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Series GSE265888 Query DataSets for GSE265888
Status Public on Apr 27, 2024
Title Loop Stacking Attenuates Chromatin Boundaries in TCR Loci During Thymocyte Development
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Expression profiling by high throughput sequencing
Summary Topologically Associating Domains (TADs) partition the genome into self-interacting regions through boundaries. Chromatin configuration plays a crucial role in TCR gene rearrangements, thereby affecting repertoire diversity. To assess the dynamics of chromatin boundaries within TCR genes, we conducted Hi-C assays on double-negative (DN) and double-positive (DP) cells from RAG-deficient mice. A chromatin boundary at the 3' end of the Tcrb locus observed in DN cells dissipated in DP cells, thereby altering interactions between the main Vβ cluster and the recombination center. Additionally, the INTs boundary in the Tcra-Tcrd locus disappeared in DP cells, leading to enhanced interactions between the proximal Vα region and recombination center at the Jα segments. Subsequent analysis revealed that the disappearance of boundaries was not attributable to diminished CTCF binding but rather heightened activity within these regions. This study illuminates the developmental dynamics of TAD boundaries in TCR genes, enriching our understanding of their evolving nature.
 
Overall design Hi-C analysis of EACBE+/+Rag1-/- and EACBE-/-Rag1-/- DN thymocytes;Hi-C analysis of EACBE+/+Rag1-/- DP thymocytes;3C-HTGTS analysis of EACBE+/+Rag1-/- DN and/or DP thymocytesusing different baites(Trbv12-2,Trbv5，Eb,Trav21,Trdv2-2);3C-HTGTS analysis of EACBE+/+Rag1-/- and/or EACBE-/-Rag1-/- DN thymocytes using different baites(Ea,INT2,Trdv2-2,Trdd2,Trdv5,TEA);HTGTS-VDJ analysis of EACBE+/+Rag1-/- and EACBE-/-Rag1-/- DN or DP thymocytes at the baits from Trdj1 or Traj61;ATAC-seq analysis of EACBE+/+Rag1-/- and EACBE-/-Rag1-/- DN thymocytes;ATAC-seq analysis of EACBE+/+Rag1-/- DP thymocytes.
 
Contributor(s) Zhu Y, Dai R, Hao B
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 25, 2024
Last update date Apr 22, 2025
Contact name Hao bingtao
E-mail(s) haobingtao@gmail.com
Phone 18578669173
Organization name Southern Medical University
Street address ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province
City Guangzhou
ZIP/Postal code haobingtao@gmail.com
Country China
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (92)
GSM8230919 EACBEwt-Rag1ko-DN-DpnII-HiC-rep1
GSM8230920 EACBEwt-Rag1ko-DN-DpnII-HiC-rep2
GSM8230921 EACBEwt-Rag1ko-DN-DpnII-HiC-rep3
Relations
BioProject PRJNA1104639

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE265888_EACBEko-Rag1ko-DN-DpnII-HiC.allValidPairs.hic 6.6 Gb (ftp)(http) HIC
GSE265888_EACBEko-Rag1ko-DN-DpnII-HiC.allValidPairs.txt.gz 6.6 Gb (ftp)(http) TXT
GSE265888_EACBEwt-Rag1ko-DN-DpnII-HiC.allValidPairs.hic 6.4 Gb (ftp)(http) HIC
GSE265888_EACBEwt-Rag1ko-DN-DpnII-HiC.allValidPairs.txt.gz 6.6 Gb (ftp)(http) TXT
GSE265888_EACBEwt-Rag1ko-DN-DpnII-HiC_all_chr_compartments.bw 433.3 Kb (ftp)(http) BW
GSE265888_EACBEwt-Rag1ko-DP-DpnII-HiC.allValidPairs.hic 6.8 Gb (ftp)(http) HIC
GSE265888_EACBEwt-Rag1ko-DP-DpnII-HiC.allValidPairs.txt.gz 5.2 Gb (ftp)(http) TXT
GSE265888_EACBEwt-Rag1ko-DP-DpnII-HiC_all_chr_compartments.bw 426.4 Kb (ftp)(http) BW
GSE265888_RAW.tar 3.5 Gb (http)(custom) TAR (of BED, BEDGRAPH, BEDPE, BROADPEAK, BW, CSV, MATRIX, TXT)
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Raw data are available in SRA
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