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Sample GSM7224211 Query DataSets for GSM7224211
Status Public on Mar 01, 2024
Title LP1, control, H3K27ac ChIP, biorep2
Sample type SRA
 
Source name Haematopoietic and Lymphoid
Organism Homo sapiens
Characteristics tissue: Haematopoietic and Lymphoid
cell line: LP-1
cell type: Plasma Cell Myeloma
genotype: WT
Sex: Female
treatment: control
chip antibody: H3K27ac antibody (07-360; Merck)
Treatment protocol Cells were transduced with TLCV2-containing virus and selected with 0.5 µg/ml puromycin for 72H. Transduced cells were subjected to 1 µg/ml Doxycycline to induce Cas9 expression before GFP sorting.
Growth protocol Cells were cultured in RPMI 1640 media with 2.05 mM L-Glutamine (SH30027.01; Hyclone).
Extracted molecule genomic DNA
Extraction protocol Cells were fixed in 1% formaldehyde for 12 minutes, swelled in 0.5% SDS buffer then lysed in 0.5% SDS + 5% Triton buffer (2:1). Genomic DNA was sheared to 100-500bp by sonication.
ChIP libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing Reads aligned to hg38 using bowtie2 and filtered for duplicates, poor quality and blacklisted regions
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls
 
Submission date Apr 24, 2023
Last update date Mar 01, 2024
Contact name Yinghui Li
E-mail(s) liyh@ntu.edu.sg
Organization name Nanyang Technological University
Department School of Biological Sciences
Lab 05n-21
Street address 60 Nanyang Drive
City Singapore
State/province Singapore
ZIP/Postal code 637551
Country Singapore
 
Platform ID GPL20795
Series (2)
GSE230466 Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [ChIP-seq]
GSE230526 Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma
Relations
BioSample SAMN34367449
SRA SRX20095598

Supplementary file Size Download File type/resource
GSM7224211_p52KD_H3K27ac_LP1_ctrl_rep2.bw 226.6 Mb (ftp)(http) BW
GSM7224211_p52KD_H3K27ac_LP1_ctrl_rep2.narrowPeak.gz 881.6 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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