|
| Status |
Public on Jul 14, 2023 |
| Title |
Rpb1 KO Guide 2- H3K4me3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
CML
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: K562
treatment: Pol II guide 2 6 days
antibody: H3K4me3 Rb Ab ab8580 GR3264490-1 Abcam
|
| Treatment protocol |
K562 and MLLAF9 Cas9 cells (10x10^6 per cell line) were infected with lentiviral sgRNA libraries at a multiplicity of infection of 0.3. Infected cells were selected with 2ug/ml puromycin for 72hrs, commencing 48hrs after transduction. ~ 100x10^6 cells were fixed/sonicated and ChIP performed at indicated timepoints from approx- 20-30 million cells per ChIP
|
| Growth protocol |
Cells were cultured in RPMI-1640 supplemented with 2mM Glutamax, 100IU/ml Penicillin, 100 ug/ml Streptomycin and 10%HI-FCS in 5% CO2 37degrees.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP DNA was purified using qiagen PCR clean up columns
Library prep was performed on ChIP DNA using rubicon kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with cutadapt.
K562 ChIP-seq reads were aligned to the GRCh37.73 ensembl genome assembly using BWA. MLLAF9 ChIP-seq reads were aligned to the Mm10 genome assembly using BWA.
Sam files were converted into Bam files using samtools. Tdf files were generated using igvtools.
Peak calling was performed using MACS2.
Genome_build: GRCh37.73 and Mm10
Supplementary_files_format_and_content: Bed files
|
| |
|
| Submission date |
Dec 23, 2021 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Mark Dawson |
| E-mail(s) |
mark.dawson@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Cancer Research
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE192555 |
CRISPR-ChIP to identify mechanisms of chromatin regulation [ChIP-seq] |
| GSE192562 |
CRISPR-ChIP to identify mechanisms of chromatin regulation |
|
| Relations |
| BioSample |
SAMN24369079 |
| SRA |
SRX13497470 |
