ATAC-seq protocol

[mantis]

Hi Runuply,

Yes, I did a 1.6V ampure treatment: The small primers won't bind to the peaks with this DNA/beads ratio.

Good luck!

[Runuply]

Originally Posted by mantis

Hi Runuply,

Yes, I did a 1.6V ampure treatment: The small primers won't bind to the peaks with this DNA/beads ratio.

Good luck!

Thanks Mantis.
I did the AMpure , it looks good.
By the way, may I know that, normally how much DNA can you get after lysis if you use 50K cells? Do you check the concentration before PCR amplification.

[mantis]

Originally Posted by Runuply

Thanks Mantis.
I did the AMpure , it looks good.
By the way, may I know that, normally how much DNA can you get after lysis if you use 50K cells? Do you check the concentration before PCR amplification.

I never did...

[puraskar_theaward]

Originally Posted by Zaag

I have sent some of them out this morning, I don't know when I get my results, but I will post the bio-analyser traces and some sequencing QC when I get it back.

I also got the similar peak at the 55bp. Ppl reported that to be either the adapter 50-53bp.

So I tried using a AmpureXP x1.8V cleanup. It cleared the band.

[puraskar_theaward]

Hi Mantis,
I got similar BA image post AmpureXP cleanup.


1] I was wondering what was the conversion factor you used to calculate the DNA concentration of the libraries for the cluster generation.

1.1 Did you use the broad range like 150-1200bp in BA and found out the pM concentration from BA region table? or
1.2 used some conversion tables for the ng/uL for each region of library? or
1.3 Did a Qubit HS DNA concentration of the libraries?

2] Illumina tells to normalize libraries to 2nM before adding them to cBOT prep tubes. Did you normalize to 2nM? If so did you use Tris-HCl pH8.5 with 0.1% Tween 20 or used the regular TE buffer which had DNA eluted post Ampure XP purification.

3] Did you use phiX control at 1-5% before loading on the cBot?

Originally Posted by mantis

hi everyone,

I just tried my first ATAC-seq on cells and using the protocol of Buenrostro and I obtain good results: sharp peaks, low background, (appr. 50000 cells).

I included my HS picture.

After measuring the molarity for each fragment, I obtained a good nucleosome distribution (also indicated on the gel, in the right). Before putting on the HS chip, I Ampured (1.6V) the sample.

[LOH]

Originally Posted by Zaag

I used this protocol and got this after adapter-PCR:





Can anyone comment? Is it completely crap or not?

To me sample 2 looks better than sample 1, but I have no real clue as in how it should look.

You have huge peaks at size > 1kb region, indicating your libraries are over enriched with fragments >1kb. Fragments >1kb will decrease the sequencing efficiency and is not suitable for Illumina sequencer.

[Runuply]

Originally Posted by LOH

You have huge peaks at size > 1kb region, indicating your libraries are over enriched with fragments >1kb. Fragments >1kb will decrease the sequencing efficiency and is not suitable for Illumina sequencer.

Hi LOH
Could you please tell us, what should be the factors to get large size libraries sizes over 1kb. Do you think it is under-tagmentation, cell number dependent?

Best


Runuply

[mantis]

Originally Posted by puraskar_theaward

Hi Mantis,
I got similar BA image post AmpureXP cleanup.


1] I was wondering what was the conversion factor you used to calculate the DNA concentration of the libraries for the cluster generation.

1.1 Did you use the broad range like 150-1200bp in BA and found out the pM concentration from BA region table? or
1.2 used some conversion tables for the ng/uL for each region of library? or
1.3 Did a Qubit HS DNA concentration of the libraries?

2] Illumina tells to normalize libraries to 2nM before adding them to cBOT prep tubes. Did you normalize to 2nM? If so did you use Tris-HCl pH8.5 with 0.1% Tween 20 or used the regular TE buffer which had DNA eluted post Ampure XP purification.

3] Did you use phiX control at 1-5% before loading on the cBot?

Hi puraskar theaward,

To answer your questions:
1.1 Yes, I used the full range. So, my average size was around 450-500 for each sample; I calculated the molarity from that to obtain eventually 4 nM in the end.
1.2 So, I did not specify for every region of the library.
1.3 I indeed measured the concentration with the Qubit.

For questions 2 en 3 I unfortunately cannot help you. I handed in pooled 4 nM libraries to our sequencing facility. (I elute my DNA from the beads with MilliQ.) The subsequent dilutions and processing are done by the facility.

[paramita7]

Originally Posted by Runuply

Hi guys, I also used that protocol for ATAC-seq from frozen tissue, PCR amplification 5 cycles; and 7 cycles for qPCR(1 to 3rd of Max Fluorescent). It is a little hard for me to control the exact cell number, but after transposition and purification I will use 1ul to check by Qubit, which usually shows around 10ng/ul in 10ul (this should be equal to 25k cells or less). And after I did PCR amplification (in total 5+7 cycles), the purified DNA will be about 50ng/ul in 20ul.
The Bio analyzer is attached.

Hi Runuply,
i am also doing ATAC-seq from froze tissue. Can you give me an idea how you dissociate cells from tissue? I am having difficulty with it. Thank you,

[Runuply]

Originally Posted by Wonghe

Hi All, I've been trying to do ATAC-seq on nuclei isolated from frozen tissues with sucrose gradient. Although I am able to obtain a nucleosome-like pattern (see above attachment) but after sequencing I get many background peaks which are very noisy and the peaks at the TSS were not distinct. Anyone has any idea to improve the method and reduce the background peaks?

Hi Wonghe did you solve the problem？
What kind of frozen tissue do you use？ I feel like the cell isolation process is most important.

[Runuply]

Originally Posted by paramita7

Hi Runuply,
i am also doing ATAC-seq from froze tissue. Can you give me an idea how you dissociate cells from tissue? I am having difficulty with it. Thank you,

Hi paramita7

I am using frozen cartilage for ATAC-seq. I use collagenase to dissociate the chondrocytes.
What kind of frozen tissue do you use?

[paramita7]

Hi Runuply,
I have frozen brain tissue and I am just using grind and strain method. But after purification steps I am loosing a lot of DNA.

[maddy2016]

Hi All, I am also planning to start ATAC-seq using fresh cells. My question is how do I harvest the cells..is it by scraping cells in 1x cold PBS and then counting them on hemocytometer to make sure how many cells I am staring with. Also what should be the best internal control during sequencing? I assume cells without treatment with Transposase? Any help is highly appreciated. Thanks in advance.

[seed222222]

Originally Posted by maddy2016

Hi All, I am also planning to start ATAC-seq using fresh cells. My question is how do I harvest the cells..is it by scraping cells in 1x cold PBS and then counting them on hemocytometer to make sure how many cells I am staring with. Also what should be the best internal control during sequencing? I assume cells without treatment with Transposase? Any help is highly appreciated. Thanks in advance.

Hi maddy,
I am also trying to perform ATAC-seq on fresh cell. Did you solve the cell collection problem? Are you use trypsin or harvest cell by scraping? Thank you.

[milevskiy]

I have tried the standard protocol on COMMA-D mouse mammary cell line with limited success. We appear to have a log of smaller fragments and not getting the nice banding pattern typical of this technique. I have tried to optimise the TD reaction but that seems to have little effect. Has anyone gotten this to work on cell lines or cells which might be harder to lyse than blood cells?

[maddy2016]

Originally Posted by seed222222

Hi maddy,
I am also trying to perform ATAC-seq on fresh cell. Did you solve the cell collection problem? Are you use trypsin or harvest cell by scraping? Thank you.

Yes, I made the ATAC-seq libraries and sent my samples for sequencing. I started with 54,000 cells and performed the TD reaction.
For collecting cells, first I discarded the media, washed cells in PBS twice. Added TryPLE to detach cells and scraped them gently in regular media. Followed by counting cells in hemocytometer.
Hope this helps. Good luck!

[Vgamma4]

Hi ATAC-fanatics.

Since my experience with ATAC is only 2 weeks old, I have a question regarding the quality of my ATAC library. I used 50.000 cells and followed the instruction as described in Buenrostro et al.
The Bioanalyzer gave me the following picture. It seems the DNA size of the libraries is quite small, no?
Do you guys think that its sequenceable??

[ScottC]

Does anyone here use NexteraXT rather than Nextera for ATAC-seq library construction?

[jamesdinn]

Originally Posted by Runuply

Thanks Mantis.
I did the AMpure , it looks good.
By the way, may I know that, normally how much DNA can you get after lysis if you use 50K cells? Do you check the concentration before PCR amplification.

Hi Runuply & Mantis,
I'm new user for ATAC-seq experiment, i see that you use AMpure beads to clean DNA, could i use it for the each purification step (after 30 min tagmentation, after PCR cycles...?) or only before loading in Bioanalyser?

thank you

[atacseq01]

Hi all -

For those of you who prepare ATAC libraries followed by sequencing on Illumina hiseq2000
- what specific illumina-based protocols and reagents are you using? (for cbot, Hiseq, etc.)?

thanks.