ENCODE data submission: WTC11 NGN2 Diff for cs-555 and cs-556

[twang15]

cs-555: https://www.encodeproject.org/experiments/ENCSR110BQW/ cs-556: https://www.encodeproject.org/experiments/ENCSR431UCR/ Experiment series: https://www.encodeproject.org/experiment-series/ENCSR575GUR/

Right now, cs-556 is missing its IPs.

[twang15]

Steps:

0. submission w/ code for each experiment
1. link biosamples: 1 is the parent of 3 and 2 is the parent of 4. (manual)
   • add 1 as “originated_from” for 3
   • add 2 as “originated_from” for 4, rep1 for rep1, rep2 for rep2
2. GMs submission: a. 1 (GM1_on_ENCODE_portal = ENCGM156EZW) b. 2 (ENCGM156EZW, GM2_in_Pulsar) c. 3 (ENCGM156EZW) d. 4 (ENCGM156EZW, GM2_in_Pulsar)
3. IP submission for rep1 and rep2 of 2 and 4 respectively (code)
4. NIC or mouse organism
5. Biosample ontology submission: "biosample_ontology": "/biosample-types/in_vitro_differentiated_cells_CL_0008030/" for a. biosamples in 3 and 4
6. Link the two experiments with Differentiation series a. https://docs.google.com/spreadsheets/d/1bYJ8w2XqfR9El0dXEl9QJKXAjy58zL8b/edit#gid=2018381402

[twang15]

Hi Annika,

Ips for cs-556 are missing. Could you please let me know when they are available?

Thanks, Tao

[twang15]

Hi Tao,

We recommend using the Differentiation Series object for these submissions. This is less generic than the Experiment Series and will help indicate that the datasets specifically investigated the differentiation of WTC-11. The schema information is available here: https://www.encodeproject.org/profiles/differentiation_series

The structure of these objects is very similar to Experiment Series, so you should be able to use a nearly identical submission format. Please let me know if you have any questions about this!

Best, Jennifer

[twang15]

Hi Jennifer,

Could you help remove the experiment series? https://www.encodeproject.org/profiles/differentiation_series

I will resubmit it as a differentiation series.

Thanks, Tao

[twang15]

Hi Tao,

I have deleted /experiment-series/ENCSR575GUR/. Please let me know if you'd like to remove the associated alias information as well.

Thanks, Jennifer

[twang15]

Hi Jennifer,

Please help me delete the associated alias information as well.

Thanks, Tao

[twang15]

Hi Jennifer,

Could you please let me know whether the alias has been deleted or not? I am still seeing the following error:

2022-04-13 20:04:33,333:eu_debug: {'@type': ['HTTPConflict', 'Error'], 'status': 'error', 'code': 409, 'title': 'Conflict', 'description': 'There was a conflict when trying to complete your request.', 'detail': "Keys conflict: [('alias', 'michael-snyder:NGN2_ENCSR110BQW_ENCSR431UCR')]"} 2022-04-13 20:04:33,334:eu_debug: >>>>>>GET michael-snyder:NGN2_ENCSR110BQW_ENCSR431UCR From DCC with URL https://www.encodeproject.org/michael-snyder:NGN2_ENCSR110BQW_ENCSR431UCR/?format=json&datastore=database

Thanks, Tao

[twang15]

Differentiation series posted

[twang15]

IP for cs-556 posted: reused from cs-555, because no other changes to the bio samples except they are differentiated.