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Sample GSM2067931 Query DataSets for GSM2067931
Status Public on Feb 22, 2016
Title H3K4me3 WT OIS (SC OIS H3K4me3)
Sample type SRA
Source name IMR90 Lung Fibroblasts
Organism Homo sapiens
Characteristics genotype/variation: WT
treatment: 4-OHT induced H-Ras V12
ChIP: H3K4me3
antibody: Abcam, ab8580
Treatment protocol Senescence was induced with 4-OHT (Sigma-Aldrich). For the viral transfections, IMR90 fibroblasts were infected with virus (scrambled control (SC) or MLL1 KD shRNA) at 60% confluency on 10-cm2 plates for 24 h in the presence of polybrene. Forty-eight hours following infections, cells underwent selection with puromycin to obtain completely puromycin-resistant cell populations. Senescent cells were maintained in dishes for 10 d to ensure growth termination. Senescence was determined by monitoring CDKN2A/P16 up-regulation and down-regulation of cyclin genes and by SA-β-gal (Chemicon International).
Growth protocol IMR90 cells (obtained from Coriell Institute for Medical Research) were grown in DMEM without phenol with 10% FBS and 1% penicillin/streptomycin at 3% oxygen. The cells were generated by retrovirally infecting normal IMR90 fibroblasts with pLNCX-ER:Ras.
Extracted molecule genomic DNA
Extraction protocol Cells in 10-cm2 dishes were fixed in 1% formaldehyde for 5 min, and fixation was quenched with addition of glycine to 125 mM for an additional 5 min. Cells were harvested by scraping from plates and were washed twice in 1× PBS before storage at −80°C. ChIP was performed as previously described (Shah et al. 2013) except that extracts were sonicated nine times for 5 min each round (30 sec of sonication with intermediate incubation of 30 sec per round) using a Bioruptor (Diagenode). All ChIPs were performed using 500 µg of extract and 2 µg of antibody per sample. Thirty microliters of Protein G Dynabeads (Invitrogen, 100.02D) was used per ChIP.
ChIP DNA was used to make sequencing libraries using NEBNext (New England Biolabs). Libraries were quantified (Kapa Biosystems), and sequencing was performed on either Hi-Seq or NextSeq platforms (50-bp, single-end reads) (Illumina).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Demultiplexing: data were demultiplexed from the raw reads using Illumina's BCL2Fastq version 2.15.
Alignment: demultiplexed data were aligned to UCSC reference genome build hg19 downloaded from iGenomes. Alignments were generated with Bowtie 2.2.4, allowing for one distinct alignment and one mismatch per seed region (-N1 -K1). All other default parameters were used.
Track creation: reads were counted to 100-bp fixed bins using featureCounts from the Subreads package version 1.4.6-p2. Normalized TPTM was used. Input was subtracted from γH2A.X, while all H3K4me3 tracks had H3 divided to account for the extensive histone loss seen in senescence.
Genome_build: hg19
Supplementary_files_format_and_content: BigWigs: bigWig files represent the distribution of H3K4me3 and gH2A.x genome-wide in 100bp contiguous, non-overlapping bins, weighted per 10 million aligned reads, and adjusted for local sonication efficiency biases by dividing by H3 or subtracting input (also weighted per 10 million aligned reads), respectively. The file is the subtraction of the OIS scramble control from the OIS MLL1 knockdown track.
Submission date Feb 22, 2016
Last update date May 15, 2019
Contact name Gregory Donahue
Organization name The University of Pennsylvania
Department Cell & Developmental Biology
Lab Zaret Lab
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL18573
Series (2)
GSE78141 MLL1 is essential for the senescence-associated secretory phenotype [ChIP-Seq]
GSE78142 MLL1 is essential for the senescence-associated secretory phenotype
BioSample SAMN04505927
SRA SRX1595743

Supplementary file Size Download File type/resource 163.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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