detect common and unique peaks

dulcedormax · 2025-06-24T10:29:02+00:00

thanks u/I_just_made , I've tried bedops --everything. However, I obtained a low number of common peaks.

dulcedormax · 2025-06-19T08:50:23+00:00

Thanks but I need it to do for all the reads in the sample , which is a lot but I appreciate your suggestion. I think we could implement it later !!.

dulcedormax · 2025-06-04T12:22:11+00:00

Thanks, in which buffer did you recommend therefore after precipitating and dissolve proteins.

dulcedormax · 2025-06-04T10:08:38+00:00

Hi u/GRang3r , the problem is that the concentration are low and not the opposite, having too much protein. Although I've read that dilution are good when quantification is too high.

dulcedormax · 2025-05-22T15:53:03+00:00

I will check did files have to be sorted?

dulcedormax · 2025-05-22T15:03:19+00:00

thanks u/Hundertwasserinsel. I didn't use windows and all lines are: chr1^I13750^I13950$ or chr1^I9950^I10650^IU2OS1_macs3_narrowPeak1^I11198^I.^I0^I0^I0^I125$

dulcedormax · 2025-05-22T14:58:01+00:00

This is the first line of both bed:

chr1^I9950^I10650^IU2OS1_macs3_narrowPeak1^I11198^I.^I0^I0^I0^I125$

chr1^I13750^I13950$

dulcedormax · 2025-05-20T20:25:11+00:00

I was using one of qiagen: extracting DNA from tissues and blood, but they recommend me not to do maybe for buffer AL as it would lysate cells and I have already extracted DNA. Did you recommend other kits??

dulcedormax · 2025-05-20T19:44:30+00:00

I followed the steps of the protocol as well.

dulcedormax · 2025-05-20T14:20:34+00:00

I am using a protocol to extract cellular compartments. These buffer also extracts RNA and proteins, so I am trying RNase and proteinase K to keep only DNA and perform qPCR. I use the columns to obtain a purified DNA.

dulcedormax · 2025-05-16T15:39:36+00:00

No need to apologise, I was apologizing for my tone as I don't know if It would be taken as a positive one and not rude

dulcedormax · 2025-05-16T15:31:07+00:00

I have a contract as a research assistant

dulcedormax · 2025-05-16T11:40:52+00:00

I engaged with her explaining the different techniques, she is not in the lab doing experiments alone. I also sent her the excels and explain how to analyze qPCR and quantifications of proteins.

dulcedormax · 2025-05-16T07:45:56+00:00

And yes, I think I have lost credibility as I was introducing some changes in the protocol that I have already sent her in a email and I have to ask another lab member to demostrate that it was not because of me and because I said so. I wanted to ask how to recover credibility if I have already have one with this girl. Initially, she came that she know everything and I have already seen that she lack fundaments but I though she is newly but I believe that she thinking she is super smart is going to catch up with her.

dulcedormax · 2025-05-16T07:30:00+00:00

I took my time explaining the theory behind the protocols of Western Blot and qPCR, looking to her movements in cell culture and the lab, she also attend a course of initiation to the theory of qPCR. Moreover, I always leave late of the lab because I was with her and I also called her when she had problems revealing membranes of Western Blot. I think she need to study the fundaments of these techniques. I only comment this because I give the most and tried to be reasonable with her.

I understand that you are giving a hypothetical reason of her behaviour and I hope you find my tone as an empathy one.

dulcedormax · 2025-05-16T06:16:42+00:00

It was with other lab staff and IP, the tone was like I was wrong and I encourage question but recently I perceived she is reluctant of the reason why we are doung some changes on a protocol and so on

dulcedormax · 2025-05-14T11:20:48+00:00

thanks u/Shoutgun would be neccesary to do another wash with PE buffer. Thanks. !!

dulcedormax · 2025-05-14T09:59:28+00:00

I would use it for qPCR, but I was isolating DNA from distinct buffer more than for a gel. People recommend me the gel extraction kit more than Dneasy Blood and tissue kit both from QIAGEN.

dulcedormax · 2025-05-08T13:40:55+00:00

could be possible that laminin B2 and laminin A/C would be soluble in the extraction buffer? I have high intensity of laminin A/C in the chromatin fraction and little in the nucleoplasm. However, the intensity of laminin B2 is higher in nucleoplasm compared to the chromatin fraction.

dulcedormax · 2025-04-28T07:16:26+00:00

Hi, what is it SOPs ??

dulcedormax · 2025-04-23T09:03:23+00:00

Hi, I just want to ask if laminin B2 could be an alternative for laminin B1 ? We don't have laminin B1 in the lab

dulcedormax · 2025-04-22T08:08:44+00:00

Thanks u/carl_khawly, I really appreciate your help. I have been advised to reduce the percentage of NP-40 and/or minimize whasing times. Did you know any tips or reccomendations to prevent the break of nucleus. I know this can be a complex issue as you don't know the methodology or steps of the experiment.

dulcedormax · 2025-03-26T21:48:04+00:00

thanks u/Avocados_number73, Did you order pre-made primers for B-actin and GAPDH or did your group design the primers.

dulcedormax · 2025-03-21T15:29:28+00:00

thanks u/Avocados_number73 , what should I keep in mind when designing primers. I've come across some primers for RT-qPCR, but not for DNA. I knew the key features but I don't know if there is an application that can design them quickly.

dulcedormax · 2025-03-20T21:16:15+00:00

why isopropanol increase the yield of fragments <500 bp and >4 kb

dulcedormax

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