NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4486257 Query DataSets for GSM4486257
Status Public on Apr 14, 2021
Title H3K79me2_veh rep1
Sample type SRA
 
Source name H3K79me2_veh rep1
Organism Homo sapiens
Characteristics cell type: LNCap cell line
antibody: Anti-H3K79me2
vendor: Abcam
catalog #: ab8898
treatment: DMSO
Treatment protocol 10 nM DHT was added before cell collection for MNase-seq/ MNase-ChIP-seq of histone markers assay.
Growth protocol LNCaP cells were cultured in 10% FBS RPMI 1640 medium, 1:2.5 split every 2 days. Cells are cultured in 5% charcoal stripped FBS RPMI-1640 medium
Extracted molecule genomic DNA
Extraction protocol extract 1: For ChIP-exo, after treatment with 10 nm DHT or vehicle for 4 h, LNCaP cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GATA2 antibody and T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.
extract2: For Mnase-ChIP-seq, chromatin was isolated from freshly cultured cells and Mono-nucleosomes with solubilized chromatin was achieved by MNase digestion at 37 °C, then immunoprecipitated with antibody-conjugated magnetic beads. DNA is phenol extracted and ethanol precipitated.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment 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, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 3000 following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Description Extraction protocol 2
Data processing hIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version with parameters '-k 2 -v 2' to report up to two valid alignments
Read with multiple valid alignments were removed using a Perl program
Uniquely mapped reads from replicates of the same sample were pooled
Peaks were called using MACS2 with parameters '-m 3,30 -g hs -p 1e-8'
ChIP-exo data were processed using ePEST with parameters '-p 1e-8 -R 25 -c 0.05 -k 2.0'
BigWig file was generated by deeptools for visualization
Genome_build: GRCh37/hg19
 
Submission date Apr 20, 2020
Last update date Mar 28, 2022
Contact name Tianbao Li
E-mail(s) tianbaoli89@gmail.com
Organization name University of Texas Health Science Center at San Anotnio
Department Molecular Medicine
Lab Victor Jin
Street address 7703 Floyd Curl
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
 
Platform ID GPL21290
Series (1)
GSE148935 LNCap cell nucleosome footprint elicits novel noncanonical GATA2 pioneer model
Relations
BioSample SAMN14644721
SRA SRX8142303

Supplementary file Size Download File type/resource
GSM4486257_H3K79me2_veh_rep1.bigWig 317.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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