Sam Siljee

8 Questions 20 Answers 0 Followers

Questions related from Sam Siljee

Basic question - how to make a cell dissociation buffer?

Dear All, I'm looking to make a cell dissociation buffer from lyophilised collagen I (Gibco, 12648010). The protocols I've been looking at all specify concentrations of enzymes in terms of...

07 October 2020 647 3 View

Expected phosphopeptide numbers from primary lung basal cells

Hi all, I have recently done a pilot protein extraction from primary lung basal cells with phosphopeptide enrichment using the protocol described by Humphrey et. al, and found 2433...

01 January 1970 1,171 6 View

Distribution of club cells in airway epithelium

Dear all, I am growing human primary airway epithelial cells from excised normal lung tissue in 2D ALI culture. In order to validate my model, I am doing immunofluorescence staining of the...

01 January 1970 2,896 0 View

Artefact in volcano plot

Hi all, I've noticed a suspicious pattern in some volcano-plots I've made of proteomics data. Specifically, I've noticed points lining up, seeming to show a direct mathematical relationship...

01 January 1970 3,602 4 View

Bridging channels and TMT in mass spectrometry for proteomics

Dear all, I'm working on the finer details of my experimental design, and have some questions regarding bridging channels for TMT based experiments. I have two conditions to test, across nine...

01 January 1970 8,870 1 View

Over-representated vs Upregulated

Hi all, I'm busy building a shiny analysis pipeline to analyse protemics data from mass spectrometry, and I was wondering what the exact difference is between the terms Over-represented, and...

01 January 1970 4,139 3 View

GO term enrichment analysis for proteomics in R

Dear all, I'm building a shiny application for analysis of mass-spectrometry based proteomics data (for non-coders), and am working on the section for GO term enrichment. There are a wide variety...

01 January 1970 4,802 5 View

Cryopreservation media for primary lung basal cells

Hi all, I'm growing primary basal cells from lung digests, and was wondering if anyone has recommendations for cell freezing media for primary lung basal cells. Previously I have been using...

01 January 1970 6,378 8 View