spatial transcriptomics data

[pitviper6]

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:

• raw image (.tiff)
• fastq file
• loupe-alignment json file

Output files (using spaceranger)

• image files
• BAM files
• feature matricies

See attached doc for details

[pitviper6]

Meeting notes from November 2021

[pitviper6]

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

• filtered_feature_bc_matrix.h5
• metrics_summary.csv
• molecule_info.h5
• raw_feature_bc_matrix
• raw_feature_bc_matrix.h5

web_summary.html

[pitviper6]

RFC for the new template sent to Nick and Leo.

[pitviper6]

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