|
| Status |
Public on Mar 28, 2024 |
| Title |
ATAC-Seq - Treg WT ex vivo stimulated 1 |
| Sample type |
SRA |
| |
|
| Source name |
Children’s Hospital of Philadelphia
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
treatment: stimulated
tissue: Tregs dervived from spleen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
One hundred thousand cells were lysed with 50 ul of cold lysis buffer (10mM Tris pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged at 550g for 10 minutes at 4C. Supernatants were discarded and nuclear pellets were subjected to Tn5 transposition using Nextera DNA preparation kits (cat #1502812). DNA was purified from transposition reaction using Qiagen Min-Elute PCR purification kits.
Transposed DNA fragments were PCR amplified and indexed using Nextera index kits. PCR reaction products were size selected using AMpure-XP beads and DNA fragments were re-suspended in 10 mM Tris-HCl. DNA concentration was determined by Qubit, and ATAC seq library quality was checked on a bioanalyzer. Dual indexed libraries were sequenced on the Illumina NovaSeq 6000 platform.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ATAC_Treg_WT_Stim_1
|
| Data processing |
Bases were called using Illumina bcl2fastq2 conversion v2.29
Reads were aligned using bowtie2 implimented in the ENCODE pipeline. Reads alignment by offsetting +4bp for all the reads aligned to the forward strand, and -5bp for all the reads aligned to the reverse strand
Open chromatin regions (OCRs) were called using MACS2 implimented in the ENCODE pipeline with the following parameters -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits. The encode blacklist regions (wgEncodeDacMapabilityConsensusExcludable.bed.gz) were removed from called peaks.
Assembly: mm9
Supplementary files format and content: comma deliminated files
|
| |
|
| Submission date |
Apr 05, 2022 |
| Last update date |
Mar 28, 2024 |
| Contact name |
Matthew C Pahl |
| E-mail(s) |
pahlm@email.chop.edu
|
| Phone |
5704282303
|
| Organization name |
Children's Hospital of Philadelphia
|
| Department |
Center for Spatial and Functional Genomics
|
| Lab |
Struan Grant and Andrew Wells
|
| Street address |
3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE200176 |
Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function [ATAC-Seq] |
| GSE200179 |
Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function |
|
| Relations |
| BioSample |
SAMN27305320 |
| SRA |
SRX14743249 |
