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gao-lab · Jun 15, 2022 · 9f37e40 · 9f37e40
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diff --git a/docs/data.rst b/docs/data.rst
@@ -5,81 +5,90 @@ By courtesy of the original authors, we provide here the following preprocessed
 data files used in our paper:
 
 .. list-table::
-   :widths: 15 15 5 5 35 25
+   :widths: 15 15 5 5 32 3 25
    :header-rows: 1
 
    * - Dataset
      - Protocol
      - Species
      - Organ
      - Publication
+     - Source
      - Processed files
    * - Chen-2019
      - SNARE-seq
      - Mouse
      - Cortex
-     - `High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell <https://doi.org/10.1038/s41587-019-0290-0>`_
-     - | `Chen-2019-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/Chen-2019-RNA.h5ad>`_,
-       | `Chen-2019-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/Chen-2019-ATAC.h5ad>`_
+     - `High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell <https://doi.org/10.1038/s41587-019-0290-0>`__
+     - `GEO <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126074>`__
+     - | `Chen-2019-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/Chen-2019-RNA.h5ad>`__,
+       | `Chen-2019-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/Chen-2019-ATAC.h5ad>`__
    * - Ma-2020
      - SHARE-seq
      - Mouse
      - Skin
-     - `Chromatin potential identified by shared single-cell profiling of RNA and chromatin <https://doi.org/10.1016/j.cell.2020.09.056>`_
-     - | `Ma-2020-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/Ma-2020-RNA.h5ad>`_,
-       | `Ma-2020-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/Ma-2020-ATAC.h5ad>`_
+     - `Chromatin potential identified by shared single-cell profiling of RNA and chromatin <https://doi.org/10.1016/j.cell.2020.09.056>`__
+     - `GEO <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140203>`__
+     - | `Ma-2020-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/Ma-2020-RNA.h5ad>`__,
+       | `Ma-2020-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/Ma-2020-ATAC.h5ad>`__
    * - 10x-Multiome-Pbmc10k
      - 10x Multiome
      - Human
      - PBMC
      -
-     - | `10x-Multiome-Pbmc10k-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/10x-Multiome-Pbmc10k-RNA.h5ad>`_,
-       | `10x-Multiome-Pbmc10k-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/10x-Multiome-Pbmc10k-ATAC.h5ad>`_
+     - `10x Demo <https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/1.0.0/pbmc_granulocyte_sorted_10k>`__
+     - | `10x-Multiome-Pbmc10k-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/10x-Multiome-Pbmc10k-RNA.h5ad>`__,
+       | `10x-Multiome-Pbmc10k-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/10x-Multiome-Pbmc10k-ATAC.h5ad>`__
    * - Saunders-2018
      - Drop-seq
      - Mouse
      - Cortex
-     - `Molecular diversity and specializations among the cells of the adult mouse brain <https://doi.org/10.1016/j.cell.2018.07.028>`_
-     - `Saunders-2018.h5ad <http://download.gao-lab.org/GLUE/dataset/Saunders-2018.h5ad>`_
+     - `Molecular diversity and specializations among the cells of the adult mouse brain <https://doi.org/10.1016/j.cell.2018.07.028>`__
+     - `dropviz <http://dropviz.org/>`__
+     - `Saunders-2018.h5ad <http://download.gao-lab.org/GLUE/dataset/Saunders-2018.h5ad>`__
    * - Luo-2017
      - snmC-seq
      - Mouse
      - Cortex
-     - `Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex <https://doi.org/10.1126/science.aan3351>`_
-     - `Luo-2017.h5ad <http://download.gao-lab.org/GLUE/dataset/Luo-2017.h5ad>`_
+     - `Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex <https://doi.org/10.1126/science.aan3351>`__
+     - `annoj <https://brainome.ucsd.edu/annoj/brain_single_nuclei/>`__
+     - `Luo-2017.h5ad <http://download.gao-lab.org/GLUE/dataset/Luo-2017.h5ad>`__
    * - 10x-ATAC-Brain5k
      - 10x ATAC
      - Mouse
      - Cortex
      -
-     - `10x-ATAC-Brain5k.h5ad <http://download.gao-lab.org/GLUE/dataset/10x-ATAC-Brain5k.h5ad>`_
+     - `10x Demo <https://support.10xgenomics.com/single-cell-atac/datasets/1.1.0/atac_v1_adult_brain_fresh_5k>`__
+     - `10x-ATAC-Brain5k.h5ad <http://download.gao-lab.org/GLUE/dataset/10x-ATAC-Brain5k.h5ad>`__
    * - Cao-2020
      - sci-RNA-seq3
      - Human
      - 15 organs
-     - `A human cell atlas of fetal gene expression <https://doi.org/10.1126/science.aba7721>`_
-     - `Cao-2020.h5ad <http://download.gao-lab.org/GLUE/dataset/Cao-2020.h5ad>`_
+     - `A human cell atlas of fetal gene expression <https://doi.org/10.1126/science.aba7721>`__
+     - `GEO <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156793>`__
+     - `Cao-2020.h5ad <http://download.gao-lab.org/GLUE/dataset/Cao-2020.h5ad>`__
    * - Domcke-2020
      - sci-ATAC-seq3
      - Human
      - 15 organs
-     - `A human cell atlas of fetal chromatin accessibility <https://doi.org/10.1126/science.aba7612>`_
-     - `Domcke-2020.h5ad <http://download.gao-lab.org/GLUE/dataset/Domcke-2020.h5ad>`_
+     - `A human cell atlas of fetal chromatin accessibility <https://doi.org/10.1126/science.aba7612>`__
+     - `GEO <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149683>`__
+     - `Domcke-2020.h5ad <http://download.gao-lab.org/GLUE/dataset/Domcke-2020.h5ad>`__
    * - Muto-2021
      - | snRNA-seq,
        | scATAC-seq
      - Human
      - Kidney
-     - `Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney <https://doi.org/10.1038/s41467-021-22368-w>`_
-     - | `Muto-2021-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/Muto-2021-RNA.h5ad>`_,
-       | `Muto-2021-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/Muto-2021-ATAC.h5ad>`_
-
-
-.. * - Yao-2021
-..   - | 10x RNA v3,
-..     | snATAC-seq
-..   - Mouse
-..   - MOp
-..   - `A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex <https://doi.org/10.1038/s41586-021-03500-8>`_
-..   - | `Yao-2021-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/Yao-2021-RNA.h5ad>`_,
-..     | `Yao-2021-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/Yao-2021-ATAC.h5ad>`_
+     - `Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney <https://doi.org/10.1038/s41467-021-22368-w>`__
+     - `GEO <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151302>`__
+     - | `Muto-2021-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/Muto-2021-RNA.h5ad>`__,
+       | `Muto-2021-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/Muto-2021-ATAC.h5ad>`__
+   * - Yao-2021
+     - | 10x RNA v3,
+       | snATAC-seq
+     - Mouse
+     - MOp
+     - `A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex <https://doi.org/10.1038/s41586-021-03500-8>`__
+     - `NeMO <https://assets.nemoarchive .org/dat-ch1nqb7>`__
+     - | `Yao-2021-RNA.h5ad <http://download.gao-lab.org/GLUE/dataset/Yao-2021-RNA.h5ad>`__,
+       | `Yao-2021-ATAC.h5ad <http://download.gao-lab.org/GLUE/dataset/Yao-2021-ATAC.h5ad>`__