Skip to content

Commit

Permalink
update docs
Browse files Browse the repository at this point in the history
  • Loading branch information
@OnlyBelter
OnlyBelter committed Feb 2, 2024
1 parent c69bf1d commit 00754c7
Show file tree
Hide file tree
Showing 2 changed files with 179 additions and 64 deletions.
85 changes: 46 additions & 39 deletions docs/datasets.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,48 +3,55 @@ Datasets

Datasets used in DeSide
***
## scRNA-seq datasets

| Dataset ID | Journal | DOI | Publish Date | Reported cells (total) | Organism | Tissue | Data location | Sequencing method | #patients |
|-------------|----------------------|-----------------------------|--------------|------------------|------------------------|----------------------------------|-----------------------------------|-------------------------|-----------|
| hnscc_cillo_01 | Immunity | 10.1016/j.immuni.2019.11.014 | 20200107 | 131,224 | 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 | Human | Pancreatic Ductal Adenocarcinoma (PDAC)| [Link](https://bigd.big.ac.cn/gsa/browse/CRA001160) | 10x Single Cell 3' v2 | 22 |
| hnscc_puram_03 | Cell | 10.1016/j.cell.2017.10.044 | 20171130 | 5,902 | Human | Head and Neck Cancer (HNSC) | GSE103322 | Smart-seq2 | 16 |
| pdac_steele_04 | Nat Cancer | 10.1038/s43018-020-00121-4 | 20201026 | 124,898 | 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 | 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 | 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 | Human | Cancer cell lines | GSE157220 | Illumina NextSeq 500 | - |


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

## Merged datasets and Synthetic datasets

| Dataset name | #samples | Sampling method | Filtering | #cell types | #genes | Input dataset | GEPs <br/>(type, fortmat) | Dataset type | Notation |
|:--------------------------------------:|----------|-----------------|-----------|-------------|--------|--------------------------------|:-------------------------------:|:-----------------------------:|:----------:|
| TCGA | 7,699 | - | - | - | 19,712 | - | MCT, `TPM` | Downloaded from TCGA | DA |
| merged_7_sc_datasets | 135,049 | - | - | 11 | 12,114 | 7 collected scRNA-seq datasets | Single cell, <br/>`log2(TPM+1)` | Raw dataset from scRNA-seq | S0 |
| SCT_POS_N10K | 110,000 | n_base=100 | - | 11 | 12,114 | S0 | SCT, `log2(TPM+1)` | Used to simulate MCT datasets | S1 |
| Mixed_N100K_random | 100,000 | Random | No | 11 | 12,114 | S1 | MCT, `log2(TPM+1)` | Training set | D0 |
| Mixed_N100K_segment | 100,000 | Segment | Yes | 11 | 6,168 | S1 | MCT, `log2(TPM+1)` | Training set | D1 |
| Mixed_N100K_segment_<br/>without_filtering | 100,000 | Segment | No | 11 | 12,114 | S1 | MCT, `log2(TPM+1)` | Training set | D2 |
| Test_set_random | 3,000 | Random | No | 11 | 12,114 | S1 | MCT, `log2(TPM+1)` | Test set | T0 |
| Test_set1 | 3,000 | Segment | Yes | 11 | 6,168 | S1 | MCT, `log2(TPM+1)` | Test set | T1 |
| Test_set2 | 3,000 | Segment | No | 11 | 12,114 | S1 | MCT, `log2(TPM+1)` | Test set | T2 |
| SCT_POS_N100 | 1100 | n_base=100 | - | 11 | 12,114 | S0 | SCT, `log2(TPM+1)` | Test set | T3 |

- MCT: Bulk gene expression profile with multiple different cell types
- SCT: Bulk gene expression profile with single cell type (scGEP)

## Merged datasets and Synthetic datasets (Table S1)

| Dataset name | #samples | Sampling method | Filtering | #cell types | #genes | Input dataset | GEPs <br/>(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, <br/>`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_<br/>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](https://bigd.big.ac.cn/gsa/browse/CRA001160) | 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
- TCGA: [download link](https://figshare.com/articles/dataset/Merged_gene_expression_profiles_TPM_/23047547)
- merged_7_sc_datasets (S0): [download link](https://figshare.com/articles/dataset/Dataset_S0/23283908)
- SCT_POS_N10K (S1): [download link](https://figshare.com/articles/dataset/Dataset_S1/23043560)
- Mixed_N100K_random (D0): [download link](https://figshare.com/articles/dataset/Dataset_D0/23283932)
- Mixed_N100K_segment (D1): [download link](https://figshare.com/articles/dataset/Dataset_D1/23047391)
- Mixed_N100K_segment_without_filtering (D2): [download link](https://figshare.com/articles/dataset/Dataset_D2/23284256)
- All Test Sets: [download link](https://figshare.com/articles/dataset/All_Test_Sets/23283884)
- TCGA (DA): [merged_tpm.csv.zip](https://doi.org/10.6084/m9.figshare.23047547.v1)
- merged_12_sc_datasets (S0): [merged_12_sc_datasets_231003.h5ad](https://doi.org/10.6084/m9.figshare.23283908.v2)
- SCT_POS_N10K (S1): [simu_bulk_exp_SCT_N10K_S1_16sct.h5ad](https://doi.org/10.6084/m9.figshare.23043560.v2)
- Mixed_N100K_random (D0): [simu_bulk_exp_Mixed_N100K_random_log2cpm1p.h5ad](https://doi.org/10.6084/m9.figshare.23283932.v2)
- Mixed_N100K_segment (D1): [simu_bulk_exp_Mixed_N100K_D1.h5ad](https://doi.org/10.6084/m9.figshare.23047391.v2)
- Mixed_N100K_segment_without_filtering (D2): [simu_bulk_exp_Mixed_N100K_D2.h5ad](https://doi.org/10.6084/m9.figshare.23284256.v2)
- All Test Sets: [all_test_sets.zip](https://doi.org/10.6084/m9.figshare.23283884.v3)
- Test_set_random (T0)
- Test_set1 (T1)
- Test_set2 (T2)
Expand Down
Loading

0 comments on commit 00754c7

Please sign in to comment.