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Sample GSM2495558 Query DataSets for GSM2495558
Status Public on Jul 04, 2017
Title 4C_Dup-syn_IhhTSS_rep_1
Sample type SRA
Source name E14.5 digit forelimb, Dup-syn
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: Dupsyn/+
age: E14.5
tissue: forelimb (digit 2-5)
viewpoint: Ihh TSS
Extracted molecule genomic DNA
Extraction protocol 4C-seq libraries were generated from microdissected E14.5 mouse forelimb tissues (digit 2-5) as described previously (van de Werken et al., 2012). The starting material for all 4C-seq libraries was 5000000-10000000 cells. All 4C-seq experiments were carried out in heterozygous animals and were compared to wildtype. 4-bp cutters were used as primary (Csp6I) and secondary (BfaI) restriction enzymes. A total of 1 to 1.6 µg DNA was amplified by PCR (Primer sequence: Ihh_promoter_1:ACAGCTGGGGACCCTATAC; Ihh_promoter_2:CCCGTCAGGAGGACAATC). 4C-seq experiments were carried out in two biological replicates in wildtype, Dupint/+ and Dupsyn/+ mutants.
All samples were sequenced with Illumina Hi-Seq technology according to standard protocols.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
Description Processed data file: 4C_Ratio_Dup-syn_vs_WT.bedgraph
Data processing Library strategy: 4C-seq
4C-seq reads were cleaned of the primer sequence and mapped to a corresponding reference (NCBI37/mm9) using BWA-MEM (v0.7.12-r1044) with default settings.
4C-seq contacts were analyzed in the murine region chr1:74500000-75500000.
To calculate read count profiles, the viewpoint and adjacent fragments 1.5 kb up- and downstream were removed. A sliding window of 2 fragments was chosen to smooth the data and data was normalized to reads per million mapped reads (RPM).
To compare interaction profiles of different samples, we obtained the log2 fold change for each window of normalized reads.
To obtain ratios, duplicated regions were excluded for calculation of the scaling parameter used in RPM normalization.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files of the coverage and the calculated ratios.
Submission date Feb 18, 2017
Last update date May 15, 2019
Contact name Darío G Lupiáñez
Organization name Max Planck Institute for Molecular Genetics
Street address Ihnestrasse 73
City Berlin
ZIP/Postal code 14195
Country Germany
Platform ID GPL18480
Series (1)
GSE95062 A multipartite enhancer ensemble coordinates pleiotropic developmental functions of Indian hedgehog
BioSample SAMN06347086
SRA SRX2576224

Supplementary file Size Download File type/resource
GSM2495558_4C_Dup-syn_IhhTSS_rep_1.bedgraph.gz 17.7 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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