Contract M13 phage ssDNA Production - Revision history

ShawnDouglas at 22:13, 31 January 2011

2011-01-31T22:13:16Z

←Older revision		Revision as of 22:13, 31 January 2011
Line 1:		Line 1:
-	~~==Contract M13 phage ssDNA Production==~~
-	The following outlines my recent experience with contract research. We attempted to outsource the production and purification of single-stranded DNA produced by M13 phage. It wasn't a happy experience, but hopefully someone will find this useful. For example: I generated an extensive list of contract research companies in the process.
-
	===Companies Contacted===		===Companies Contacted===
	'''No response'''		'''No response'''
Line 29:		Line 26:
	*[http://altheatech.com/ Althea Technologies] (emailed 4/4, response 4/6)		*[http://altheatech.com/ Althea Technologies] (emailed 4/4, response 4/6)
	*[http://plasmidfactory.com/ Plasmid Factory] (emailed 4/4, response 4/11)		*[http://plasmidfactory.com/ Plasmid Factory] (emailed 4/4, response 4/11)
-
-	~~===Quotes Received===~~
-	~~{\| {{table}}~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''Company'''~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''10 mg'''~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''20 mg'''~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''50 mg'''~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''100 mg'''~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''500 mg'''~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''1000 mg'''~~
-	\|-
-	~~\| [http://www.ocimumbio.com/web/research_services/research_con.asp Ocimum Bio]\|\| \|\|$1,250 \|\|$3,900 \|\|$5,900 \|\|$18,500 \|\|$25,000~~
-	\|-
-	~~\| [http://fermentas.com/ Fermentas]\|\|$6,300\|\| \|\|$10,200 \|\|$14,400 \|\|$25,700 \|\|$42,100~~
-	\|-
-	~~\| [http://www.seqwright.com/ Seqwright] \|\| \|\| \|\| \|\| \|\|$28,000 \|\|~~
-	\|-
-	~~\| [http://www.lofstrand.com/ Lofstrand] \|\| \|\|$4,000 \|\|$7,000 \|\|$12,000 \|\|$50,000 \|\|$90,000~~
-	\|-
-	~~\| [http://aldevron.com/ Aldevron] \|\| \|\| \|\| \|\| $16,000 \|\| \|\| $90,000~~
-	\|-
-	~~\| [http://cmt-inc.net/ CMT] \|\| \|\| \|\| \|\| $82,240+<sup>*</sup> \|\| \|\|~~
-	\|}
-	~~<nowiki>* - CMT would not guarantee yields.</nowiki>~~
-
-	~~===Orders placed===~~
-	We placed an order with Ocimum Biosolutions for 1000 mg of ssDNA. The contract they proposed was to deliver 100-200 mg within 14 days, 300 mg within 21 days, and the remaining 500-600 mg within 28 days. After 21 days, Ocimum was able to deliver 10 mg of highly-contaminated ssDNA (see the nice smear in the last two lanes of the gel below).
-
-	~~[[Image:p7308-comparison.png\|thumb\|2% agarose 10 mM {{mgcl2}}]]~~
-	~~{\| {{table}}~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''Lane'''~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''Contents'''~~
-	~~\| align="center" style="background:#f0f0f0;"\|'''Loading Buffer'''~~
-	\|-
-	~~\| 0\|\|[[:Image:1kb.png\|1kb DNA ladder]] (4 {{ul}})\|\|~~
-	\|-
-	~~\| 1\|\|Shih Lab ssDNA (1 {{ul}})\|\|AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})~~
-	\|-
-	~~\| 2\|\|Shih Lab ssDNA (5 {{ul}})\|\|AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})~~
-	\|-
-	~~\| 3\|\|Ocimum ssDNA (1 {{ul}})\|\|AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})~~
-	\|-
-	~~\| 4\|\|Ocimum ssDNA (5 {{ul}})\|\|AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})~~
-	\|}
-
-	~~===Outcome===~~
-	We went with the deceptively low bid, and after 3 weeks we received what ''would'' have amounted to 1/50th of what we were promised by that time, and 1/100th of our total order -- that is, if it had been clean, usable DNA. In the subsequent two weeks of extremely tedious negotiations, Ocimum refused to offer any discount or compensation, and failed to guarantee any future delivery schedule, and we were ultimately forced to cancel our order.

ShawnDouglas at 18:22, 7 May 2009

2009-05-07T18:22:16Z

←Older revision		Revision as of 18:22, 7 May 2009
Line 1:		Line 1:
	==Contract M13 phage ssDNA Production==		==Contract M13 phage ssDNA Production==
-	The following outlines my recent experience with contract research. We attempted to outsource the production and purification of single-stranded DNA produced by M13 phage. It wasn't a happy experience, but hopefully someone will find this useful.	+	The following outlines my recent experience with contract research. We attempted to outsource the production and purification of single-stranded DNA produced by M13 phage. It wasn't a happy experience, but hopefully someone will find this useful. For example: I generated an extensive list of contract research companies in the process.

	===Companies Contacted===		===Companies Contacted===

ShawnDouglas: /* Quotes Received */

2006-06-14T12:30:24Z

Quotes Received

←Older revision		Revision as of 12:30, 14 June 2006
Line 52:		Line 52:
	\| [http://cmt-inc.net/ CMT] \|\| \|\| \|\| \|\| $82,240+<sup>*</sup> \|\| \|\|		\| [http://cmt-inc.net/ CMT] \|\| \|\| \|\| \|\| $82,240+<sup>*</sup> \|\| \|\|
	\|}		\|}
-	<nowiki>* - CMT would not guarantee yields.<nowiki>	+	<nowiki>* - CMT would not guarantee yields.</nowiki>

	===Orders placed===		===Orders placed===

ShawnDouglas: /* Quotes Received */

2006-06-14T12:29:59Z

Quotes Received

←Older revision		Revision as of 12:29, 14 June 2006
Line 50:		Line 50:
	\| [http://aldevron.com/ Aldevron] \|\| \|\| \|\| \|\| $16,000 \|\| \|\| $90,000		\| [http://aldevron.com/ Aldevron] \|\| \|\| \|\| \|\| $16,000 \|\| \|\| $90,000
	\|-		\|-
-	\| [http://cmt-inc.net/ CMT] \|\| \|\| \|\| \|\| $82,240+(<sup>*</sup> \|\| \|\|	+	\| [http://cmt-inc.net/ CMT] \|\| \|\| \|\| \|\| $82,240+<sup>*</sup> \|\| \|\|
	\|}		\|}
-	*CMT would not guarantee yields.	+	<nowiki>* - CMT would not guarantee yields.<nowiki>

	===Orders placed===		===Orders placed===

ShawnDouglas: /* Quotes Received */

2006-06-14T12:28:47Z

Quotes Received

←Older revision		Revision as of 12:28, 14 June 2006
Line 50:		Line 50:
	\| [http://aldevron.com/ Aldevron] \|\| \|\| \|\| \|\| $16,000 \|\| \|\| $90,000		\| [http://aldevron.com/ Aldevron] \|\| \|\| \|\| \|\| $16,000 \|\| \|\| $90,000
	\|-		\|-
-	\| [http://cmt-inc.net/ CMT] \|\| \|\| \|\| \|\| $82,240+ \|\| \|\|	+	\| [http://cmt-inc.net/ CMT] \|\| \|\| \|\| \|\| $82,240+(<sup>*</sup> \|\| \|\|
	\|}		\|}
-		+	*CMT would not guarantee yields.

	===Orders placed===		===Orders placed===

ShawnDouglas at 12:20, 14 June 2006

2006-06-14T12:20:58Z

New page

==Contract M13 phage ssDNA Production==
The following outlines my recent experience with contract research. We attempted to outsource the production and purification of single-stranded DNA produced by M13 phage. It wasn't a happy experience, but hopefully someone will find this useful.

===Companies Contacted===
'''No response'''
*[http://www.lamdabiotech.com/displaycategory.asp?Categoryid=36 Lambda biotech] (emailed 3/2/06)
*[http://www.wisbio.com/ Wisconsin Bioproducts] (voicemail left 3/3/06)
*[http://www.geneblitz.com/dna_preparation.htm Geneblitz] (emailed 3/8/06)
*[http://www.fitbiotech.com/products/t_prod8.htm FIT biotech] (emailed 3/8/06)
*[http://www.cbi-biotech.com/cbi Commonwealth Biotech] (emailed 4/12/06)
*[http://www.maxim-asia.com/xyen/Index.asp Maxim Biotech] (emailed 4/12/06)
*[http://www.atglabsinc.com/ ATG Labs] - info@atglabsinc.com (emailed 4/12/06)
*[http://seracare.com/ Seracare] (emailed 4/12/06)
*[http://www.retrogen.com/ Retrogen] (emailed 4/12/06)
*[http://www.usbio.net/Home.aspx US Biological] - service@usbio.net (emailed 4/12/06)

'''Initial response promising a quote, followed by zero communication'''
*[http://www.marinbio.com/molecularbio2.html Marinbio] (emailed 3/8/06, 3/26/06, 4/4/06, 4/12,06. last response was 3/26/06)
*[http://www.natx.com/PlasmidLargeScale.html Nature Technology Corporation (natx)] - (emailed 3/2, 3/8, 3/23, 3/27, 4/3, 4/12) Shipped them a sample to begin pre-production on 3/27. Was informed that my sample was "quarantined" on 4/3, and then no further responses were received.

'''Response received, but not offering M13 ssDNA production'''
*[http://www.genscript.com/clone_exp.html Genscript] (emailed 3/9, response 3/9)
*[http://www.lark.com/services%5ccustom_services.html Lark] (emailed 3/9, responses 3/9, 3/13, 3/14)
*[http://www.agencourt.com/ Agencourt] (emailed 3/6, response 3/7, 3/13)
*[http://www.invitrogen.com/content.cfm?pageid=11035 Invitrogen] (emailed 3/8, response 3/15)
*[http://www.puresyn.com/ Puresyn] (emailed 4/4, response 4/5, including phone call followup)
*[http://www.mwgbiotech.com/html/all/index.php MWG Biotech] (emailed 4/12, response 4/12)
*[http://paragonbioservices.com/ Paragon] (emailed 4/12, response 4/12)
*[http://altheatech.com/ Althea Technologies] (emailed 4/4, response 4/6)
*[http://plasmidfactory.com/ Plasmid Factory] (emailed 4/4, response 4/11)

===Quotes Received===
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Company'''
| align="center" style="background:#f0f0f0;"|'''10 mg'''
| align="center" style="background:#f0f0f0;"|'''20 mg'''
| align="center" style="background:#f0f0f0;"|'''50 mg'''
| align="center" style="background:#f0f0f0;"|'''100 mg'''
| align="center" style="background:#f0f0f0;"|'''500 mg'''
| align="center" style="background:#f0f0f0;"|'''1000 mg'''
|-
| [http://www.ocimumbio.com/web/research_services/research_con.asp Ocimum Bio]|| ||$1,250 ||$3,900 ||$5,900 ||$18,500 ||$25,000
|-
| [http://fermentas.com/ Fermentas]||$6,300|| ||$10,200 ||$14,400 ||$25,700 ||$42,100
|-
| [http://www.seqwright.com/ Seqwright] || || || || ||$28,000 ||
|-
| [http://www.lofstrand.com/ Lofstrand] || ||$4,000 ||$7,000 ||$12,000 ||$50,000 ||$90,000
|-
| [http://aldevron.com/ Aldevron] || || || || $16,000 || || $90,000
|-
| [http://cmt-inc.net/ CMT] || || || || $82,240+ || ||
|}

===Orders placed===
We placed an order with Ocimum Biosolutions for 1000 mg of ssDNA. The contract they proposed was to deliver 100-200 mg within 14 days, 300 mg within 21 days, and the remaining 500-600 mg within 28 days. After 21 days, Ocimum was able to deliver 10 mg of highly-contaminated ssDNA (see the nice smear in the last two lanes of the gel below).

[[Image:p7308-comparison.png|thumb|2% agarose 10 mM {{mgcl2}}]]
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Lane'''
| align="center" style="background:#f0f0f0;"|'''Contents'''
| align="center" style="background:#f0f0f0;"|'''Loading Buffer'''
|-
| 0||[[:Image:1kb.png|1kb DNA ladder]] (4 {{ul}})||
|-
| 1||Shih Lab ssDNA (1 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
|-
| 2||Shih Lab ssDNA (5 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
|-
| 3||Ocimum ssDNA (1 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
|-
| 4||Ocimum ssDNA (5 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
|}

===Outcome===
We went with the deceptively low bid, and after 3 weeks we received what ''would'' have amounted to 1/50th of what we were promised by that time, and 1/100th of our total order -- that is, if it had been clean, usable DNA. In the subsequent two weeks of extremely tedious negotiations, Ocimum refused to offer any discount or compensation, and failed to guarantee any future delivery schedule, and we were ultimately forced to cancel our order.