|
| Status |
Public on May 26, 2023 |
| Title |
BB_DMSO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Hoxb8-ER cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: myeloid progenitors
treatment: DMSO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hoxb8-ER cells were transduced with ERG variants and treated with either DMSO or BRD3308. Cells were fluidized in TRIzol reagent, and RNA was purified using the TRIzolTM Plus RNA Purification Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ER-Hoxb8 cells transduced with an empty lenti-viral vector treated with DMSO
|
| Data processing |
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt; resulting reads shorter than 30bp were discarded.
Reads were mapped to the M. musculus reference genome GRCm38 using STAR, supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04).
Expression levels for each gene were quantified using htseq-count, using the gtf above.
Differentially expressed genes were identified using DESeq2 with the betaPrior, cooksCutoff and independentFiltering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Assembly: GRCm38
Supplementary files format and content: count matrix with raw reads per sample
|
| |
|
| Submission date |
Apr 07, 2022 |
| Last update date |
May 26, 2023 |
| Contact name |
Eitan Kugler |
| E-mail(s) |
et.kugler@gmail.com
|
| Organization name |
Rabin medical center
|
| Department |
Hematology
|
| Street address |
Zeev Jabutinsky Rd 39
|
| City |
Petah Tikva |
| State/province |
Please make your selection |
| ZIP/Postal code |
49100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE200391 |
The NCOR-HDAC3 co-repressive complex modulates the leukemogenic potential of ERG. |
| GSE200393 |
A single amino acid at the PNT domain of ERG mediates its leukemogenic activity through interaction with the NCoR-HDAC3 co-repressor complex. |
|
| Relations |
| BioSample |
SAMN27403307 |
| SRA |
SRX14775822 |
