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| Status |
Public on Mar 22, 2024 |
| Title |
CHiC_HL_Shox2trac_E135_DECOM |
| Sample type |
SRA |
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| Source name |
Embryonic Hindlimb
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| Organism |
Mus musculus |
| Characteristics |
background: G4
tissue: Embryonic Hindlimb
embryonic stage: E13.5
genotype: Shox2trac
facs-sorted status: dmCherry-/EYFP+
biological replicate: rep1
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| 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.
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| 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.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Shox2 Agilent probes C-HiC
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| 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
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| Submission date |
Mar 20, 2024 |
| Last update date |
Mar 22, 2024 |
| Contact name |
Guillaume Andrey |
| E-mail(s) |
guillaume.andrey@unige.ch
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| Phone |
+41223795703
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| Organization name |
University of Geneva
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| Department |
Department of Genetic Medicine and Development
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| Street address |
Rue Michel-Servet 1
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| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| 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 |
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| Relations |
| BioSample |
SAMN40556270 |
| SRA |
SRX24003474 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8155813_CHiC_HL_Shox2trac_E135_DECOM_S8_L001_R1_2_001.hicup.MAPQ30.KR_5kb.WashU.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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