NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4133299 Query DataSets for GSM4133299
Status Public on Dec 31, 2020
Title ATACseq_rep1_HEK293
Sample type SRA
 
Source name Human embryonic kidney cell-line 293
Organism Homo sapiens
Characteristics 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 ATAC-seq, cells (5 x 104) were incubated with DNase I (Worthington cat# LS002007) to remove DNA from dead cells, washed with PBS, resuspended in lysis buffer, and treated with transposase from Nextera DNA sample Prep Kit (Illumina, cat# FC-121-1030).
Libraries were made through adding adpators on purified tagmented DNA, followed by double-sided bead purification. Purified products were sequenced with PE 150 cycles on an Illumina Nextseq500 system
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing ATAC-seq Reads aligned to hg19 using BWA. Properly aligned reads were filtered to exclude PCR duplicates and processed as previously described (PMC3959825). Read start positions were shifted towards the 3’ end by 4 bp in for reads aligning to plus strand and 5 bp towards the 5’ end for reads aligning to minus strand.
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 SAMN13070672
SRA SRX7030828

Supplementary file Size Download File type/resource
GSM4133299_YET121_ATAC_HEK293.bw 385.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap