|
| Status |
Public on Jul 27, 2020 |
| Title |
cord blood CD34+, OP9-GFP_Ctrl_2 |
| Sample type |
SRA |
| |
|
| Source name |
cord blood CD34+
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: cord blood-derived HPC
feeder: OP9-GFP (Notch-OFF)
construct: LIE-Ctrl
|
| Treatment protocol |
Precultured CD34+ cells were transduced with HES1-or HES4-encoding retrovirus and cultured for one day on OP9-GFP or OP9-DLL1. Subsequently eGFP+CD45+CD34+Lin- were sorted.
|
| Growth protocol |
CD34+ were isolated from cord blood and cultured for two days in complete IMDM containing 10% heat-inactivated FCS, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 mM L-glutamine, supplemented with 20 ng/ml TPO, 100 ng/ml SCF and 100 ng/ml FLT3L.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from sorted cells was harvested using Trizol reagent and the miRNeasy Micro Kit (Qiagen)
RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files were mapped against GRCh38p5 using STAR 2.4.2a.
Counts were called by specifying the quantMode flag during mapping and by providing an approriate gtf file obtained from gencode (v20).
Raw counts were normalized using the DESeq2 package in R.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include DESeq2-normalized values for each sample.
|
| |
|
| Submission date |
May 02, 2019 |
| Last update date |
Jul 27, 2020 |
| Contact name |
Matthias De Decker |
| E-mail(s) |
[email protected]
|
| Organization name |
Ghent University
|
| Department |
Diagnostic Sciences
|
| Lab |
Immunology
|
| Street address |
Corneel Heymanslaan 10
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE130614 |
HES1 and HES4 have both unique and overlapping roles as downstream mediators of Notch-dependent hematopoietic lineage decisions in human |
|
| Relations |
| BioSample |
SAMN11557609 |
| SRA |
SRX5781376 |
