|
| Status |
Public on May 23, 2021 |
| Title |
SEM nascent RNA-seq RUNX1 siRNA rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Leukemia cell line (SEM)
|
| Organism |
Homo sapiens |
| Characteristics |
sirna: RUNX1 siRNA (Dharmacon J-003926-05)
cell line: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
|
| Treatment protocol |
Cells were electroporated with non-targeting or RUNX1 targeting siRNA
|
| Growth protocol |
Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10e8 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
DNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7765).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Nascent RNA-seq in SEM cells treated with RUNX1 siRNA
SEM_RUNX1_KD2
|
| Data processing |
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using Picard MarkDuplicates
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 28, 2020 |
| Last update date |
May 23, 2021 |
| Contact name |
Thomas Milne |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oxford
|
| Department |
Radcliffe Department of Medicine
|
| Lab |
Milne Lab
|
| Street address |
MRC MHU, WIMM, John Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE151385 |
A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes [RNA-seq] |
| GSE151390 |
A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes. |
|
| Relations |
| BioSample |
SAMN15048511 |
| SRA |
SRX8418554 |
