search

StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
3 stars 1 forks source link

ENCODE submission: dataset patch on ENCODE portal #970

Open twang15 opened 1 year ago

twang15 commented 1 year ago

Hi Tao,

I realized there is one more piece of metadata that we should update. Assuming it is the same as previous experiments, I think the scRNA-seq biosamples are missing the property "subcellular_fraction_term_name" of "nucleus". Here is an example of an older sample: https://www.encodeproject.org/biosamples/ENCBS315KVT/

Does it make sense to add subcelllular_fraction_term_name for all the Biosamples in this table? https://www.encodeproject.org/report/?type=Experiment&assay_title=scRNA-seq&lab.title=Michael+Snyder%2C+Stanford&replicates.library.biosample.subcellular_fraction_term_name!=*&status!=deleted&field=%40id&field=biosample_summary&field=replicates.library.biosample.accession&field=aliases

Please let me know if the other patch we discussed is complete as well.

Thanks, Jennifer

twang15 commented 1 year ago

Hi Jennifer,

I will ask around and get back to you asap.

Thanks, Tao