|
| Status |
Public on Jun 26, 2023 |
| Title |
Hnf4ctrl.mTEC.H3K27me3.rep#2 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
strain: C57BL/6
genotype: Foxn1cre(+/-)Hnf4a(fl/+)Hnf4g(+/-)
cell type: mTEC
antibody: H3K27me3
|
| Treatment protocol |
mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, fixing cells for 1 minute at RT in 0.1% PFA, flow sorting mTECs into PBS, extracting nuclei and freezing at -80C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN protocol for genomic DNA extraction
CUTANA CUT&RUN Library Prep Kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CUT&RUN
WT_H3K27me3.merged.CPM.bigwig
|
| Data processing |
Fastq data were trimmed using TrimGalore
Reads were aligned to mm10 reference genome using bowtie2 v.2.3.4.3 with parameters --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 1000
Non-unique, duplicated and ChrM reads were removed using SAMTools view and Picard MarkDuplicates.
Bam files were converted bigWig using deepTools 3.5.0 with the following parameters --binSize 1 --normalizeUsing CPM --effectiveGenomeSize 2407883318
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Feb 20, 2023 |
| Last update date |
Jun 26, 2023 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
|
| Phone |
617-432-7747
|
| Organization name |
Harvard Medical School
|
| Department |
Microbiology and Immunobiology
|
| Lab |
CBDM
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE225657 |
Hnf4 controls gut and liver gene programs in the thymus [CUT&RUN] |
| GSE225661 |
Hnf4 controls gut and liver gene programs in the thymus |
|
| Relations |
| BioSample |
SAMN33386113 |
| SRA |
SRX19447686 |
