 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 17, 2021 |
| Title |
H3K27Ac.CTRL |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic spheroids
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Pancreatic epithelial cells
growth protocol: DMEM/F12 1:1 supplemented with 2.5 mM L-Glutamine, 15 mM HEPES Buffer (HyClone), 5 mg/ml D-glucose (Sigma Aldrich), 1.22 mg/ml nicotinamide (Sigma Aldrich), 5 nM 3,3,5-Tri-iodo-L-thyronine (Sigma Aldrich), 0.5 μM hydrocortisone Solution (Sigma Aldrich), 100 ng/ml cholera toxin (Sigma Aldrich), 0.5 % insulin-transferrin-selenium (Corning), 100 μg/ml penicillin/streptomycin (Gibco), 0.1 mg/ml soybean trypsin inhibitor (Sigma Aldrich), 20 ng/ml EGF (Peprotech), 25 μg/ml bovine pituitary extract (Invitrogen), and 5% Nu Serum IV Culture Supplement (BD)
antibody: Anti H3K27ac (Abcam, ab4729)
treatment: Untreated
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP lysates were generated from 50x10^6 cells. 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 AMPure XP SPRI (Beckman Coulter) and quantified using Quantifluor (Promega). ChIP DNA was prepared for HiSeq2000 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 H3K27ac
|
| Data processing |
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38), then reads were aligned to mouse genome build GRCm38/mm10 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS 1.4 with the “--nomodel” and “--shiftsize 125” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.bed, list of the peaks called by MACS 1.4
|
| |
|
| Submission date |
Jul 15, 2021 |
| Last update date |
Sep 17, 2021 |
| 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 |
GPL13112 |
| Series (2) |
| GSE180199 |
Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis [ChIP-seq] |
| GSE180212 |
Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis |
|
| Relations |
| BioSample |
SAMN20250504 |
| SRA |
SRX11472095 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5455392_H3K27Ac.CTRL.bed.gz |
541.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
