ENCODE data submission: treatment for Betty Liu from Greenleaf lab

[twang15]

The submission sheet preparation was done by Annika and Tao

https://docs.google.com/spreadsheets/d/1KxSKLNLf2MueCo-gbw5pVCBfSvGbfOOZ/edit#gid=1176823628

[twang15]

Hi Tao and Annika,

I am not sure what are these experiments: https://www.encodeproject.org/report/?type=Experiment&status=in+progress&internal_status=unreviewed&status=submitted&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&audit.ERROR.category!=missing+raw+data+in+replicate&audit.ERROR.category!=missing+possible_controls&assay_title=total+RNA-seq&field=accession&field=biosample_summary&field=aliases&limit=100

If I am to believe the aliases, they are lacking treatments? They are to be organized into series? Do we have RIN values for these RNA libraries? It looks like 7 of them (https://www.encodeproject.org/report/?type=Experiment&status=in+progress&internal_status=unreviewed&status=submitted&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&audit.ERROR.category!=missing+raw+data+in+replicate&audit.ERROR.category!=missing+possible_controls&assay_title=total+RNA-seq&field=accession&field=biosample_summary&field=aliases&limit=100&audit.NOT_COMPLIANT.category=missing+spikeins) don’t have spikeins? Can they be processed (are all the FASTQ files submitted?)

It would be great to get answers before the break, especially if these could be processed or not by the pipeline

Thanks,

Idan

[twang15]

Please see my answers in the text below. Thanks, A.

On Dec 16, 2021, at 9:49 AM, Idan Gabdank gabdank@stanford.edu wrote:

Hi Tao and Annika,

I am not sure what are these experiments: https://www.encodeproject.org/report/?type=Experiment&status=in+progress&internal_status=unreviewed&status=submitted&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&audit.ERROR.category!=missing+raw+data+in+replicate&audit.ERROR.category!=missing+possible_controls&assay_title=total+RNA-seq&field=accession&field=biosample_summary&field=aliases&limit=100

They are bulk RNA-seq experiment from Greenleaf’s lab (PhD student: Betty)

If I am to believe the aliases, they are lacking treatments?

Tao, there were treatments specified in the submission sheet that we worked on with Betty. Were they not submitted or attached to the experiments? Could you please submit the treatments?

They are to be organized into series?

Yes

Do we have RIN values for these RNA libraries?

I don’t think so, but I will confirm with Betty..

It looks like 7 of them (https://www.encodeproject.org/report/?type=Experiment&status=in+progress&internal_status=unreviewed&status=submitted&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&audit.ERROR.category!=missing+raw+data+in+replicate&audit.ERROR.category!=missing+possible_controls&assay_title=total+RNA-seq&field=accession&field=biosample_summary&field=aliases&limit=100&audit.NOT_COMPLIANT.category=missing+spikeins) don’t have spikeins?

Those are old submissions from Eyal from the Greenleaf lab. They didn’t do spike-ins for them. Will wants to release them with exemption and I believe I mentioned that before to you or Ingrid but if now, sorry about that.

Can they be processed (are all the FASTQ files submitted?)

Yes

It would be great to get answers before the break, especially if these could be processed or not by the pipeline

Thanks,

Idan

[twang15]

Hi Betty,

Could you confirm if you have RIN scores for your RNA-seq experiments that we submitted to the ENCODE portal for you? And if so, could you please send them over?

Thanks, Annika

[twang15]

Hi Annika,

I don’t think I have that information.

Betty

[twang15]

Hi Ingrid,

We were asked by Idan to submit treatment for recent submission of Greenleaf lab datasets. Annika and I have prepared the submission sheet here:

https://docs.google.com/spreadsheets/d/1KxSKLNLf2MueCo-gbw5pVCBfSvGbfOOZ/edit#gid=1176823628

But I do not have the privilege to do so, could you please help us finish the registration?

2021-12-17 16:28:36,109:eu_debug: Failed to POST will-greenleaf:DMSO_4 2021-12-17 16:28:36,110:eu_debug: <<<<<< DCC POST RESPONSE: 2021-12-17 16:28:36,110:eu_debug: { "@type": [ "HTTPForbidden", "Error" ], "code": 403, "description": "Access was denied to this resource.", "detail": "Unauthorized: collection_add failed permission check", "status": "error", "title": "Forbidden" }

Thanks, Tao

[twang15]

Hi Tao,

I was unable to open the spreadsheet. Would you be able to double check the sharing permissions? The DCC can post the treatment objects using your submission file.

Thanks, Jennifer

[twang15]

Hi Jennifer, I just changed the permission. THanks, Annika

[twang15]

Hi Annika and Tao,

I have submitted the 48 treatments to production. Please let us know if you need anything else to proceed with the submissions.

Best, Jennifer

[twang15]

Hi Jennifer,

Thanks for your help. Could you please fill the ENC numbers in column A for all treatments? https://docs.google.com/spreadsheets/d/1KxSKLNLf2MueCo-gbw5pVCBfSvGbfOOZ/edit#gid=1176823628

Best, Tao

[twang15]

Hi Tao,

Sure. Since treatments do not have accessions, I have filled in their @id instead -- let me know if that works for you.

Jennifer

[twang15]

Hi Jennifer,

IDs also works.

Thanks, Tao

[twang15]

Hi Idan,

Treatments have been associated with the biosamples.

Best, Tao