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| Status |
Public on Apr 25, 2020 |
| Title |
GT_E15_5_WT_Hoxd13VP |
| Sample type |
SRA |
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| Source name |
genital tubercule
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| Organism |
Mus musculus |
| Characteristics |
genotype: wildtype
developmental stage: E15.5
strain: CBA / C57BL/6 mix
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Circular chromosome conformation capture (4C-seq) was performed as described in (Noordermeer et al., 2011). Briefly, tissues (20-40 GT or 40 cloaca) were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated to single cell by collagenase treatment. Samples were fixed in 2% formaldehyde, lysed, and stored at −80°C. Samples were primarily digested with NlaIII (NEB, R0125L) followed by ligation under diluted conditions. After decrosslinking and DNA purification DpnII (NEB, R0543M) was used for the second restriction. All ligation steps were performed using highly concentrated T4 DNA ligase (Promega, M1794). For each viewpoint approximately 1μg of DNA was amplified by using 12 individual PCR reactions.
Libraries were constructed with inverse primers for different viewpoints (see Table 5) containing Illumina Solexa adapter sequences and sequenced on an Illumina HiSeq 2500 sequencer, as single-end reads (read length 100 base pairs or 80 base pairs). In some samples 4-bp barcodes were added between the adapter and each specific viewpoint to allow sample multiplexing.
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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-seq
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly, and analyzed using the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) or using a local version of it using the facilities of the Scientific IT and Application Support Center of EPFL. Profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph
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| Submission date |
Oct 07, 2019 |
| Last update date |
Apr 26, 2020 |
| Contact name |
Ana Rita Amandio Lhopitallier |
| E-mail(s) |
rita.lhopitallier@epfl.ch
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| Organization name |
EPFL
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| Department |
SV-ISREC-EPFL
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| Lab |
Laboratory of Developmental Genomics
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| Street address |
SV2842, Station 19
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| City |
Lausanne |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE138507 |
A complex regulatory landscape involved in the development of external genitals [4C-seq] |
| GSE138514 |
A complex regulatory landscape involved in the development of external genitals |
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| Relations |
| BioSample |
SAMN12982923 |
| SRA |
SRX6958301 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4110069_GT_E15_5_WT_Hoxd13VP.bedGraph.gz |
2.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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