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Sample GSM8295483 Query DataSets for GSM8295483
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
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
 
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

Supplementary file Size Download File type/resource
GSM8295483_2705177_Foxp3_NC_1.CRall.bw 229.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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