GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1587927 Query DataSets for GSM1587927
Status Public on Sep 25, 2015
Title K562_CDK8_untreated_18
Sample type SRA
Source name K562
Organism Homo sapiens
Characteristics cell line: K562
cell type: CML
treatment protocol: untreated
chip epitope: CDK8
chromatin prep#: 18
ca sensitivity: insensitive
Growth protocol K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for Illumina sequencing were prepared using the Illumina TruSeq ChIP Sample Preparation kit with the following exceptions. After end-repair and A-tailing, ChIP DNA or whole cell extract DNA was ligated to Illumina RNA adaptors with unique indices. Alternatively, libraries were prepared using the KAPA Hyper Prep Kit for Illumina and ligated to unique Bioo Scientific NEXTflex barcode adaptors. Following ligation, libraries were amplified with 16-18 cycles of PCR and were then size-selected using a 2% gel cassette in the Pippin Prep System from Sage Science. For histone modifications and RNA pol II, DNA fragments of size 200-500bp were captured. For CDK8 and MED1, DNA fragments of size 200-450bp were captured. Libraries were quantified by qPCR utilizing the KAPA Biosystems Illumina Library Quantification kit.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description matched input: K562_input_8260
Data processing Basecalls performed using CASAVA version 1.4
FastQC v.0.10.1 was used to check read quality metrics. If necessary, trim_galore v.0.3.3 was used with default settings to remove adapters, low-quality bases and trimmed reads < 20nt long after trimming.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v.1.0.0 with flags -n 1 -m 1 --best --strata
Duplicate reads were removed with MarkDuplicates (picard tools v.1.79(1282))
In cases where peaks were used without subsequent ROSE enhancer analysis, SPP was used both for cross-correlation analysis and for peak finding using default parameters or FDR < 0.05. MACS2 was used either with default parameters or using --shiftsize to set the strand shift to match the SPP peak cross-correlation size. Peaks identified by both peak finders were retained. Regions on chrM or overlapping repeat elements (RepeatMasker bed file downloaded from UCSC 16 Nov. 2012) by > 70% were routinely excluded.
In cases where ROSE was used to identify enhancers and super-enhancers, MACS v.1.4 was run with the suggested parameters, namely -p 1e-9 --keep-dup=auto. MACS v1.4 peak bed files were converted to GFF format and used for ROSE with suggested parameters : -s 12500 -t 2000.
Genome_build: hg19
Submission date Jan 21, 2015
Last update date May 15, 2019
Contact name Matthew D. Shair
Organization name Harvard University
Department Chemistry and Chemical Biology
Lab Shair
Street address 12 Oxford Street
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
Platform ID GPL16791
Series (2)
GSE65138 Effect of cortistatin A (CA) on enhancer occupancy in CA-sensitive and -insensitive human cell lines
GSE65161 Mediator kinase inhibition further activates super-enhancer-associated genes in AML
BioSample SAMN03290586
SRA SRX849404

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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