SOPs

164 SOPs visible to you, out of a total of 311

Explains the different steps involved in building the core dynamic model of glycolysis, pyruvate metabolism and ATPase in M. pneumoniae
-Construction of the model
-Parameter estimation, selection of best parameter set

Creator: Niels Zondervan

Contributor: Niels Zondervan

Initial configuration and parameters of the Bioleaching

steps conducted to pellet cells for RNA and protein extraction

Creator: Stephan Christel

Contributor: Stephan Christel

Method extraction of intracellular metabolites in Lactococcus lactis

No description specified
No description specified

Oxygen gradients were developed as a quick and easy way to simultaneously adapt (recombinant) strains to decreasing levels of oxygen and monitor their progress over multiple days. This SOP can be used for o/n checks or for adaptation experiments spanning over multiple days. For the latter, a time-lapse camera setup is recommended.
This SOP can also be applied to check the oxygen requirements of unknown strains.

Creators: Linde Kampers, Fons Stams

Contributor: Linde Kampers

The reverse transcriptase synthesizes DNA, which complements the mRNA template
(complementary DNA, cDNA). Cy3/Cy5-dCTP are incorporated into cDNA during Reverse transcription. The obtained Cy3/Cy5 cDNA are then competitively hybridised onto Agilent microarray slide and subsequently scanned.

Standard Operating Procedure describing the process and software used in generating a Genome Scale Metabolic model of M. hyopneumoniae.
Used software:
Pathway tools
PathLogic
Cobrapy
the Cobra Toolbox
libSBML

This protocol describes the analysis of RNA-Seq data to identify differential expressed genes between two samples. The protocol is simply the analysis of the data and do not include the sequencing protocol.

Creator: Vânia Pobre

Contributor: Vânia Pobre

No description specified

Creator: Theresa Kouril

Contributor: Theresa Kouril

This SOP describes the SUMO procedure for determining B-galactosidase activities.

This protocol describes the transcriptional profiling of E. coli cultures using microarrays. The protocol utilises RNA isolated as described in another SOP (SUMO RNA isolation from E. coli) and with hybridisation to Ocimum Ocichip E. coli K-12 microarrays.

For the study of mRNA decay rates, transcription was inhibited with ActinomycinD, and RNA splicing with Sinefungin, at different time points, in the Matthews lab. rRNA depleted RNA was extracted from each of the samples in the Clayton lab, and sent for deep sequencing at the BioQuant facility in Heidelberg

Sample preparation procedure for metabolic footprint analysis on T. b. brucei 427 using LC/MS

No description specified
No description specified

Creator: Michael Kohlstedt

Contributor: Michael Kohlstedt

This is a well-established, classical genetic method of constructing chromosomal monolysogenic fusions to a promoterless lacZ gene.

ClosTron mutants should always be subjected to Southern blot analysis to ensure that only
one intron insertion has occurred.

Creators: Ying Zhang, Nigel Minton

Contributor: Ying Zhang

No description specified
No description specified

SOPs related with medium composition, fermentation and stocking of S. solfataricus.

Standard procedure regarding intracellular metabolome analysis using GC-MS.

Protocol for RNA isolation, cDNA synthesis and labeling and hybridization and cleanup of Sulfolobus solfataricus microarray

Standard operating procedures regarding iTraq based proteomics.

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