14 Jan 2008
1. Long Paired End Library prep. for Lemtinula54A con't
The sheared, methylated DNA was end polished, ligated with hairpin adaptor and treated with exonucleases. The "hairpin-adapted" DNA fragments were now digested overnignt with EcoRI.
Patrick

9 Jan 2009
1. Long Paired End DNA Library of Le-54A
Today we start the DNA fragmentation (Hydroshear) of 4.3 ug Le-54A genomic DNA. The fragmented DNA was treated with EcoRI methyltransferase to methylate all EcoRI sites. Below is the Agilent 2100 trace of the fragmented and ampured Le-54A DNA.

7 Jan 2009
1. We got 65Mbp data from the shotgun run of Pleurotus cDNA. The unexpected low throughput is due to about 40% the reads are short reads with read length less than 50 bp. Here are the assembly result using the GS De novo Assembler.
no. of contigs: 10,988
no. of contigs >500 bp: 1,602
average contig size:658 bp
largest contig size:1,490 bp

2. Training for ABI 7500 was finished today.

Patrick

6Jan2009
Today Winnie and I start the shotgun sequencing run for Pleurotus cDNA. There are almost 900,000 raw reads with the key sequences which means that we should be able to get more than 100 Mbp. See whether we have luck tomorrow.
Patrick

5 January 2009

1. Additional 6 emulsion PCR were performed for the Pleurotus cDNA library.
2. Emulsion breaking
3. DNA quantification for Salmonella and Vibrio DNA

Sample	AU	AU	Average	dilution	Concentration(ng/ul)	5ug (ul)
Lentinula L54A	178	188	183	2000	15.68973116	318.6797753
VP4-430-1	3160	2751	2955.5	2000	278.5368004	17.95094937
VP4-434-1	310	279	294.5	2000	27.32481269	182.983871
VP4-430-2	246	230	238	2000	21.68356104	230.5894309
VP4-434-2	1188	1066	1127	2000	104.7157338	47.7483165
STYM4650/95	3781	3822	3801.5	2000	333.2745703	15.0026448
STYM4848/06	3446	3296	3371	2000	303.7461437	16.46111434
STYM6988/94	1460	1458	1459	2000	128.6910533	38.85273973
STYM728/07	4236	3803	4019.5	2000	373.3803438	13.39117092
STYM90184/93	2524	2601	2562.5	2000	222.4768621	22.47424723

Patrick