|
Status |
Public on Nov 09, 2021 |
Title |
Kelly_lacZ_H3K27ac |
Sample type |
SRA |
|
|
Source name |
Neuroblastoma
|
Organism |
Homo sapiens |
Characteristics |
cell line: Kelly cell type: Neuroblastoma chip antibody: H3K27ac antibody manu.: Millipore antibody catalog: MABE647 antibody lot: VP2010161
|
Growth protocol |
Human cell lines were cultured in RPMI media containing 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. All cell lines were routinely validated to be free of Mycoplasma species and used within 10 passages after thawing.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
CUT&RUN sequencing was performed by standard methodology, using reagents from Epicypher Inc. H3K27ac and IgG CUT&RUN validated antibodies were obtained from Epicypher Inc. Briefly, Kelly-cas9 expressing cells were infected with lentiviruses encoding sgRNAs to TFAP2b (TFAP2b-1,2) or control loci (ch2.2, LACZ) and grown in selection media containing puromycin at 5ug/mL. At day 6 post-infection, 500,000 live cells per sample were permeabilized and processed by CUT&RUN by standard protocols. Samples were internally controlled by spiking in exogenous E.coli DNA relative to cell number, per the manufacturer’s protocol.
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|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Library strategy: CUT&RUN Reads were aligned to the NC_008253.1 version of the E. coli reference genome using bowtie v1.2.2 in single-end mode with parameter -k 1 –best. Reads not aligned to E. coli were retained and aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 in single-end mode with parameters -k 2 -m 2 –best. hg19 Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are normalized to millions of mapped reads
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|
|
Submission date |
Sep 05, 2021 |
Last update date |
Nov 09, 2021 |
Contact name |
Brian J Abraham |
Organization name |
St. Jude Children's Research Hospital
|
Department |
Computational Biology
|
Street address |
262 Danny Thomas Blvd
|
City |
Memphis |
State/province |
TN |
ZIP/Postal code |
38112 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (2) |
GSE159617 |
EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma |
GSE183475 |
EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma [CUT&RUN] |
|
Relations |
BioSample |
SAMN21238302 |
SRA |
SRX12020300 |