|
| Status |
Public on Jan 18, 2016 |
| Title |
H3K4me1.CFPAC1 |
| Sample type |
SRA |
| |
|
| Source name |
H3K4me1.CFPAC1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: CFPAC1
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 |
Iscove's Modified Dulbecco Medium (IMDM) 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 |
SAMN03273819 |
| SRA |
SRX825373 |
