|
| Status |
Public on Aug 15, 2023 |
| Title |
ChIP seq Input for chALL patient sample 3 |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF4 childhood ALL patient 3 blasts
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: acute lymphoblastic leukemia (ALL)
treatment: N/A
individual: 3-year old MLL-AF4 ALL patient
tissue: Bone marrow aspirate
chip antibody: none
|
| Growth protocol |
Infant (<1 year old) and childhood ALL samples were obtained from Blood Cancer UK Childhood Leukemia Cell Bank, UK (REC: 16/SW/0219). All ALL samples were anonymized at source, assigned a unique study number and linked. Cryopreserved samples were thawed, and immediately processed.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed with PBS and fixed in 2mM DSG for 30 minutes and 1% FA for 30 minutes. Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext Ultra DNA II library preparation kit for Illumina (Cat no. E7645).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP-seq performed in MLL-AF4 patient blasts
|
| 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
Peak calling and annotation using Homer v4.7
Bigwig generation using DeepTools
Assembly: hg19
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
May 07, 2022 |
| Last update date |
Aug 15, 2023 |
| Contact name |
Thomas A Milne |
| E-mail(s) |
thomas.milne@imm.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
MRC Weatherall Institute of Molecular Medicine
|
| Street address |
John Radcliffe Hospital, Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE202449 |
MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia [ChIP-seq] |
| GSE202451 |
MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia |
|
| Relations |
| BioSample |
SAMN28131857 |
| SRA |
SRX15203356 |
