|
| Status |
Public on May 16, 2022 |
| Title |
Empty vector_3 |
| Sample type |
SRA |
| |
|
| Source name |
Cord blood progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cord blood progenitor cells
sorted cells: CD34+ cells, GFP+
treatment: control
|
| Treatment protocol |
Each biological replicate composed of three different cord blood units
|
| Growth protocol |
The cells were cultured for five days in-vitro (SCF, Flt3L, and TPO) , sorted for GFP positive, and sent for bulk RNA-sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD34 positive cord blood cells were isolated using magnetic beads from fresh cord blood (For each biological replicate, three different cord blood samples were mixed). The cell were retrovirally infected with ETV6-NCOA2 or empty vector and cultured in IMDM supplemented with hSCF, hTPO, hFlt3L (100 ng/ml) for 5 days. The positive cells were sorted (GFP). We extracted RNA from the samples and performed bulk RNA-sequencing.
RNA was purified, analyzed by bioanalyzer (Agilent 2100), cDNA libraries were prepared using Using PrepX mRNA Library kit (WaferGen), and Apollo 324 NGS automatic library prep system. Using the universal (SR) and index-specific primer with limited PCR cycle number (~13), a sample-specific index was added to each adaptor-ligated cDNA sample. Libraries were clustered onto Illumina’s TruSeq SR Cluster kit v3, and sequenced for 50 cycles using TruSeq SBS kit on Illumina HiSeq system
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
EV_3
Human CD34 positive cord blood cells were retrovirally infected with MigR1-IRES-GFP expression
|
| Data processing |
Reads were aligned to the reference genome using TopHat
Differential expression analysis was performed using the DESeq package
Genome_build: GRCh38
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Nov 27, 2020 |
| Last update date |
May 16, 2022 |
| Contact name |
Gilgi Friedlander |
| Organization name |
Weizmann Institute of Science
|
| Street address |
Hertzel st
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL15433 |
| Series (2) |
| GSE162230 |
RNA sequencing of ETV6-NCOA2 expression in CD34 positive cord blood cells |
| GSE162338 |
ETV6-NCOA2 expression in CD34 positive cord blood cells |
|
| Relations |
| BioSample |
SAMN16934850 |
| SRA |
SRX9596381 |
