|
| Status |
Public on Dec 09, 2022 |
| Title |
SETD1AKO_FKBP-SETD1A_dTAG_RNAP2 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
MOLM-13
|
| Organism |
Homo sapiens |
| Characteristics |
vector: HA-FKBP-hSETD1A-puro;Cas9-Blast;SETD1A Ex8 sgRNA-GFP
chip antibody: RNAP2 (diagenode C15100055)
stimulation: dTAG-13
time: 24h
|
| Treatment protocol |
HA-FKBP-hSETD1A expression vector, Cas9 expression vector and SETD1A sgRNA expression vector were introduced with lentivirus and stable expressing single cell clone was established. Cells were treated with DMSO or 500 nM dTAG-13 for 24 hours.
|
| Growth protocol |
MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SETD1AKO_FKBP-SETD1A_dTAG_RNAP2
|
| Data processing |
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.1.0.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-1.56.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Dec 15, 2021 |
| Last update date |
Dec 10, 2022 |
| Contact name |
Masaki Fukuyo |
| E-mail(s) |
fukuyo@chiba-u.jp
|
| Organization name |
Chiba University
|
| Department |
Department of Molecular Oncology
|
| Street address |
1-8-1 Inohana, Chuo-ku
|
| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE189894 |
SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia |
| GSE190994 |
SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN24103658 |
| SRA |
SRX13440041 |
