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Steven Roberts wrote a new post, Sifting Sands, on the site half-shell 3 years, 5 months ago
Below is a quick workflow I am using to help Drinan annotate ~1.5 million sequences from an amplicon targeting NGS effort of sand.
head […]
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Steven Roberts wrote a new post, Finishing out with the mechanical, on the site half-shell 3 years, 6 months ago
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Steven Roberts wrote a new post, Another day, another species, on the site half-shell 3 years, 6 months ago
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Steven Roberts wrote a new post, Big day, big clam, on the site half-shell 3 years, 6 months ago
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Steven Roberts wrote a new post, Dirty and crude with Oly qPCR, on the site half-shell 3 years, 6 months ago
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Steven Roberts wrote a new post, Alternative splicing and germline methylation, on the site half-shell 3 years, 7 months ago
One of the premises related to germline methylation in oysters is that genes with limited methylation will have more alternatively spliced products. One of our most robust identification of alternatively spliced […]
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Steven Roberts wrote a new post, No code required, on the site half-shell 3 years, 7 months ago
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Steven Roberts wrote a new post, Second look at Geoduck transcriptome, on the site half-shell 3 years, 7 months ago
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Steven Roberts wrote a new post, First look at Geoduck transcriptome, on the site half-shell 3 years, 7 months ago
Here is first look at annotations from a gonad transcriptome assembly.
Also available @…[Read more]
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Steven Roberts commented on the post, There is something about TEs, on the site half-shell 3 years, 7 months ago
fu- the direction of methylation in TEs in predominantly hypo, or loss of methylation.
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Steven Roberts wrote a new post, There is something about TEs, on the site half-shell 3 years, 7 months ago
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Steven Roberts wrote a new post, Heat Stress DDMRs, on the site half-shell 3 years, 7 months ago
Here is a summary of 10 Dramatically Differentially Methylated Regions (DDMRs), that is, those covered in this post that are found across a majority of the oysters exposed to acute heat shock.
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Steven Roberts wrote a new post, A closer look at DMRs, on the site half-shell 3 years, 7 months ago
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Steven Roberts wrote a new post, Side track with tracks, on the site half-shell 3 years, 8 months ago
Today working on our paper looking at heat stress and DNA methylation I dived deeper into the array data in the search for what should be called a DMR.
As a refresher we have tracks from the core that have 1.8+ […]
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Steven Roberts wrote a new post, Passing Flanks , on the site half-shell 3 years, 8 months ago
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Steven Roberts wrote a new post, First steps at an aggregated view of all DNA methylation data (updated), on the site half-shell 3 years, 8 months ago
Seems like I have gotten close (see here) but do not have a canonical IGV session that has all of our DNA methylation data. The goal here is to generate such a product (and publish, so I do not lose it).
All data […]
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Steven Roberts wrote a new post, Quick Carmalign, on the site half-shell 3 years, 8 months ago
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Steven Roberts wrote a new post, Wayback to just-MBD, on the site half-shell 3 years, 8 months ago
Prior to bisulfite sequencing we did do a couple of MBD enrichment libraries to describe DNA methylation in oysters. Results even were snuck into this perspective.
While I am sure there are genome tracks […]
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Steven Roberts commented on the post, Bioanalyzer – Geoduck Gonad RNA Quality Assessment, on the site Sam's Notebook 3 years, 9 months ago
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Steven Roberts commented on the post, RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks, on the site Sam's Notebook 3 years, 10 months ago
Hindsight- she did have some issues with proper preservation on some occasions- using wrong sequence of chemicals and/or not getting into building?
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I know we discussed this in person, but I’ll post here for posterity.
As far as I can tell from her notebook, there didn’t seem to be any issues. However, most of the samples that I have been unable to get RNA from are from the very first set that she prepped with the PAXgene Tissue Stabilizer. Could just be coincidence.
Anyway, as discussed,…[Read more]
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fu- the direction of methylation in TEs in predominantly hypo, or loss of methylation.