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Sample GSM4133288 Query DataSets for GSM4133288
Status Public on Dec 31, 2020
Title H3K27Ac_rep2_HEK293_ChIPsep
Sample type SRA
 
Source name Human embryonic kidney cell-line 293
Organism Homo sapiens
Characteristics chip antibody: H3K27Ac antibody (Active motif, cat#, lot#10918010)
cell status: native cells
cell line: HEK293
Growth protocol U2OS cells and HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin until 80% confluent. HepG2 cells were grown in EMEM with 10% FBS and 1% penicillin and streptomycin. K562 cells were grown in RPMI supplemented with 10% heat-inactivated FBS, 2 mM GlutaMax, and 1% penicillin and streptomycin.
Extracted molecule genomic DNA
Extraction protocol For ChIP-seq, chromatin from 1% formaldehyde-fixed cells were fragmented to 200-500 bps by sonication for 5-6 mins using the Branson sonifer SFX250
Sequencing libraries were prepared with 3 ng of each H3K27Ac ChIP DNA and input sample using SMARTer ThruPLEX DNA-seq kit (Takara, Cat# R400675). Libraries were sequenced with single-end (SE) 75 cycles on an Illumina Nextseq 500 system
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq reads were aligned to human reference genome hg19 using Burrows-Wheeler Alignment (BWA) tool (PMC2705234). Genome-wide coverage was calculated after extending to 200 bases(approximate fragment size) and averaged over 25 bp windows using igvtools (https://doi.org/10.1093/bib/bbs017). Coverage was then normalized and scaled using RSeqC (http://rseqc.sourceforge.net/#normalize-bigwig-py)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization on igv
 
Submission date Oct 21, 2019
Last update date Jan 01, 2021
Contact name Keith Joung
E-mail(s) esther.ygt@gmail.com
Organization name MGH
Street address 149 13th st
City Charlestown
State/province MA
ZIP/Postal code 02129
Country USA
 
Platform ID GPL18573
Series (1)
GSE139190 Chromatin status and transcriptomics of HEK293, U2OS, HepG2 and K562
Relations
BioSample SAMN13070683
SRA SRX7030817

Supplementary file Size Download File type/resource
GSM4133288_YET160_rep2_HEK293_H3K27Ac.bw 178.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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