NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3020125 Query DataSets for GSM3020125
Status Public on Feb 11, 2019
Title CHIPseq-MCF10A Epithelial-treated with DMSO-CHIP for H3K27ac
Sample type SRA
 
Source name Breast mammary gland
Organism Homo sapiens
Characteristics treatment: DMSO
antibody: H3K27ac
Treatment protocol To induce p53 activation, cells were treated with Nutlin-3A (5 mM final) or DMSO (vehicle control) for 6 hours.
Growth protocol MCF10A epithelial cells were cultured in HuMEC Complete media (Gibco, #12752010) and skin fibroblast cells were cultured in DMEM media (with 10% FBS and 1% Pen/Strep, Gibco)
Extracted molecule genomic DNA
Extraction protocol For RNA-Seq: Total mRNA was extracted with E.Z.N.A. Total RNA kit (Omega; R6834-02) and Poly(A)+ RNA was isolated by double selection with poly-dT beads, using 2.5 mg total RNA, which is then followed by first- and second-strand synthesis
For RNA-Seq: Libraries were prepared using NEXTflex Rapid Illumina DNA-Seq Library Prep Kit (Bioo Scientific).
For ChIP-Seq: Cells were crosslinked at 80% confluency with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 125mM glycine and the resulting pellet was washed twice with cold PBS and lysed. Samples were subjected to sonication with Diagenode Bioruptor Plus for 40 cycles (30 sec on/off at high setting) for shearing chromatin to 150-500 bp average size. Immunoprecipitation reactions were performed with Diagenode IP-Star Compact Atuomated System with mentioned antibodies. Immunoprecipitated DNA was reverse-crosslinked at 65°C for 4 hours and then eluted from beads, purified using SPRI beads, and used to construct sequencing libraries.
For ChIP-Seq: Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Raw fastq reads were processed for quality control using FastQC v0.11.5
Reads were aligned to the reference genome (hg19) using STAR v 2.5.3a. Genome indices for STAR were built using the parameters --runThreadN 12 --runMode genomeGenerate --sjdbOverhang 100
Indexes built in the aforementioned step were then used to align reads with STAR using the parameters --runThreadN 12 --genomeDir <genomeDir> --readFilesIn <Sample.fastq.gz> --readFilesCommand zcat --outSAMstrandField intronMotif --outFilterIntronMotifsRemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outFileNamePrefix Sample. --limitBAMsortRAM 61675612266
Gene counts were calculated using HTSeq v 0.9.1 with -f bam -s no -I gene_id -m intersection-strict parameters
Genome_build: hg19
Supplementary_files_format_and_content: The count files are tab-delimited text files with first column as geneNames and second column as geneCounts
 
Submission date Feb 22, 2018
Last update date Feb 11, 2019
Contact name Morgan A Sammons
E-mail(s) masammons@albany.edu
Organization name University at Albany - SUNY
Department Biological Sciences
Lab Sammons
Street address 1400 Washington Ave, Life Sciences 2075
City Albany
State/province NY
ZIP/Postal code 12222
Country USA
 
Platform ID GPL18573
Series (1)
GSE111009 Cell type-dependent control of enhancer and p53 transcriptional activity by p63
Relations
BioSample SAMN08581026
SRA SRX3734310

Supplementary file Size Download File type/resource
GSM3020125_MCF10A_DMSO_H3K27ac_peaks.narrowPeak.gz 1.7 Mb (ftp)(http) NARROWPEAK
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