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Sample GSM1279840 Query DataSets for GSM1279840
Status Public on Jun 19, 2014
Title telencephalon
Sample type SRA
 
Source name Telencephalon
Organism Mus musculus
Characteristics tissue: Telencephalon
developmental stage: E11.5 (44-45 somites)
1st restriction enzyme: NlaIII
2nd restriction enzyme: DpnII
viewpoint: Ptch1 promoter – chr13:63669139
Treatment protocol Forelimbs from 20 embryos were split into posterior and anterior parts. Telencephalic vesicles were processed in parallel as a control tissue
Growth protocol E11.5 mouse embryos were collected in ice cold 10% FCS in PBS.
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description 4C PCR product
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
 
Submission date Dec 04, 2013
Last update date Nov 17, 2021
Contact name DBM Bioinformatics Core Facility
Phone +41612073541
Organization name University of Basel
Department Departement of Biomedicine
Street address Hebelstrasse 20
City Basel
State/province BS
ZIP/Postal code 4053
Country Switzerland
 
Platform ID GPL16417
Series (1)
GSE52988 Attenuated sensing of SHH underlies adaptive evolution of bovine limbs
Relations
BioSample SAMN02436023
SRA SRX387190

Supplementary file Size Download File type/resource
GSM1279840_1.nearcis.norm.txt.median.scales.txt.gz 48.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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