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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).
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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
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|
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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 |