|
| Status |
Public on Mar 05, 2018 |
| Title |
DNase-seq Late Th2 WT-1 |
| Sample type |
SRA |
| |
|
| Source name |
Late Th2
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: Bcl11b[fl/fl]-CreERT2 mice on C57BL/6 background
isolated cell type: Naive CD4 T cells
sorting condition: CD4+CD44high
culture condition: Late Th2
genotype/variation: Bcl11b WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq experiments were performed following iDeal ChIP-seq Kit for Histones (C01010051, Diagenode) using anti-H3K27ac (C15410196, Diagenode). DNase-Seq followed the protocols described previously in (PMID: 26605532).
Library constructions ChIP-Seq and DNase-Seq follow the protocols described previously in (PMID: 19528076) and (PMID: 26605532).
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
GB4917
Cell culture
DNase-Seq
|
| Data processing |
Basecalls performed using CASAVA 2.18.
Sequence reads were mapped to mouse genome (mm9) by using bowtie 2 with default settings (PMID: 22388286 ). Reads mapped to multiple positions (MAPQ < 10) were discarded. Only one read for genomic site with multiple alignment hits were retained.
SICER v1.1 was used to call peaks (window size is 200bp, gap size is 400bp, bp-shift is 75, E-value = 1 and others by defaults) (PMID: 19505939).
Genome_build: mm9
Supplementary_files_format_and_content: *.scoreisland.txt.gz: gzipped peak file recoding peak call from SICER. Columns from left to right denote: chrom, start, end, score.
|
| |
|
| Submission date |
Dec 29, 2017 |
| Last update date |
Mar 05, 2018 |
| Contact name |
Andrew J Oler |
| E-mail(s) |
[email protected]
|
| Organization name |
NIAID/NIH
|
| Department |
Bioinformatics and Computational Biosciences Branch (BCBB)
|
| Lab |
Computational Biology Section
|
| Street address |
31 Center Drive, Room 3B62E
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE108633 |
Bcl11b, a Novel GATA3-Interacting Protein, Suppresses Th1 while Limiting Th2 Cell Differentiation (H3K27ac and DNase-Seq) |
| GSE109109 |
Bcl11b, a Novel GATA3-Interacting Protein, Suppresses Th1 while Limiting Th2 Cell Differentiation |
|
| Relations |
| BioSample |
SAMN08275892 |
| SRA |
SRX3521781 |
