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StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
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ENCODE data submission: scRNA patch subcellular_fraction_term_name #806

Closed twang15 closed 2 years ago

twang15 commented 2 years ago

Hi Tao and Annika,

Another lab is looking at the single-cell data on the portal, and noticed that these 5 scRNA-seq datasets (each belonging to MultiomicsSeries) don't have 'subcellular_fraction_term_name': 'nucleus' specified on their biosamples. Could you check that these are actually multiome samples/datasets, and patch the biosamples as appropriate? https://www.encodeproject.org/report/?type=Experiment&assay_title=scRNA-seq&lab.title=Michael+Snyder%2C+Stanford&replicates.library.biosample.subcellular_fraction_term_name!=*&related_series=*&field=%40id&field=biosample_summary&field=related_series.accession&field=replicates.library.biosample.subcellular_fraction_term_name

Let me know if you have any questions! Thanks, Ingrid

twang15 commented 2 years ago

Hi Tao, can you please patch this?

subcellular_fraction_term_name': 'nucleus'

Thanks, Annika

twang15 commented 2 years ago

Hi Annika and Ingrid,

These biosamples have been patched properly. But I am not sure why they have the field subcellular_fraction_term_name missing since the bug has been fixed when the submission was made.

Ingrid, please let me know if you see any other cases like these.

Thanks, Tao