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Sample GSM5558173 Query DataSets for GSM5558173
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.
 
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
 
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

Supplementary file Size Download File type/resource
GSM5558173_Kelly_lacZ_H3K27ac.RPM.wig.gz 140.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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