NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1574248 Query DataSets for GSM1574248
Status Public on Jan 18, 2016
Title H3K4me1.HPAF2
Sample type SRA
 
Source name H3K4me1.HPAF2
Organism Homo sapiens
Characteristics cell line background: HPAF2
cell type: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line
chip antibody: Anti-H3K4me1
chip antibody vendor: Abcam
chip antibody cat.#: ab8895
Treatment protocol No treatment
Growth protocol Eagle's Minimal Essential Medium (EMEM) supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep
Extracted molecule genomic DNA
Extraction protocol ChIP lysates were generated from 2-5x10^6 cells for histone marks or 20-40x10^6 cells for transcription factors. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chromatin IP against H3K4me1
Data processing Reads quality filtered according to the Illumina pipeline
Reads were mapped to the human hg19 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters, nomodel and bw=300 (except for the H3K27ac of PDACs for which a bw=100 was used). Each IP was compared to input DNA.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS
 
Submission date Dec 29, 2014
Last update date May 15, 2019
Contact name Chiara Balestrieri
E-mail(s) balestrieri.c@gmail.com
Organization name IRCCS San Raffaele Scientific Institute
Department Center for Omics Sciences
Street address Via Olgettina 58
City Milan
ZIP/Postal code 20132
Country Italy
 
Platform ID GPL11154
Series (2)
GSE64557 Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer [ChIP-seq]
GSE64560 Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer.
Relations
BioSample SAMN03273797
SRA SRX825374

Supplementary file Size Download File type/resource
GSM1574248_H3K4me1.HPAF2_vs_INPUT.CAPAN1_peaks.bed.gz 1.4 Mb (ftp)(http) BED
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