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Sample GSM3666011 Query DataSets for GSM3666011
Status Public on Nov 21, 2019
Title Sample 16_exvivo_PNT_S1_ab
Sample type SRA
 
Source name exvivo_PNT
Organism Homo sapiens
Characteristics age: 8 years
tissue/cell type source: Thymus
cell type: alpha beta thymocytes
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 ftp.Ensembl.org.
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
E-mail(s) dvermijl@ulb.ac.be
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
Relations
BioSample SAMN11105686
SRA SRX5507761

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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