|
| Status |
Public on Aug 15, 2023 |
| Title |
Input for PAF1 TOPmentation in DMSO-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V) |
| Sample type |
SRA |
| |
|
| Source name |
Leukemia cell line (SEM)
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: DMSO for 24h
cell type: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
|
| Treatment protocol |
See sample table
|
| Growth protocol |
Cells were continuously grown in IMDM (SEM) or RPMI (RS4;11) 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 and HT-CM) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (TFs). Cells were sonicated to give fragments of 100-300bp followed by IP.
IPed chromatin was tagmented by incubating in 29 µl Tagmentation Buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 10% dimethylformamide) and adding 1 µl of transposase (Illumina) at 37 ˚C for 10 min. Tagmented DNA was amplified and indexed with NEBNext Ultra II Q5 Master Mix (NEB).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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
Assembly: hg19
Supplementary files format and content: Peak calling and annotation using Homer v4.7
Supplementary files format and content: Bigwig generation using DeepTools
|
| |
|
| Submission date |
May 09, 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) |
| GSE202451 |
MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia |
| GSE202569 |
MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia [TOPmentation data] |
|
| Relations |
| BioSample |
SAMN28163635 |
| SRA |
SRX15213652 |
