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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 28, 2023 |
| Title |
Crypts, EPR cKO, 43 |
| Sample type |
SRA |
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| Source name |
colon
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| Organism |
Mus musculus |
| Characteristics |
tissue: colon
strain: C57BL/6
cell type: epithelial
genotype: EPR cKO
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| Treatment protocol |
Crypts were isolated from 12-16-week-old mice
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| Growth protocol |
Hi-C was performed in crypts from mouse proximal colon using the Arima-HiC Kit according to the manufacturer?s instructions (Arima Genomics). Briefly, crypts were isolated from two distinct EPR fl/fl and two EPR cKO mice, snap-frozen and weighted (100-130 ?g/sample). Hundred ?g crypts were resuspended in PBS and crosslinked in 2% formaldehyde for 10 min. at room temperature, digested with a restriction enzyme cocktail, end-labeled with Biotin-14-dATP and then ligated. The ligated chromatin was reverse cross-linked and fragmented using Bioruptor (Diagenode) to obtain an average fragment size of 400bp. Fragmented DNA was then size-selected to have a size distribution between 200-600 bp, and finally subjected to biotin enrichment. Then, DNA libraries were prepared according to the procedure detailed in the Arima Capture-HiC Kit User Guide for mammalian cells (https://arimagenomics.com/wp-content/files/User-Guide-Arima-Capture-HiC-for-Mammalian-Cell-Lines.pdf). The Arima Mouse Promoter Panel was designed to the promoters of 25,752 genes from the Mouse GRCm38 Ensemble database, version 94, including: 21,088 protein-coding genes, 207 antisense RNAs, 544 lincRNAs, 1,015 miRNAs, 1,494 snoRNAs, and 1,383 snRNAs. Capture probes were designed to the restriction fragment of each of the promoters. The probes were manufactured using 1x tiling with repeat masking and balance boosting. Arima Capture-HiC libraries were sequenced via Illumina sequencers in ?paired-end? mode and sequence analyzed according to the Arima Capture-HiC Analysis Pipeline. Data were pre-processed using HiCUP and loops called using CHiCAGO at Arima Genomics.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
chromatin from crypts was crosslinked and digested using a restriction enzyme cocktail. The 5’-overhangs are then filled in, causing the digested ends to be labeled with a biotinylated nucleotide. Next, spatially proximal digested ends of DNA are ligated, capturing the sequence and structure of the genome. The ligated DNA is then purified, producing pure proximally-ligated DNA. The proximally-ligated DNA is then fragmented, and the biotinylated fragments are enriched. The enriched fragments are then subjected to a custom library preparation protocol utilizing the Arima Library Prep Module . Following Library prep we perform shallow sequencing (500k-2M paired-end reads) to assess the libraries’ quality in terms of library complexity and long-range interaction information prior to proceeding with the capture. Once Hi-C is complete, the sample is pre-cleared to remove carry over biotinylated Hi-C molecules. The interactions of interest are then enriched using biotinylated RNA probes from the Arima Mouse Promoter Panel
paired-end
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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 |
Arima Mouse Promoter Panel Design The Arima Mouse Promoter Panel was designed to the promoters of 25,752 genes from the Mouse GRCm38 Ensemble database, version 94, including: 21,088 protein-coding genes, 207 antisense RNA’s, 544 lincRNA’s, 1,015 miRNA’s, 1,494 snoRNA’s, and 1,383 snRNA’s.
bigwig files generated using bamCoverage (deeptools) with defaults parameters
Assembly: mm10
Supplementary files format and content: bigwig
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| Submission date |
Dec 07, 2022 |
| Last update date |
Mar 28, 2023 |
| Contact name |
gabriele bucci |
| E-mail(s) |
bucci.gabriele@hsr.it
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| Phone |
+39026439140
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| Organization name |
IRCCS Ospedale San Raffaele
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| Department |
CTGB
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| Street address |
via olgettina 58
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20100 |
| Country |
Italy |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE220309 |
LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis [Hi-C] |
| GSE220310 |
LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis |
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| Relations |
| BioSample |
SAMN32092062 |
| SRA |
SRX18524365 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6798161_S43.bigwig |
96.8 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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