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Sample GSM6226219 Query DataSets for GSM6226219
Status Public on Apr 28, 2023
Title CHi-C of Del(CBS1-5) stembryos at 120h
Sample type SRA
Source name stembryo
Organism Mus musculus
Characteristics tissue: stembryo
cell type: mES cells
genotype: Del(CBS1-5)
stage (in_hours_after_aggregation): 120
Extracted molecule genomic DNA
Extraction protocol Collected stembryos were pooled and fixed for 10 min in 1% formaldehyde at room temperature and stored at -80°C until further use.
Lysis was performed with TissueLyser II and metallic beads for 30 sec at 30 hertz before incubation at 4° for 30 min. The rest of the protocol for the capture Hi-C library generation is described in (Bolt et al., 2021). The costume SureSelectXT RNA probe used for DNA capture covers the region chr2:72240000-76840000 (mm9).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing All scripts are available on
Trimmed reads were processed with HiCUP version 0.6.1 (doi: 10.12688/f1000research.7334.1) with default paramters on mm10 or on the corresponding mutant genome.
The output BAM was converted to Juicebox format thanks to a custom python script available in
Only pairs with both mates falling into the capture region (mm10:chr2:72402000-77000000) and with both mates with quality above 30 were kept.
Filtered pairs were loaded into 2kb and 5kb matrices with cooler version 0.7.4 (Abdennur, N., and Mirny, L. (2019),
The matrices were balanced with cooler balance (--cis-only).
For the mutant Del(subTAD1), the balancing was done with the option --ignore-diags 5 instead of --ignore-diags 2 to discard the bias due to the presence of a BAC containing the region (mm10:chr2:74747769-74913171).
Assembly: mm10 for wt samples and Del(CBS*) samples and mutant genomes for Del(d1-d4) and Del(sub-TAD1)
Supplementary files format and content: *_validPairs_*.txt.gz: all valid pairs from HiCUP in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse) pos = middle of the fragment)
Supplementary files format and content: *_*kb_Balanced_*.cool: balanced matrix at 2 or 5kb-bins only in the captured region
Library strategy: Capture Hi-C
Submission date Jun 09, 2022
Last update date Apr 28, 2023
Contact name Lucille Lopez-Delisle
Organization name EPFL
Street address Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
Platform ID GPL19057
Series (2)
GSE205778 Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [cHi-C]
GSE205783 Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos
BioSample SAMN28944794
SRA SRX15652889

Supplementary file Size Download File type/resource 7.4 Mb (ftp)(http) COOL 4.0 Mb (ftp)(http) COOL
GSM6226219_Del_CBS1-5_120h_CHiC_validPairs_mm10.txt.gz 937.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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