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Sample GSM8155812 Query DataSets for GSM8155812
Status Public on Mar 22, 2024
Title CHiC_HL_Shox2trac_E125_MAINTAIN
Sample type SRA
 
Source name Embryonic Hindlimb
Organism Mus musculus
Characteristics background: G4
tissue: Embryonic Hindlimb
embryonic stage: E12.5
genotype: Shox2trac
facs-sorted status: dmCherry+/EYFP+
biological replicate: rep1
Growth protocol Forelimbs and Hindlimbs from E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted based on the dmCherry and EYFP fluorescent signal.
Extracted molecule genomic DNA
Extraction protocol Tissues were homogenized in typsin-EDTA solution, fixed with 2% PFA at room temperature 10 min. Then fixation was halted with 1M glycine and the cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 1mM EGTA, Protease Inhibitor, #04693159001). Upon PBS wash, samples were frozen and stored at -80°C. Samples were then digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was then sheared and adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions. Libraries were sequenced an Illumina HiSeq 4000 or Illumina NovaSeq 6000 sequencer.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description Shox2 Agilent probes C-HiC
Data processing Sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v0.6.1. The pipeline was set up with Bowtie2 v2.3.4.2 for short read mapping. In case replicates were available, they were combined before the processing with the HiCUP pipeline. Juicer command line tools v1.9.9 was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing. For binning and normalization, only the genomic region chr3: 65,000,001-68,500,000 was considered. Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb resolution. Subtraction maps were produced from theKR normalized maps and scaled together across their subdiagonals. CHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 99-th percentile were truncated for visualization purposes.
Assembly: mm9
Supplementary files format and content: Text files indicating interaction frequency of valid pairs of the binned contact map
 
Submission date Mar 20, 2024
Last update date Mar 22, 2024
Contact name Guillaume Andrey
E-mail(s) guillaume.andrey@unige.ch
Phone +41223795703
Organization name University of Geneva
Department Department of Genetic Medicine and Development
Street address Rue Michel-Servet 1
City Geneva
ZIP/Postal code 1211
Country Switzerland
 
Platform ID GPL21103
Series (2)
GSE262003 Temporal constraints on enhancer usage shape the regulation of limb gene transcription
GSE262006 Temporal constraints on enhancer usage shape the regulation of limb gene transcription
Relations
BioSample SAMN40556271
SRA SRX24003473

Supplementary file Size Download File type/resource
GSM8155812_CHiC_HL_Shox2trac_E125_MAINTAIN_cat_R1_2_001.hicup.MAPQ30.KR_5kb.WashU.txt.gz 1.9 Mb (ftp)(http) TXT
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Raw data are available in SRA

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