|
| Status |
Public on Dec 29, 2023 |
| Title |
BL6_IL4 |
| Sample type |
SRA |
| |
|
| Source name |
Pritoneal Macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Macrophage
strain: C57BL/6
treatment: treated with A fusion protein of mouse IL-4 with the Fc portion of IgG1
|
| Treatment protocol |
IL4 treated for 4 days for both BL/6 and BALB/c strains
|
| Growth protocol |
Macrophage cells were isolated from the peritoneal cells by using EasySep™ Mouse F4/80 Positive Selection Kit (100-0659, Stemcell Technologies)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin interaction (Hi-C) libraries preparations were performed by Arima Genomics (https://arimagenomics.com/) using the Arima-HiC kit
HiC-seq samples were pooled and sequenced on NovaSeq and paired-end sequencing
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
TheReal Time Analysis software (RTA 3.4.4) was used for processing raw data files, the Illumina bcl2fastq v2.20 was used to demultiplex and convert binary base calls and qualities to fastq format.
All Hi-C data were processed with Juicer (v.1.6 ), pipelines with default settings.
MEME-FIMO (5.4.1) was uesd to scan for the locations of strain-specific active transcription factors (TFs) within promoter-distal regions (enhancers)
Juicebox (2.3.0)was used to visualize the Hi-C heatmap.
Assembly: mm10
Supplementary files format and content: Loops hic files are generated by Juicer (v.1.6 )
|
| |
|
| Submission date |
Nov 16, 2023 |
| Last update date |
Dec 29, 2023 |
| Contact name |
Mingming Zhao |
| E-mail(s) |
mingming.zhao@nih.gov
|
| Organization name |
national institutes of health
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE248029 |
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [Hi-C] |
| GSE248038 |
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS |
|
| Relations |
| BioSample |
SAMN38285935 |
| SRA |
SRX22550691 |
