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| Status |
Public on Sep 29, 2022 |
| Title |
cHiC__ESC_G4_deltaPromoterRex1_mouse_Rep-1 |
| Sample type |
SRA |
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| Source name |
ESC
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| Organism |
Mus musculus |
| Characteristics |
tissue: ESC
cell line: G4
genotype: del chr8 43302254 43332347
treatment: deltaPromoter-Rex1
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| Treatment protocol |
HiC libraries were prepared as described in a previously published in situ protocol (Melo et al., 2020; Rao et al., 2014). Briefly, ∼1 million cells were fixed in 2% formaldehyde, lysed, and stored at -80°C.
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| Growth protocol |
Embryonic limb cells were isolated from chicken or opossum embryos through limb dissection, trypsinization, filtration (100 µm) and centrifugation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
A S-Series 220 Covaris was used to shear the DNA to fragments of 300–600 bp for library preparation, and biotin-filled DNA fragments were pulled down using Dynabeads MyOne Streptavidin T1 beads. DNA ends were subsequently repaired using T4 DNA polymerase and the Klenow fragment of DNA polymerase I and phosphorylated with T4 Polynucleotide Kinase NK. DNA was further prepared for sequencing by ligating adaptors to DNA fragments, using the NEBNext Multiplex Oligos for Illumina kit. Indexes were added via PCR amplification (4–8 cycles) using the NEBNext Ultra II Q5 Master Mix. PCR purification and size selection were carried out using Agencourt AMPure XP beads. Libraries were sequenced on a x platform yielding x bp paired-end reads. For each sample, the HiC library was created by pooling a total of four technical replicates generated from two different cell isolations cultures in order to ensure higher complexity of the sequencing library
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Fastq files were processed with the Juicer pipeline v1.5.6 (Durand et al., 2016) (CPU version) using bwa v0.7.17 (Li and Durbin, 2010) for mapping short reads to the reference genomes mm10 (mouse), hg19 (human), galGal6 (chicken), monDom5 (opossum), susScr11.1 (pig), and AmexG_v6.0-DD (axolotl), respectively.
Replicates were merged after the mapping, filtering and deduplication steps of the Juicer pipeline. Juicer tools v1.7.5 (Durand et al., 2016) were used to generate binned and KR normalized HiC maps from read pairs with MAPQ≥30.
For compartment analysis, hic-files were converted at 100kb bin size to the cool format using hic2cool (v0.8.2) (https://github.com/4dn-dcic/hic2cool) and balanced using cooler (v0.8.5) (Abdennur and Mirny, 2020). Afterwards, compartment analysis was performed using cooltools (v0.3.0) (https://github.com/open2c/cooltools) and using the GC content as reference track. TADs were identified by applying TopDom v.0.0.228 on 50-kb binned and KR-normalized maps using a window size of 10 (Shin et al., 2016).
Assembly: mondom5 and galgal6
Supplementary files format and content: .hic
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| Submission date |
Aug 19, 2022 |
| Last update date |
Oct 01, 2022 |
| Contact name |
Michael I Robson |
| E-mail(s) |
robson@molgen.mpg.de
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| Organization name |
Max Planck Institute for Molecular Genetics
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| Street address |
Max Planck Institut für molekulare Genet, Ihnestrasse 63-73
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| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE185768 |
Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [Hi-C] |
| GSE185775 |
Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes |
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| Relations |
| BioSample |
SAMN30416582 |
| SRA |
SRX17156368 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6482919_mpimg_L25648-1_DRex1Prom_S128_75bp_R1_2_001_enriched_only_MAPQ30.hic |
18.6 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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