BioHackerLab/Experimental - Revisjonshistorikk

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2017-09-06T10:28:37Z

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Jarlemag: /* 11 Jul 2016 - Bitraf PCR #3 */

2016-07-24T20:19:09Z

‎11 Jul 2016 - Bitraf PCR #3

Jarlemag: Added July 11 PCR results picture

2016-07-24T20:17:01Z

Added July 11 PCR results picture

Jarlemag: /* Expected results/bioinformatics analysis */

2016-07-20T11:49:49Z

‎Expected results/bioinformatics analysis

Jarlemag på 20. jul. 2016 kl. 11:37

2016-07-20T11:37:36Z

Jarlemag på 20. jul. 2016 kl. 08:45

2016-07-20T08:45:43Z

Jarlemag på 20. jul. 2016 kl. 08:44

2016-07-20T08:44:44Z

Jarlemag på 20. jul. 2016 kl. 08:44

2016-07-20T08:44:23Z

Jarlemag: /* 11 Jul 2016 - Bitraf PCR #3 */

2016-07-19T19:12:55Z

‎11 Jul 2016 - Bitraf PCR #3

Jarlemag på 19. jul. 2016 kl. 18:23

2016-07-19T18:23:43Z

← Eldre revisjon		Revisjonen fra 6. sep. 2017 kl. 10:28
Linje 44:		Linje 44:

	Finally, a blastn search was likewise performed with the reverse complement of the ITS4 primer sequence. The search returned 200 hits and 100 sequences producing significant alignments, including several hits with 100% query coverage and 100% identity. The lowest E value was 0.49.		Finally, a blastn search was likewise performed with the reverse complement of the ITS4 primer sequence. The search returned 200 hits and 100 sequences producing significant alignments, including several hits with 100% query coverage and 100% identity. The lowest E value was 0.49.
		+
		+	[[Category:Biohacking]]

← Eldre revisjon		Revisjonen fra 24. jul. 2016 kl. 20:19
Linje 26:		Linje 26:

	[1]: Liquid cultures provided by Heikki. To prepare template, 50 uL liquid culture was incubated at 98C for 10 min in OpenPCR.		[1]: Liquid cultures provided by Heikki. To prepare template, 50 uL liquid culture was incubated at 98C for 10 min in OpenPCR.
		+
		+	The samples were analzyed by electrophoresis July 24 2016. See the picture below:

	[[Fil:July11PCRresult.jpg\|miniatyr\|sentrer\|The result after electrophoresis of the PCR samples from the meetup 11 july 2016. Unfortunately, the results were rather disappointing. Out of the six PCR reactions, it appears that only one resulted in succesful amplification. Sample 5, using 1 uL of the solution previously prepared from dry baker's yeast as template, gave the expected band. There are several possible explanations for the failure of the other reactions to produce visible bands, including differences in template preparation, amount of template used and genetic differences between the yeast types. From left to right: DSbio 1kb ladder, PCR samples #1 , 2, 3, 4, 5, 6 and 7 (negative control). Electrophoresis was performed with 1% agarose at 100 V for 30 min.]]		[[Fil:July11PCRresult.jpg\|miniatyr\|sentrer\|The result after electrophoresis of the PCR samples from the meetup 11 july 2016. Unfortunately, the results were rather disappointing. Out of the six PCR reactions, it appears that only one resulted in succesful amplification. Sample 5, using 1 uL of the solution previously prepared from dry baker's yeast as template, gave the expected band. There are several possible explanations for the failure of the other reactions to produce visible bands, including differences in template preparation, amount of template used and genetic differences between the yeast types. From left to right: DSbio 1kb ladder, PCR samples #1 , 2, 3, 4, 5, 6 and 7 (negative control). Electrophoresis was performed with 1% agarose at 100 V for 30 min.]]

← Eldre revisjon		Revisjonen fra 24. jul. 2016 kl. 20:17
Linje 26:		Linje 26:

	[1]: Liquid cultures provided by Heikki. To prepare template, 50 uL liquid culture was incubated at 98C for 10 min in OpenPCR.		[1]: Liquid cultures provided by Heikki. To prepare template, 50 uL liquid culture was incubated at 98C for 10 min in OpenPCR.
		+
		+	[[Fil:July11PCRresult.jpg\|miniatyr\|sentrer\|The result after electrophoresis of the PCR samples from the meetup 11 july 2016. Unfortunately, the results were rather disappointing. Out of the six PCR reactions, it appears that only one resulted in succesful amplification. Sample 5, using 1 uL of the solution previously prepared from dry baker's yeast as template, gave the expected band. There are several possible explanations for the failure of the other reactions to produce visible bands, including differences in template preparation, amount of template used and genetic differences between the yeast types. From left to right: DSbio 1kb ladder, PCR samples #1 , 2, 3, 4, 5, 6 and 7 (negative control). Electrophoresis was performed with 1% agarose at 100 V for 30 min.]]

	==Expected results/bioinformatics analysis==		==Expected results/bioinformatics analysis==

← Eldre revisjon		Revisjonen fra 20. jul. 2016 kl. 11:49
Linje 37:		Linje 37:
	A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the expected number of identical results encountered by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.		A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the expected number of identical results encountered by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.

−	Likewise a search was performed with the ITS1 primer sequence as query. The search returned 194 hits and 94 sequences producing significant alignments. Several hits had 100% query coverage and 100% identity. However, the lowest E value reported was 25.	+	Likewise a blastn search was performed with the ITS1 primer sequence as query. The search returned 194 hits and 94 sequences producing significant alignments. Several hits had 100% query coverage and 100% identity. However, the lowest E value reported was 25. Search with megablast/discontigous megablast did not return any hits.
		+
		+	Finally, a blastn search was likewise performed with the reverse complement of the ITS4 primer sequence. The search returned 200 hits and 100 sequences producing significant alignments, including several hits with 100% query coverage and 100% identity. The lowest E value was 0.49.

← Eldre revisjon		Revisjonen fra 20. jul. 2016 kl. 11:37
Linje 36:		Linje 36:

	A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the expected number of identical results encountered by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.		A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the expected number of identical results encountered by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.
		+
		+	Likewise a search was performed with the ITS1 primer sequence as query. The search returned 194 hits and 94 sequences producing significant alignments. Several hits had 100% query coverage and 100% identity. However, the lowest E value reported was 25.

← Eldre revisjon		Revisjonen fra 20. jul. 2016 kl. 08:45
Linje 35:		Linje 35:
	'''BLAST search:'''		'''BLAST search:'''

−	A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the ~~probability~~ of ~~observing the result~~ by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.	+	A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the expected number of identical results encountered by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.

← Eldre revisjon		Revisjonen fra 20. jul. 2016 kl. 08:44
Linje 35:		Linje 35:
	'''BLAST search:'''		'''BLAST search:'''

−	A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence ( for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the probability of observing the result by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.	+	A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the probability of observing the result by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.

← Eldre revisjon		Revisjonen fra 20. jul. 2016 kl. 08:44
Linje 34:		Linje 34:

	'''BLAST search:'''		'''BLAST search:'''
		+
		+	A BLAST search was performed in the GCA_000340765.1 assembly with the expected PCR product sequence ( for amplification with primers ITS1 and ITS4 from S. cerevisiae, as determined by in silico PCR ([https://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=500810913_rmZAxNnexxkDaK66dHwLt86MeALA&org=S.+cerevisiae&db=sacCer3&wp_target=genome&wp_f=TCCGTAGGTGAACCTGCGG&wp_r=TCCTCCGCTTATTGATATGC&Submit=submit&wp_size=4000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0 link]). The search returned 15 hits ("Sequences producing significant alignments". The longest 100% matching sequence stretch was 17 bp long, having an Expectation value ("E value"; roughly, the probability of observing the result by chance) of 5.1. The hit with lowest Expectation value and the only hit with an E value below 1, is a 34bp stretch with 28/34(82%) matching nucleotides and an E value of 0.42.

← Eldre revisjon		Revisjonen fra 19. jul. 2016 kl. 19:12
Linje 26:		Linje 26:

	[1]: Liquid cultures provided by Heikki. To prepare template, 50 uL liquid culture was incubated at 98C for 10 min in OpenPCR.		[1]: Liquid cultures provided by Heikki. To prepare template, 50 uL liquid culture was incubated at 98C for 10 min in OpenPCR.
		+
		+	==Expected results/bioinformatics analysis==
		+
		+	'''Reference sequence:'''
		+
		+	One of the yeast samples was described as Brettanomyces. The most relevant organism in this genus appears to be Brettanomyces bruxellensis. The organism overview page at http://www.ncbi.nlm.nih.gov/genome/11901 lists Brettanomyces bruxellensis CBS 2499 (assembly Dekkera bruxellensis CBS 2499 v2.0, Assembly accession no. GCA_000340765.1) as the representative genome for this organism.
		+
		+	'''BLAST search:'''

@@ Linje 17: / Linje 17: @@
 * #1/HS1A: 1 uL yeast sample #1. (S. Cerevisiae [1])
 * #2/HS1B: 2 uL yeast sample #1. (S. Cerevisiae [1])
-* #3/HS2A: 1 uL yeast sample #2. (Brettanomyces [1]?)
+* #3/HS2A: 1 uL yeast sample #2. (Brettanomyces? [1])
-* #4/HS2B: 2 uL yeast sample #2. (Brettanomyces [1]?)
+* #4/HS2B: 2 uL yeast sample #2. (Brettanomyces?[1])
 * #5/P1: 1 uL S. cerevisiae (Idun tørrgjær. Template prepared 5 july stored in freezer)
 * #6/P2: 2 uL S. cerevisiae (Idun tørrgjær. Template prepared 5 july stored in freezer)