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Sample GSM6443271 Query DataSets for GSM6443271
Status Public on Dec 09, 2022
Title SETD1AKO_FKBP-SETD1A_dTAG_1h_RNAP2
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 (#14958, Cell Signaling)
stimulation: dTAG-13
time: 1h
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 NovaSeq 6000
 
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.
Assembly: hg19
Supplementary files format and content: bigwig
 
Submission date Aug 10, 2022
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 GPL24676
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 SAMN30242881
SRA SRX17024516

Supplementary file Size Download File type/resource
GSM6443271_SETD1AKO_FKBP-SETD1A_dTAG_1h_RNAP2.bigwig 177.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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