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| Status |
Public on May 08, 2015 |
| Title |
Epha4_WT_mm9 |
| Sample type |
SRA |
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| Source name |
distal forelimb E11.5
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| Organism |
Mus musculus |
| Characteristics |
strain: 129/Sv x C57BL/6
tissue: distal forelimb
age: E11.5
genotype: wild type
1st restriction enzymes: BglII
2nd restriction enzymes: Csp6I
viewpoint: Epha4
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| Treatment protocol |
Distal forelimbs were microdissected and dissociated using a Trypsin solution (0.05%).
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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 |
4C-seq libraries were generated from microdissected tissues or cells as described previously (van de Werken et al., 2012). BglII or HindIII (6-bp cutters) were used as primary restriction enzymes. Csp6I or DpnII were used as secondary restriction enzymes. For each viewpoint, a total of 1.6 mg of each library was amplified in 8 or 16 PCR reactions, depending on PCR efficiencies. Samples were multiplexed and sequenced with Ilumina Hi-Seq technology. The following primers were used: Wnt6_promoter_forward: CTACACGACGCTCTTCCGATCTCCACAGATGCCTACATCAG, Wnt6_promoter_reverse: CAGACGTGTGCTCTTCCGATCTCAGTTGGACAGCCTTCTACC, Ihh promoter_forward: CTACACGACGCTCTTCCGATCTCTTGCTCGGGATTCAGAT, Ihh_promoter_reverse: CAGACGTGTGCTCTTCCGATCTGCATGTCTAGCATGGTGGTA, mm1036_forward: CTACACGACGCTCTTCCGATCTACCTTATCTTGGCCTTCAA, mm1036_reverse: CAGACGTGTGCTCTTCCGATCTCCATAACCCAGACTGAGATG, Epha4_promoter_forward: CTACACGACGCTCTTCCGATCTTGGCTTTTACCGAAAATAAA, Epha4_promoter_reverse: CAGACGTGTGCTCTTCCGATCTTCGTAGTCTAGGTGGAGGAA Pax3_promoter_forward: CTACACGACGCTCTTCCGATCTTTCTATCTCCCCATGACACC, Pax3_promoter_reverse: CAGACGTGTGCTCTTCCGATCTTCCTCCAAACGTGCTCTG
Samples were multiplexed and sequenced with Ilumina Hi-Seq technology according to the manufacturer´s protocol.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
Library strategy: 4C-Seq
Reads were mapped by Novoalign (Novoalign V2.07; www.novocraft.com) to the reference sequences NCBI37/mm9.
To visualize the data, we created files in bedGraph track format for the readcounts of each fragment or in a specified window of fragments.
The viewpoint, adjacent undigested fragment and fragments 10 kb up and downstream were removed.
4C-seq contacts were analyzed in the mouse region chr1:73000000-79000000. A range of 5 fragments was used to normalize the data per million reads (RPM) over a sliding window and display the continuous-valued data in the figures. Log2 ratios were calculated by dividing fragment reads between different samples.
Genome_build: mm9
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph).
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| Submission date |
Feb 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Darío G Lupiáñez |
| E-mail(s) |
lupianez@molgen.mpg.de
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| Organization name |
Max Planck Institute for Molecular Genetics
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| Street address |
Ihnestrasse 73
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| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
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| Platform ID |
GPL15103 |
| Series (2) |
| GSE66379 |
Disruptions of Topological Chromatin Domains Causes Pathogenic Rewiring of Gene-Enhancer Interactions [4C-Seq-mouse] |
| GSE66383 |
Disruptions of Topological Chromatin Domains Causes Pathogenic Rewiring of Gene-Enhancer Interactions |
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| Relations |
| BioSample |
SAMN03379890 |
| SRA |
SRX893597 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1621279_Epha4_WT_mm9.bedgraph.gz |
5.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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