title: Locational memory of macrovessel vascular cells is transcriptionally imprinted

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

summary: The locational predisposition of vascular pathologies illustrates the need for a better insight into vascular heterogeneity. To investigate the transcriptomic basis of angiodiversity, we isolated and analyzed transcriptomes from endothelial cells and vascular smooth muscle cells from nine different adult canine macrovessels: the aorta, coronary artery, vena cava, portal vein, femoral artery, femoral vein, saphenous vein, pulmonary vein, and pulmonary artery. We identified both reported and novel expression patterns defining specialized adult blood vessels. Our findings also show that adult vascular cells in culture express a remarkably high number of transcription factors crucial to organ development in the embryo. The persistent expression of these genes in culture indicates that these genes are not regulated by the flow or surrounding cell types but are rather fixed in the molecular memory. Therefore, our findings prompt the re-thinking of the extrapolation of results from single-origin endothelial cell systems.

overall_design: Whole transcriptome data of primary adult canine endothelial and vascular smooth muscle cells of 9 macrovessels, produced on Illumina NextSeq500 using a single-end 75 bp configuration

first: Talitha

last: Spanjersberg

first: Loes

last: Oosterhoff

first: Hedwig

last: Kruitwagen

first: Noortje

last: van den Dungen

first: Magdalena

last: Harakalova

first: Michal

last: Mokry

first: Bart

last: Spee

middle: G

first: Hans

last: Vernooij


title: Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan

status: Public on Aug 16 2023

city: Sydney

first: Fabio

last: Luciani

state: NSW

address: Kensington Campus

country: Australia

institute: UNSW Sydney

type: Expression profiling by high throughput sequencing

summary: CD8+ T-cells provide robust anti-viral immunity, yet how epitope-specific T-cells evolve across the human lifespan is unknown. We defined CD8+ T-cell immunity directed at the prominent influenza epitope, HLA-A*02:01-M158-66 (A2/M158) across four age groups (newborns, children, adults and elderly) ex vivo at phenotypic, single cell sequence (transcriptomic), clonal and functional levels. We identified a linear differentiation trajectory from newborns to children then adults, followed by divergence and a clonal reset in older adults. Gene profiles in older adults closely resembled those observed in newborns and children, despite being clonally-different. However, only child- and adult-derived A2/M158+CD8+ T-cells had the potential to differentiate into highly cytotoxic epitope-specific CD8+ T-cells, which was linked to highly functional public TCRab-signatures. Suboptimal TCRab-signatures detected in older adults led to poorer proliferation, polyfunctionality, avidity and recognition of peptide mutants, although displayed no signs of exhaustion. Our study suggests that priming T-cells at different stages of life might greatly affect CD8+ T-cell responses towards viral infections.

overall_design: human PBMCs derived from newborns, children adults and older adults were stained using the A2/M158 tetramer followed by tetramer associated magnetic enrichment (TAME) and further stained with a larger phenotypic panel. A2/M158-specific cells were isolated based on their tetramer fluorescence using FACS index-sorting and further analyzed using scRNAseq

first: Katherine

last: Kedzierska

first: Carolien

middle: E

last: van de Sandt

first: Jerome

last: Samir


title: Differences in nucleus accumbens transcriptome are associated with high motivation for palatable reward in C3H/hen male mice exposed to maternal separation [medial prefrontal cortex]

status: Public on Jul 24 2023

city: Jouy-en-Josas

first: Anne

last: GABORY

address: Domaine de Vilvert

country: France

institute: INRAE

summary: The aim of this study was to determine the impact of early life stress on the motivation for a palatable nutritional reward in two mouse strains. Our data showed that MS associated with unpredictable chronic mild stress in lactating dams exacerbated motivation for a palatable food reward (sweetened milk) in both males and females C3H/HeN mice. Interestingly, no effect of MS was reported on motivation in C57Bl/6J mice strain. The transcriptomic analysis revealed that exacerbated motivation in MS C3H/HeN male mice was associated with marked changes in gene expressions in the NAc, whereas no significant changes were reported in PFC or hypothalamus.

overall_design: Gene expression the in the hypothalamus, the nucleus accumbens and the medial prefrontal cortex, to examine the brain changes associated with maternal separation in C3H/HeN mice.

first: Simon

last: BENOIT

first: Mathilde

last: HENRY

first: Sara

last: FNEICH

first: Alexia

last: MATHOU

first: Lin

last: XIA

first: Aline

last: FOURY

first: Claudine

last: JUNIEN

first: Lucile

last: CAPURON

first: Claire

last: Naylies

first: Yannick

last: Lippi

first: Luc

last: JOUNEAU

first: Marie-Pierre

last: MOISAN

first: Cyrille

last: DELPIERRE

first: Muriel

last: DARNAUDERY


title: Differences in nucleus accumbens transcriptome are associated with high motivation for palatable reward in C3H/hen male mice exposed to maternal separation [hypothalamus]

overall_design: Gene expression the in the hypothalamus, the nucleus accumbens and the median prefrontal cortex, to examine the brain changes associated with maternal separation in C3H/HeN mice.


title: Differences in nucleus accumbens transcriptome are associated with high motivation for palatable reward in C3H/hen male mice exposed to maternal separation

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Time-course transcriptome of wild type and PRC2 mutant mouse embryonic stem cells during ground state conversion

status: Public on Jul 18 2023

city: San Antonio

first: Alexey

middle: A

last: Soshnev

state: TX

address: 1 UTSA Cir

department: Neuroscience, Developmental, and Regenerative Biology

country: USA

institute: University of Texas at San Antonio

summary: Mouse embryonic stem cells (mESCs) represent an exceptional model for understanding how transcriptional responses are regulated by signalling pathways during development. Treatment with a cocktail of MEK and GSK3β inhibitors (“2i”) induces ground state pluripotency, characterized by increased self-renewal, reduced DNA methylation, and uniformly high expression of pluripotency markers. Polycomb Repressive Complex 2 (PRC2) is a key developmental regulator controlling stem cell self-renewal and differentiation decisions, and altered expression of PRC2 target genes is a signature of 2i-mediated ground state conversion. Here, we generated a comprehensive RNA sequencing dataset from mESCs subjected to 2i conversion time-course across five time points, representing six population doublings. We analysed two independently derived wild type lines, and two isogenic Cas9-edited lines carrying loss-of-function mutations in core PRC2 subunits Enhancer of Zeste Homolog 2 (Ezh2) or Embryonic Ectoderm Development (Eed). These data may provide a comprehensive resource to understand the temporal patterns of transcriptional responses to MEK and GSK3β inhibitors and explore the role of PRC2 function in regulation of pluripotency circuit.

overall_design: We generated a comprehensive RNA sequencing dataset from mESCs subjected to 2i conversion time-course across five time points, representing six population doublings. We analyzed two independently derived wild type lines, and two isogenic Cas9-edited lines carrying loss-of-function mutations in core PRC2 subunits Enhancer of Zeste Homolog 2 (Ezh2) or Embryonic Ectoderm Development (Eed).

first: Cameron

middle: M

last: Chapa

first: Dustin

middle: R

last: Fetch

first: Amina

last: Jumamyradova


title: Differences in nucleus accumbens transcriptome are associated with high motivation for palatable reward in C3H/hen male mice exposed to maternal separation [nucleus accumbens]

first: Anne

last: GABORY

first: Simon

last: BENOIT

first: Mathilde

last: HENRY


title: Establishment of palbociclib resistant metastatic breast cancer patient-derived xenograft models

status: Public on Jul 10 2023

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

summary: Identify therapeutic vulnerabilities of palbociclib resistance in metastatic breast cancer patient-derived xenograft models and identify key biomarkers that correlate with development of resistance to inform new treatment directions

overall_design: Comparative gene expression profiling analysis of RNA-seq data of palbociclib resistant patient-derived xenograft

first: Nicole

last: Kettner

first: Juliana

last: Navarro-Yepes

first: Xiayu

last: Rao

first: Jing

last: Wang

first: Xian

last: Chen

first: Kurt

middle: W

last: Evans

first: Funda

last: Meric-Bernstam

first: Kelly

middle: K

last: Hunt


title: Establishment of bovine trophoblast stem cells [RNA-seq]

status: Public on Jul 20 2023

city: Gainesville

first: Zongliang

last: Jiang

state: Florida

address: 2033 Mowry Rd, Cancer & Genetics Research Bldg, Room 303

department: Dept. of Animal Sciences

institute: University of Florida

summary: Here we report that a chemical cocktail (LCDM: hLIF, CHIR99021, DiM and MiH) previously reported for extended potential pluripotent stem cells enables the de novo derivation and long-term culture of bovine trophoblast stem cells (TSCs). Bovine TSCs exhibit transcriptomic and epigenetic features characteristic of trophectoderm cells from bovine embryos and retain developmental potency to differentiate into functional trophoblasts in vitro and in vivo

overall_design: RNA-seq analysis was performed using bTSC, differentiates TSC (day2, 3, 4, 5 and 6), Day7 IVF blastocyst (BL) and isolated trophectoderm (TE).

first: Yinjuan

first: Jie

last: Li


title: Epigenetic landscape of Human Brain by Single Nucleus Methylation Sequencing

status: Public on Jul 05 2023

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the human brain is critical to understanding its diverse functions and complex animal behaviors. Single nucleus methylation sequencing was applied to regions of human brains. we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster.

overall_design:
Apply snmC-seq3 to brain regions to identify epigenomic landcape of the adult human brains.

This project includes the following series:
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GSE167577 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167577
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GSE168482 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168482
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GSE168761 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168761
GSE179129 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179129
GSE179610 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179610
GSE179696 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179696
GSE179761 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179761
GSE179971 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179971
GSE180011 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180011
GSE180049 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180049
GSE180293 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180293
GSE195653 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195653
GSE195672 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195672
GSE196225 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196225
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GSE196521 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196521
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GSE199897 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199897
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GSE202341 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202341
GSE202393 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202393
GSE202412 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202412
GSE202908 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202908
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GSE202999 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202999
GSE203103 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203103
GSE203133 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203133
GSE203205 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203205
GSE203373 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203373
GSE203616 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203616
GSE204677 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE204677
GSE204713 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE204713
GSE204792 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE204792
GSE204827 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE204827
GSE205705 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205705
GSE205722 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205722
GSE205760 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205760
GSE205789 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205789
GSE205809 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205809
GSE205820 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205820
GSE207507 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207507
GSE207558 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207558
GSE207583 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207583
GSE207599 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207599
GSE207674 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207674
GSE207694 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207694
GSE207752 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207752
GSE207774 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207774
GSE207953 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207953
GSE208024 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208024
GSE208051 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208051
GSE208392 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208392
GSE208553 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208553
GSE208580 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208580
GSE208643 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208643
GSE208673 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208673
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GSE208780 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208780
GSE209544 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209544
GSE209709 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209709
GSE209576 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209576
GSE209830 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209830
GSE209905 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209905
GSE209930 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209930
GSE210907 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210907
GSE211016 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211016
GSE211139 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211139
GSE211239 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211239
GSE211453 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211453
GSE211564 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211564
GSE212268 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212268
GSE212335 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212335
GSE212426 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212426
GSE212555 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212555
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GSE212764 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212764
GSE212781 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212781
GSE212830 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212830
GSE212850 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212850
GSE212932 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212932
GSE212967 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212967
GSE213027 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213027
GSE216539 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216539
GSE216615 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216615
GSE216696 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216696
GSE216778 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216778
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GSE217228 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217228
GSE217335 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217335
GSE218321 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218321
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GSE219113 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219113
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GSE220431 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE220431
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GSE220857 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE220857
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GSE220984 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE220984
GSE221010 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221010
GSE221040 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221040
GSE221089 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221089
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GSE221368 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221368
GSE221393 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221393
GSE221445 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221445
GSE221452 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221452
GSE221463 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221463
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GSE221523 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221523
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GSE223427 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223427
GSE223431 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223431
GSE223443 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223443
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GSE223696 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223696
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GSE230015 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230015
GSE230070 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230070
GSE230159 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230159
GSE230209 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230209
GSE230312 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230312
GSE230595 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230595
GSE230684 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230684
GSE230823 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230823
GSE231537 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231537
GSE231622 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231622
GSE231722 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231722
GSE231811 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231811
GSE232006 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232006
GSE232116 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232116
GSE232210 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232210
GSE232229 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232229
GSE232321 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232321
GSE232420 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232420
GSE232442 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232442
GSE232492 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232492
GSE232494 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232494
GSE232495 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232495
GSE232499 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232499
GSE233154 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233154
GSE233243 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233243
GSE233325 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233325
GSE234066 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234066
GSE234152 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234152
GSE234175 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234175
GSE234208 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234208
GSE234264 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234264
GSE234321 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234321

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Huaming


title: Establishment of bovine trophoblast stem cells

type: Genome binding/occupancy profiling by high throughput sequencing


title: Establishment of novel murine cell lines with defined mutations for preclinical in vitro and in vivo investigations of syngeneic epithelial ovarian cancer with different histological subtypes and inflammatory profiles

status: Public on Jul 01 2023

city: Pittsburgh

first: Anda

middle: M.

last: Vlad

state: PA

address: 204 Craft Avenue, B403

institute: Magee-Womens Research Institute

summary: Preclinical modeling of epithelial ovarian cancer in immune competent mice progressing to spontaneous tumors is challenging, requiring multiple genetic modifications in the host. We have generated a total of 28 immortalized cell lines with distinct genetic traits. Primary OSE cells were propagated in vitro and reached immortalization after an average of 8-10 months in culture. The cells were further engineered via deletion of Trp53, activation of oncogenic KrasG12D, deletion of Pten tumor suppressor or KrasG12D/Pten-/- combination. Cellular transformation was confirmed in vivo, via orthotopic tumor growth syngeneic hosts. Two different Trp53 null cell lines recapitulate high grade serous histology, Pten deletion triggers aggressive, high grade endometrioid tumors, and cells with dual KrasG12D activation and Pten deletion model carcinosarcoma. The cells express different tumor antigens, secrete various levels of chemoattracting cytokines and chemokines and trigger diverse in vivo inflammation profiles, including intratumoral T and B lymphocyte conglomerates. RNAseq data from 16 cell lines reveal the gene expression profile of several distinct models for high grade serous, endometrioid and carcinosarcoma histotypes. This versatile collection of murine cell lines significantly broadens the preclinical modeling capacity in ovarian cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 28 immortalized and/or transformed mouse ovarian cell lines and some reference cell lines (2F8,2F8cis, ID8, and ID8-VEGF).

first: Lixin

last: Zhang


title: Simultaneous profiling of chromatin architecture and transcription in single cells

status: Public on Jul 08 2023

city: Guangzhou

first: Jiale

last: Qu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Street, Yuexiu District

department: Zhongshan School of Medicine

country: China

institute: Sun Yat-sen University

summary: Three-dimensional (3D) chromatin structure plays a crucial role in development and diseases, which are associated with transcriptional changes. However, given the heterogeneity in single-cell chromatin architecture and transcription, the regulatory relationship between 3D chromatin structure and gene expression is difficult to explain based on the cell populations. Here we developed a single-cell multimodal omics method for simultaneously detecting chromatin architecture and mRNA expression by sequencing (scCARE-seq). Applying scCARE-seq to examine chromatin architecture and transcription from naïve to primed single mouse embryonic stem cells (mESCs), we observed correlated changes between 3D chromatin structure and expression in the cell fate transition. In addition, we defined cell cycle phase of each cell through chromatin architecture extracted by CARE-seq, and found that periodic changes in chromatin architecture were in parallel with transcription during the cell cycle. These findings indicate that scCARE-seq allows comprehensive analysis of chromatin architecture and transcription in the same single cell.

overall_design: chromatin architecture and gene expression profiling by high throughput sequencing

first: Jun

last: Sun

first: Junjun

last: Ding


title: Inverse Agonists of the Androgen Receptor

status: Public on Jun 25 2023

city: Cleveland

first: Hyunmin

last: Kim

state: OH

address: 10900 Euclid Ave.

department: genetics and genome sciences

institute: Case western reserve university

summary: We report the efficacy of androgen receptor inverse agonists (ARIAs) in altering androgen receptor (AR) transcriptional activity. Through RNA-sequencing studies in a panel of prostate cancer cell lines and patient derived xenograft models, we demonstrate ARIAs succcessfully inhibit androgen response gene sets. ChIP-seq and CUT&RUN studies demonstrate H3K27ac decreases at AR-target genes in response to treatment. AR and NCOR1/2 localizes at these regions of acetylation loss. HiChIP further revealed loss of 3D connectivity in reponse to ARIA treatment,

overall_design: RNA-seq studies of prostate cancer (PCa) cell lines or patient derived xenograft models treated with controls or androgen receptor inverse agonists (ARIA). CUT&RUN or ChIP-seq with control or ARIA treatment in PCa cell lines with IP targets including AR, H3K27ac, NCOR1, and NCOR2/SMRT. HiChIP with control or ARIA treatment in PCa cell lines with IP targets of AR, H3K27ac, and CTCF.

first: Berkley

last: Gryder


title: Single-cell transcriptomics of primary human pancreatic islet cells exposed to stress conditions associated with beta-cell failure.

status: Public on Jun 19 2023

city: Leiden

first: Françoise

last: Carlotti

state: FN

address: Albinusdreef 2

department: Internal Medicine

institute: Leiden University Medical Center

summary: Diabetes mellitus (DM) is a chronic disease associated with elevated blood glucose level and resulting from a loss of functional beta-cell mass. The goal of this study is to investigate the response of human pancreatic cells to pathophysiological conditions associated with beta-cell dysfunction, ultimately to identify molecular mechanisms contributing to the development of diabetes. Isolated primary human islets from three non-diabetic donors were exposed in vitro to pro-inflammatory, oxidative, metabolic and endoplasmic reticulum stress for up to 3 days. Subsequently the cells were processed for single-cell RNA sequencing (scRNA-seq). Analysis of the dataset revealed both common and specific molecular response of each pancreatic cell type to the various stress conditions.

overall_design: Pancreatic islet cells from non-diabetic donors were treated with stressors (glucose (22 mM) and/or palmitate (0.5 mM), thapsigargin (0.1 μM), IL-1β (1 ng/ml) and/or IFNγ (1000 U/ml), IFNα (2000 U/ml), hydrogen peroxide (H2O2, 50 μM), FGF2 (100 ng/ml), hypoxia) and untreated as control for 24h and 72h

first: Nathalie

last: Groen

first: Amadeo

last: Munoz-Garcia

first: Eelco

last: de Koning


title: Identification of an outer membrane protease of Rickettsia rickettsii responsible for maturation of surface exposed autotransporters

status: Public on Jul 06 2023

city: Hamilton

first: Ted

last: Hackstadt

state: MT

address: 903 S. Forth St

institute: NIAID

summary: Members of the spotted fever group rickettsia express four large, surface-exposed autotransporters, at least one of which is a known virulence determinant. Autotransporter translocation to the bacterial outer surface, also known as type V secretion, involves formation of a b-barrel autotransporter domain in the periplasm that inserts into the outer membrane to form a pore through which the N-terminal passenger domain is passed and exposed on the outer surface.  Two major surface antigens of Rickettsia rickettsii, are known to be exposed and the passenger domain cleaved from the autotransporter domain.  A highly passaged strain of R. rickettsii, Iowa, fails to cleave these autotransporters and is avirulent.  We have identified a putative peptidase, truncated in the Iowa strain, that when reconstituted into Iowa restores appropriate processing of the autotransporters as well as restoring a modest degree of virulence.

sample_organism:
Rickettsia rickettsii
Chlorocebus aethiops

overall_design: Comparative gene expression profiling analysis of Rickettsia rickettsii infected Vero cells at 4, 24, 48 hours post infection.


title: High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.

status: Public on Jun 03 2023

city: Chicago

first: Ruli

last: Gao

state: IL

address: Simpson Querrey, 7th Floor

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Single cell Nanopore sequencing of full-length RNAs (scNanoRNAseq) is transforming single cell multi-omics analysis, however it is computationally challenged and relying on paralleled short-read sequencing to curate errors. We developed scNanoGPS to calculate same-cell genotypes-phenotypes from scNanoRNAseq data and eliminate dependance on short-reads guidance. To test its accuracy, robustness and applications, we analyzed 6 single nuclei transcriptomes composited of 4 frozen tumors and 2 cancer cell lines. Our results showed that scNanoGPS accurately deconvoluted raw long-reads into single-cells and single-molecules without short-reads guidance and calculated same-cell gene expressions, isoforms, and mutations and copy numbers simultaneously for thousands of cells. In a kidney tumor, we can identify cell-type-specific alternatively spliced genes enriched in important tumorigenic pathways, in addition to expression levels. Further, we detected transcriptome-wide mutations of each cell-type, enabling direct cell-lineage (genotype) and cell-fate (phenotype) alignment to investigate tumor progression. Together, scNanoGPS addresses major computational challenges and largely simplifies experimental workflow of scNanoRNAseq.

overall_design: Single nucleus suspensions of all samples were loaded onto 10X Genomics Chromium instrucment for barcoding with scRNAseq protocol.  A portion of barcoded cDNAs were fragmented to perform paralleled 3'scRNAseq on Novaseq 6000.  Another portion of full-length cDNAs were sent for Oxford Nanopore sequencing on PromethION.

first: Cheng-Kai

last: Shiau

first: Lina

last: Lu

first: Rachel

last: Kieser

first: Kazutaka

last: Fukumura

first: Hsiao-Yun

last: Lin

first: Jie

last: Yang

first: Jason

last: Huse


title: The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells snRNA-Seq

status: Public on May 31 2023

city: Ann Arbor

first: Andrew

last: Lieberman

state: MI

address: 1150 W Medical Center Drive

department: Pathology

institute: University of Michigan

summary: Cholesterol is required for oligodendrocyte maturation and CNS myelination. Here, we demonstrate an essential role for the intracellular cholesterol transporter NPC1 in these processes. NPC1 functions in late endosomes and lysosomes to efflux unesterified cholesterol, and its deficiency causes Niemann-Pick disease Type C, an autosomal recessive lysosomal disorder characterized by progressive neurodegeneration and early death. To identify cell types and pathways affected early in pathogenesis, we performed single nuclear RNA-seq on the forebrain of Npc1-/- mice at P16. This analysis uncovered striking transcriptional changes in the oligodendrocyte lineage during the period of developmental myelination, accompanied by diminished maturation of myelinating oligodendrocytes. Unexpectedly, we identified a significant upregulation of genes associated with neurogenesis and synapse formation in Npc1-/- oligodendrocyte lineage cells, reflecting diminished gene silencing by H3K27me3 and H3K9me3.

overall_design: Nuclei were isolated from the forebrains of  3 WT and 3 Npc1-null mice at P16. Single-nuclear RNA-seq on approximately 10,000 cells from each sample was performed.

first: Thaddeus

middle: J

last: Kunkel

first: Alice

last: Townsend

first: Kyle

last: Sullivan

first: Jean

last: Merlet

first: Daniel

last: Jacobson

middle: P


title: Albumin-binding RNAi Conjugate for Carrier Free Treatment of Arthritis

status: Public on May 30 2023

city: Nashville

first: Juan

last: Colazo

state: TN

address: 2301 Vanderbilt Place PMB 351826

department: Biomedical Engineering

institute: Vanderbilt University

summary: Osteoarthritis (OA) and rheumatoid arthritis (RA) are joint diseases that are associated with pain and lost quality of life. No disease modifying OA drugs are currently available. RA treatments are better established but are not always effective and can cause immune suppression. Here, an MMP13-selective siRNA conjugate (Albumin-binding siMMP13<(EG18L)2) was developed that, when delivered intravenously, docks onto endogenous albumin and promotes preferential accumulation in articular cartilage and synovia of post-traumatic OA (PTOA) and RA (K/BxN) joints. MMP13 expression was diminished upon intravenous delivery of MMP13 siRNA conjugates, consequently decreasing multiple histological and molecular markers of disease severity, while also reducing clinical manifestations such as swelling (RA) and joint pressure sensitivity (RA and OA). Importantly, MMP13 silencing provided more comprehensive OA treatment efficacy than standard of care (steroids) or experimental MMP inhibitors. These data demonstrate the utility of albumin ‘hitchhiking’ for drug delivery to arthritic joints, and establish the therapeutic utility of systemically delivered anti-MMP13 siRNA conjugates in OA and RA.

overall_design:
For the Osteoarthritis treatment studies, groups are either healthy mice (no osteoarthritis) or subjected to an acute PTOA model of noninvasive, repetitive joint loading by subjecting the knee joints of 8-week-old C57BL/6 mice to 250 cycles of compressive mechanical loading at 9N (adapted from Poulet B, et al. Arthritis and rheumatism. 2011. PubMed PMID: 20882669). This procedure was repeated three times per week over a period of 1 week. PTOA groups were either left untreated or treated with MMP13-specific albumin-binding small interfering RNA (siRNA) conjugate. The knee joints were studied 10 days after treatment with subsequent loading cycles still occurring.

For the Rheumatoid Arthritis treatment studies, groups are either healthy mice (no arthritis) or injected with K/BxN serum. K/BxN groups were either left untreated or treated with MMP13-specific albumin-binding small interfering RNA (siRNA) conjugate 2 days after serum transfer. 10 days after serum transfer (8 days after treatment), the hindpaw joints were studied.

first: Craig

middle: L

last: Duvall


title: Integrated single-cell chromatin and transcriptomic analyses of human scalp reveal etiological insights into genetic risk for hair and skin disease

status: Public on May 09 2023

city: Stanford

first: Benjamin

last: Ober-Reynolds

address: 279 Campus Drive West

department: Genetics

institute: Stanford University


title: Dynamic liposomal and transcriptomic profiling reveal the metabolic  network and regulators governing TAGs formation in seeds of safflower

status: Public on May 20 2023

city: Guiyang; Huaxi

first: dan

middle: dan

last: Li

address: Jiaxiunan road

institute: Guizhou university

summary: In this study, depending on quantitative liposome and transcriptomic analyses, we unveiled safflower seed lipidic landscapes at 5 different developmental stages of seeds and revealed a parallel classification of 417 lipid compounds and their co-expressed genes into 7 distinct lipidic metabolites vs gene modules (MM vs GM). An essential transcriptional regulatory network for major lipid compounds changes that occurred throughout the seed growth cycle was constructed via integrative bioinformatics coupled with functional genomic assays. Sixteen transcription factors were identified that regulate the accumulation of triacylglycerols (TAGs) and fatty acids (FAs). Our findings thus shed light on the seeds of safflower metabolic regulatory network involved in the biosynthesis of major lipid compounds and provide a prospective resource for the designed improvement of oilseed quality.

overall_design: Seeds in 5 different developmental stages were executed the analysis by lipisome and transcripome, three biologycal duplicates.

first: Dandan

first: Qing

last: Wang

first: Jiang

last: Chen

first: Wei

last: Wu


title: Chidamide combined with cytarabine plays a role in the treatment of AML by down-regulating the MYC-RRP9 pathway

status: Public on May 12 2023

city: chengdu

first: qing

last: li

state: Sichuan

address: No.37 Guoxue Lane, Wuhou District

department: Hematology

institute: West China Hospital of Sichuan University

summary: To provide a new treatment strategy for patients with acute myeloid leukemia (AML), we investigated the therapeutic effect and mechanism of chidamide combined with cytarabine in AML.

overall_design: RNA-seq was performed after 24 h of treatment of MV4-11 cells with chidamide and cytarabine alone or in combination, and the obtained data were analyzed for gene expression profiling.

first: Yu


title: Comparative transcriptome analysis between six adipose depots in buffaloes

status: Public on May 17 2023

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

summary: To characterize the transcriptome differences between different adipose depots, a total of 36 adipose samples were used for high-throughput sequencing. At last, about 23,000 transcripts were identified.

overall_design: A total of 36 adipose samples were used for RNA sequencing, including 3 subcutaneous adipose tissue (SAT) depots (back subcutaneous adipose tissue, BSAT; sternum subcutaneous adipose tissue, SSAT; inguinal adipose tissue, IAT) and 3 visceral adipose tissue (VAT) depots (omental adipose tissue, OAT; pericardial adipose tissue, PCAT; perirenal adipose tissue, PRAT) in 6 buffaloes.

first: Jieping

last: Huang


title: miRNA sequence analysis of primary lesions, brain metastases, and normal lung tissues in lung adenocarcinoma

status: Public on Apr 26 2023

city: Kagoshima

first: Yuya

last: Tomioka

country: Japan

institute: Kagoshima University

type: Non-coding RNA profiling by high throughput sequencing

summary: We obtained primary lesions, brain metastases, and normal lung tissues from lung adenocarcinoma patients. Next generation sequencing was performed to assess the expressions of miRNA in these specimens.

overall_design: A total of 15 samples (5 normal lung tissues, 5 primary tumors, and 5 brain metastases) were analyzed using small RNA sequencing technology to generate a miRNA expression signature.

first: Kengo

last: Tanigawa

first: Naohiko

last: Seki


title: Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos

status: Public on Apr 28 2023

city: Hull

first: Lauric

last: Feugere

address: Cottingham Road

department: Biological and Marine Sciences

country: United Kingdom

institute: University of Hull

summary: Heat alters biology from molecular to ecological levels, but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here, we provide a comprehensive picture of the molecular signatures of this process, by integrating multiomic and phenotypic data. In individual zebrafish embryos, repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow-down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur-containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response, extracellular signalling, glycosaminoglycan/keratan sulphate, and lipid metabolism. Consequently, non-heat-exposed receivers (exposed to stress metabolites only) experienced accelerated catch-up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most, mediated by apelin signalling. Our results prove the concept of indirect heat-induced stress propagation towards naive receivers, inducing phenotypes comparable to those resulting from direct heat exposure, but utilising distinct molecular pathways. Group-exposing a non-laboratory zebrafish line, we independently confirm that the glycosaminoglycan biosynthesis-related gene chs1, and the mucus glycoprotein gene prg4a, functionally connected to the candidate stress metabolite classes sugars and phosphocholine, are differentially expressed in receivers. This hints at the production of Schreckstoff-like cues in receivers, leading to further stress propagation within groups, which may have ecological and animal welfare implications for aquatic populations in a changing climate.

overall_design: Zebrafish embryos were exposed for 24 hours to thermal stress (TS) and stress metabolites (SM) released by heat-stressed zebrafish embryos, in a two-way factorial design (TSxSM), yielding four experimental treatments: fresh medium at 27°C (control C), fresh medium with thermal stress (TS), medium containing stress metabolites at 27°C (SM), and medium containing stress metabolites with thermal stress (TS+SM). Each treatment contains n = 3 biological replicates, each representing the pooled gene expression from 20 individual embryos.

first: Adam

last: Bates

first: Timothy

last: Emagbetere

first: Emma

last: Chapman

first: Linsey

last: Malcolm

first: Kathleen

last: Bulmer

first: Jörg

last: Hardege

first: Pedro

last: Beltran-Alvarez

first: Katharina

middle: C

last: Wollenberg Valero


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance (mouseRNAseq)

status: Public on May 02 2023

city: Cambridge

first: Sara

middle: Jane

last: Dubbury

state: MA

address: 500 Main Street, 76-417

department: Koch Institute

institute: MIT

summary: RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We find disrupted nuclear RNA surveillance is oncogenic. Cyclin Dependent Kinase 13 (CDK13) is mutated in melanoma and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. Mutant CDK13 fails to activate nuclear RNA surveillance, causing aberrant protein-coding transcripts to be stabilized and translated. Forced aberrant RNA expression accelerates melanoma in zebrafish. We find recurrent mutations in genes encoding nuclear RNA surveillance components in many malignancies, establishing nuclear RNA surveillance as a tumor-suppressive pathway. Activating nuclear RNA surveillance is crucial to avoid accumulation of aberrant RNAs and their ensuing consequences in development and disease.

overall_design: V6.5 mouse embryonic stem cells with endogenous Cdk13 knock out complemented by doxycycline (Dox)-inducible Flag- HA- epitope tagged Cdk13 transgene (Cdk13△) were grown in the presence of Cdk13 (+Dox) or were depleted of Cdk13 (-Dox). RNA sequencing experimental design: PolyA-selected RNA was isolated from two independently derived Cdk13△ clones each in biological duplicate for cells maintained in Dox (+Dox), withdrawn from Dox for 48 hours (-Dox 48hrs), or withdrawn from Dox for 72 hours (-Dox 72hrs). A total of 12 libraries were prepared and sequenced.

first: Paul

last: Boutz

first: Phillip

last: Sharp


title: Vascularization of pluripotent stem cell-derived islet organoids improves β-cell function

status: Public on May 01 2023

city: Irvine

first: Christopher

last: Hatch

address: 2400 Biological Sciences III

institute: University of California, Irvine

summary: Blood vessels play a critical role in pancreatic islet health and function, yet current culture methods to generate islet organoids from human pluripotent stem cells (SC-islets) lack a vascular component. Here, we engineered 3D vascularized SC-islet organoids by assembling SC-islet cells, human primary endothelial cells (ECs) and fibroblasts both in a non-perfused model and a microfluidic device with perfused vessels. Vasculature improved stimulus-dependent Ca2+ influx into SC-β-cells; a hallmark of β-cell function that is blunted in non-vascularized SC-islets. We show that an islet-like basement membrane is formed by vasculature and contributes to the functional improvement of SC-β-cells. Furthermore, cell-cell communication networks based on scRNA-seq data predicted BMP2/4-BMPR2 signaling from ECs to SC-β-cells. Correspondingly, BMP4 augmented the SC-β-cell Ca2+ response and insulin secretion. The here-described vascularized SC-islet models will enable further studies of crosstalk between β-cells and ECs and serve as an in vivo-mimicking platform for disease modeling and therapeutic testing.

overall_design: In this analysis, we used single-cell RNA-seq (scRNA-seq) to profile 1809 vasculature forming cells (endothelial cells and fibroblasts). We annotate cell types based on the known marker genes. Through cell-cell communication network analyses, we predicted heterotypic cell-cell interactions between beta cells, endothelial cells and fibroblasts.

first: Stephanie

last: Hachey

first: R

middle: H

last: Bender

first: Duc

middle: T

last: Phan

last: Hughes


title: Integrated single-cell chromatin and transcriptomic analyses of human scalp reveal etiological insights into genetic risk for hair and skin disease [scRNA-Seq]

first: Benjamin

last: Ober-Reynolds

summary: In this study, we use single-cell ATAC sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) to map chromatin accessibility and gene expression in human scalp samples from healthy patients and patients with alopecia areata

overall_design: We generated single-cell ATAC-seq and single-cell RNA-seq libraries from human scalp tissue from three sources: punch biopsy samples from healthy control volunteers (C_PB, n = 3), punch biopsies from patients with clinically active alopecia areata (AA, n = 5), and discarded normal peripheral surgical tissue from patients undergoing dermatologic surgeries on the scalp (C_SD, n = 7)


title: TGFβ blockade in pancreatic cancer enhances sensitivity to combination chemotherapy

status: Public on Apr 23 2023

city: Boston

last: Dougan

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

summary: We evaluated the TGFβ blocking antibody NIS793 in combination with either gemcitabine/n(ab)-paclitaxel or FOLFIRINOX chemotherapy in orthotopic pancreatic cancer. Blockade of TGFβ with chemotherapy reduced tumor burden in poorly immunogenic pancreatic cancer, without affecting the metastatic rate of cancer cells. TGFβ blockade decreased total aSMA+ fibroblasts but had minimal effect on fibroblast heterogeneity.

overall_design: 6694c2 tumor cells were inoculated orthotopically into C57BL/6 mice treated with αTGFβ or Isotype, +/- GnP or FOLFIRINOX (5mg/kg oxaliplatin, 75mg/kg leucovorin, 50mg/kg irinotecan, and 75mg/kg 5-FU; dosed by i.v. at day 3 and day 6). Tumors were harvested on day 14, digested, and enriched for fibroblasts using antibodies against CD31 and CD90, followed by positive selection with magnetic beads and single cell transcriptional analysis. n = 5 tumors pooled per group.

first: Li

last: Qiang

first: Megan

last: Hoffman

first: Lestat

last: Ali

first: Jaime

middle: I

last: Castillo Silva

first: Lauren

last: Kageler

first: Ayantu

last: Temesgen

first: Patrick

last: Lenehan

first: S

last: Wang

first: Elisa

last: Bello

first: Victoire

last: Cardot-Ruffino

first: Annan

last: Yang

first: Michael

first: Andrew

last: Aguirre

first: Srivatsan

last: Raghavan

first: Marc

last: Pelletier

first: Viviana

last: Cremasco


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [humanpolyARNAseq]

status: Public on Apr 21 2023

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

overall_design: 3' RNA-seq data from the A375 melanoma cell line with perturbations of genes encoding PAXT modulators

last: Insco

first: Brian

last: Abraham

first: Sara

last: Dubbury

first: Ines

last: Kaltheuner

first: Sofia

last: Dust

first: Constance

last: Wu

first: Kevin

middle: Y

last: Chen

first: David

last: Liu

first: Stanislav

last: Bellaousov

first: Anna

last: Cox

first: Benjamin

last: Martin

first: Tongwu

last: Zhang

first: Calvin

middle: G

last: Ludwig

first: Tania

last: Fabo

first: Rodsy

last: Modhurima

first: Dakarai

last: Esgdaille

first: Telmo

last: Henriques

last: Brown

first: Stephen

last: Chanock

first: Matthias

last: Geyer

first: Karen

last: Adelman

first: Phillip

last: Sharp

first: Paul

last: Boutz

first: Leonard

last: Zon


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [zf3primeseq]

first: Richard

middle: A

last: Young

first: Megan

last: Insco

first: Brian

last: Abraham

first: Sara

last: Dubbury

first: Ines

last: Kaltheuner

first: Sofia

last: Dust

first: Constance

last: Wu

first: Kevin

last: Chen

last: Liu

middle: E


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [humanTTseq]

first: David

first: Stanislav

last: Bellaousov

first: Anna

middle: M

last: Cox

first: Benjamin

last: Martin

first: Tongwu

last: Zhang

first: Calvin

last: Ludwig

first: Tania

last: Fabo

first: Rodsy

last: Modhurima

last: Esgdaille

last: Henriques


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [humanMut3primeseq]

last: Young

last: Insco

first: Dakarai

first: Telmo

last: Brown

first: Stephen

last: Chanock

first: Matthias

last: Geyer

first: Karen

last: Adelman

first: Phillip

last: Sharp

first: Paul

last: Boutz

first: Leonard

last: Zon


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [humanRibominusRNAseq]

first: Richard

first: Megan

first: Brian

last: Abraham

first: Sara

last: Dubbury

first: Ines

last: Kaltheuner

first: Sofia

last: Dust

first: Constance

last: Wu

first: Kevin

last: Chen

last: Liu

last: Bellaousov

last: Cox


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance (zfRNAseq)

last: Young

overall_design: RNA-Seq in zebrafish melanoma expressing EGFP or mutant CDK13

last: Insco

first: David

first: Stanislav

first: Anna

first: Benjamin

last: Martin

first: Tongwu

last: Zhang

first: Calvin

last: Ludwig

first: Tania

last: Fabo

first: Rodsy

last: Modhurima

last: Esgdaille

last: Henriques


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance (zfChIPseq)

last: Abraham

last: Dubbury

first: Dakarai

first: Telmo

last: Brown

first: Stephen

last: Chanock

first: Matthias

last: Geyer

first: Karen

last: Adelman

first: Phillip

last: Sharp

first: Paul

last: Boutz

first: Leonard

last: Zon


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance (humanChIPseq)

first: Richard

last: Young

overall_design: ChIP-Seq in human melanoma cells expressing CLOVER or mutant CDK13

first: Megan

last: Insco

first: Brian

first: Sara

first: Ines

last: Kaltheuner

first: Sofia

last: Dust

first: Constance

last: Wu

first: Kevin

last: Chen

last: Liu

last: Bellaousov

last: Cox


title: Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance

sample_organism:
Danio rerio
Homo sapiens
Mus musculus

platform_organism:
Danio rerio
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

last: Abraham

last: Dubbury

first: David

first: Stanislav

first: Anna

first: Benjamin

last: Martin

first: Tongwu

last: Zhang

first: Calvin

last: Ludwig

first: Tania

last: Fabo

first: Rodsy

last: Modhurima

last: Esgdaille

last: Henriques


title: Differential Deep RNA Sequencing Revealed Various Bacterial Infections and Host Responses in Inflammatory Cardiomyopathy

status: Public on Apr 10 2023

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

summary: We reported 4 single-sample cases and 3 control-sample cases of inflammatory cardiomyopathy using deep RNA-seq for detection of pathogenic agents. We identified various bacterial infections, analyzed genetic variants in patients and their differential gene expression caused by these infections in control-sample cases.

overall_design: Deep RNA-seq of lesioned sample for detection of pathogenic agents in single-sample cases; differential deep RNA-seq of both lesioned and control samples for detection of pathogenic agents and characterization of host response in control-sample cases.


title: Effect of repeated optogenetic stimulation on chromatin accessibility in the mouse dentate gyrus [ATAC-seq]

status: Public on Mar 31 2023

city: Toyoake

first: Tomoyuki

last: Murano

address: 1-98 Dengakugakubo, Kutsukake-cho

institute: Fujita Health University

summary: To investigate the effect of repeated neural overactivation in the chromatin accessibility of dentate gyrus neurons, we optogenetically stimulated mouse dentate gyrus repeatedly.

overall_design:
We then performed chromatin accessibility profiling using data obtained from ATAC-seq of mice in two different stimulation conditions and no stimulation condition.
Comparative chromatin accessibility profiling of ATAC-seq data for mouse dentate gyrus neurons in three differnet conditions (No Stimulation, Stimx3+2wks, and Stimx10+2wks).


title: Jakyak-gamcho-tang ameliorates dexamethasone-induced muscle atrophy and muscle dysfunction

status: Public on Mar 21 2023

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

summary: This SuperSeries is composed of the SubSeries listed below.


title: IL-13 promotes sensory-sympathetic neurons crosstalk in asthma [RNA-seq II]

status: Public on Mar 23 2023

city: Montréal

first: Theo

last: Crosson

state: Quebec

address: 2900 Boulevard Edouard Montpetit

country: Canada

institute: Université de Montréal

overall_design: RNA sequencing of cultured JNC nociceptors exposed to BDNF, IL-1β, and TNF-α.

first: Shreyas

last: Bhat

first: Jo-Chiao

last: Wang

first: Clara

last: Salaün

first: Katiane

last: Roversi

first: Sebastien

last: Talbot


title: A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

status: Public on Mar 25 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

summary: Extensive studies of the model plant Arabidopsis has enabled a deep understanding of organs and tissues throughout plant development. Yet, a fundamental understanding of cell types and states across organs and development is still lacking. Here, we present a single-nucleus transcriptome atlas of Arabidopsis seed-to-seed development encompassing diverse tissues across ten developmental time points. Analysis of over 400,000 nuclei revealed 183 major and 653 subclusters that demarcate cell type and state. Cross-organ analyses revealed that the transcriptional identity of many cell types is conserved across development but influenced by the organ of origin and developmental timing. In addition, groups of transcription factors were enriched and uniquely expressed in individual organs and time points, suggesting developmental gatekeeping of transcription factor activation. Finally, we employed spatial transcriptomics to validate our findings in the highly complex silique organ.

overall_design: Using a standardized nucleus extraction method, single-nucleus RNA seq was performed on whole Arabidopsis organs and tissues, including seeds, seedlings, rosettes, stems, flowers, and siliques, at ten developmental timepoints throughout the entire lifecycle of the plant. A minimum of four single-nucleus RNA-seq runs were performed per tissue and timepoint.

first: Travis

last: Lee

first: Tatsuya

last: Nobori

first: Natanella

last: Illouz-Eliaz

first: Bruce

last: Jow

last: Nery


title: Integrated single-cell chromatin and transcriptomic analyses of human scalp reveal etiological insights into genetic risk for hair and skin disease [scATAC-Seq]

first: Benjamin

last: Ober-Reynolds


title: Transcriptional profile regulated by 1,25-dihydroxyvitamin D (Calcitriol) in primary Human Monocyte-Derived Macrophages infected by zika virus

status: Public on Mar 15 2023

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

summary: ZIKA virus (ZIKV) infection is characterized by alterations in gene expression profile on host cells that consequently lead to an immune response. Here, we used RNA sequencing to analyze the mRNA and miRNA expression profile in human monocyte-derived macrophages (MDMs) differenitated in presenece of 1,25-dihydroxyvitamin D (Calcitriol) and infected with a Zika virus strain COL345Si-Asian at MOI of 5 and analized 24 hpi.

overall_design: Human peripheral blood mononuclear cells (PBMCs) from blood samples of 4 healthy donors mixed with 2% EDTA, were isolated through density gradient with Lymphoprep. Monocytes-derived Macrophages (MDM) were obtained from total PBMCs by adherence to the plastic and differentiation to macrophages was allowed to occur for 6 days in RPMI-1640 medium supplemented with 10% (v/v) FBS, 4 mM L-glutamine, 0.3% (v/v) NaCO3, and 1% (v/v) antibiotic-antimycotic solution 100X (complete medium), at 37 °C and 5% CO2, without growth factors. Additionally, MDMs were differentiated in presence of 1,25 di-hydroxyvitamin D3 to obtain D3-MDM. 1,25 di-hydroxyvitamin D3 was added to the culture media at a final concentration of 1 nM and replenished every 24 h for six days. MDM and D3-MDM monolayers were washed with warm PBS and were infected with  Zika virus strain COL345Si-Asian at MOI of 5. Three hpi, the cells were washed with warm PBS to remove unbound virus. Then 24 hpi, macrophage monolayers were used for sample collection.

first: Geysson

last: Fernandez

first: Silvio

last: Urcuqui-Inchima


title: Jakyak-gamcho-tang ameliorates dexamethasone-induced muscle atrophy and muscle dysfunction [C2C12]

last: Park

summary: Jakyak-gamcho-tang (JGT) is a herbal medicine that has been traditionally prescrived for pain control including muscular pain.  This transcriptome analysis aims to investigate the changes in global gene expression profile in differentiated murine C2C12 myotube cells treated with JGT extract.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for C2C12 myotubes treated with increasing doses of JGT (20, 100, and 500 μg/mL) or vehicle control (0.1% DMSO) for 24 hrs.
The dried powders of Paeoniae radix and Glycyrrhizae radix et rhizoma at 1:1 weight ratio was subjected to extraction in a 10-fold volume of hot distilled water for 3 h in a reflux extraction system.  The extract solution was filtered through a 53 micrometer mesh filter, concentrated in a rotary evaporator system and lyophilized in a freeze dryer to get a final JGT extract.  The JGT stock solution was prepared at 10 mg/mL in PBS containing 2% DMSO.

first: Seongwon

last: Cha

first: No

middle: S

last: Kim


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [SC-islet snRNA-seq]

status: Public on Mar 02 2023

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and from primary childhood and adult pancreas for comparison. We delineate major cell types, define their regulomes, and describe spatiotemporal regulatory relationships between transcription factors. CDX2 emerged as a regulator of enterochromaffin-like cells, which we show resemble a previously unrecognized, transient CDX2-expressing β-cell-related population in fetal pancreas, arguing against a non-pancreatic origin as proposed. Furthermore, we observe insufficient activation of signal-dependent transcriptional programs during in vitro β-cell maturation and identify sex hormones as drivers of childhood β-cell proliferation. Altogether, our analysis provides a comprehensive understanding of cell fate acquisition in stem cell-derived islets and a framework for manipulating cell identities and maturity.

overall_design: In this analysis, we used single nucleus RNA-seq (snRNA-seq) to profile 28,059 cells during human pluripotent stem cell differentiation into islets at D21, D32, D39. We characterized transcriptome signatures of pancreatic progenitors, endocrine progenitors, and fully differentiated SC-islet endocrine cell types. We integrated this data with snATAC-seq data from the same batch of differentiation for gene regulatory network (GRN) analysis. Comparing this SC-islet GRN to similarly integrated datasets from primary endocrine cells from childhood and adult human pancreas allowed us to identify gene regulatory differences between SC-islet cell types and primary childhood and adult islet cell types.


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [SC-islet_snATAC]

overall_design: In this analysis, we used single nucleus ATAC-seq (snATAC-seq) to analyze 65,255 cells during human pluripotent stem cell differentiation into islets at D11, D14, D21, D32, D39. We characterized accessible chromatin profiles of pancreatic progenitors, endocrine progenitors, and fully differentiated SC-islet endocrine cell types. Through integrative analysis with scRNA-seq data from the same batch of differentiation, we established a gene regulatory network to describe gene regulatory mechanisms of islet lineage progression in vitro.


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain

status: Public on Apr 13 2023

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design:
Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain.

This project includes the following series:
GSE213221 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213221
GSE213259 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213259
GSE213353 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213353
GSE215147 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215147
GSE215213 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215213
GSE215342 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215342
GSE215422 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215422
GSE215779 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215779
GSE215809 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215809
GSE215913 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215913
GSE215958 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215958
GSE215995 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215995
GSE216014 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216014
GSE216041 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216041
GSE216188 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216188
GSE216224 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216224
GSE216240 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216240
GSE216300 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216300
GSE216331 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216331
GSE216436 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216436
GSE230219 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230219
GSE230220 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230220
GSE230221 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230221
GSE230222 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230222
GSE230223 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230223
GSE230224 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230224
GSE230225 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230225
GSE230226 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230226
GSE230242 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230242
GSE230248 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230248
GSE230335 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230335
GSE230336 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230336
GSE230338 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230338
GSE230339 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230339
GSE232593 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232593
GSE232663 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232663
GSE232668 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232668
GSE232768 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232768
GSE232909 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232909
GSE232945 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232945
GSE233185 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233185
GSE233268 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233268
GSE234950 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234950
GSE235004 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235004
GSE236274 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236274
GSE236428 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236428
GSE236451 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236451
GSE236574 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236574
GSE236583 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236583
GSE236612 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236612
GSE236699 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236699
GSE236893 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236893
GSE236973 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236973
GSE237288 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237288
GSE237325 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237325
GSE237437 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237437
GSE237455 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237455
GSE237580 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237580
GSE237699 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237699
GSE237781 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237781

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Cell type-specific and disease-associated eQTL in the human lung

status: Public on Mar 20 2023

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

summary: Understanding how the genetic control of gene expression varies between cell types and contexts is key for our understanding of complex traits including disease. To this end, we leveraged single cell RNA sequencing (scRNA-seq) to characterize the genetic architecture of gene regulation in an organ with one of the most cellularly diverse organs, the human lung. We profile these effects across two conditions, tissue samples from healthy controls and patients with pulmonary fibrosis (PF), a chronic, progressive condition characterized by the scarring of lung tissue. In total, we have generated expression profiles of 475,047 cells from primary human lung tissue from 116 individuals, including 67 with PF and 49 unaffected donors. Employing a pseudo-bulk approach, we have mapped expression quantitative trait loci (eQTL) across 38 cell types, identifying shared and cell type-specific effects. Further, we identify disease-interaction eQTL demonstrating this class of associations are more likely to be cell-type specific and linked to key drivers of dysregulation in PF. Finally, we connect PF risk variants implicated by genome-wide association studies to their regulatory targets in disease-relevant cell types. This study represents the first use of scRNA-seq to identify cell type level eQTL in the human lung, and one of only a small number of studies to carry out these characterizations in solid tissues. These results provide valuable insights into lung biology and disease risk.

overall_design: Lung tissue samples were collected from a total of 60 individuals, including 33 ILD cases and 27 nonfibrotic controls, and processed as previously described by Habermann et al (Sci Adv 6, eaba1972, 2020): ILD tissue samples were obtained from lungs removed at the time of lung transplantation at either Vanderbilt University Medical Center (VUMC) or the National Thoracic Institute (NTI). Control tissue samples were obtained from lungs declined for organ donation either at the Donor Network of Arizona (DNA) or VUMC. Tissue sections were taken from multiple peripheral (within ~2 cm of the pleural surface) regions in each lung. For ILD lungs, representatively diseased areas were selected on the basis of preoperative chest CT, while for control lungs, the most normal-appearing region was identified by gross inspection and selected for biopsy. For ILD lungs, diagnoses were determined according to the American Thoracic Society/European Respiratory Society consensus criteria.

first: Heini

last: Natri

first: Christina

middle: B

last: Del Azodi

first: Lance

last: Peter

first: Chase

last: Taylor

first: Sagrika

last: Chugh

first: Robert

last: Kendle

first: Jonathan

last: Kropski

first: Davis

last: McCarthy


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [Childhool snRNA-seq]

first: Maike

last: Sander

overall_design: In this analysis, we used single nucleus RNA-seq (snRNA-seq) to analyze cells from childhood human pancreas (age: 13 months to 9 years). We obtained transcriptomic signatures  from both exocrine and endocrine pancreas, but focused on α-, β-, δ- and γ-cells (3,296 cells in total) for downstream analysis. We integrated these data with snATAC-seq data from the same donors for gene regulatory network (GRN) analysis. Comparing this primary childhood GRN to similarly integrated datasets from human pluripotent stem cell-derived islets and primary adult human pancreatic endocrine cells allowed us to identify gene regulatory differences between SC-islet cell types and primary childhood and adult islet cell types.


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [childhool scRNA-seq]

overall_design: In this analysis, we used single cell RNA-seq (scRNA-seq) to analyze cells from primary childhood human islets (age: 2 years). We obtained transcriptomic signatures from exocrine and endocrine cells, but focused on α-, β-, δ- and γ-cells (250 cells in total) for downstream analysis. We used this dataset to demonstrate similarity between snRNA-seq and scRNA-seq data, and to justify the use of snRNA-seq data for our network analysis.


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [Childhood snATAC-seq]

overall_design: In this analysis, we used single nucleus ATAC-seq (snATAC-seq) to analyze cells from childhood human pancreas (age: 13 months to 9 years). We characterized accessible chromatin profiles from both exocrine and endocrine pancreas, but only focused on α-, β-, δ- and γ-cells (6,840 cells in total) for downstream analysis. We integrated this data with snRNA-seq data from the same donors for gene regulatory network (GRN) analysis. Comparing this primary childhood GRN to similarly integrated datasets from SC-islets and primary adult human pancreatic endocrine cells allowed us to identify gene regulatory differences between SC-islet cell types and primary childhood and adult islet cell types.


title: IL-13 promotes sensory-sympathetic neurons crosstalk in asthma

first: Theo

last: Crosson


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [SC-islet scRNA-seq]

overall_design: In this analysis, we used single cell RNA-seq (scRNA-seq) to profile 25,686 cells during human pluripotent stem cell differentiation into islets at D11, D14, D21, D32, D39. We characterized transcriptomic signatures of pancreatic progenitors, endocrine progenitors, and fully differentiated SC-islet endocrine cell types. Through integrative analysis with snATAC-seq data obtained from the same batch of differentiation, we established a gene regulatory network to describe gene regulatory mechanisms of islet lineage progression in vitro.


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [CDX1 snRNA-seq]

overall_design: In this analysis, we used single nucleus RNA-seq (snRNA-seq) to profile 11,201 cells from D21 SC-islets derived from wild type (WT) or CDX2 knockout (CDX2 KO) H1 hESC lines. In both cell lines, we characterized transcriptomic signatures of pancreatic progenitors, endocrine progenitors, and fully differentiated SC-islet endocrine cell types. We found a significant reduction of SC-β-cell and SC-EC populations, which are compensated for by an increase of SC-α-cell numbers. Comparing WT and CDX2 KO transcriptomes in each cell type, we identified lower expression levels of genes involved in serotonin synthesis in CDX2 KO SC-ECs.


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [CDX2 ChIP-seq]

overall_design: In this analysis, we used ChIP-seq to assess genomewide CDX2 binding in day 21 human pluripotent stem cell-derived islets. Two biological replicates were included and raw chromatin without CDX2 antibody co-immunoprecipitation (input) was used as background control.


title: Single-cell transcriptomics of chimeric antigen receptor (CAR) T cell infusion products

status: Public on Mar 12 2023

city: Houston

first: Navin

last: Varadarajan

address: 4722 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

summary: Adoptive immunotherapy with T cells expressing chimeric antigen receptors (CARs) for B-cell malignancies serves as a model for identifying subsets with superior clinical activity. We profiled the infusion products (IP) of 9 patients with large B-cell lymphoma (LBCL) using scRNA-sequencing to reveal the therapeutic potential of CD19-specific CAR+ T cells. ScRNA-seq demonstrated that T cells from responders were enriched in pathways related to T-cell killing, migration and actin cytoskeleton, and TCR clustering.

overall_design:
Leftover CD19-targeted CAR T cells from patients with LBCL were analyzed using scRNA sequencing to determine the differences between the responders and non-responders to the therapy in terms of gene expression.
Total of 9 samples: 5 patients with complete response (CR), 2 patients with progressive disease (PD), and 2 patients with partial response (PR) after 3 months of follow-up after the therapy.
After a 6-month follow-up, the responses were as follows:
4 patients with complete response (CR), 3 patients with progressive disease (PD), and 2 patients with partial response (PR)

first: Ali

last: Rezvan


title: Differential Expression of MED12-Associated Coding RNA 2 transcripts in Uterine Leiomyomas

status: Public on Mar 01 2023

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

summary: The objective of this study was to elucidate the expression profile of coding RNA transcripts in leiomyomas with and without MED12 mutation and their paired myometrium.

overall_design: Comparative gene expression profiling analysis of RNA-seq data based on MED12 mutation status in 19 paired myometrim and leiomyoma specimens.

first: Tsai-Der

last: Chuang

first: Jianjun

last: Gao

first: Derek

last: Quintanilla

first: Hayden

last: McSwiggin

first: Drake

last: Boos

first: Wei

last: Yan


status: Public on Feb 28 2023

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

summary: Gynogenetic development in fish is induced by activation of eggs with irradiated spermatozoa followed by exposure of the activated eggs to the temperature or high hydrostatic pressure (HHP) shock that prevents 1st cell cleavage. Produced specimens are fully homozygous fish also known as Doubled Haploids. Gynogenetic DH individuals might be used aquaculture and developmental biology unfortunately; the potential application of DHs is limited by a rather low survival rate of such specimens. However, observed variation in the survival rates of the gynogenetic embryos originated from different clutches suggests that eggs from some females have increased ability for gynogenetic development than others. Taking into account that first 10 cell cleavages in the fish embryos rely on the maternal RNA, it is tempting to assume that the ova showing such a vast difference in potential for gynogenesis may have also had different biological characteristics including alterations in maternal gene expression profiles. If so, then genes that up- or down –regulated expression in eggs increases competence for gynogenetic development in trout might be considered as candidate genes for gynogenesis in rainbow trout. Thus, the main goal of the project is identification of genes that increase ability of rainbow trout eggs for gynogenetic development. Within the project, we tried to verify following hypotheses: 1. Eggs from different females have different potential for gynogenesis in rainbow trout. 2. Eggs with different ability for gynogenetic development with all maternal inheritance have different biological characteristics including morphology and anti-ROS enzyme activities. 3. Eggs with increased competence for gynogenesis have altered transcriptomic profiles. 4. There are some particular genes that altered expression in trout eggs enable development of gynogenetic embryos. Gynogenetic rainbow trout specimens were produced in the course of activation of eggs with UV-irradiated spermatozoa and High Hydrostatic Pressure shock (HHP) applied around 1st cell cleavage. Eggs from several females were used in the experiment. Survival rates of gynogenetic rainbow trout was monitored since fertilization. Quality of eggs was examined by assessment of their morphology and activity of anti-ROS (reactive oxygene species) enzymes. Transcriptome of eggs showing increased and decreased developmental competence for gynogenesis was analyzed using RNA-seq approach and results compared to find out any alterations related to survival of gynogenetic trout.

overall_design:
Rainbow trout eggs originated from 7 females were stripped. Eggs from each female were divided into two batches and fertlized separately by the UV-irradiated (G) and non-irradiated sperm to develop into gynogenetic (G) and normal (F) (control) offspring. Samples of eggs from each female and each batch were collected and stored in RNA later for the RNA extraction. Eggs fertilized with UV-irradiated sperm were exposed for high hydrostatic pressure shock to recover diploid state in gynogenetically activated eggs. Provided within such procedure zygotes were fully homozygoous gynogenetic Doubled Haploids with only maternal chromosomes. Eggs from both, gynogenetic and control groups were incubated to monitor development of embryos. Survival before hatching and after hatching was assessed. RNA was extracted from collected eggs and their transcriptomic profiles have been provided. Expression profiles of maternal RNA in eggs from each batch and group were compared with the survival of embryos to find out any connection between increased efficiency of gynogenesis and expression of particular maternal transcripts. Genes with altered expression in relation to high survival of Doubled Haploids would be treated as candidate genes realted with increased competence of eggs for gynogenesis.

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Grant number: 2020/39/B/NZ9/00865

Title: Fishing for genes that affect efficiency of gynogenesis in rainbow trout (Oncorhynchus mykiss)

Name of the funding source: National Science Center (Poland)
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first: Konrad

last: Ocalewicz

first: Igor

last: Jasielczuk

first: Tomasz

last: Szmatoła


title: Single cell RNA-seq (scRNA-seq) of 48h GCBC cultures with either of these two stimuli or with the combination of IL-21R/CD40 and BCR stimulation.

status: Public on Feb 16 2023

city: Pittsburgh

first: Mark

last: Shlomchik

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary:
Purpose:Flow cytometric analysis showed that after 48h of culture with T cell- and Ag-derived stimuli, GCBC alter their TF expression and begin to differentiate. However, only a subset of cells undergoes this process, for reasons that are unclear. To better define the nature of this heterogeneity, and to further define the differences between IL-21R/CD40 vs BCR/CD40 signals, we performed single cell RNA-seq (scRNA-seq) of 48h GCBC cultures with either of these two stimuli or with the combination of IL-21R/CD40 and BCR stimulation.
Methods: we performed scRNA-seq using 10X Genomics Chromium system .
Results: Single cell analysis demonstrated surprisingly little overlap between the clusters derived from IL-21/⍺-CD40 stimulation and those derived from BCR/⍺-CD40 ligation, thus establishing at molecular and cellular detail how distinct these two types of selection signals are for GCBC

last: Luo

first: Shuchi

last: Smita

first: Laura

last: Conter

middle: J


title: Single nucelus RNA sequencing of 14 week EGA fetal skin

status: Public on Feb 08 2023

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

institute: Lancaster University

summary: Based on snSeq of back, dorsal digit and ventral digit skin from 2 fetal donations at 14 weeks EGA we report differential expression of signaling and structural molecules between different skin regions, specifically as related to the distinction between hair follicle producing and dermatoglyph producing skin.

overall_design:
Examination of differential gene expression in epithelial and mesenchymal cells from different locations on the body.
Please note that raw data is not provided, due to patient privacy concerns.

first: Denis

last: Headon

first: James

last: Glover


title: Effect of repeated optogenetic stimulation on gene expression in the mouse dentate gyrus [RNA-seq]

first: Tomoyuki

last: Murano

summary: To investigate the effect of repeated neural overactivation in the transcriptome of dentate gyrus neurons, we optogenetically stimulated mouse dentate gyrus repeatedly.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of mice in four different stimulation conditions and no stimulation condition.
Comparative gene expression profiling analysis of RNA-seq data for mouse dentate gyrus neurons in five differnet conditions (No Stimulation, Stimx3+24hrs, Stimx3+2wks, Stimx10+24hrs, and Stimx10+2wks).


title: Mechanical Tension Mobilizes Lgr6+ Epidermal Stem Cells to Drive Skin Growth (I)

status: Public on Feb 03 2023

city: baltimore

first: Yingchao

last: Xue

state: MD

address: 1500 orleans st, room 216

institute: johns hopkins university

summary: Uniquely among mammalian organs, skin is capable of dramatic size change in adults, yet the mechanisms underlying this striking capacity are unclear. Here, we utilize a system of controlled tissue expansion in mice to uncover cellular and molecular determinants of skin growth. Through machine learning-guided three-dimensional tissue reconstruction, we capture morphometric changes in growing skin. We find that most growth is driven by the proliferation of the epidermis in response to mechanical tension, with more limited changes in dermal and subdermal compartments. Epidermal growth is achieved through preferential activation and differentiation of not Lgr5+, but instead Lgr6+ stem cells of the interfollicular epidermis, driven in part by the Hippo pathway. By single-cell RNA sequencing, we uncover further changes in mechanosensitive and metabolic pathways underlying growth control in the skin. These studies point to therapeutic strategies to enhance skin growth and establish a platform for understanding organ size dynamics in adult mammals.

overall_design: scRNA profiles of 8- week-old expander-implanted male mice. The ones with expansion induced as E, and the ones are not induced as NE(ctrl).

first: Chenyi

last: Lyu

first: Luis

last: Garza

first: Sashank

last: Reddy


title: IL-13 promotes sensory-sympathetic neurons crosstalk in asthma [RNA-seq I]

status: Public on Jan 20 2023

first: Theo

last: Crosson

summary: Sequencing of different cell populations of the Jugular-nodose complex (JNC) in a mouse model of Allergic inflammation, and sequencing of cultured JNC nociceptors exposed to IL-13.

overall_design:
The samples 1A-6A, 1B-6B, 1C-6Ccorrespond to:
NaV1.8cre::tdTomatofl/wt mice were injected intranasally with the retrotracer DiD’ every day for 3 consecutive days, and underwent (samples 2, 4, 6) or not (samples 1, 3, 5) the OVA model of Allergic Airway Inflammation (AAI). Mice were sacrificed at the peak of inflammation (day 18 of AAI protocol), 15 days after the first tracer injection. For each sample, JNC from 4 mice (2 males and 2 females) were dissected out and pooled together. Ganglia were enzymatically dissociated, nucleus stained with SYTO40, and cells sorted by flow cytometry and collected into Trizol. Airway nociceptors (samples 1A-6A) were gated as Syto40+tdTomato+DiD+, other visceral nociceptors (samples 1B-6B) as Syto40+tdTomato+DiD-, and glial/stromal Nav1.8- cells (samples 1C-6C)  as Syto40+tdTomato-.

The samples C1-C6 correspond to:
NaV1.8cre::tdTomatofl/wt mice were sacrificed and their JNC harvested. For each sample, JNC from 2 males and 2 females were pooled and enzymatically dissociated, seeded at 10000 neurons per well, and cultured with (samples C2, C4, C6) or without (samples C1, C3, C5) 100 ng/mL IL-13 for 24 hours. Cells were then mechanically detached with a cell scraper, sorted by flow cytometry and collected into Trizol. Nociceptors were gated as tdTomato+.

RNA from all samples were extracted using the the kit PureLink™ RNA Micro Scale (Thermofisher #12183016), quality controlled, before mRNA library preparation mRNA KAPA mRNA HyperPrep Kit (KapaBiosystems #KR1352). All barcoded samples were then sequenced with a Nextseq500 (Illumina) with 75-cycle single-end read. For analysis, sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1. Gene expressions were obtained from STAR as readcounts and computed using RSEM in order to obtain normalized gene and transcript level expression in FPKM.

first: Shreyas

last: Bhat

first: Jo-Chiao

last: Wang

first: Clara

last: Salaün

first: Katiane

last: Roversi

first: Sebastien

last: Talbot


title: Sleep dependent changes in the transcriptome of wild type mice at four different developmental stages.

status: Public on Jan 16 2023

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

summary: This dataset constitutes the first RNA-Seq study of gene expression following sleep deprivation in wild type mice at four different developmental stages, P16, P24, P40 and P90

overall_design: 52 total samples were analyzed. Pre-frontal cortex tissue of P16, P24 and P30 animals was collected at 3 hours of sleep deprivation (SD), prefrontal cortex tissue of P90 animals was collected after 5h of sleep deprivation starting at ZT0 (Lights on). Animals that were left to sleep in their homecage were dissected at the same time of day to control for variations due to circadian rhythms (HC).

first: Christine

last: Muheim

first: Kaitlyn

last: Ford

first: Elizabeth

last: Medina

first: Marcos

last: Frank


title: Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer′s disease-specific cis regulatory elements [ChIP-seq]

status: Public on Jan 09 2023

city: Huntsville

first: Lindsay

last: Rizzardi

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer’s Disease (AD) and unaffected controls have been well-documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq + snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell-type specific transposase accessible regions that are enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglial links were globally enriched for heritability of AD risk and previously identified active regulatory regions.

overall_design: We performed single nucleus multiomics (snRNA+snATAC) on postmortem DLPFC tissues from 7 AD and 8 unaffected donors.

first: Ashlyn

last: Anderson

first: Jacob

last: Loupe

middle: F


title: Deletion of the RS domain in RBM20 leads to dilated cardiomyopathy

status: Public on Jan 02 2023

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Human patients carrying genetic mutations in RBM20 develop a clinically aggressive dilated cardiomyopathy (DCM) characterized by early onset heart failure, high mortality, and sudden death, which is recapitulated in animal models. RBM20 has two primary domains, an RNA recognition motif (RRM) that binds RNA and an arginine/serine (RS)-rich domain that mediates spliceosome assembly and nuclear localization. Reported data showed that mutations in the RS domain lead to severe DCM. Loss of the RRM domain in RBM20 has been shown to disrupt the splicing of RBM20 target transcripts but does not lead to DCM. The objectives of the present study were to determine the functional role of the RS domain in DCM and examine the mechanisms. Mice expressing RBM20 lacking the RS domain (Rbm20ΔRS) were generated using CRISPR/Cas9 technology. Male and female Rbm20ΔRS mice developed a DCM-like phenotype characterized by ventricular dilation and impaired systolic function, that is more severe in females. Splicing of RBM20 target genes, including Ttn, was disrupted in both Rbm20ΔRS and Rbm20ΔRRM mice. However, RBM20 was mis-localized to the sarcoplasm only in the hearts of Rbm20ΔRS mice, indicating that mis-localization of RBM20 rather than disrupted splicing is key in DCM pathogenesis.

first: Wei

last: Guo

first: Camila

middle: U

last: Braz

first: Yanghai

last: Zhang

first: Zachery

last: Gregorich


title: Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [Adult-snRNA-seq]

first: Maike

last: Sander

state: CA

overall_design: In this analysis, we used single nucleus RNA-seq (snRNA-seq) to analyze cells from adult human pancreas (ages: 20 - 31 years). We obtained transcriptomic signatures from both exocrine and endocrine cells, but focused on α-, β-, δ- and γ-cells (1,859 cells in total) for downstream analysis. We integrated these data with snATAC-seq data from adult human pancreas for gene regulatory network (GRN) analysis. Comparing this GRN from adult endocrine cells to similarly integrated datasets from human pluripotent stem cell-derived islets (SC-islets) and childhood human pancreatic endocrine cells allowed us to identify gene regulatory differences between SC-islet cell types and primary childhood and adult islet cell types.


title: Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer′s disease-specific cis regulatory elements