Data submission to ENCODE: cs-388

[twang15]

https://pulsar-encode.herokuapp.com/chipseq_experiments/388 also only has replicate 3.

Ask Lixia about it.

[twang15]

Hi Lixia,

CS-388 (https://pulsar-encode.herokuapp.com/chipseq_experiments/388) in pular only has replicate 3. Is it part of a previous ChIP experiment?

[twang15]

https://github.com/StanfordBioinformatics/pulsar_lims/issues/441

CS-388 (add as technical rep to rep 1 to old exp ENCSR727GPE) https://www.encodeproject.org/experiments/ENCSR727GPE/

[twang15]

move L-11342 https://pulsar-encode.herokuapp.com/libraries/11342 as one replicate of cs-41 (https://pulsar-encode.herokuapp.com/chipseq_experiments/41).

It should be biological rep 1's technical rep 2. But I cannot modify it on the portal, since it has been revoked. If it is technical rep2 of biological rep 1, should they use the same biosample?

[twang15]

Hi Annika,

As requested, I submitted a new replicate (rep 3) for experiment https://www.encodeproject.org/experiments/ENCSR727GPE/.

But I have one question: If it is technical rep3 of biological rep 1, should they use the same biosample?

Best, Tao

[twang15]

Hi Jessica,

I submitted a new technical replicate for this experiment https://www.encodeproject.org/experiments/ENCSR727GPE/.

It should be biological rep 1’s technical rep2. However, I cannot make the change since the experiment status is “revoked”. Could you modify it for me?

Thanks, Tao

[twang15]

Hi Tao,

I believe it may be clearer to submit your new replicate to entirely new datasets, but I'd like to get a better picture of how the new data relates to the old data first. The same questions apply to your other email about Cs-41, but we can work out some details in this thread to keep the information in one place. Is the new replicate sequencing a new library generated from the old biosample cells? Or is there a new cell sample generated before the library was prepared? After this new replicate, will there be another one submitted so that processing will occur between 2 new replicates? Or is there a possibility that one of the revoked/potentially contaminated replicates is safe to use? And overall, I'm aware of 17 total revoked and potentially contaminated datasets. Could you and Annika update me on whether you would submit new sequencing to all 17, or if you are still trying to determine if some need to be repeated? I'm looking at these here: https://www.encodeproject.org/report/?type=Experiment&accession=ENCSR445FHB&accession=ENCSR171TDM&accession=ENCSR748HJZ&accession=ENCSR149KGC&accession=ENCSR106GVM&accession=ENCSR282NLQ&accession=ENCSR474KBG&accession=ENCSR581GUY&accession=ENCSR742RUA&accession=ENCSR727GPE&accession=ENCSR300BTC&accession=ENCSR723BZO&accession=ENCSR101DNY&accession=ENCSR776WLL&accession=ENCSR810YED&accession=ENCSR738VSK&accession=ENCSR136OFY&accession=ENCSR781EUA&accession=ENCSR048BRQ&accession=ENCSR335SUD&accession=ENCSR713OLH&accession=ENCSR360HZO&accession=ENCSR679XED&accession=ENCSR061BVP&accession=ENCSR102UFK&accession=ENCSR897LCR&accession=ENCSR326AQV&field=accession&field=submitter_comment&status=revoked

Thank you! -Ingrid

[twang15]

Hi Ingrid,

I was asked by Annika to submit the new replicate to cs-41 and cs-45. So she has clearer answer than I do on these questions.

Annika, please share your thoughts when you have time.

Thanks, Tao

[twang15]

Hi Annika,

Is there any update on this issue?

Thanks, Tao

[twang15]

Hi everyone,

I apologize that this fell through the cracks.

1) I asked Tao to submit them as technical replicates to the existing experiments (rep3 is technical rep of rep1). For some reason, Chicago only sent one replicate but I am reminding them since a while to send the other rep (=rep 4) as well asap. So there would be two new replicates to process. Those are technical replicates, so they have the same biosample ID than the previous ones because we are quite sure that the contamination occurred during library prep not before.

2) For the other 17 experiments: I have just sent another email to Chicago to ask about the status of the K562 data sets and will update you asap on those. 4 of the 17 are from our lab: ENCSR360HZO was repeated and it released (ENCSR288NNJ) ENCSR713OLH won’t be repeated because we have this TF in K562 as well which will hopefully be able to be released soon ENCSR742RUA is on our to do list for transfection into A549 ENCSR149KGC won’t be repeated at this point, maybe if we have time later (haha).

Thanks and sorry again for the late reply! Thanks for reminding me, Tao!

Annika

[twang15]

Hi Annika,

As I am combing through the input library control experiments with “Missing Biosample Characterization”, I found the 17 revoked ChIPs actually determine what to do for the input library experiments.

Could you update us on the status of these 17 ChIPs, especially the implications on their corresponding input library experiments?

Thanks, Tao