|
| Status |
Public on Aug 07, 2019 |
| Title |
WT_Treg_Foxp3_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bcl11b sufficient Treg cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Sorted CD4+YFP+ cells
genotype: Foxp3-IRES-YFP-Cre
antibody: Foxp3
|
| Growth protocol |
Single cell supensions were prepared from drainig lymphnodes and spleen. Respective cell population were sorted using BD Moflo-XDP cell sorter and fixed.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sheared Chromatin were cleared and protein-DNA complexes were isolated with antibody-magnetic bead complex.
ChIP-seq library for each sample were prepared according to manufacturer (NEXTFLEX® ChIP-Seq Kit 5143-01) protocols. Briefly,purified immunoprecipitated DNA were end-repaired and size selected for 200–400-bp fragments with Agencourt AMPure XP beads (A63880) followed by Adenylation, barcoded adaptor-ligation and PCR amplification (15 cycles). Size distribution and concentration of each library was checked using Agilent Bioanalyzer. Equivalent amounts of barcoded libraries were pooled and sequenced using HiSeq 2500 (Illumina) instruments.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Foxp3 ChIP DNA
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_Bcl11b-KO-Treg-Foxp3-specific.bed
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_common.bed
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_WT-Treg-Foxp3-specific.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_WT-Treg-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_WT-Treg-Foxp3-specific_.bed
|
| Data processing |
The quality of sequenced reads (50 bp; paired-end) was measured using FastQC , and low quality portions of the sequenced reads were trimmed using Trim Galore (version 0.4.2; with Cutadapt (version 1.12).
The trimmed reads were mapped to the mouse genome (reference assembly mm10) using HISAT2 (version 2.1.0).
The mapped reads were sorted by genomic positions using Samtools (version 1.3) , and duplicated mapped reads were removed using Sambamba (version 0.6.5).
Biological replicates for each conditions were merged and the genomic binding sites (peaks) of a given protein were identified using HOMER (version 4.10.1) with a FDR-adjusted p-value cutoff of 0.001
The peaks overlapped with the blacklisted regions that show anomalous, unstructured, and high signal/read counts were discarded.
To identify reliable target genes of a given protein, peaks located 20 kb outside of the gene’s transcription start sites were removed.
To identify common (or specific) peaks between given conditions, the identified peaks in each condition were merged.
Merged peaks were used to define common or specific peaks using HOMER (getDifferentialPeaks) with default parameters.
Deeptools (version 2.5.3-2-503c71b) was used to draw heatmaps
Genome_build: mm10
Supplementary_files_format_and_content: BED format (peak positions)
|
| |
|
| Submission date |
Oct 08, 2018 |
| Last update date |
Aug 07, 2019 |
| Contact name |
Keunsoo Kang |
| E-mail(s) |
kangk1204@gmail.com
|
| Organization name |
Dankook University
|
| Street address |
119 Dandae-ro
|
| City |
Cheonan |
| ZIP/Postal code |
31119 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE120947 |
Bcl11b prevents catastrophic autoimmunity by controlling multiple aspects of regulatory T-cell gene expression program [ChIP-Seq] |
| GSE120948 |
Bcl11b prevents catastrophic autoimmunity by controlling multiple aspects of regulatory T-cell gene expression program |
|
| Relations |
| BioSample |
SAMN10218726 |
| SRA |
SRX4814135 |
