search

ListerLab / pfc_development

14 stars 1 forks source link

Metadata in Human cell atlas (HCA) portal #11

Closed koh2ng0 closed 12 months ago

koh2ng0 commented 1 year ago

Hi,

First of all, thank you for sharing great data. I downloaded and used fastq data via the Human Cell Atlas ([https://data.humancellatlas.org/explore/projects/77dedd59-1376-4887-9bca-dc42b56d5b7a]). When I checked the metadata uploaded on the HCA, the supplementary table of the paper, and the data information posted on the GEO site, I confirmed that certain content was recorded incorrectly. Some records in the 'Specimen from organism' sheet of the metadata do not match with other resources, such as the supplementary data of the paper and GEO. The 'Biomaterial Name' column and 'Biomaterial ID' column do not correspond to each other, and there are incorrect entries when matching the 'Biomaterial ID' with GEO. I have attached the file that I corrected, and I would appreciate it if you could review it.

humanCorticalDevelopmentLandscape_metadata_09-12-2022.xlsx

+) I found something wrong in the manifest file in the HCA portal, too. The sample with SRA number 'SRR13873129' and donor ID 'RL2373' was sequenced by snATAC-seq, but the library is incorrectly written as '10x 3' v3' instead of '10x scATAC-seq' on the manifest. If it is convenient for you, I would greatly appreciate your assistance in verifying the matter.

herrinca commented 12 months ago

Thank koh, this has been corrected.