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| Status |
Public on Oct 31, 2024 |
| Title |
Atria_rep2_CAV1_GATC_CATG |
| Sample type |
SRA |
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| Source name |
Adult mouse atria
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: atria
age: 8 weeks
Sex: male
gentoype: Wild type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Heart were dissected and atria tissue were micro-dissected. Pools of 20 atria were dissociated to obtain single cells preparations with collagenase. Chromatin was fixed with 2% formaldehyde for 10 min at room temperature and the reaction was quenched on ice with glycine. After fixation, pools were lysed in 50mM Tris-HCl pH7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 and 1x complete protease inhibitor (Roche), digested first with DpnII (New England Biolabs, Cat. No. R0543M), ligated with T4 DNA ligase (Promega) followed by either NlaIII (New England Biolabs, Cat. No. R0125L) or Csp6I (Fermentas, cat.no. ER0211) digestion, depending on the initial design of the 4C viewpoint, and re-ligated with T4 DNA ligase (Promega).
500ng of 4C templates were amplified using Expand Long Template Polymerase enzyme (Roche) and inverse PCR primers flanked with barcodes allowing multiplexing. The Illumina adaptors used were 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' for the reading primers and 5'-CAAGCAGAAGACGGCATACGA-3' for the non-reading. Specific primer information for each viewpoint is displayed in the related publication.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Library strategy: 4C
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) genome using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped within fragments with a DpnII at one end and a NlaIII or Csp6I at the other end were kept. Fragments smaller than 40 bp, or within a window of 10 kilobase (kb) around the viewpoint were filtered out.
Mapped reads were then converted to reads per first enzyme fragment ends and smoothened using a 30-fragment mean running window algorithm. Smoothened scores of each experiment were then normalized by the total number or reads
For contact estimation, the reference genome was digested in silico according to the first and second restriction enzymes (NlaIII or Csp6I). Then, processed reads were assigned to their corresponding first cutter (DpnII) digested genome fragment, filtering out reads on fragments located 5kb around the viewpoint. Quantification was performed considering each fragment end as one captured site if one or more sequences mapped to it. The number of captured sites was summarized per 30 fragments window (max of 60 captured sites per window). The frequency of captured sites per window was used to fit a distance decreasing monotone function and Z-scores were calculated from its residuals using a modified version of FourCSeq (Klein et al. 2015). Significant contacts were considered in cases where the Z-score was >2 in both replicates and deviated significantly (adjusted p value <0.05) from its normal cumulative distribution in at least one of the replicates. After data analysis, processed reads and interactions were visualized at the WashU EpiGenome Browser Mouse genome (mm9).
Individual viewpoint fastq files were reconstructed form the individual viewpoint sorted.bam files using BEDtools toolset (https://bedtools.readthedocs.io/en/latest/)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files contain smoothed and normalized data for each replicate. These processed files can be directly uploaded to UCSC or WashU Browsers for visualization.
Supplementary_files_format_and_content: bed file contains the coordinates of significative interactions. These processed files can be directly uploaded to WashU Browser for visualization.
Supplementary_files_format_and_content: txt file contains paired interactions between the viewpoint and the genome. These processed files can be directly uploaded to WashU Browser for visualization.
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| Submission date |
Jul 19, 2021 |
| Last update date |
Oct 31, 2024 |
| Contact name |
Raquel ROUCO GARCIA |
| E-mail(s) |
raquel.roucogarcia@unige.ch
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| Phone |
+41 22 379 57 11
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| Organization name |
University of Geneva
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| Department |
Department of Genetic Medicine and Development
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| Lab |
Epigenetic control of developmental processes
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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 |
GPL17021 |
| Series (1) |
| GSE180396 |
Cis-regulatory elements control gene expression in time and space |
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| Relations |
| BioSample |
SAMN20307285 |
| SRA |
SRX11499831 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5462294_Atria_CAV1_REP2_smooth_30_frags.bedGraph.gz |
4.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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