Showing 24 of 24 results

• Publication

  released

  Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

  Linda Kachuri, Angel C. Y. Mak, Donglei Hu, et al.

  Nat Genet. 2023-05-25;55(6):952-963.

  • PMID:37231098
  • doi:10.1038/s41588-023-01377-z
  • PMCID:PMC10260401

• 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

• Publication

  released

  Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts

  Benjamin H. Mullin, Jennifer Tickner, Kun Zhu, et al.

  Genome Biology. 2020-03-26;20(1):80.

  • PMID:32216834
  • PMCID:PMC7098081
  • doi:10.1186/s13059-020-01997-2

  URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01997-2

• Publication

  released

  CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

  Ruilin Tian, Mariam A Gachechiladze, Connor H Ludwig, et al.

  Neuron. 2019-10-23;104(2):239-255.e12.

  • doi:10.1016/j.neuron.2019.07.014
  • PMID:31422865
  • PMCID:PMC6813890

• Publication

  released

  The single-cell transcriptomic landscape of early human diabetic nephropathy

  Parker C Wilson, Haojia Wu, Yuhei Kirita, et al.

  Proc Natl Acad Sci U S A. 2019-09-24;116(39):19619-19625.

  • PMID:31506348
  • PMCID:PMC6765272
  • doi:10.1073/pnas.1908706116

• Publication

  released

  Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

  Thomas M Norman, Max A Horlbeck, Joseph M Replogle, et al.

  Science. 2019-08-23;365(6455):786-793.

  • doi:10.1126/science.aax4438
  • PMID:31395745
  • PMCID:PMC6746554

• Publication

  released

  Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

  Jason C Klein, Aidan Keith, Sarah J Rice, et al.

  Nat Commun. 2019-06-04;10(1):2434.

  • doi:10.1038/s41467-019-10439-y
  • PMID:31164647
  • PMCID:PMC6547687

• Publication

  released

  Gain-of-Function Mutations of SLC16A11 Contribute to the Pathogenesis of Type 2 Diabetes

  Yongxu Zhao, Zhuanghui Feng, Yongxian Zhang, et al.

  Cell Rep. 2019-01-22;26(4):884-892.e4.

  • doi:10.1016/j.celrep.2018.12.100
  • PMID:30673611

• Publication

  released

  High-throughput characterization of genetic effects on DNA-protein binding and gene transcription

  Cynthia A Kalita, Christopher D Brown, Andrew Freiman, et al.

  Genome Res. 2018-09-25;28(11):1701-1708.

  • doi:10.1101/gr.237354.118
  • PMID:30254052
  • PMCID:PMC6211638

• Publication

  released

  Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

  Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, et al.

  Cell Stem Cell. 2018-08-02;23(2):276-288.e8.

  • doi:10.1016/j.stem.2018.06.014
  • PMID:30033119
  • PMCID:PMC6084406

• Publication

  released

  Single-cell RNA-seq analysis reveals the progression of human osteoarthritis

  Quanbo Ji, Yuxuan Zheng, Guoqiang Zhang, et al.

  Ann Rheum Dis. 2018-07-19;78(1):100-110.

  • doi:10.1136/annrheumdis-2017-212863
  • PMID:30026257
  • PMCID:PMC6317448

• Publication

  released

  Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey

  Cassandra N Spracklen, Jinxiu Shi, Swarooparani Vadlamudi, et al.

  PLoS Genet. 2018-04-05;14(4):e1007275.

  • doi:10.1371/journal.pgen.1007275
  • PMID:29621232
  • PMCID:PMC5886383

• Publication

  released

  A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression

  Ina Kycia, Brooke N Wolford, Jeroen R Huyghe, et al.

  Am J Hum Genet. 2018-04-05;102(4):620-635.

  • doi:10.1016/j.ajhg.2018.02.020
  • PMID:29625024
  • PMCID:PMC5985342

• Publication

  released

  Integrative analysis of super enhancer SNPs for type 2 diabetes

  Weiping Sun, Sihong Yao, Jielong Tang, et al.

  PLoS One. 2018-01-31;13(1):e0192105.

  • doi:10.1371/journal.pone.0192105
  • PMCID:PMC5792005
  • PMID:29385209

• Publication

  released

  Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes

  Sílvia Bonàs-Guarch, Marta Guindo-Martínez, Irene Miguel-Escalada, et al.

  Nat Commun. 2018-01-22;9(1):321.

  • doi:10.1038/s41467-017-02380-9
  • PMID:29358691
  • PMCID:PMC5778074

• Publication

  released

  Data of methylome and transcriptome derived from human dilated cardiomyopathy

  Bong-Seok Jo, In-Uk Koh, Jae-Bum Bae, et al.

  Data Brief. 2016-09-14;9:382-387.

  • doi:10.1016/j.dib.2016.09.006
  • PMID:27699191
  • PMCID:PMC5035344

• Publication

  released

  Epigenomic profiling reveals an association between persistence of DNA methylation and metabolic memory in the DCCT/EDIC type 1 diabetes cohort

  Zhuo Chen, Feng Miao, Andrew D Paterson, et al.

  Proc Natl Acad Sci U S A. 2016-05-24;113(21):E3002-11.

  • doi:10.1073/pnas.1603712113
  • PMID:27162351
  • PMCID:PMC4890596

• Publication

  released

  Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types

  Jin Li, Johanna Klughammer, Matthias Farlik, et al.

  EMBO Rep. 2016-02-17;17(2):178-87.

  • doi:10.15252/embr.201540946
  • PMCID:PMC4784001
  • PMID:26691212

• Publication

  released

  Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions

  Shimrat Mamrut, Nili Avidan, Elsebeth Staun-Ram, et al.

  Epigenetics. 2015-10-09;10(10):943-57.

  • doi:10.1080/15592294.2015.1084462
  • PMID:26291385
  • PMCID:PMC4844205

• Publication

  released

  Research resource: the pdx1 cistrome of pancreatic islets

  Cynthia Khoo, Juxiang Yang, Samuel A Weinrott, et al.

  Mol Endocrinol. 2012-03-01;26(3):521-33.

  • doi:10.1210/me.2011-1231
  • PMCID:PMC3286194
  • PMID:22322596

• Publication

  released

  The type 2 diabetes-associated HMG20A gene is mandatory for islet beta cell functional maturity

  Jose M Mellado-Gil, Esther Fuente-Martín, Petra I Lorenzo, et al.

  Cell Death Dis. 2018-02-15;9(3):279.

  • doi:10.1038/s41419-018-0272-z
  • PMID:29449530
  • PMCID:PMC5833347

• Publication

  released

  A Whole-Genome RNA Interference Screen Reveals a Role for Spry2 in Insulin Transcription and the Unfolded Protein Response

  Zachary Pappalardo, Deeksha Gambhir Chopra, Thomas G Hennings, et al.

  Diabetes. 2017-02-28;66(6):1703-1712.

  • doi:10.2337/db16-0962
  • PMID:28246293
  • PMCID:PMC5440024