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Series GSE161378 Query DataSets for GSE161378
Status Public on Jan 23, 2021
Sample organisms Gallus gallus; Mus musculus
Experiment type Other
Third-party reanalysis
Summary During tetrapod limb development, the HOXA13 and HOXD13 transcription factors are critical for the emergence and organization of the autopods, the most distal aspect where digits will develop. Since previous work had suggested that the Dbx2 gene is a target of these factors, we set up to analyze in detail this potential regulatory interaction. We used a chromatin conformation capture approach (4Cseq) to characterize the regulatory domain and interactions of the transcription factor Dbx2 and of its neighboring genes Nell2 and Ano6 in distal and/ or proximal forelimbs of E12 mouse embryos. In particular, we analyzed their interaction with distal limb specific regulatory elements (DLE1 and DLE2) by the analysis of H2K27ac coverages (Beccari et al 2016) and Hoxa13/Hoxd13 binding (Sheth R et al 2016). We report that Dbx2, Nell2 and Ano6 are expressed in distal limb buds and are controlled by the same enhancers located close to Dbx2. As the Nell2 and Ano6 genes are localized into two different topologically associating domains (TADs) flanking the Dbx2 locus, we conclude that these enhancers can overcome TAD boundaries in either direction, to co-regulate a set of genes located in distinct chromatin domains.
Overall design HiC reanalysis of GSM2713716 from Rodriguez-Carballo et al. 2017, GSM2533818 to GSM2533821 and GSM2533839 to GSM2533842 from Bonev et al. 2017 and GSE115562 from Yakushiji-Kaminatsui et al.
Data Processing:
For capture Hi-C on chicken, data were processed independently using HiCUP v0.8.0 ( on galGal6. Valid pairs were obtained using a custom python script.
For downstream analysis FL and HL valid pair files were concatenated.
For data from Bonev et al. 2017, valid pairs were downloaded from GSEXXXXX.
For all, the valid pairs of all studies were loaded in cool file using cooler version 0.8.10 ( using resolution of 5Kb, 20Kb or 40Kb. Matrices were balanced using cooler balance –cis-only. The TAD-separation score and the domains were obtained using hicFindTADs version 3.5.2 (,, with --minBoundaryDistance 100000 and either default parameters for the choice of window size or a fixed window size of 120Kb.
all scripts are available at at
Genome build: mm10, galGal6
Files: *validPairs*: valid pairs in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2><frag2> <mapq1> <mapq2> with str = strand (0 for forward, anything else for reverse), pos = middle of the fragment.) *.cool: matrices in cool format balanced using cooler *domains.bed.gz: TAD coordinates (default were obtained with default parameters, 120kb were obtained with fixed window size of 120kb)
Contributor(s) Lopez-Delisle L, Beccari L, Duboule D
Citation(s) 33497014
Submission date Nov 12, 2020
Last update date Feb 01, 2021
Contact name Lucille Lopez-Delisle
Organization name EPFL
Street address Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
This SubSeries is part of SuperSeries:
Reanalysis of GSM2533818
Reanalysis of GSM2533819
Reanalysis of GSM2533820
Reanalysis of GSM2533821
Reanalysis of GSM2533839
Reanalysis of GSM2533840
Reanalysis of GSM2533841
Reanalysis of GSM2533842
Reanalysis of GSM2713716
Reanalysis of GSM3182470
Reanalysis of GSM3182471

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
GSE161378_E12_DL_40kb.120kb_domains.bed.gz 57.1 Kb (ftp)(http) BED 39.6 Mb (ftp)(http) COOL
GSE161378_E12_DL_40kb.default_domains.bed.gz 67.9 Kb (ftp)(http) BED
GSE161378_E14_Cortex_chr15_5kb.120kb_domains.bed.gz 5.7 Kb (ftp)(http) BED 36.5 Mb (ftp)(http) COOL
GSE161378_E14_Cortex_chr15_5kb.default_domains.bed.gz 5.7 Kb (ftp)(http) BED
GSE161378_ES_chr15_5kb.120kb_domains.bed.gz 6.4 Kb (ftp)(http) BED 36.5 Mb (ftp)(http) COOL
GSE161378_ES_chr15_5kb.default_domains.bed.gz 6.4 Kb (ftp)(http) BED
GSE161378_HH20_FL_WT_CHi-C.validPairs.csort.txt.gz 649.6 Mb (ftp)(http) TXT
GSE161378_HH20_HL_FL_20kb.120kb_domains.bed.gz 54.9 Kb (ftp)(http) BED 54.6 Mb (ftp)(http) COOL
GSE161378_HH20_HL_FL_20kb.default_domains.bed.gz 55.0 Kb (ftp)(http) BED
GSE161378_HH20_HL_WT_CHi-C.validPairs.csort.txt.gz 722.3 Mb (ftp)(http) TXT
GSE161378_README.txt 30.5 Kb (ftp)(http) TXT
Processed data are available on Series record

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