Showing 3 of 3 results

• Publication

  released

  Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex

  Ana Uzquiano, Amanda J Kedaigle, Martina Pigoni, et al.

  Cell. 2022-09-29;185(20):3770-3788.e27.

  • doi:10.1016/j.cell.2022.09.010
  • PMID:36179669
  • PMCID:PMC9990683

  Available supplemental data: website

  URL: https://www.synapse.org

  Data summary: Read-level data from scRNA-seq, scATAC-seq, SHARE-seq, and Slide-seq data, supporting the findings…See more

  Available supplemental data: website

  URL: https://singlecell.broadinstitute.org/single_cell/study/SCP1756

  Data summary: The count-level data and meta-data have been deposited at the Single Cell Portal.

  Available supplemental data: website

  URL: https://doi.org/10.17632/7cxccpv4hg.1

  Data summary: Supplemental data related to Figures 1, ​,3,3, ​,4,4, ​,5,5, ​,6,6, and ​and77 has been deposited…See more

  Available supplemental data: website

  URL: https://github.com/AmandaKedaigle/OrganoidAtlas

  Data summary: Code used during data analysis is available at GitHub. d Any additional information required to…See more

  Available supplemental data: website

  URL: http://solo.bmap.ucla.edu/shiny/webapp/

  Data summary: Data from previous publications that was used in this study can be found at the Gene Expression…See more

• Publication

  released

  Single-nucleus chromatin accessibility profiling highlights distinct astrocyte signatures in progressive supranuclear palsy and corticobasal degeneration

  Nils Briel, Viktoria C. Ruf, Katrin Pratsch, et al.

  Acta Neuropathol. 2022-08-17;144(4):615–635.

  • doi:10.1007/s00401-022-02483-8
  • PMID:35976433
  • PMCID:PMC9468099

  Available supplemental data: website

  URL: https://github.com/nes-b/snATAC-seq_psp_cbd

  Data summary: All scripts for pre-processing and analyzing the snATAC-seq data from PSP/CBD frontal cortex and…See more

• Publication

  released

  Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

  Chongyuan Luo, Hanqing Liu, Fangming Xie, et al.

  Cell Genom. 2022-03-09;2(3):100107.

  • doi:10.1016/j.xgen.2022.100107
  • PMID:35419551
  • PMCID:PMC9004682

  Available supplemental data: website

  URL: http://neomorph.salk.edu/Human_cells_snmCT-seq.php

  Data summary: Raw and processed data included in this study were deposited to NCBI GEO/SRA with accession number…See more

  Available supplemental data: website

  URL: http://neomorph.salk.edu/human_frontal_cortex_ensemble.php

  Data summary: snmCAT-seq generated from brain tissues can be visualized at…See more

  Available supplemental data: website

  URL: https://assets.nemoarchive.org/dat-s3creyz

  Data summary: snRNA-seq data is available for download from the Neuroscience Multi-omics Archive…See more

  Available supplemental data: website

  URL: https://github.com/mukamel-lab/SingleCellFusion

  Data summary: The code for SingleCellFusion is available from https://github.com/mukamel-lab/SingleCellFusion.

  Available supplemental data: website

  URL: https://github.com/lhqing/snmCAT-seq_integration

  Data summary: The code benchmarking computational integration methods are available from…See more

  Available supplemental data: website

  URL: https://github.com/FangmingXie/mctseq_over_under_splitting/blob/master/over-under-splitting-analysis.ipynb

  Data summary: The code reproducing the over- and under-splitting analysis are available from…See more

  Available supplemental data: website

  URL: https://www.protocols.io/view/snmcat-v1-bwubpesn

  Data summary: A detailed bench protocol for snmCAT-seq and future updates to the method can be found at…See more