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Status |
Public on May 29, 2024 |
Title |
2705177_Foxp3_NC_1 |
Sample type |
SRA |
|
|
Source name |
Spleen and lymph nodes
|
Organism |
Mus musculus |
Characteristics |
tissue: Spleen and lymph nodes antibody: anti-Foxp3 cell type: ex vivo cultured nTreg cells genotype: sgNC in RosaCas9/+ Foxp3gfp treatment: anti-CD3/anti-CD28 restimulation
|
Extracted molecule |
genomic DNA |
Extraction protocol |
CD4 T cells were enriched by EasySep Mouse CD4 T Cell Isolation Kit (STEMCELL) from lymph nodes and spleens. naive T cells (CD4+GFP-CD44loCD62Lhi), Natural Treg cells (CD4+GFP+) T cells, resting Treg cells (rTreg: CD4+GFP+CD44loCD62Lhi), activated Treg cells (aTreg: CD4+ GFP+CD44hiCD62Llo) were further sorted by FACS. Libraries were prepared with precipitated DNA using KAPA Hyper Prep Kit (Kapa Biosystems). The library DNA was enriched by size selection with AMPure XP beads.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
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Data processing |
Trim_Galore(v0.4.4) is used to quality trim 3’ reads raw reads with the cutadapt (DOI: 10.14806/ej.17.1.200) program. A quality score cutoff of Q20 is used. Trimmed reads are mapped to the mm10(Gencode GRCm38) reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943). biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads and non-duplicated reads were kept by samtools (parameter “-q 1 -F 1804” version 1.2). All samples have more than 5 million fragments as suggested by CUT&RUN protocol paper. We generated bigwig files using the center 80 bp of fragments smaller than 2000 bp and normalized to 10 million fragments. We confirmed the replicability between replicates. Assembly: mm10(Gencode GRCm38) Supplementary files format and content: bigwig Library strategy: Cut&Run
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Submission date |
May 29, 2024 |
Last update date |
May 29, 2024 |
Contact name |
Beisi Xu |
E-mail(s) |
beisi.xu@stjude.org
|
Organization name |
St Jude Children's Research Hosipital
|
Department |
Center for Applied Bioinformatics
|
Street address |
262 Danny Thomas Pl
|
City |
Memphis |
State/province |
Tennessee |
ZIP/Postal code |
38105 |
Country |
USA |
|
|
Platform ID |
GPL24247 |
Series (2) |
GSE149674 |
Dynamic Foxp3-chromatin interaction controls tunable Treg cell function |
GSE268623 |
Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [Cut&Run Foxp3 Batf Ets1] |
|
Relations |
BioSample |
SAMN41592496 |
SRA |
SRX24744433 |