|
| Status |
Public on Aug 10, 2020 |
| Title |
Th9 WT1 |
| Sample type |
SRA |
| |
|
| Source name |
Th9
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
tissue: spleen
treated: in vitro culture
|
| Growth protocol |
Naïve T cells culture under Th2, Th9 and Th17 condition
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed by 1X PBS and re-suspended in cold PBS. Collected cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% IGEPAL CA-630) and the nuclei were pelleted and resuspended in Tn5 enzyme and transposase buffer (Illumina Nextera® DNA library preparation kit, FC-121-1030).
The resulting ATAC-seq libraries were sequenced on Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine and paired-end 50 bp reads were generated
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Th9 WT1
|
| Data processing |
Libraries were sequenced with 2×50 bp paired-end configuration on an Illumina NovaSeq 6000.
Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3.
The resulting high-quality reads were aligned to the mouse reference genome mm10 using bowtie2.
Duplicate reads were discarded with Picard.
Reads mapped to mitochondrial DNA together with low mapping quality reads were excluded from further analysis.
Peaks were detected with MACS2 (version 2.1.0) with parameters "-f BAMPE --nolambda -broad".
Genome_build: UCSC mm10
Supplementary_files_format_and_content: broadPeak BED files were generated from MACS2
|
| |
|
| Submission date |
Feb 19, 2020 |
| Last update date |
Aug 11, 2020 |
| Contact name |
Mark H Kaplan |
| E-mail(s) |
mkaplan2@iupui.edu
|
| Phone |
317-278-3696
|
| Organization name |
Indiana University
|
| Department |
Microbiology and Immunology
|
| Street address |
635 Barnhill Dr. MS 420
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE145512 |
STAT5 is a pioneer factor for BATF-mediated plasticity at the Il9 locus [ATAC-Seq] |
| GSE145541 |
STAT5 promotes accessibility and is required for BATF-mediated plasticity at the Il9 locus |
|
| Relations |
| BioSample |
SAMN14134138 |
| SRA |
SRX7747628 |
