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| Status |
Public on Jun 20, 2022 |
| Title |
4C_Hoxd9_E95_PT_rep2 |
| Sample type |
SRA |
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| Source name |
posterior trunk
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: E9.5
strains: CD1
genotype: WT
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| Treatment protocol |
A portion of tissue corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, was micro-dissected from approximately fifteen E9.5 embryos.
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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 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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| Description |
4C
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| Data processing |
Library strategy: 4C-seq
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly and on GRCg6a/galGal6 chicken assembly, and analyzed using a local version of the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) 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
Data was mapped on simplified genome assemblies comprising chromosomes only.
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph), when multiple biological replicates were done, the average was done.
Supplementary_files_format_and_content: HoxD_minusNextVP (bedgraph) is the score of the viewpoint minus the score of the next viewpoint (i.e.Hoxd1 minus Hoxd4 and Hoxd4 minus Hoxd9)
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly and on GRCg6a/galGal6 chicken assembly, and analyzed using a local version of the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) using the facilities of the Scientific IT and Application Support Center of EPFL.
First, scores were normalized to million mapped reads
Then, profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Data was mapped on simplified genome assemblies comprising chromosomes only.
processed data files format and content: bw: 4C coverage normalized by the number of reads mapped.
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| Submission date |
Jan 27, 2022 |
| Last update date |
Jun 20, 2022 |
| Contact name |
Aurelie Hintermann |
| E-mail(s) |
aur.hin@gmail.com
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| Organization name |
University of Geneva
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| Department |
Genetics and Evolution
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| Street address |
30 quai Ernest-Ansermet
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| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE195591 |
Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [4C-seq] |
| GSE195592 |
Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds |
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| Relations |
| BioSample |
SAMN25338805 |
| SRA |
SRX13954090 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5841332_4C_Hoxd9_E95_PT_rep2.bedgraph.gz |
1.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM5841332_segToFrag_4C_Hoxd9_E95_PT_rep2.bw |
369.9 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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