@steven-roberts
active 4 months, 2 weeks ago-
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
Currently there is a pretty robust spreadsheet and over the past few days Jake has cranked through some reps to see how the oysters that were mechanically stressed hold up. Below is how these data are […] -
Steven Roberts wrote a new post, Another day, another species, on the site half-shell 3 years, 6 months ago
Today we sampled Jesse, the Olympia oyster selected for genome sequencing. Not as big of a specimen as yesterday, but made up for it with video.The oyster was collected in Fidalgo Bay, weighing in at 58.99 grams […]
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Steven Roberts wrote a new post, Big day, big clam, on the site half-shell 3 years, 6 months ago
Today we sampled the geoduck (Panopea generosa) for genome sequencing. Here is how things went down.It was an early morning for the clam, peaking out to see a glorious sunrise on the porch.
From there it was […]
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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
Taking the most decent Ct values, I did the simple and crude calculation, normalizing with EF1 and looking at fold over minimum.Seems to be EF1 data is skewing. Will take a look with actin and also compare […]
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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 […] -
Steven Roberts wrote a new post, No code required, on the site half-shell 3 years, 7 months ago
Today Sam and I took care of the daily maintenance of F2 Olympia oysters grown at the Ken Chew Shellfish Hatchery at Manchester, WA. In short, larvae are being described from Fidalgo (North: NF), Oyster Bay […] -
Steven Roberts wrote a new post, Second look at Geoduck transcriptome, on the site half-shell 3 years, 7 months ago
Last week I popped out a quick assembly and annotation on our geoduck gonadal transcriptome. A second assembly was also done using Trinity.Updates
August 3 – Confirmed//in file location had no impact on […] -
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
For purposes of proposaling and reports, I have gone back to look at a small project done in collaboration with scientist at IFREMER looking at pesticide exposure on oyster larvae methylation.The control […]
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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
A detailed look at DMRs that hold true across oysters exposed to heat shock.Updated July 6, 2015 – added three more DMRs (at bottom of post)
Going down the list, scaffold418_576986 is a feature that […]
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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
A first look at population differences at qPCR primer sites for three population of Olympia oystersPlate 1 (
samwhite_112381) included, BMP2, CARM, HSPb11, and PGEEP4. At the bottom is a full list of qPCR […] -
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
The first batch of sequencing came into today to verify sequence of Olympia oyster qPCR primers.1) imported
.ab1files into CLC,2) trimmed “CARM” sequences
3) aligned to
comp7220_c0_seq2 -
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.