Difference between revisions of "2017 Feb Taeyoung Lab note"
(→2017.2.22) |
|||
Line 96: | Line 96: | ||
===2017.2.22=== | ===2017.2.22=== | ||
+ | [[File:2017022201.jpg|frameless|2017.2.22 LIPs-13a Gradient using CS-14 and W82 Tm:50-65 130ml gel 1% Agar 100v 1h]] | ||
+ | |||
+ | 2017.2.22 | ||
+ | |||
+ | LIPs-13a Gradient using CS-14 and W82 | ||
+ | |||
+ | Tm:50-65 | ||
+ | |||
+ | 130ml gel | ||
+ | |||
+ | 1% Agar 100v 1h |
Revision as of 07:19, 22 February 2017
2017.2.2
PCR with LIP short primer
Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order
LIP01-24
Last 4 bands are Tubulin control in CS-12,CS-14,KS-04,W82
1% agar, 100V, 1h, Tm:56,
2017.2.3
PCR with LIP short primer
Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order
SLIP01,02,03,06,07,09,13,14,15,16,20,24
Last 3 bands are Tubulin control in CS-12,CS-14,W82
1% agar, 100V, 1h, Tm:56,
2017.2.6
PCR with LIP short primer
Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order
SLIP01,02,03,06,07,13,14,15,16,20,24
Last 3 bands are Tubulin control in CS-12,CS-14,W82
1% agar, 100V, 1h, Tm:56,
2017.2.7
PCR with LIP short primer
Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order
2017.02.07 SLIP-08,12,13,20 with Wild and W82
Last 3 bands are Tubulin control in CS-12,CS-14,W82
1% agar, 100V, 1h, Tm:56,
Primer re-design
SLIP-13 and 16 is re-designed
python ~/py/LIP/6-1.manual_primer_design.py CS-14-contigs.fa.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates
2017.2.8~2.10
Field work
2017.2.13
LIPs-13 and 16 re-design
python ~/py/LIP/6-1.manual_primer_design.py CS-14-contia.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates
e-PCR
re-PCR -S ../../CS-14/qvalue/CS-14-contigs.hash -n1 -g1 CS-14.short.primer.fa.2candidates.sts -o CS-14.short.primer.fa.2candidates.sts.out
Primer order
OrthoMcl of Jatropha organ
all done
Draw venn diagram using Jatropha organ data
require(Vennerable) Data <- read.table("group.txt.binary.parsed.rawinput.endosperm",col.names="") Organ <- c("SG","LG","Y","B") png(filename="Venn.endosperm.png",width=2000,height=2000) plot(Venn(SetNames=Organ,Weight=as.vector(Data$X)),doWeights=F,type="ellipses") dev.off()
OrthoMcl of Jatropha species
all done
Drawing venn diagram using Jatropha species data
done
BLASTP for Ks calculation among Jatropha species
193:/data2/alima90/Jatropha/KaKs_nocdhit$python blastp.py # blastp -db Jct.cds.fa.pep.complete.fa -evalue 1e-10 -outfmt 6 -num_threads 20 -num_alignments 5 -query Rco.cds.fa.pep.complete.fa -out Jct.Rco.blastp.1e-10.na5.outfmt6
2017.2.20
LIPs-13a,16a with CS-14 and W82
Tm:56
1% agar 130ml gel 100v 1h
2017.2.22
2017.2.22
LIPs-13a Gradient using CS-14 and W82
Tm:50-65
130ml gel
1% Agar 100v 1h