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| Status |
Public on Aug 27, 2016 |
| Title |
121211-allmis-ms-meth-ux1 |
| Technology type |
in situ oligonucleotide |
| Distribution |
custom-commercial |
| Organism |
Alligator mississippiensis |
| Manufacturer |
NimbleGen |
| Manufacture protocol |
see http://www.nimblegen.com/technology/manufacture.html
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| Description |
The array used for the differential methylation analysis was a DNA methylated custom array by Roche Nimblegen that consisted of a Whole Genome Tiling Array of the American Alligator (Alligator mississippiensis) made of two chip set arrays with a 200bp resolution (121211-allmis-ms-meth-ux1). Probe sizes were 50-75mer in length and median probe spacing was 200bp.
The December 2014 report of the Alligator mississippiensis genome produced by the Genome Sequencing Center was retrieved (http://crocgenome.hpc.msstate.edu/crocbase/gbrowsers.html, http://crocgenome.hpc.msstate.edu/gb2/gbrowse/gator/). A seed file was constructed and a BSgenome package was forged for using the Alligator DNA sequence in the R code (Herve Pages BSgenome: Infrastructure for Biostrings-based genome data packages. R package version 1.24.0). This sequence was used to design the custom tiling arrays and to perform the bioinformatics.
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| Submission date |
Jun 06, 2016 |
| Last update date |
Aug 27, 2016 |
| Contact name |
Michael K Skinner |
| E-mail(s) |
skinner@mail.wsu.edu
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| Organization name |
WSU
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| Department |
SBS
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| Street address |
Abelson 507
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| City |
Pullman |
| State/province |
WA |
| ZIP/Postal code |
99163 |
| Country |
USA |
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| Samples (4) |
GSM2293612, GSM2293613, GSM2293614, GSM2293615 |
| Series (1) |
| GSE82318 |
Epigenetic Programming Alterations in Alligators from Environmentally Contaminated Lakes |
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| Supplementary file |
Size |
Download |
File type/resource |
| GPL21985_121211_allMis1_1of2_MS_Meth_UX1.ndf.gz |
266.8 Mb |
(ftp)(http) |
NDF |
| GPL21985_121211_allMis1_1of2_MS_Meth_UX1.pos.gz |
33.2 Mb |
(ftp)(http) |
POS |
| GPL21985_121211_allMis1_2of2_MS_Meth_UX1.ndf.gz |
266.6 Mb |
(ftp)(http) |
NDF |
| GPL21985_121211_allMis1_2of2_MS_Meth_UX1.pos.gz |
33.1 Mb |
(ftp)(http) |
POS |
| GPL21985_ReadmeDesignFile.pdf |
14.0 Kb |
(ftp)(http) |
PDF |
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