7_Submit single cell data to GEO

prepare your data

1. Wherever your experiment is located, create a 'geo_upload' folder

2. Prepare single cell data

Copy filtered_featured_matrices or fastqs of sample runs to folder, make sure they have unique file names

Then in R:

meta<-seu@meta.data
names(meta) # double check that you want to keep all the columns of your metadata, if not subset columns above

#add umap coordinates to metadata 

meta$UMAP_1<-seu@reductions$umap@cell.embeddings[,1]
meta$UMAP_2<-seu@reductions$umap@cell.embeddings[,2]

write.csv(meta, file.path( "geo_upload/metadata.csv"))

3. Export processed count matrices, if you have more assays (ADT,ATAC, etc) create separate files

sct_mat<-seu@assays$SCT@data %>% as.sparse()

write.csv(sct_mat, file.path("geo_upload/rna_counts_processed.csv"))

upload

4. Go here: https://www.ncbi.nlm.nih.gov/geo/info/seq.html and click on

It will direct you to making an NCBI account if you don't already have one

5)Fill out your profile. Here is an example. Hit 'save'.

6. Then go back a page and hit 'transfer files' again. Something like this should pop up.

find this

and this

7. Edit these lines of code, then run on terminal/bash on r markdown

ncftp
set passive on
set so-bufsize 33554432

#make sure below line is geoftp:PASSWORD FROM ABOVE@ftp-private.ncbi.nlm.nih.gov
#so for me it looks like 

open ftp://geoftp:inAlwokhodAbnib5@ftp-private.ncbi.nlm.nih.gov

#change this to your directory found in step 6
cd uploads/owaltner@orcid_MlmJa2eM

#change this to the path to your geo_upload directory
put -R /fh/fast/furlan_s/.../geo_upload

8. Nagivate to geo_upload directory and get Md5 checksums

cd /fh/fast/furlan_s/.../geo_upload
md5sum rna_counts_processed.csv
#i got this string: f2a01b9c6ee751a97ddeda99301da43a
md5sum metadata.csv
#returned this: edfeaa082abe9797b4033be75dd905da 

9. navigate here