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| Status |
Public on Sep 17, 2021 |
| Title |
ATAC.Day28.DCLK1 |
| Sample type |
SRA |
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| Source name |
Ex vivo samples from pancreas
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| Organism |
Mus musculus |
| Characteristics |
cell type: Primary pancreatic epithelial cells
growth protocol: Ex vivo samples, no need to grow
treatment: Harvest at 28 days after Caerulein treatment
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50000-100000 cells were pelleted by centrifugation and re-suspended in 100 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin). After incubation on ice for five minutes, lysis was washed out by adding 1 mL of lysis buffer without NP40 and digitonin. Nuclei were pelleted by centrifugation for 10 min at 500g, 4 ºC. The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1.5 µl of Tn5 transposase (Illumina), 10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), 16.5 µl PBS, 0.5 µl of 1% digitonin, 0.5 µl of 10% Tween-20. The reaction was incubated at 37ºC for 30 minutes with 600 RPM mixing and cleaned up with PCR purification kit. The eluted DNA were then used for library preparation and sequenced on an Illumina Hiseq4000/HiseqX platform.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Reads were pre-processing (filtering, quality trimming and adapter clipping) using cutadapt, then paired-end with min 36-bp reads length were aligned to mouse genome build GRCm38/mm10 using Bowtie2 v2.2.6 (PMID: 22388286) 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. Then read positions were corrected for transposon insertion offset as described in (PMID:24097267).
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 146”, “--qvalue 1E‐4”, "--nolambda" and "--keep-dup all" flags and arguments.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.narrowPeak (list of the peaks called by MACS2) or *.bigwig (normalized signal tracks generated with bamCoverage)
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| Submission date |
Jul 15, 2021 |
| Last update date |
Sep 17, 2021 |
| Contact name |
Chiara Balestrieri |
| E-mail(s) |
balestrieri.c@gmail.com
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| Organization name |
IRCCS San Raffaele Scientific Institute
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| Department |
Center for Omics Sciences
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| Street address |
Via Olgettina 58
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| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE180192 |
Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis [ATAC-seq] |
| GSE180212 |
Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis |
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| Relations |
| BioSample |
SAMN20248528 |
| SRA |
SRX11470409 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5455112_ATAC.Day28.DCLK1.bw |
402.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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