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| Status |
Public on Jun 19, 2014 |
| Title |
anterior_limb |
| Sample type |
SRA |
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| Source name |
Anterior Limb
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| Organism |
Mus musculus |
| Characteristics |
tissue: Anterior Limb
developmental stage: E11.5 (44-45 somites)
1st restriction enzyme: NlaIII
2nd restriction enzyme: DpnII
viewpoint: Ptch1 promoter – chr13:63669139
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| Treatment protocol |
Forelimbs from 20 embryos were split into posterior and anterior parts. Telencephalic vesicles were processed in parallel as a control tissue
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| Growth protocol |
E11.5 mouse embryos were collected in ice cold 10% FCS in PBS.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
A single cell suspension was achieved by digestion of the dissected tissues with 1mg/ml Collagenase D in HBSS at 37°C and gentle pippeting.
The procedure was performed as previously described (Simonis et al., Nature Methods, 2006; van de Werken et al., Methods in Enzymology, 2012). Briefly, dissociated cells were cross-linked with 2% formaldehyde for 10 min at room temperature in PBS containing 10%FC. After nuclei isolation, chromatin was digested with NlaIII as primary restriction enzyme and subsequently ligated under dilute conditions. After crosslink reversal, DNA was purified and digested with the second restriction enzyme (DpnII). After a second re-ligation step the sample was purified and a 4C inverse PCR was performed using primers annealing to the viewpoint fragment-end of interest. Primers contained non-annealing dangles with Illumina adapter sequences, allowing immediate sequencing of purified PCR products.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
4C PCR product
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| Data processing |
Only first 50bp from each 4C-seq read were analyzed using “4Cseqpipe” (Landan et al., 2012).
Briefly, sequenced reads were mapped to a pre-built database of restriction fragment locations and fragment end sequences, representing a reduced genome defined by the primary and secondary restriction enzymes.
Mapping takes into account fragment end uniqueness and mappability, and utilizes base-calling qualities to partially apportion reads according to mismatch probabilities.
Dense genomic profiles were created for four distinct classes of fragment ends by linear interpolation of mapped reads.
One interpolated profile was selected and the three other profiles were quantile-normalized to match its distribution. Resulting profiles were combined by direct summation, resulting in a coverage profile.
Finally, medians of normalized coverage, as well as 20th and 80th percentiles, were calculated for sliding windows ranging from 2kb to 50kb in size.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: ID.nearcis.norm.median.scales – Median of normalized contact intensity in 1kb genomic bins. Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns:
Supplementary_files_format_and_content: column 1 – the starting coordinate of the 1kb bin
Supplementary_files_format_and_content: column 2 – the median of values within a 2kb window, centered on the 1kb genomic bin
Supplementary_files_format_and_content: column 3 – the 80th percentile of values in the window
Supplementary_files_format_and_content: column 4 – the 20th percentile of values in the window
Supplementary_files_format_and_content: Column 5-145 – as columns 2-4, but with linearly increasing window size, going up to 50kb
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| Submission date |
Dec 04, 2013 |
| Last update date |
Nov 17, 2021 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
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| Organization name |
University of Basel
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| Department |
Departement of Biomedicine
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| Street address |
Hebelstrasse 20
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| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE52988 |
Attenuated sensing of SHH underlies adaptive evolution of bovine limbs |
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| Relations |
| BioSample |
SAMN02436026 |
| SRA |
SRX387191 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1279841_2.nearcis.norm.txt.median.scales.txt.gz |
46.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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