Skip to content

7_Submit single cell data to GEO

Jump to bottom
Olivia Waltner edited this page Dec 26, 2023 · 4 revisions

prepare your data

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

  2. Prepare single cell data

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"))
  1. 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"))

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

image

If you have something like this, then your folder is ready!

upload

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

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'. image

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

find this image

and this image

  1. 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
  1. 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
  1. Insert md5sum values in sheet 2 of GEO metadata excel spreadsheet
image
  1. navigate to GEO submission page and select:
image

Clone this wiki locally