|
| Status |
Public on Jul 12, 2023 |
| Title |
MUTZ3 - CTBP2 Input - PLASS ctrl Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow
cell line: MUTZ3
cell type: acute myelomonocytic leukemia
genotype: p50MX-3xFLAG-3xNLS-4xPLASS-Zeo
treatment: PLASS
antibody: None
protocol: Single crosslink
|
| Growth protocol |
The MOLM-1 cell line was cultured in RPMI with 10% FCS. The MUTZ3 cell lines were cultured in αMEM with 20% FCS and 20% conditioned 5637 medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear lysates were sonicated and pulled down with antibody according to one of three different protocols: the Upstate histone protocol, with a single formaldehyde crosslink, or with a double DSG crosslink (see methods)
ChIP samples were processed according to the Illumina TruSeq ChIP Sample Preparation Protocol (Illumina) or Diagenode Library V3 preparation protocol (Diagenode) and either sequenced single-end (1 × 50 bp) on the HiSeq 2500 platform (Illumina) or paired-end (2 × 100 bp) on the Novaseq 6000 platform (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling was conducted with bcl2fastq v1.8.4 for runs sequenced on the Hiseq 2500 and v2.20.422 for runs sequenced on the Novaseq 6000
ChIP-seq reads were aligned to the human reference genome build hg19 with either BBMap (v34.92) or bowtie (v1.1.1)
Peak calling was performed with MACS2 (v 2.1.2) using the default settings, using input sequencing data as controls.
Bigwig files were generated for visualization with deepTools bamCoverage (v3.5.1) and the options --normalizeUsing RPKM --smoothLength 100 --binSize 20
Assembly: hg19
Supplementary files format and content: narrowPeak (except for Input samples)
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Jun 28, 2023 |
| Last update date |
Sep 18, 2023 |
| Contact name |
Ruud Delwel |
| E-mail(s) |
[email protected]
|
| Organization name |
Erasmus MC
|
| Street address |
Dr. Molewaterplein 40
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE236010 |
Oncogene EVI1 Drives Acute Myeloid Leukemia Via a Targetable Interaction with CTBP2 [ChIP-Seq] |
| GSE243621 |
Oncogene EVI1 Drives Acute Myeloid Leukemia Via a Targetable Interaction with CTBP2 |
|
| Relations |
| BioSample |
SAMN36019553 |
| SRA |
SRX20804914 |
