|
| Status |
Public on Nov 21, 2019 |
| Title |
Sample 12_OP9DL1_Control_S3 |
| Sample type |
SRA |
| |
|
| Source name |
OP9DL1_Control
|
| Organism |
Homo sapiens |
| Characteristics |
age: Term delivery
tissue/cell type source: Hematopoietic stem and progenitor cells (HSPC)
cell type: gamma delta T cells (HSPC derived)
|
| 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: CMP_OP9DL1.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 |
SAMN11105690 |
| SRA |
SRX5507757 |
