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| Status |
Public on May 28, 2024 |
| Title |
2317016_aFoxp3-aTreg-1 |
| Sample type |
SRA |
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| Source name |
Spleen and lymph nodes
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen and lymph nodes
cell type: activated Treg
genotype: Foxp3gfp-DTR
treatment: No
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| 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. CD4 naïve T cells (Tn: CD4+ CD25-CD44loCD62Lhi), natural Treg cells (CD4+GFP+) T cells, CD4 effector T cells (Te, CD4+GFP-CD44hiCD62Llo), 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 |
library strategy: Cut&Tag
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. 15bp from 5' were also trimmed to reduce Tn5 bias.
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 4 million fragments as CUT&TAG protocol paper suggested > 3 million. 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
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| Submission date |
Oct 11, 2023 |
| Last update date |
May 28, 2024 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
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| Organization name |
St Jude Children's Research Hosipital
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| Department |
Center for Applied Bioinformatics
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE149674 |
Dynamic Foxp3-chromatin interaction controls tunable Treg cell function |
| GSE245101 |
Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [Cut&Tag Foxp3] |
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| Relations |
| BioSample |
SAMN37778777 |
| SRA |
SRX22067220 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7836337_2317016_aFoxp3-aTreg-1.CRall.bw |
29.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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