bases) were mapped against the human reference genome (GRCh38) using STAR_2.5.3a software to generate read alignments for each sample. Annotations Homo_sapiens.GRCh38.90.gtf were obtained from
After transcripts assembling, gene level counts were obtained using HTSeq, followed by a library size normalization data processing step
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file include CPM (count per million) values for each Sample.
Submission date Mar 12, 2019
Last update date Nov 21, 2019
Contact name David Vermijlen
Organization name Université Libre de Bruxelles
Street address Boulevard de Triomphe, accès 2 (CP205/3)
City Brussels
ZIP/Postal code 1050
Country Belgium
Platform ID GPL24676
Series (1)
GSE128163 The human fetal thymus generates effector invariant γδ T cells in a Lin28b-dependent manner
BioSample SAMN11105679
SRA SRX5507768

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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