Datasets

Datasets used in DeSide

Merged datasets and Synthetic datasets (Table S1)

Dataset name

#samples

Sampling method

Filtering

#cell types

#genes

Input dataset

GEPs
(type, fortmat)

Dataset type

Notation

TCGA

7,699

-

-

-

19,712

-

MCT, TPM

Downloaded from TCGA

DA

merged_7_sc_datasets

325,474

-

-

19

17,834

12 collected scRNA-seq datasets

Single cell,
log2(TPM+1)

Raw dataset from scRNA-seq

S0

SCT_POS_N10K

10,000 x 16

n_base=100

-

16

17,834

S0

SCT, log2(TPM+1)

Used to simulate MCT datasets

S1

Mixed_N100K_random

100,000

Random

No

16

17,834

S1

MCT, log2(TPM+1)

Training set

D0

Mixed_N100K_segment

100,000

Segment

Yes

16

9,028

S1

MCT, log2(TPM+1)

Training set

D1

Mixed_N100K_segment_
without_filtering

100,000

Segment

No

16

17,834

S1

MCT, log2(TPM+1)

Training set

D2

Test_set_random

3,000

Random

No

16

17,834

S1

MCT, log2(TPM+1)

Test set

T0

Test_set1

3,000

Segment

Yes

16

9,028

S1

MCT, log2(TPM+1)

Test set

T1

Test_set2

3,000

Segment

No

16

17,834

S1

MCT, log2(TPM+1)

Test set

T2

SCT_POS_N100

100 x 16

n_base=100

-

16

17,834

S0

SCT, log2(TPM+1)

Test set

T3

  • MCT: Bulk gene expression profiles with multiple different cell types

  • SCT: Bulk gene expression profiles with single cell type (sctGEPs)

  • GEPs: Gene expression profiles

Collected scRNA-seq datasets (Table S2)

Dataset ID

Journal

DOI

Publish Date

Reported cells (total)*

Integrated cells (used)

Organism

Tissue

Data location

Sequencing method

#patients**

hnscc_cillo_01

Immunity

10.1016/j.immuni.2019.11.014

20200107

131,224

57,034

Human

Head and Neck Cancer (HNSC)

GSE139324

10x Single Cell 3’ v2

26

pdac_pengj_02

Cell Res

10.1038/s41422-019-0195-y

20190704

57,530

37,079

Human

Pancreatic Ductal Adenocarcinoma (PDAC)

Link

10x Single Cell 3’ v2

22

hnscc_puram_03

Cell

10.1016/j.cell.2017.10.044

20171130

5,902

4,647

Human

Head and Neck Cancer (HNSC)

GSE103322

Smart-seq2

16

pdac_steele_04

Nat Cancer

10.1038/s43018-020-00121-4

20201026

124,898

32,062

Human

Pancreatic Ductal Adenocarcinoma (PDAC)

GSE155698

10x Single Cell 3’ v2

15

luad_kim_05

Nat Commun

10.1038/s41467-020-16164-1

20200508

208,506

49,959

Human

Lung Adenocarcinoma (LUAD)

GSE131907

10x Single Cell 3’ v2

13

nsclc_guo_06

Nature Medicine

10.1038/s41591-018-0045-3

20180625

12,346

4,050

Human

Non-Small-Cell Lung Cancer (NSCLC)

GSE99254

Smart-Seq2

13

pan_cancer_07

Nat Genet

10.1038/s41588-020-00726-6

20201030

53,513

30,681

Human

Cancer cell lines

GSE157220

Illumina NextSeq 500

-

prad_cheng_08

Nat Cell Biol

10.1038/s41556-020-00613-6

20211108

36,424

28,253

Human

Prostate cancer (PRAD)

https://www.weizmann.ac.il/sites/3CA/prostate

10X Genomics

12

prad_dong_09

Commun Biol

10.1038/s42003-020-01476-1

20201216

21,292

16,472

Human

Prostate cancer (PRAD)

https://www.weizmann.ac.il/sites/3CA/prostate

10X Genomics

6

hcc_sun_10

Cell

10.1016/j.cell.2020.11.041

20201123

16,498

11,365

Human

Hepatocellular carcinoma (HCC)

https://www.weizmann.ac.il/sites/3CA/liverbiliary

10X Genomics

16

gbm_neftel_11

Cell

10.1016/j.cell.2019.06.024

20190618

24,131

16,835

Human

Glioblastoma multiforme (GBM)

https://www.weizmann.ac.il/sites/3CA/brain (GSE131928)

10X Genomics

36

gbm_abdelfattah_12

Nat Commun

10.1038/s41467-022-28372-y

20220909

201,986

37,037

Human

Glioblastoma multiforme (GBM)

GSE182109

10× Chromium / HiSeq 4000

8

  • * The number of reported cells may include cells that don’t originate from solid tumors, which were removed during integrating.

  • ** The count considered only the number of patients (samples) in the data that were integrated into the final dataset.

Download

.h5ad files can be opened by the function scanpy.read_h5ad() in Scanpy or the class deside.utility.read_file.ReadH5AD in DeSide.