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| Status |
Public on Jul 13, 2023 |
| Title |
org_fetal_rep2_hic |
| Sample type |
SRA |
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| Source name |
small intestinal epithelium derived organoids
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| Organism |
Mus musculus |
| Characteristics |
tissue: small intestinal epithelium derived organoids
developmental state: E16.5
strain: C57BL/6J
treatment: untreated
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| Growth protocol |
Fetal spheroids and adult organoids derived from E16.5 fetal epithelial fragments or scraped adult crypts harvested from proximal small intestine using 2mM EDTA were embedded in Matrigel droplets and cultured in advanced DMEM/F12 with GlutaMAX and Penicillin/Streptomycin supplemented with 50 ng/ml EGF, 100 ng/ml Noggin, and 500 ng/ml, R-Spondin1, 3 µM CHIR99021 and 10 mM Nicotinamide.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fetal spheroids and adult organoids corresponding to approximately one million cells per replicate were released from Matrigel and fragmented by repeated washing with cold PBS with 0.1% BSA. The organoid fragments were cross-linked in 2% formaldehyde for 20 minutes, quenched, and washed. Following, the cells were lysed and chromatin was digested with 2 units of DNase I for 5 minutes.
The nuclei were purified with AMPure XP beads and washed followed by end repair and dA-tailing reactions. Biotin-labeled bridge adapters were then ligated overnight to the fragments followed by another round of purification with AMPure XP beads and washing. The nuclei were treated with PNK to phosphorylate adapters and ligation prior to reversal of cross-linking, DNA precipitation and purification. The ligation products with biotin were then pulled down with MyOne C1 beads followed by washing and end repair, dA-tailing, and ligation of sequencing adapters. The libraries were amplified for 14 PCR cycles with primers containing Nextera barcodes for sample multiplexing: N701 (TCGCCTTA), N702 (CTAGTACG), N703 (TTCTGCCT), and N704 (GCTCAGGA). Libraries were then purified and quantified with Qubit and Fragment Analyzer (Agilent) and the four libraries were pooled and paired-end sequenced with Illumina NextSeq.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequencing reads were converted by using bcf2fastq and demultiplexed according to the indexes
The reads were quality trimmed with Trim Galore and mapped and processed with HiC-Pro.
We used MAPQ score threshold 30 and excluded read pairs mapping within 1kb, to retain valid pairs and generate ICE normalised contact maps at 100kb resolution.
Genome_build: mm10
Supplementary_files_format_and_content: Contact matrixes of all valid read pairs are stored in Juicebox viable .hic file.
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| Submission date |
Oct 29, 2020 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Laura Maarit Pikkupeura |
| Organization name |
University of Copenhagen
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| Department |
BRIC
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| Lab |
Jensen lab
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| Street address |
Ole Maaloes vej 5
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| City |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE160449 |
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [I] |
| GSE228519 |
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation |
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| Relations |
| BioSample |
SAMN16596934 |
| SRA |
SRX9401585 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4873514_F2_allValidPairs.hic |
101.4 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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