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Series GSE81553 Query DataSets for GSE81553
Status Public on Apr 25, 2018
Title TSA-Seq Mapping of Nuclear Genome Organization [seq]
Organism Homo sapiens
Experiment type Other
Summary We describe TSA-Seq, a new mapping method able to estimate mean chromosomal distances from nuclear speckles genome-wide and predict several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple, spatially separated nuclear domains, including two types of transcription ?hot-zones?. Transcription hot-zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers.
 
Overall design We used TSA-Seq to study genome organization relative to nuclear speckles and the nuclear lamina. For nuclear speckles, we performed TSA-Seq using two different antibodies against the protein SON and an antibody against a phosphorylated epitope of the protein SC35. We also performed TSA-Seq using an antibody against RNA Pol II as a general marker for active nuclear domains to compare with the speckle TSA-Seq chromosome patterns. For the nuclear lamina, we performed TSA-Seq using antibodies against lamin B and Lamin A/C. For each TSA-Seq experiment, a no primary control experiment was done in parallel, where the same TSA-Seq procedure is performed but with no added primary antibody.
 
Contributor(s) Chen Y, Zhang L, Belmont AS
Citation(s) 30154186
NIH grant(s)
Grant ID Grant title Affiliation Name
U54 DK107965 Combined Cytological, Genomic, and Functional Mapping of Nuclear Genome Organization UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN Andrew Steven Belmont
R01 GM058460 Chromatin Domain Structure and Function UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN Andrew Steven Belmont
Submission date May 18, 2016
Last update date Nov 26, 2023
Contact name Andrew S Belmont
E-mail(s) asbel@illinois.edu
Phone (217) 244-2311
Organization name University of Illinois at Urbana-Champaign
Street address 601 S Goodwin Ave, CLSL B509
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
 
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (43)
GSM2157129 No Primary Control_for_SON TSA-Seq
GSM2157130 input_for_No Primary Control_for_SON TSA-Seq
GSM2157131 SON TSA-Seq Condition 1 (TSA only)
This SubSeries is part of SuperSeries:
GSE66019 TSA-Seq Mapping of Nuclear Genome Organization
Relations
BioProject PRJNA321975
SRA SRP075320

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
GSE81553_K562_GRO-Seq_binned_20kb.bw 992.8 Kb (ftp)(http) BW
GSE81553_K562_HiC_100kb_Eigenvector.bw 475.2 Kb (ftp)(http) BW
GSE81553_K562_RNA-Seq_binned_20kb.bw 1.2 Mb (ftp)(http) BW
GSE81553_K562_Smoothed_Pol2_ChIP-Seq.bw 156.3 Mb (ftp)(http) BW
GSE81553_K562_Transcription_Hot-Zone_Peaks.bb 48.3 Kb (ftp)(http) BB
GSE81553_LaminAC_TSA-Seq_Condition2.bw 144.8 Mb (ftp)(http) BW
GSE81553_LaminAC_TSA-Seq_Conditoin2_Replicate.bw 142.4 Mb (ftp)(http) BW
GSE81553_LaminB_TSA-Seq_Condition2.bw 151.3 Mb (ftp)(http) BW
GSE81553_LaminB_TSA-Seq_Conditoin2_Replicate.bw 148.4 Mb (ftp)(http) BW
GSE81553_NoPrimaryCtrl_for_GSE81553_LaminAC_TSA-Seq.bw 144.6 Mb (ftp)(http) BW
GSE81553_NoPrimaryCtrl_for_GSE81553_LaminAC_TSA-Seq_Replicate.bw 140.2 Mb (ftp)(http) BW
GSE81553_NoPrimaryCtrl_for_GSE81553_LaminB_TSA-Seq.bw 149.1 Mb (ftp)(http) BW
GSE81553_NoPrimaryCtrl_for_GSE81553_LaminB_TSA-Seq_Replicate.bw 149.2 Mb (ftp)(http) BW
GSE81553_NoPrimaryCtrl_for_GSE81553_pSC35_TSA-Seq_Replicate.bw 143.4 Mb (ftp)(http) BW
GSE81553_NoPrimaryCtrl_for_SON_TSA-Seq.bw 149.4 Mb (ftp)(http) BW
GSE81553_NoPrimaryCtrl_for_pol2_TSA-Seq_Replicate.bw 143.5 Mb (ftp)(http) BW
GSE81553_Pol2_TSA-Seq_Condition1.bw 151.2 Mb (ftp)(http) BW
GSE81553_Pol2_TSA-Seq_Condition1_Replicate.bw 148.2 Mb (ftp)(http) BW
GSE81553_SON_TSA-Seq_Ab2_Condition2.bw 141.4 Mb (ftp)(http) BW
GSE81553_SON_TSA-Seq_Condition1.bw 152.5 Mb (ftp)(http) BW
GSE81553_SON_TSA-Seq_Condition1_Replicate.bw 150.9 Mb (ftp)(http) BW
GSE81553_SON_TSA-Seq_Condition1_Replicate_2nd_pulldown.bw 150.3 Mb (ftp)(http) BW
GSE81553_SON_TSA-Seq_Condition2.Replicate.bw 148.5 Mb (ftp)(http) BW
GSE81553_SON_TSA-Seq_Condition2.bw 147.9 Mb (ftp)(http) BW
GSE81553_SON_TSA-Seq_Condition3.bw 135.5 Mb (ftp)(http) BW
GSE81553_SON_TSA-Seq_Decile_Color_Condition2.bed.gz 87.2 Kb (ftp)(http) BED
GSE81553_Speckle_distance_Condition1.bw 177.0 Mb (ftp)(http) BW
GSE81553_Speckle_distance_Condition2.bw 171.5 Mb (ftp)(http) BW
GSE81553_Speckle_distance_Condition3.bw 145.2 Mb (ftp)(http) BW
GSE81553_pSC35_TSA-Seq_Condition1.bw 151.5 Mb (ftp)(http) BW
GSE81553_pSC35_TSA-Seq_Condition1_Replicate.bw 143.0 Mb (ftp)(http) BW
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