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README.md

FUMA scRNA-seq data sets

This is a github repository for pre-process script of scRNA-seq data sets used on FUMA web application (http://fuma.ctglab.nl). Processed data sets can also be downloaded from this repository to run MAGMA by yourself.

updates

  • 5 Aug 2019: Updated citation
  • 19th May 2019:
    Added: PsychENCODE, GSE97478, GSE106707
  • 13th Feb 2019:
    Added: Allene Brain Atlas Cell Type second release,10X dataset
    Updated: Tabula Muris FACS
  • 19th Jul 2018:
    First release

Preparation of genes

Human Ensembl genes (GRCh37 v92)

The list of genes with Ensembl ID are in ENSG.genes.txt

Mapping of mouse gene ID to human gene ID

The script is available under scripts/mm2hs.R. The output file is mm2hs.RData

Data sets

The list of data sets are available at FUMA tutorial page.

Preprocess of each data set is available in one of the following R scripts.

  1. Allen_Brain_Atlas_Cell_Type.R
    2 human and 3 mousebrain data sets from Allen Brain Atlas.
  2. Allen_Brain_Atlas_Cell_Type_prev.R
    3 mouse data sets from Allen Brain Atlas (previously released datasets).
  3. DroNc.R
    2 data sets (human and mouse) from Habib et al. Nat. Meth. (2017)
  4. DropViz.R
    Data set from http://dropviz.org.
  5. Linnarsson_MouseBrainAtlas.R
    Data sets from http://mousebrain.org.
  6. TabulaMuris.R
    2 data sets (FACS and droplet) from The Tabula Muris Consortium.
  7. MouseCellAtlas.R
    Data set from http://bis.zju.edu.cn/MCA/.
  8. Linnersson_lab.R
    Other data sets from Linnarsson's group.
  9. 10X.R
    PBMC data set downloaded from 10X Genomics.
  10. PsychENCODE.R
    2 data sets from PsychENCODE.
  11. GEO.R
    Everything else.

Citation

K. Watanabe et al. Genetic mapping of cell type specificity for complex traits. Nat. Commun. 10:3222. (2019).
https://www.nature.com/articles/s41467-019-11181-1

Additional process prior to the process in R scripts

1. GSE67602 (Linnarsson's lab)

Metadata for cells were extracted from family soft file by the following commands.

echo -e "cell_id\tcell_type" > GSE67602_celltype.txt
gzip -cd GSE67602_family.soft.gz | grep Sample_title | sed 's/!Sample_title = //' > title.txt
gzip -cd GSE67602_family.soft.gz | grep "cell type level 1" | sed 's/!Sample_characteristics_ch1 = cell type level 1: //' > celltype.txt
paste title.txt celltype.txt >>GSE67602_celltype.txt

2. GSE75330 (Linnarsson's lab)

Metadata for cells were extracted from family soft file by the following commands.

echo -e "cell_id\ttissue\tage\ttreatment\tcell_type" > GSE75330_metadata.txt
gzip -cd GSE75330_family.soft.gz | grep Sample_title | sed 's/^!Sample_title = //' >title.txt
gzip -cd GSE75330_family.soft.gz | grep Sample_source_name_ch1 | sed 's/^!Sample_source_name_ch1 = //' >tissue.txt
gzip -cd GSE75330_family.soft.gz | grep "= age:" | sed 's/^!Sample_characteristics_ch1 = age: //' >age.txt
gzip -cd GSE75330_family.soft.gz | grep "= treatment:" | sed 's/^!Sample_characteristics_ch1 = treatment: //' >treatment.txt
gzip -cd GSE75330_family.soft.gz | grep "inferred cell type:" | sed 's/^!Sample_characteristics_ch1 = inferred cell type: //' >celltype.txt
paste title.txt tissue.txt age.txt treatment.txt celltype.txt >>GSE75330_metadata.txt

3. GSE78845 (Linnarsson's lab)

Metadata for cells were extracted from family soft file by the following commands.

echo -e "cell_id\tcell_type\tage" >GSE78845_metadata.txt
gzip -cd GSE78845_family.soft.gz | grep Sample_title | sed 's/^!Sample_title = //' >title.txt
gzip -cd GSE78845_family.soft.gz | grep celltype | sed 's/^!Sample_characteristics_ch1 = celltype identifier: //' >celltype.txt
gzip -cd GSE78845_family.soft.gz | grep "= age:" | sed 's/^!Sample_characteristics_ch1 = age: //' >age.txt
paste title.txt celltype.txt age.txt >>GSE78845_metadata.txt

4. GSE95315 (Linnarsson's lab)

Metadata for cells were extracted from family soft file by the following commands.

echo -e "cell_id\tcell_type\tpostnatal_day" >GSE95315_metadata.txt
gzip -cd GSE95315_family.soft.gz | grep Sample_title | sed 's/^!Sample_title = //' >title.txt
gzip -cd GSE95315_family.soft.gz | grep "cell cluster:" | sed 's/^!Sample_characteristics_ch1 = cell cluster: //' >celltype.txt
gzip -cd GSE95315_family.soft.gz | grep "postnatal day:" | sed 's/^!Sample_characteristics_ch1 = postnatal day: //' >age.txt
paste title.txt celltype.txt age.txt >>GSE95315_metadata.txt

5. GSE95752 (Linnarsson's lab)

Metadata for cells were extracted from family soft file by the following commands.

echo -e "cell_id\tcell_type\tpostnatal_day" >GSE95752_metadata.txt
gzip -cd GSE95752_family.soft.gz | grep Sample_title | sed 's/^!Sample_title = //' >title.txt
gzip -cd GSE95752_family.soft.gz | grep "cell cluster:" | sed 's/^!Sample_characteristics_ch1 = cell cluster: //' >celltype.txt
gzip -cd GSE95752_family.soft.gz | grep "postnatal day:" | sed 's/^!Sample_characteristics_ch1 = postnatal day: //' >age.txt
paste title.txt celltype.txt age.txt >>GSE95752_metadata.txt

6. GSE81547

Metadata for cells were extracted from family soft file and expression data was concatanaged into a single matrix by the following commands.

# metadata
gzip -cd GSE81547_family.soft.gz | grep "SAMPLE = " | sed 's/^\^SAMPLE = //' >sample.txt
gzip -cd GSE81547_family.soft.gz | grep "donor_age:" | sed 's/^!Sample_characteristics_ch1 = donor_age: //' >age.txt
gzip -cd GSE81547_family.soft.gz | grep "inferred_cell_type:" | sed 's/^!Sample_characteristics_ch1 = inferred_cell_type: //' >celltype.txt
echo -e "cell_id\tage\tcell_type" >GSE81547_metadata.txt
paste sample.txt age.txt celltype.txt >> GSE81547_metadata.txt
rm sample.txt age.txt celltype.tt

# expression matrix
mkdir GSE81547_raw
mv GSE81547_RAW.tar GSE81547_raw
cd GSE81547_raw
tar -xvf GSE81547_RAW.tar
files=($(ls GSM*))
f=${files[0]}
pre=${f%%_*}
echo -e "gene\t$pre" >../GSE81547_count.txt
gzip -cd $f >>../GSE81547_count.txt
echo ${#files[@]}
for i in {1..2543}; do
        f=${files[$i]}
        pre=${f%%_*}
        echo $pre >tmp.txt
        gzip -cd $f | cut -f 2 >>tmp.txt
        paste ../GSE81547_count.txt tmp.txt >exp.txt
        mv exp.txt ../GSE81547_count.txt
done
cd ../
rm GSE81547_raw/*.gz
gzip GSE81547_count.txt

7. GSE67835

Metadata for cells were extracted from family soft file and expression data was concatanaged into a single matrix by the following commands.

# metadata
echo -e "cell_id\tcell_type\tage" > GSE67835_metadata.txt
gzip -cd GSE67835_family.soft.gz | grep "SAMPLE = " | sed 's/^\^SAMPLE = //' >sample.txt
gzip -cd GSE67835_family.soft.gz | grep "= cell type:" | sed 's/!Sample_characteristics_ch1 = cell type: //' > celltype.txt
gzip -cd GSE67835_family.soft.gz | grep "= age: " | sed 's/!Sample_characteristics_ch1 = age: //'>age.txt
paste sample.txt celltype.txt age.txt >>GSE67835_metadata.txt

# expression matrix
mkdir GSE67835_raw
mv GSE67835_RAW.tar GSE67835_raw
cd GSE67835_raw
tar -xvf GSE67835_RAW.tar
files=($(ls GSM*))
f=${files[0]}
pre=${f%%_*}
echo -e "gene\t$pre" >../GSE67835_count.txt
gzip -cd $f >>../GSE67835_count.txt
echo ${#files[@]}
for i in {1..465}; do
	f=${files[$i]}
	pre=${f%%_*}
	echo $pre >tmp.txt
	gzip -cd $f | cut -f 2 >>tmp.txt
	paste ../GSE67835_count.txt tmp.txt >exp.txt
	mv exp.txt ../GSE67835_count.txt
done
cd ../
rm GSE67835_raw/*.gz
gzip GSE67835_count.txt

8. GSE89232

Metadata for cells were extracted from family soft file by the following commands.

gzip -cd GSE89232_family.soft.gz | grep Sample_title | sed 's/^!Sample_title = //' >title.txt
gzip -cd GSE89232_family.soft.gz | grep "cell type:" | grep -v "(" | sed 's/!Sample_characteristics_ch1 = cell type: //' >celltype.txt
echo -e "cell_id\tcell_type" >GSE89232_celltype.txt
paste title.txt celltype.txt >>GSE89232_celltype.txt

9. GSE97478

Metadata for cells were extracted from family soft file by the following commands.

gzip -cd GSE97478_family.soft.gz | grep Sample_title | sed 's/^!Sample_title = //' >title.txt
gzip -cd GSE97478_family.soft.gz | grep "cell type:" | grep -v "(" | sed 's/!Sample_characteristics_ch1 = cell type: //' >celltype.txt
echo -e "cell_id\tcell_type" >GSE97478_celltype.txt
paste title.txt celltype.txt >>GSE97478_celltype.txt

10. GSE106707

Metadata for cells were extracted from family soft file by the following commands.

gzip -cd GSE106707_family.soft.gz | grep Sample_title | sed 's/^!Sample_title = //' >title.txt
gzip -cd GSE106707_family.soft.gz | grep "cell type:" | grep -v "(" | sed 's/!Sample_characteristics_ch1 = cell type: //' >celltype.txt
gzip -cd GSE106707_family.soft.gz | grep "postnatal days:" | grep -v "(" | sed 's/!Sample_characteristics_ch1 = postnatal days: //' >pd.txt
echo -e "cell_id\tcell_type\tpd" >GSE106707_celltype.txt
paste title.txt celltype.txt pd.txt >>GSE106707_celltype.txt

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Descriptions/scripts for pre-process and processed data for FUMA cell specificity analyses (scRNA-seq)

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