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Sage-Bionetworks / sysbioDCCjsonschemas

SysBio DCC JSON schemas
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spatial transcriptomics data #141

Open pitviper6 opened 2 years ago

pitviper6 commented 2 years ago

PI: Keri Martinowich Institution: LIBD

Keri is contributing Visium spatial transcriptomics data.

  1. What output/file types do we need from them?
  2. What metadata do we need?

Input files:

Output files (using spaceranger)

See attached doc for details

pitviper6 commented 2 years ago

Meeting notes from November 2021

pitviper6 commented 2 years ago

Cellranger files we should receive, according to documentation Nicole put together:

10x Cellranger

Preferably all output files, except BAM, should be uploaded. At minimum, we need all the bulleted files. Note: Still need the raw fastq files.

analysis cloupe.cloupe filtered_feature_bc_matrix

web_summary.html

pitviper6 commented 2 years ago

RFC for the new template sent to Nick and Leo.

pitviper6 commented 2 years ago

Per 10X website, we should get from the DC:

  1. R1 and R2 FASTQs;
  2. Image (submitted as processed data file)

https://kb.10xgenomics.com/hc/en-us/articles/360024716391-What-format-of-10x-Genomics-data-should-I-submit-to-NCBI-GEO-SRA-?source=search

SpatialDB record: http://www.spatialomics.org/SpatialDB/st_29925878_browse.php?gene=KCTD12&sample=P24&log=log2