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Table 1 Datasets and sources

From: Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets

sample ID

organism

common name

tissue

10X version

FACS sorted

source

reference

ensembl reference version

dr-RGC-larva-s1

D. rerio

zebrafish

Retinal ganglion cells (RGCs)

2

yes

GSE152842

Koelsch et al., 2020

101

dr-RGC-adult-s17

D. rerio

zebrafish

RGCs

2

yes

GSE152842

Koelsch et al., 2020

101

dr-pineal-s1

D. rerio

zebrafish

pineal gland

2

no

SRR8315377/SRR8315378

[7]

101

dr-pineal-s2

D. rerio

zebrafish

pineal gland

2

no

SRR8315379/SRR8315380

[7]

101

nf-embryo-s1

N. furzeri

killifish

tail blastema

2

no

SRR11886701

[8]

101

nf-embryo-s2

N. furzeri

killifish

tail blastema

2

no

SRR11917464

[8]

101

am-hk-cave

A. mexicanus

mexican cavefish

head kidney

3

yes

GSE128306/L39134

[6]

100

am-hk-surf

A. mexicanus

mexican cavefish

head kidney

3

yes

GSE128306/L39132

[6]

100

dm-brain-s1

D. melanogaster

drosophila

brain

2

no

SRR6327103

[2]

100

dm-brain-s2

D. melanogaster

drosophila

brain

2

no

SRR6327104

[2]

100

ce-embryo-s1

C. elegans

C. elegans

embryo

2

no

SRR8611991

[4]

100

ce-embryo-s2

C. elegans

C. elegans

embryo

2

no

SRR8611992

[4]

100

ci-larva-s1

C. intestinalis

ciona

larva

2

no

SRR9051005

[1]

100

ci-larva-s2

C. intestinalis

ciona

larva

2

no

SRR9051006

[1]

100

hs-pbmc-4 k-v2

H. sapiens

human

pbmc

2

no

*

10X Genomics

100

hs-pbmc-8 k-v2

H. sapiens

human

pbmc

2

no

*

10X Genomics

100

mm-neuron-2 k-v2

M. musculus

mouse

neurons

2

no

*

10X Genomics

100

mm-neuron-9 k-v2

M. musculus

mouse

neurons

2

no

*

10X Genomics

100

hs-pbmc-10 k-v3

H. sapiens

human

pbmc

3

no

*

10X Genomics

100

hs-pbmc-1 k-v3

H. sapiens

human

pbmc

3

no

*

10X Genomics

100

mm-neuron-10 k-v3

M. musculus

mouse

neurons

3

no

*

10X Genomics

100

mm-neuron-1 k-v3

M. musculus

mouse

neurons

3

no

*

10X Genomics

100

      

* https://support.10xgenomics.com/single-cell-gene-expression/datasets