|
| Status |
Public on May 23, 2021 |
| Title |
Reference normalised ChIP-seq input for RUNX1 and MLL-N in SEM cells following KD siRNA treatment |
| Sample type |
SRA |
| |
|
| Source name |
Leukemia cell line (SEM)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Bone marrow aspirate from a 15-year old MLL-AF4 ALL patient
chip antibody: none
sirna: RUNX1 siRNA (Dharmacon J-003926-05)
|
| Treatment protocol |
Cells were either untreated, or 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 |
genomic DNA |
| Extraction protocol |
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (EZH2). For reference normalisation 10% S2 cells were spiked in prior to sonication. Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-seq performed using RUNX1 and MLL-N antibody in SEM cells following KD siRNA treatment
SEM_RUNX1-KD_RUNX1_peaks.txt
|
| Data processing |
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Supplementary_files_format_and_content: Peak calling using Homer v4.7
|
| |
|
| Submission date |
Mar 30, 2021 |
| 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 |
GPL16791 |
| Series (2) |
| GSE151386 |
A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes [ChIP-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 |
SAMN18543090 |
| SRA |
SRX10484573 |
