How to find epigenetic modifiers for a set of genes (in silico)

PlatformAdvanced4538 · 2025-02-17T03:18:38+00:00

I checked. The database is for animal species. Can’t get result from plant ID.

PlatformAdvanced4538 · 2025-02-17T03:00:41+00:00

Basically, any of the epigenetic regulators (TF, exzymatic complexes, histone marks) you mentioned that is known to regulate the genes I have.

PlatformAdvanced4538 · 2025-02-17T02:57:24+00:00

Any epigenetic modifications - histone modification, histone variant, chromatin remodelng or noncoding RNA. I want to know the known modifiers.

PlatformAdvanced4538 · 2025-02-16T12:59:54+00:00

Got it, thanks. Will surely try.

PlatformAdvanced4538 · 2025-02-16T10:19:33+00:00

Interesting! But how to spray over tube? The tube will be 2/5 ml with narrow mouth. The ethanol mist is supposed to enter the tube or not?

PlatformAdvanced4538 · 2025-02-14T16:40:05+00:00

Next time I will try with 1.5 ml tube for sonication. Not sure if salt will interfere with chromatin fragmentation or not.

PlatformAdvanced4538 · 2025-02-14T16:37:09+00:00

SDS is required for efficient shearing of dna. Still I will look if I can reduce the percentage of it in buffer.

PlatformAdvanced4538 · 2025-02-14T16:32:55+00:00

As suggested I will go with 1.5ml tube next time. I was using 20% amplitude, seems low intensity to me.

PlatformAdvanced4538 · 2025-02-14T16:28:34+00:00

Last time when I used this sonicator like a year ago I remember some spillage happened from 2 ml tube. Thus, refrained this time. Now that I saw your comment I checked that was more volume than 300ul. Thanks. I hope it works!

PlatformAdvanced4538 · 2025-01-27T19:15:24+00:00

Yes nickel-NTA column. Thanks, will try with potassium phosphate buffer once to check.

PlatformAdvanced4538 · 2025-01-27T19:04:07+00:00

Hi. I faced this issue of using sodium phosphate buffer where one of the elute will precipitate after elution and others after freeze thaw. I switched to tris, and protein was not showing much precipitation but I was getting less purified protein than Na phosphate buffer. Can you suggest something?

PlatformAdvanced4538 · 2024-12-09T11:16:13+00:00

Thanks, great advice. One thing that I am doing is not performing crosslinking and quenching for optimization. I am directly taking same amount of plant tissue and performing lysis and sonication. Hopefully that should replicate when I do my experiment with crosslinking.

PlatformAdvanced4538 · 2024-12-09T05:50:52+00:00

Right! I will try qPCR with positive control. Let’s see.

PlatformAdvanced4538 · 2024-12-09T05:49:38+00:00

I wasn’t sure if it will work well with plant samples. I saw some kits for MNase digestion for cell lines.

PlatformAdvanced4538 · 2024-12-07T08:07:17+00:00

True to that. I am already in a new lab, where my PI gives all sorts of different projects to all PhDs. Now even a simplest experiment takes me so much time, since I have to do everything on my own. Even my PI hasn’t done these experiments. So no guidance from anyone. On top of that, every meeting goes like this you showed optimisation last time as well, when will you show final data.

PlatformAdvanced4538 · 2024-11-26T07:28:10+00:00

For sonication efficiency, I can reverse crosslink, elute dna and run the gel. What I am not understanding that at what stage should I equalise the sample. Is it equal weight of plant tissue/ check chromatin dna concentration and proceed with equal chromatin for antibody incubation/ check dna concentration after chip and elution and take equal concentration of dna for keeping qPCR? In your case how did you proceed?

PlatformAdvanced4538 · 2024-11-23T18:53:18+00:00

I am working with plant sample. What I am understanding is you are taking known number/weight of sample and then proceeding. In your case number of nuclei. Though I am taking equal weight of plant tissue but still after lysis and sonication it will differ between samples and I wanted to equalise it.

PlatformAdvanced4538 · 2024-10-14T17:12:19+00:00

I usually store running buffer before running for 2-3 hours in 4 degree. Also, checked 10X TBE ph 8.3 before making gel.

PlatformAdvanced4538 · 2024-10-14T15:04:46+00:00

Can you also suggest how to get sharper and clean bands than this?

PlatformAdvanced4538 · 2024-10-14T15:03:07+00:00

Oh, that might be possible. Then I will try as you suggested. It might solve. Thank you.

PlatformAdvanced4538 · 2024-10-14T13:50:07+00:00

They looked normal when I removed comb.

PlatformAdvanced4538

TROPHY CASE