ENCODE data submission: bulk RNA-seq submission for Greenleaf lab

[twang15]

Hi Tao,

We have a new submission for Will Greenleaf’s lab. I am cc’ing Betty who performed the experiments. This is a simple RNA-seq submission (not single cell) that should be relatively straight forward. Please review the submission sheet. https://docs.google.com/spreadsheets/d/1KxSKLNLf2MueCo-gbw5pVCBfSvGbfOOZ/edit#gid=201466079

Betty, could you please organize access to your files with Tao. He is our data manager and will do the submission.

Thanks, Tao!

Best Annika

[twang15]

Hi Tao,

My data is currently on sherlock/oak. Can I put it in a shared folder with read permission and simply give you the path to that folder?

Betty

[twang15]

Hi Tao, I hope you had a nice Thanksgiving weekend. Could you confirm the receipt of the email and that this will be taken care of?

Thanks, Annika

[twang15]

Hi Annika and Betty,

Sorry for my late reply.

Betty, a shared folder is good enough. Please set it up and let me know the folder.

Thanks, Tao

[twang15]

Hi SRCC support team,

Betty (sunet ID: liubetty) shared me a big dataset (sunet ID: taowang9) on Sherlock. The folder path is: /scratch/users/liubetty/drugATAC_rna_fq

Could you please help grant me read access? BTW, I need to transfer this dataset to SCG, what is the best practice to achieve this?

Thanks, Tao

[twang15]

Hi Betty,

The permission has not been set up properly.

[taowang9@sh02-ln02 login ~]$ ls /scratch/users/liubetty/drugATAC_rna_fq ls: cannot access /scratch/users/liubetty/drugATAC_rna_fq: Permission denied [taowang9@sh02-ln02 login ~]$

[twang15]

Hey Tao,

I added execute access as well, which hopefully resolves the traversal issue.

Betty

[twang15]

Hi Betty,

The permission looks right now. I will let you know if I need anything else from you.

Best, Tao

[twang15]

Hi Ingrid,

I encounter the following error message. Could you help figure out what is wrong?

2021-12-06 09:48:46,102:eu_debug: <<<<<< POST library record will-greenleaf:K562_DMSO_4a_lib To DCC with URL https://www.encodeproject.org/library and this payload:

{ "aliases": [ "will-greenleaf:K562_DMSO_4a_lib" ], "award": "/awards/UM1HG009436/", "biosample": "ENCBS829GTX", "construction_platform": "OBI:0002630", "lab": "/labs/will-greenleaf/", "nucleic_acid_term_name": "RNA", "size_range": "300-600" }

2021-12-06 09:48:46,255:eu_debug: Failed to POST will-greenleaf:K562_DMSO_4a_lib 2021-12-06 09:48:46,256:eu_debug: <<<<<< DCC POST RESPONSE: 2021-12-06 09:48:46,259:eu_debug: { "@type": [ "ValidationFailure", "Error" ], "code": 422, "description": "Failed validation", "errors": [ { "description": "{'lab': '/labs/will-greenleaf/', 'award': '/awards/UM1HG009436/', 'nucleic_acid_term_name': 'RNA', 'size_range': '300-600', 'aliases': ['will-greenleaf:K562_DMSO_4a_lib'], 'construction_platform': 'OBI:0002630', 'biosample': 'ENCBS829GTX'} is not valid under any of the given schemas", "location": "body", "name": [] } ], "status": "error", "title": "Unprocessable Entity" }

Best, Tao

[twang15]

Hi Tao,

I think all you're missing here is the "strand_specificity" property, which is required since the library is composed of RNA. Please let me know if you still see an error after including that property!

Best, Ingrid

[twang15]

Ingrid, thanks for your quick reply.

Betty, could you please tell me what ‘strand_specificity’ your datasets have?

-Tao

[twang15]

Hi Betty,

assay_term_name for experiment is currently RNA-seq.

However, it must be one of the following for submission: ['CRISPR screen', 'MPRA', 'perturbation followed by scRNA-seq', 'perturbation followed by snATAC-seq', 'pooled clone sequencing', 'STARR-seq']

Which one is appropriate for your datasets?

Thanks, Tao

[twang15]

Looping in Ingrid:

It shouldn't be one of the options that Tao mentions below, Ingrid? It’s bulk RNA-seq after drug treatment.

Thanks, Annika

[twang15]

Tao, I think if you submit this as ‘experiment’ and not as ‘functional characterization experiment’ you can just choose RNA-seq. Thanks, Annika

[twang15]

Hi Annika,

In the submission sheet, the experiment type is set to be ‘functional characterization experiment’. Can we submit it as ‘experiment’ instead?

Best, Tao

[twang15]

Yes, I think so. Thanks, Annika

[twang15]

this is what we did for the ATAC counterpart so we should it for this one as well, unless Ingrid doesn’t agree, Thanks, Annika

[twang15]

Ingrid, could you please confirm this? Betty, if Ingrid agrees, you might need change the experiment type for the future submissions.

Thanks, Tao

[twang15]

Hello all,

From the information in this thread, it does sound like standard "RNA-seq", which would be an "Experiment" rather than "Functional Characterization Experiment"- applying a treatment is not unusual for Experiments.

Is this the complementary ATAC-seq data you're talking about? https://www.encodeproject.org/search/?type=Experiment&lab.title=Will+Greenleaf%2C+Stanford&status=released

I can't be certain what these data should be called without further details, but it's unlikely to be a FCE unless you are querying a large number of predetermined elements for each of their effects via RNA-seq expression or some other activity- which is why those are typically MPRA, STARR-seq, or CRISPR screens.

If you're still at all uncertain about calling it Experiment vs FCE, please send me further details about the protocol and/or experimental design.

Thanks! Ingrid

[twang15]

Okay, after reading your email, I can confirm that this should be an experiment and not a functional characterization experiment. Thanks, Annika

[twang15]

Hi Betty,

Please check out the discussion about the experiment type that you might need to use in the future.

Best, Tao

[twang15]

Hi Annika and Betty,

The datasets have been submitted successfully.

Best, Tao