April 01, 2014
taxonomic representation of OlyO transcriptome v3 cdd blast through galaxy
Phylum
 Counts
Chordata
 12403
Proteobacteria
 1433
Streptophyta
 1111
Firmicutes
 767
Arthropoda
 434
Ascomycota
 427
Euryarchaeota
 281
Echinodermata
 104
Cyanobacteria
 82
Basidiomycota
 65
Apicomplexa
 60
Chlamydiae
 47
Annelida
 38
Mollusca
 38
Bacteroidetes
 30
Tenericutes
 26
Spirochaetes
 22
Chlorophyta
 17
Deinococcus-Thermus
 17
Platyhelminthes
 16
Crenarchaeota
 7
Euglenida
 4
Nematoda
 3
Cnidaria
 2
Neocallimastigomycota
 2
Porifera
 1
Tree:
OlyO_CDD_phylogenetictree.jpg

March 27, 2014

Parameters on the RSeq Analysis:
-OlyO Transcriptome v2 as reference genome
-min read length fraction: 0.9
-max hits per read: 10

Parameters in Expression Analysis:
-unpaired two group comparison
-set expression value to unique gene reads

Info for annotating genome and location of GOSlim database
http://oystergen.es/query
https://github.com/uwescience/sqlshare/wiki/Workflow:-Annotating-Oyster-Genes

February 18, 2014

Plots:
Scatter of 106 male/female unique gene reads
Histogram of 106 male/female unique gene reads
Scatter of 108 male/female unique gene reads
Histogram of 108 male/female unique gene reads

data table for 106 Broodstock
data table for 108 Broodstock
January 28, 2014

January 21, 2014


January 07, 2014

October 16, 2013
Many of the blasts were not fully completed so they must be redone.
Re-doing failed blasts on the following databases:
Blasts using cdd_delta (Oly Blast 2) and refseq_rna (Oly Blast 10) have successfully completed

October 10, 2013
I have been having issues with the vector and pdbaa databases not blasting.

October 9, 2013

(list last revised 10/10/2013)
Blast databases tried:

Blast databases not tried:

Databases with Issues

October 3, 2013
Running some more data through blast- added to the list on October 1st.

Reminder: DIfferent Blasts

Remember- to find notebook on iPython type ipython notebook --pylab inline into the terminal

d-128-95-149-219:~ srlab$ cd /Volumes/web/scaphapoda/Hannah

d-128-95-149-219:Hannah srlab$ pwd

/Volumes/web/scaphapoda/Hannah

d-128-95-149-219:Hannah srlab$ ipython notebook -pylab inline

Google Doc of BLAST Databases


October 1, 2013
Continuing blasting Oly transcriptome against various databases in whale folder

Program blastx works for the following databases:

Program blastn works for the following databases:

September 26, 2013
Ran blast yesterday (September 25) on Olympia oyster data comparing against new databases.
Continuing blast sequences today.

September 24, 2013
Learning more about IPython and SQLshare

Changing | to tabs in IPy:
!tr '|' "\t" </Volumes/web/scaphapoda/Hannah/OlyO_trans_v3_swissprot.txt> /Volumes/web/scaphapoda/Hannah/OlyO_trans_v3_swissprot_mod.txt

Joining Tables in SQLshare:
SELECT * FROM
[wearh@washington.edu].[OlyO_trans_v3_swissprot_mod.txt]oly
left join
[sr320@washington.edu].[associations_uni_swisspro_012410]des
on
oly.Column3 = des.ID
September 18, 2013
Steven showed me how to run IPython and BLAST
What was ran:
!blastx -query /Volumes/web/scaphapoda/Hannah/Olurida_transcriptome_v3.fasta -db /Users/Shared/Apps/ncbi-blast_28/db/uniprot_sprot -out /Volumes/web/scaphapoda/Hannah/Olur_blast_sprot.txt -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 14

Program: blastx
Language: -query (file)
Database: -db (file: /Users/Shared/Apps/ncbi-blast_28/db/uniprot_sprot)
Output Location: -out (new file in .txt format)
Other Info: -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 14
September 5, 2013
Took tissue samples from breeding group SN 9 and SN 30.

Group SN 9**

Group SN 30

All of the breeding group oysters from NF, HL, and SN have been sampled. Tissue samples were placed in storage nine boxes and labeled according to the contents: NF_A, NF_B, NF_C, HL_A, HL_B, HL_C, SN_A, SN_B, and SN_C.

September 4, 2013
Took tissue samples from breeding group SN 15 and SN 21.

Group SN 15

Group SN 21

August 22, 2013
Took tissue samples from breeding group HL 19.
One of the oysters was much larger than the rest of the Hood Canal oysters sampled- about 2.5 inches length opposed to 1 inch length


August 15, 2013
Took tissue samples from breeding group HL 16.

August 09, 2013
Took tissue samples from breeding group HL 28.
One of the oysters was much larger than the rest of the Hood Canal oysters sampled- about 2.5 inches length opposed to 1 inch length
Shells from breeding group HL 4 were dried, labeled corresponding the tissue sample number and placed in individual plastic bag.

August 08, 2013
Started taking samples from a new breeding group: Hood Canal (HL). Took mantle and adductor muscle tissue samples from breeding group HL 4.
Found bags for all the dried oyster shells! They are now individually labeled and bagged.

August 06, 2013
Sampled the last group of North Sound Fidalgo Bay. Oysters were frozen so they were placed in a water bath to thaw. Took mantle and adductor tissue samples from breeding group NF #?
Dried shells from NF 8 were labeled corresponding to the tissue sample number.

July 31, 2013
Took mantle and adductor tissue samples from breeding group NF 8.
Dried shells from NF 14 were labeled corresponding to the tissue sample number.

July 30, 2013
Oyster shells from group NF 14 were labeled by writing the group and sample number directly onto the shell once dry. All oyster shells from the breeding groups will continue to be labeled in this same manner.
Took mantle and adductor tissue samples from oysters in group NF 20.

July 25, 2013
Since the commercial oyster mantle tissue samples were being stored in snap lid capsules, they needed to be better preserved so we separated the A and B samples into containers and vacuum sealed them.
Breeding Group NF14 Olympic Oyster Tissue Samples
Started collecting tissue samples from oyster breeding groups. The same methods as described previously were used to collect two samples of mantle tissue per oyster in addition to a sample of adductor muscle from each oyster. The mantle tissues were labeled as NF#A and NF#B, and all adductor tissue samples were labeled as NF#C. Breeding group NF14 contained 20 live oysters (all sampled) and zero dead/un-sampled oysters. The oyster shells from NF14 were labeled corresponding to the tissue sample number and left to dry out for future research.

July 23, 2013
Finished sampling the commercial Olympic oysters that were collected last December, 2012. There were 142 oysters that tissue was extracted from with two samples per oyster (labeled A and B).

July 19, 2013
Continued to collect mantle tissue samples from Olympic oysters using the same procedure as described on July 28, 2013. Collected 52 tissue samples and starting to get a better understanding of oyster anatomy.

July 18, 2013
First day in the lab!
Olympic Oyster Mantle Tissue Samples
Took mantle tissue of commercial raised adult Olympic oysters (Ostreola conchaphila) for DNA extraction. Oysters were sliced open by prying apart the shells at the hinge and then severing the abductor muscle to reveal the internal organs. Two tissue samples from the mantle of each oyster were taken and placed into separate snap cap tubes with a 70% ethanol solution. Forceps and tweezers used to extract the tissue sample were sanitized after each oyster in a alconox, bleach, and water bath process to avoid DNA contamination. 64 tissue samples were collected.