Lee Siggens

11 Questions 8 Answers 0 Followers

Questions related from Lee Siggens

Has anybody tested H4K20me3 antibodies for specificity in ChIP assays (specificity in terms of no cross-reactivity with H4K20me2) ?

I have found in preliminary tests that many (6 tested so far) of the commercially available H4K20me3 antibodies can be blocked in ChIP assays by K20me2 peptides as well as K20me3. Has anybody...

27 March 2019 4,643 1 View

Does formaldehyde cross-linking interfere with downstream proteomics analysis?

When performing ChIP-proteomics/ChIP-MS based techniques, if one chooses to do X-ChIP using standard 1% formaldehyde cross-linking is it necessary to reverse the cross-links before performing...

03 October 2018 1,075 3 View

Can anyone suggest 'normal' non-cancerous human cell lines that can undergo quiescence or senescence or at least come from normal tissue?

Apart from fibroblast cell lines like IMR-90 etc, are there any good human cell lines that are not derived from a tumour. I'm interested in cell lines that can undergo quiescence cell cycle arrest...

11 March 2017 2,381 12 View

What is the best plasmid transfection efficiency one can hope to achieve for AML suspension cell lines like KG1a HL-60 and U937 ?

What do people commonly get as a transfection efficiency using plasmids for commonly used AML related suspension cell lines? Is 50% good? Does anyone have any special tips and tricks?

24 February 2017 4,645 2 View

In CRISPR-Cas9 genome editing is it sure that in edited cells there will be a KO / loss of function if both alleles are mutated?

Is it a guarantee to have a loss of expression or protein function if you have introduced an indel into a gene? In other words does a 1-3 bp indel definitely introduce a frameshift mutation or can...

24 February 2017 4,260 2 View

In multiple myeloma, do the malignant cells come from the transformation of differentiated B cells or from stem cell / progenitor cells?

In one recent study (Agirre et al 2015, Genome Research) the authors suggest B cell enhancers are inactivated in multiple myeloma. In stem cells/progenitors cells the aforementioned B cell...

07 April 2016 2,688 2 View

Are there any genetic markers (ideally genetic deletions) in the commonly used U2-OS cell line ?

I was wondering if there are any genetic markers, especially deletions, in the U2-OS cell line that I can use to check if a sequencing data set is valid.

27 November 2015 1,591 2 View

Does anyone have a protocol to stimulate AR dependent gene expression with DHT in PNT2 cells?

We want to stimulate PNT2 or other prostate cells with DHT to stimulate AR dependent gene expression. What is the best way to do that and where can one buy cell culture grade DHT?

06 May 2015 1,565 1 View

Can anyone advise me on the nascent RNA-seq library preparation?

Could someone tell me - when performing nascent RNA-seq in human (or mammalian) cells is it necessary to remove ribosomal RNA during library prep? Has anyone done this with Invitrogen's Click-IT...

10 September 2014 9,611 7 View

When investigating promoter/enhancer/insulator function do DNase and MNase qPCR/sequencing give exactly the same information?

Usually there are slight differences in the protocols when we use DNase or MNase qPCR/ seq in analysing genome accessibility. Is it known if DNase sensitivity and MNase sensitivity (i.e....

12 May 2014 249 1 View

Does anybody have experience with difficult to knock-down transcripts? Do siRNA / LNA gapmers sometimes work at the protein but not the RNA level?

I have successfully knocked down several genes of interest using siRNA and LNA gapmers but have one particular gene that seems to be resistant (only one siRNA out of 7 and no LNA gamers worked)....

05 March 2014 7,924 3 View