|
| Status |
Public on May 24, 2023 |
| Title |
Pancreas-Input DNA |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreas
strain: Mixed
chip antibody: None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated pancreas and NFIC-DNA complexes were isolated with antibody.
Libraries were prepared from purified DNA using "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (ref. E7645), as per the manufacturer’s instructions. Briefly, DNA samples were processed through subsequent enzymatic treatments for fragmentation (5 min), end-repair, dA-tailing, and ligation to adapters Adapter-ligated libraries were amplified by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size was 350 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's recommendations.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Rubioseq pipeline was used to carry out the analysis:
Alignment performed using BWA aligner
Duplicates marked and removed using Picard
Normalization performed with MACS2
Peak-calling using MACS2 with --nomodel --extsize 200 --gsize mm
Genome_build: mm10
Supplementary_files_format_and_content: peak
|
| |
|
| Submission date |
Jul 29, 2021 |
| Last update date |
May 24, 2023 |
| Contact name |
Jaime Martinez de Villarreal |
| E-mail(s) |
jmartinezv@cnio.es
|
| Phone |
+34 917328000
|
| Organization name |
CNIO
|
| Department |
Molecular Oncology Programme
|
| Lab |
Epithelial Carcinogenesis Group
|
| Street address |
Melchor Fernández Almagro, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE181098 |
Genome-wide occupancy map of NFIC in mouse pancreas |
|
| Relations |
| BioSample |
SAMN20477925 |
| SRA |
SRX11600042 |
