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Sample GSM1661558 Query DataSets for GSM1661558
Status Public on Jan 01, 2017
Title HEXIM1>CDK9 reChIP on A375 cells
Sample type SRA
Source name A375 melanoma cell line
Organism Homo sapiens
Characteristics cell line: A375
Treatment protocol One hundred million A375 cells per condition were washed, proteins and DNA were cross-linked with 11% formaldehyde and cell pellets were frozen down at -80C.
Growth protocol Human A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).
Extracted molecule genomic DNA
Extraction protocol DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam) followed by CDK9 (Santa Cruz) antibodies sequentially and vice versa. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description DMSO HEXIM1>CDK9 reChIP
Data processing ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph pileup from MACS 2.0 output
Submission date Apr 20, 2015
Last update date May 15, 2019
Contact name Leonard Zon
Organization name Boston Children's Hospital
Department Oncology/Hematology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL16791
Series (2)
GSE68047 Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [reChIP-seq]
GSE68053 Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription
BioSample SAMN03492259
SRA SRX1000227

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

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