|
| Status |
Public on Jul 25, 2023 |
| Title |
ChIP-seq DNMT1 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
gender: Male
age: 2 months
antibody: DNMT1
|
| Treatment protocol |
University of Pittsburgh animal protocol
|
| Growth protocol |
Regular chow diet
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
ChIP-seq DNMT1
|
| Data processing |
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference mm10 by BWA (version 0.7.17) and sorted by SAMtools (version 1.9)
Aligned reads were filtered by SAMtools (version 1.9, samtools view -b -h -q 30 -F 256 $BAMinput > $BAMfilter) and marked duplicates by picard tools (version 2.18.12)
Peak calling was performed by MACS2 (version 2.1.1.20160309) comparing treated library and the corresponding input library
Assembly: mm10
Supplementary files format and content: BW file generated by deeptools (version 3.3.0, bamCoverage -b $BAMsort -o $BWfile)
|
| |
|
| Submission date |
Apr 08, 2022 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
shl96@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Street address |
203 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE200468 |
NOTCH-YAP1/TEAD-DNMT1 axis drives hepatocyte reprogramming into intrahepatic cholangiocarcinoma [ChIP-Seq] |
| GSE200472 |
NOTCH-YAP1/TEAD-DNMT1 axis drives hepatocyte reprogramming into intrahepatic cholangiocarcinoma |
|
| Relations |
| BioSample |
SAMN27417130 |
| SRA |
SRX14786113 |
