|
| Status |
Public on Nov 01, 2023 |
| Title |
rat_F_H3K4me1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
antibody: H3K4me1
common_name: Common rat
Sex: F
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were contructed using the NEBNext UltraII kit according to manufactor's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
merged-rat-H3K4me1-ChIP-bowtie2-30qual-filter_FE.sorted.bdg.bw
|
| Data processing |
Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
ChromHMM was used to annotate chromatin states using the rat alignments
macs was used to calculate CTCF fold-enrichment tracks
Assembly: rn6
Supplementary files format and content: Processed data
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Mariam Okhovat |
| Organization name |
Oregon Health and Science University
|
| Department |
Medicine
|
| Street address |
3030 S Moody Ave.
|
| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE197926 |
TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function |
|
| Relations |
| BioSample |
SAMN38051888 |
| SRA |
SRX22320798 |
