-
Sam White wrote a new post, Sanger Sequencing – pCR2.1/OsHV-1 ORF117, on the site Sam's Notebook 3 days, 19 hours ago
Submitted plasmid DNA isolated earlier today to Genewiz for Sanger sequencing using the M13F/R primers.Sequenced each of the two plasmids three times with each forward and reverse primer. Here’s a copy of the […]
-
Sam White wrote a new post, Plasmid Isolation – pCR2.1/OsHv-1_ORF117 Miniprep, on the site Sam's Notebook 3 days, 22 hours ago
The last run at this failed, but I think that was due to old ampicillin stocks; leading to no selective pressure for transformants that actually contained plasmid.
I’ve since remedied that.
Grew up 5mL of […]
-
Sam White wrote a new post, PCR – pCR2.1/OsHV-1_ORF117 Colony Screens, on the site Sam's Notebook 4 days, 18 hours ago
Performed PCR with M13 vector primers on the two colonies that grew from yesterday’s transformation.Master mix calcs:
2x Apex Red Master PCR Mix: 33uL
M13 forward: 1.5uL
M13 reverse: 1.5uL
H2O: 29.7uLAdded […]
-
Sam White wrote a new post, Transformation – pCR2.1/OsHV-1_ORF117 into One Shot Top10 Chemically Competent Cells, on the site Sam's Notebook 6 days, 1 hour ago
Yesterday’s transformation with freshly prepared ampicillin didn’t produce any transformants, suggesting the DNA concentration is too low.Previously, I tried to elute the DNA from one of the spots Tim sent with […]
-
Sam White wrote a new post, Transformation – pCR2.1/OsHV-1_ORF117 into One Shot Top10 Chemically Competent Cells, on the site Sam's Notebook 6 days, 18 hours ago
This is a repeat since the previous attempt at obtaining sufficient quantities of plasmid for sequencing failed. Although I’m not sure why, I figure it’s easy enough to re-do using ampicillin stocks that aren’t […]
-
Erika Lilja became a registered member 1 week ago
-
Sam White wrote a new post, Data Management – Illumina Geoduck HiSeq & MiSeq Data, on the site Sam's Notebook 1 week, 6 days ago
The HDD we received from Illumina last week only had data (i.e. fastq files) from the NovaSeq runs they performed – nothing from either the MiSeq, nor the HiSeq runs.We contacted them about the missing data, […]
-
Sam White wrote a new post, Plasmid Isolation – pCR2.1/OsHv-1_ORF117 Miniprep, on the site Sam's Notebook 2 weeks, 3 days ago
Grew up 5mL of culture from re-streaked colony #1 in 1xLB + 100ug/mL of ampicillin @ 37C on a rocking platform in a 15mL conical over night (~18hrs).
Isolated plasmid DNA from the entire 5mL of culture (repeated […]
-
Sam White wrote a new post, Goals – August 2017, on the site Sam's Notebook 2 weeks, 4 days ago
Data, data, data! That is the theme for this month.
Olympia oyster data – Going to assess and continue working on assembly the Olympia oyster genome we have from our BGI sequencing project, along with the PacBio […]
-
Sam White wrote a new post, PCR – pCR2.1/OsHV-1_ORF117 Colony Screens, on the site Sam's Notebook 2 weeks, 4 days ago
After the puzzling results from the last colony screening, I was able to get more info from Tim Green regarding the insert.The insert was generated via PCR using OsHV-1 ORF 117 primers from this paper:
<a […]
-
Sam White wrote a new post, Samples Received – Pinto Abalone Histo, on the site Sam's Notebook 2 weeks, 6 days ago
-
Sam White wrote a new post, Data Received – Geoduck Genome Sequencing by Illumina, on the site Sam's Notebook 3 weeks ago
We previously sent some geoduck samples to Illumina, as part of a pilot project for them to test out a new sequencing platform. The data has finally arrived!It was sent on a 4TB Seagate external hard drive.
Due […]
-
Sam White wrote a new post, Sample Submission – Pinto Abalone Tissue for Histology Processing, on the site Sam's Notebook 1 month ago
Tracked down and submitted four cassettes containing pinto abalone digestive gland tissue that Sean Bennett prepared, as part of his Capstone project. A full list of samples from his project is here (Google […] -
Sam White wrote a new post, Sample Submission – Olympia oyster gonad RNA to Katherine Silliman @ Univ. of Chicago, on the site Sam's Notebook 1 month ago
Sent the following RNA to Katherine Silliman at the Univ. of Chicago for RNAseq. All RNA was isolated on 20170719, except SN-10-16, which was isolated on […]
-
Sam White wrote a new post, RNA Isolation – Olympia oyster gonad tissue in paraffin histology blocks, on the site Sam's Notebook 1 month ago
My previous go at this was a little premature – I didn’t wait for Laura to fully annotate her slides/blocks. Little did I know, the tissue was mostly visceral mass and, as such, I didn’t hit much in the way of […] -
Sam White wrote a new post, PCR – pCR2.1/OsHV-1_ORF117 Colony Screens, on the site Sam's Notebook 1 month, 1 week ago
Screened five colonies from yesterday’s transformation via PCR using M13 primers.I don’t have any sequence for the actual insert, so am relying on assessing empty vector vs vector with insert, based on PCR […]
-
Sam White wrote a new post, Transformation – pCR2.1/OsHV-1_ORF117 into One Shot Top10 Chemically Competent Cells, on the site Sam's Notebook 1 month, 1 week ago
Used 5uL of the pCR2.1/OsHV-1_ORF117 plasmid provided by Tim Green to transform a single aliquot of One Shot Top10 Chemically Competent Cells (Invitrogen), according to the “Rapid Transformation” protocol.Cells […]
-
Sam White wrote a new post, RNA Isolation – Olympia oyster gonad tissue in paraffin histology blocks, on the site Sam's Notebook 1 month, 1 week ago
UPDATE 20170712: The RNA I isolated below is from incorrect regions of tissue. I misunderstood exactly what this tissue was, and admittedly, jumped the gun. The tissue is actually collected from the visceral mass […] -
Sam White wrote a new post, Data Management – SRA Submission Olympia Oyster UW PacBio Data from 20170323, on the site Sam's Notebook 1 month, 2 weeks ago
Submitted the FASTQ files from the UW PacBio Data from 20170323 to the NCBI sequence read archive (SRA).
FTP’d the data to NCBI’s servers, following their instructions. Briefly,
Change to the directory where the […]
-
Sam White wrote a new post, Data Management – Tarball of Olympia oyster UW PacBio Data from 20170323, on the site Sam's Notebook 1 month, 2 weeks ago
I’d previously attempted to archive this data set on multiple occasions, across multiple days, but network dropouts kept killing my connection to the server (Owl) and, in turn, interrupting the tarball […] - Load More
