Tag Archives: Sanger sequencing

Sample Submission – Olympia oyster & Sea Pen PCRs Sanger Sequencing

Prepared two DNA plates and corresponding primer plates for sequencing at the UW HTGC from the purified gel-purified PCRs from yesterday. Primer plates were prepared by adding 7μL of NanoPure H2O to each well and then adding 3μL of 10μM primer to the appropriate wells. For the DNA plates, added 10μL of DNA to the appropriate wells.

NOTE: The H2A_ST1 samples had insufficient volume of DNA for all four sequencing reactions. Added 30μL of NanoPure water to purified DNA, mixed and distributed to the appropriate wells.

Sequencing plates layouts can be seen here (Google Sheet): sequence_log.

Submitted the plates to the UW HTGC for Sanger sequencing.

Sequencing – C.gigas COX2/PGS2 Clone #4 from 20110728

Used new primers for sequencing (SR IDs: 1351 & 1352) clone #4. Sequenced clone two times in each direction. DNA and primers were sent for sequencing at ASU. Requested “High GC” treatment to help overcome the issue seen on 20110728.


Sequencing results received 20110810. Initial analysis suggests that we managed to fully sequence this clone! Will try to assemble a full-length CDS for COX2/PGS2.

Plasmid Isolation & Sequencing – C.gigas COX2/PGS2 Clones (from yesterday)

Isolated plasmid DNA from 3mL of liquid cultures that were inoculated yesterday using Qiagen’s miniprep kit. DNA was eluted with 50uL of EB. DNA was prepped and sent for sequencing to ASU sequencing facility. Each clone was sequenced two times in each direction. Samples are as follows:

Name – Clone # Primer

  • SJW01 – 1 M13F
  • SJW02 – 1 M13F
  • SJW03 – 1 M13R
  • SJW04 – 1 M13R
  • SJW05 – 2 M13F
  • SJW06 – 2 M13F
  • SJW07 – 2 M13R
  • SJW08 – 2 M13R
  • SJW09 – 3 M13F
  • SJW10 – 3 M13F
  • SJW11 – 3 M13R
  • SJW12 – 3 M13R
  • SJW13 – 4 M13F
  • SJW14 – 4 M13F
  • SJW15 – 4 M13R
  • SJW16 – 4 M13R

Clone #s are as follows:

1 – 5′ Library Top band

2 – 5′ Library Mid band

3 – 5′ Library Bottom band

4 – 3′ Library band


Sequencing results received 20110801. SJW15 and 16 apparently stop abruptly. The sequencing facility believes this to be caused by secondary structure of the template. Depending on how things align, I may consider using 7-daeza-GTP in a PCR reaction and re-sequencing this clone, as the 7-daeza-GTP helps relax secondary structure.

Spoke with Steven and he suggested just designing new primers closer to each other and resubmit.

Sequencing – PGS Hi 4 (PGS2/COX2)

Sent plasmid prep to ASU (5uL of plasmid + 1uL of 10uM M13F/R). SJW01 = M13F, SJW02 = M13R.


Sequencing looks great! Definitely have a portion of the second isoform of COX/PGS!! Here’s the result of the consensus BLASTed in GenBank>Nucleotide (others)>blastn:

Top hit in the db is COX1/PGS1, and, clearly, there are differences between the two sequences confirming that we have the second isoform (COX2/PGS2). Will design more RACE primers in hopes of obtaining the full-length cDNA sequence.

Sequencing – Mac methylation samples, Sam rhodopsin samples, Lisa samples

Samples were submitted for sequencing. Mac prepped all Roberts Lab samples excluding the Opsin VMC gel slice 2 from 20091217-02. The gel slice was purified with Millipore spin columns. The sample was diluted 1:1 with H2O and submitted for sequencing, one time from each direction using the Sep_Op_Fw2/Rv2 primers. Plate layout can be found here on sheet labeled “20091223”.

Sequencing – Dungan Isolates, Lake Trout HRM and Emma DD cloning

Submitted 1.5 plates for Sanger sequencing. Dungan isolates prepared by me, Lake Trout HRM prepared by Rony and Emma’s differential display cloning samples prepared by her. All primers were prepped by me. See the sequencing log for samples and plate layout.