|
| 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 |
| E-mail(s) |
lupianez@molgen.mpg.de
|
| 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 |
|
| Relations |
| BioSample |
SAMN06347086 |
| SRA |
SRX2576224 |
