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SRX863783: GSM1598310: HeLa_DHS pooled reps; Homo sapiens; DNase-Hypersensitivity
2 ILLUMINA (Illumina Genome Analyzer IIx) runs: 34.2M spots, 1.2G bases, 609.1Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Ectopic CENP-A nucleosomes localize to transcription factor hotspots and subtelomeric sites in human cancer cells
show Abstracthide Abstract
Comparison of histone variant CENP-A in different cell lines vs. DHS profiles from same cell lines. Mock IPs included. Overall design: Profiles of ectopic CENP-A IP after pre-clearing with CENP-B IPs, or profiles of DHS regions from mid-log culture SW480 colorectal cancer cell lines, HeLa cervical cancer cell lines, and EpiCo normal colon cell line were generated using deep sequencing after Mnase-based ChIP, in replicates, on the Illumina platform.
Sample: HeLa_DHS pooled reps
SAMN03325303 • SRS834714 • All experiments • All runs
Organism: Homo sapiens
Instrument: Illumina Genome Analyzer IIx
Strategy: DNase-Hypersensitivity
Selection: DNase
Layout: SINGLE
Construction protocol: For chromatin: Mnase treatment followed by mild crosslinking and low salt extraction overnight at 4C. IPs with CENP-A, HJURP or Mock. For DHS fragments: Low DNase I treatment followed by sucrose gradient purification of DHS fragments. Please see Athwal-Walkiewicz et al Epigenetics and Chromatin 8:3 for full protocol and cited references. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Experiment attributes:
GEO Accession: GSM1598310
External link:
Runs: 2 runs, 34.2M spots, 1.2G bases, 609.1Mb
Run# of Spots# of BasesSizePublished


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