|
| Status |
Public on May 27, 2021 |
| Title |
CD34 shLUC control Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
human cord blood CD34+ cells_control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34+ haematopoietic stem and progenitor cells (HSPCs)
treatment: control
|
| Treatment protocol |
Control shRNA targetting luciferase or treatment shRNA targetting ERG
|
| Growth protocol |
Human cord blood CD34+ cells pooled from multiple donors and lentivirally transduced as previously described (Unnikrishnan et al NAR 44:10644 2016)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using miRNeasy kit (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
CD34_shLUC_Exp2
|
| Data processing |
Alignment to hg19 genome with TopHat2 (standard paramters)
Differential expression analysis using DeSeq2 with standard parameters and paired sample information included as a regression variable. Calculation was performed with shLUC as the treated and shERG as the untreated sample.
Genome_build: hg19
Supplementary_files_format_and_content: text files containing normalized read counts and DeSeq2 output
|
| |
|
| Submission date |
Sep 30, 2020 |
| Last update date |
May 27, 2021 |
| Contact name |
Julie Thoms |
| E-mail(s) |
j.thoms@unsw.edu.au
|
| Organization name |
UNSW Sydney
|
| Department |
Adult Cancer Program
|
| Street address |
Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St
|
| City |
Randwick |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE158795 |
Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells [RNA-seq] |
| GSE158797 |
Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells |
|
| Relations |
| BioSample |
SAMN16302788 |
| SRA |
SRX9218989 |
