title: Evaluation of breast cancer PDX tumor heterogeneity at single cell resolution II

status: Public on Sep 30 2024

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: Breast cancer is the most commonly diagnosed cancer among women. PDXs (patient-derived xenografts) are similar to cancer cell lines but differ in that they are maintained in a physiological setting as soon as they are isolated from the patient and for subsequent passages. These models are valuable for preclinical trials because PDX models have been shown to closely match their patient counterparts, both in genomic profile and response to treatment. One challenge to treatment development is tumor heterogeneity. In this study, we profiled ER+ and triple negative breast cancer PDX models using single-cell RNA-sequencing. This data may help identify populations of cells which are susceptible to certain treatments in order to improve clinical outcomes for breast cancer patients.

overall_design:
ER+, HER2 amplified, and triple-negative mammary tumors were subjected to single-cell RNA sequencing with the goal of identifying and profiling sub-populations within models to improve outcomes of targeted treatments. This dataset contains a total of 117 samples that includes new and reanalyzed samples with and without raw data present in the SRA.

This GEO record is organized as follows: the “Samples” section below contains 23 new samples with raw data submitted to the SRA; the “Relations” section contains links to the remaining 94 reanalyzed sample GSM records (see the “GSE276609_sample_file_association_for_reanalysis.txt.gz” file for mapping to reanalyzed data and sample names); of the 94 reanalyzed samples 25 are from GSE235168 that have raw data previously submitted to the SRA and are listed in the “TABLE OF REANALYZED/REUSED DATATABLE OF REANALYZED/REUSED DATA”; the remaining 69 samples are from GEO Series GSE161529 and do not have raw data archived in the SRA. These 69 samples from GSE161529 were re-analyzed by the original authors on our request by aligning the raw data using 10X Genomics CellRanger v6 software and then sharing the read count matrices with our team who incorporated them into the same pipeline as the rest of the data in this submission. 10X formatted read count matrices and additional process data for the 69 samples from GSE161529 can be found in the tar file below named “GSE276609_GSE161529_reanalysis.tar.gz”.  Processed data, including 10X formatted read count matrices, for the 25 reanalyzed samples from GSE235168 can be found in the tar file below named “GSE276609_GSE235168_reanalysis.tar.gz”. Likewise, the read counts and other processed data files for the 23 new samples that are part of this submission can be found in the “GSE276609_RAW.tar” tar file below. For all data, the processed files with “CancerCellsOnly” in the file name contains a list of the cell barcodes that we identified as cancer cells using the inferCNV tool as described in the manuscript.  In addition to read counts and cancer cell barcode lists, we provide 5 Loupe Cell Browser files that contain the merged dataset as presented in the paper (.cloupe files).  To view layouts consistent with the manuscript, you need to change the projection to the imported “UMAP_Seurat” or the imported “tSNE_Seurat” options as the defaults are not consistent with the publication figures.  Loupe file contents are as follows: MasterMerge_AllSamples.cloupe.gz contains all 117 samples with human cells only; CancerOnlyDataset.cloupe contains the subset of identified malignant cells from the Master Merge file with all normal samples removed (the CancerCellsOnly processed data files contain a list of barcodes for each sample that are in this dataset);   CancerOnly_TNBC-Samples.cloupe is a subset of the CancerOnlyDataset file contain only TNBC samples; CancerOnly_ERpositive-Samples.cloupe is a subset of the CancerOnlyDataset file that contains only ER+ samples; WHIM30_PDX_PDXO_SamplesOnly.cloupe contains only the WHIM30 PDX and organoid samples.

*********************************************************************
The table below lists GEO accessions reused/reanalyzed for this study where fastq files are available at SRA.
*********************************************************************

first: J

last: Harrell

first: A

last: Olex

first: M

last: Dozmorov

last: Altman

first: D

last: Boyd

first: E

last: Zboril


title: Pulmonary ketogenesis promotes tolerance to bacterial infection

status: Public on Oct 12 2023

city: New York

first: Sebastian

middle: A

last: Riquelme

state: NY

address: 650W 168th Street Black Building 4th Floor Room 427

country: USA

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: Tolerance is a major defense strategy against infection. During the host response to pathogens, tolerance restricts inflammatory damage to tissues, maintaining the long-term integrity of organs. The mechanisms that establish tolerance are poorly understood. We analyzed pulmonary isolates of Pseudomonas aeruginosa that evolved to coexist with tolerant hosts and found that these opportunistic pathogens facilitate tolerance by stimulating ketogenesis. Ketone body production in the airway limits the accumulation of detrimental factors that injure the lung, such as inflammatory cytokines and effector phagocytes. Although ketones are typically synthesized in the liver, in situ metabolo-transcriptomic studies revealed that P. aeruginosa drives their generation in the lung by co-opting the metabolism of alveolar macrophages, which are pulmonary cells of hepatic origin. This phenomenon was restricted to clinical isolates and not observed with laboratory strains of P. aeruginosa , confirming the unique metabolo-tolerogenic properties of ESKAPE pathogens adapted to the human lung.

overall_design: WT or Irg1-/- C57bl/6 mice (8 week old) were treated with PBS or infected either with WT PAO1 or a mix of the 17 host-adapted P. aeruginosa clinical isolates (106 total CFU per mouse in 50uL). 16 hours after infection, mice were euthanized, their lungs were harvested, and single cell suspensions of the lungs were prepared as described. Briefly, the lungs were placed in an Eppendorf tube containing an enzymatic digestion solution of collagenase I (2 mg/mL), dispase (20 mg/mL), elastase (1 mg/mL), and DNAse (1 uL/mL) in PBS. The lungs were minced within the tube and then incubated with shaking at 37C for 30 minutes. 4 volumes of PBS supplemented with 10% FBS was added to quench the digestion, and the digestion solution was strained over a 70-micron filter. The cell suspension was spun down at 4C and 1400 rpm for 7 min. Red blood cell lysis was performed using the Invitrogen RBC lysis buffer. The resulting cell pellet was resuspended in PBS supplemented with 0.04% BSA before being loaded onto the 10X Genomics Chromium Single Cell Controller. Cell viability analysis was performed before loading the samples, and was above 95% per sample. A total of ~8000 cells were analyzed per sample. FASTQ file generation, alignment, filtering, barcode counting, and UMI counting were done using the 10X Cell Ranger software.

first: Kira

last: Tomlinson


title: Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

status: Public on Oct 24 2023

city: Philadelphia

first: Dong

last: Li

state: PA

address: 3615 Civic Center BLVD

institute: Children's Hospital of Philadelphia

summary: Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50-deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Refer to individual Series


title: Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice

status: Public on Oct 16 2023

city: Birmingham

first: Jordan

last: Whitlock

email: jwhitlock@uab.edu, bnp0001@uab.edu

state: AL

address: 1900 University Boulevard

department: Cell, Developmental and Integrative Biology

institute: The University of Alabama at Birmingham

summary:
Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS.

Grant Number: 1U54oD030167
UAB Pilot Center for Precision Animal Modeling (C-PAM)
Grantee: Brittany Lasseigne

Grant Number: 5T32GM008111-35
UAB CMDB T32
Grantee: Jordan Whitlock

overall_design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J  mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664)

middle: H

first: Tabea

middle: M

last: Soelter

first: Timothy

middle: C

last: Howton

first: Brittany

middle: N

last: Lasseigne


title: Spliceosome malfunction causes neurodevelopmental disorders with overlapping features (fly)

status: Public on Oct 25 2023

summary: Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including seven recurrent variants in 30 individuals) and six individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function of the Drosophila orthologs, U2af50 and Prp19, led to lethality, abnormal mushroom body (MB) patterning, and social deficits, differentially rescued by wild- type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50 deficient flies. Upon re-analysis of negative clinical exomes followed by data sharing, we further identified six NDD patients carrying RBFOX1 missense variants which, by in vitro testing, showed loss of function. Our study implicates three splicing factors as NDD causative genes and establishes a genetic network with hierarchy underlying human brain development and function.

overall_design: fly brain tissues harvested at the 3rd instar larval stage from WT controls and elav-Gal4 driving knockdown flies for U2af50 and Prp19


title: Molecular mechanisms associated with cis-platin intrinsic resistance in early drug-tolerant persister cells of lung adenocarcinoma cell lines

status: Public on Nov 03 2023

city: Ciudad de Mexico

first: Rodolfo

middle: Luis

last: Chavez-Dominguez

state: Ciudad de Mexico

address: Calz. de Tlalpan 4502

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

summary: To investigate the mechanism associated with cis-platin intrinsic resistance, we established a model of early drug-tolerant persister cells by exposing lung adenocarcinoma cell lines to the drug for 24 h. Then, we analyzed the transcriptome using RNA-seq from 4 different lung adenocarcinoma cell lines.

overall_design: Differential expression analysis of RNA-seq data for cis-platin persister cells and untreated controls.

first: Maribel

last: Soto-Nava

first: Santiago

last: Avila-Rios

first: Alfonso

last: Mendez-Tenorio

first: Miriam

last: Galicia-Velasco

first: Dolores

last: Aguilar-Cazares

first: Jose

middle: S

last: Lopez-Gonzalez


title: Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish]

status: Public on Oct 01 2023

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

summary: The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

overall_design: Single cell RNA-seq was performed on cells isolated from fresh retina. Fluorescence-activated cell sorting was used to collect Calcein blue(CB)-positive live cells. For some collections, CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors, respectively (Please note that he enrichment strategy was not effective for some species/samples). Approximately 8000 cells were recovered from each sample, and each cell was sequenced to a depth of ~40000 reads.

first: Aboozar

last: Monavarfeshani

first: Mu

last: Qiao

first: Allison

last: Kao

first: Yvonne

last: Kölsch

first: Ayush

last: Kumar

first: Ashley

last: Rasys

first: Rose

last: Richardson

first: Herwig

last: Baier

first: Robert

middle: J

last: Lucas

first: Wei

first: Markus

last: Meister

middle: T

last: Trachtenberg

first: Wenjun

last: Yan

first: Yi-Rong

last: Peng

middle: R

last: Sanes

first: Karthik

last: Shekhar


title: Evolution of neuronal cell classes and types in the vertebrate retina [Sheep]

overall_design: Single nucleus RNA-seq was performed on nuclei isolated from frozen retina. Fluorescence-activated cell sorting was used to collect DAPI-positive nuclei. For some collections, DAPI+ nculei were further seprated using NEUN/RBFOX3 and/or CHX10/VSX2 expression as an strategy to enrich for RGCs and/or bipolar cells, respectively (PLease note that he enrichment strategy was not effective for some species/samples). Approximately 8000 nuclei were recovered from each sample, and each nucleus was sequenced to a depth of ~40000 reads.

last: Li


title: Arraystar m6A-mRNA Epitranscriptomic Microarray Analysis of Atopic Dermatitis and healthy controls

city: Changsha

first: Zeng

last: Jinrong

address: No.138 Tongzipo Rd, Yuelu District, Changsha, Hunan, China, 410013

country: China

institute: the Third Xiangya Hospital, Central South University

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: To investigate the potential mechanism of m6A modification in the development of AD

overall_design:
In the study presented here, m6A ArrayStar apparent transcriptome profiling was performed in  skin tissues from normal human and lesional skin tissue from patients with AD
Note: These are dual channel arrays that have been analyzed as a single-channel array experiment. Therefore there is a sample (GSM) for each channel.

first: Jinrong

last: Zeng

first: Fugang

last: Xiao


title: Evolution of neuronal cell classes and types in the vertebrate retina [Squirrel]

first: Joshua

last: Hahn

first: Aboozar

last: Monavarfeshani

last: Qiao

last: Kao


title: Evolution of neuronal cell classes and types in the vertebrate retina [Rhabdomys]

first: Mu

first: Allison

last: Kölsch

last: Kumar

last: Rasys

last: Richardson


title: Evolution of neuronal cell classes and types in the vertebrate retina [Opossum]

first: Yvonne

first: Ayush

last: Baier

last: Lucas

last: Meister

last: Trachtenberg


title: Evolution of neuronal cell classes and types in the vertebrate retina [Marmoset]

first: Ashley

first: Rose

last: Yan

last: Peng

last: Sanes

last: Shekhar


title: Single cell multi-omic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma

status: Public on Dec 15 2023

city: Leipzig

first: Maximilian

last: Merz

address: Liebigstr. 22

department: Department for Hematology, Cell Therapy and Hemostaseology

country: Germany

institute: University Hospital Leipzig

summary: Markers predicting response and resistance to chimeric antigen receptor (CAR) T cells in relapsed/refractory multiple myeloma are currently missing. We subjected cells isolated from peripheral blood and bone marrow before and after the application of CAR T cells directed against B cell maturation antigen to single cell multi-omic analyses to identify markers associated with resistance and early relapse.

overall_design: Peripheral Blood Mononuclear Cells (PBMC) and Bone Marrow Mononuclear Cells (BMMC) collected at day of leukapheresis and approximately 30 days after CAR T cell infusion were subjected to Single Cell RNA, T Cell Receptor, B Cell Receptor and Surface Proteome Sequencing

first: Nora

last: Grieb


title: Evolution of neuronal cell classes and types in the vertebrate retina [ferret]

last: Hahn

last: Monavarfeshani

first: Herwig

first: Robert

first: Wei

last: Li

first: Markus


title: Evolution of neuronal cell classes and types in the vertebrate retina [Pig]

last: Qiao

last: Kao

last: Kölsch

first: Wenjun

first: Yi-Rong

first: Karthik


title: Evolution of neuronal cell classes and types in the vertebrate retina [Peromyscus]

first: Joshua

last: Kumar

last: Rasys

last: Richardson


title: Evolution of neuronal cell classes and types in the vertebrate retina [cow]

first: Aboozar

last: Baier

last: Lucas

last: Meister


title: Evolution of neuronal cell classes and types in the vertebrate retina [Lizard]

first: Mu

last: Trachtenberg

last: Yan

last: Peng


title: Influence of metaphylaxis for bovine respiratory disease on host transcriptome responses

status: Public on Sep 26 2023

city: Canyon

first: Matthew

last: Scott

state: TX

address: 3201 Russell Long Blvd

institute: Texas A&M University

summary: To evaluate how commonly-utilized antimicrobials affect the host transcriptome of commercial beef cattle overtime, we enrolled 105 feedlot beef steers randomly into seven different treatment groups (negative control, tulathromycin, tildipirosin, enrofloxacin, florfenicol, ceftiofur, oxytetracycline) to receive a one-time label dose of a commercial antimicrobial or not (negative control), and collected jugular whole blood into PAXgene RNA blood tubes at six time points: Day 0 (baseline), 3, 7, 14, 21, and 56.

overall_design: Whole blood from six randomly selected individuals per treatment group (n=7; negative control, tulathromycin, tildipirosin, enrofloxacin, florfenicol, ceftiofur, oxytetracycline) were used for gene expression profiling and differential analysis across six time points (Day 0, 3, 7, 14, 21, 56).

last: Valeris-Chacin

first: Paul

last: Morley

first: John

last: Richeson


title: Single cell sequecing analysis of exhausted CD8 T cell subsets in LCMV-clone13 infected mice

status: Public on Sep 22 2023

city: Würzburg

first: Hao

last: Wu

address: versbacherstr 7-9

institute: institute for systemsimmunology, wurzburg university

summary: To identify the subsets of exhausted T cells and to analyze the transcriptional-metabolic programs alongside their developmental trajectories at single-cell resolution, we isolated CD44+ PD-1hi CD8+ T cells from chronically infected wild-type (WT) mice 21 days after infection with the ‘clone 13’ strain of lymphocytic choriomeningitis virus (LCMV) by FACs sorting aand performed scRNA-sequencing.

overall_design: C57BL/6 WT Mice were infected with 2x10^6 IU LCMV clone13 after CD4 T cell depletion at d-2 and d0 with 300µg GK1.5 anti-CD4 antibody. At the chronic infection phase (> d21), splenocytes were isolated and CD8+, CD44+, PD-1high cells were sorted using FACS AriaIII.

first: Martin

last: Vaeth

first: Wolfgang

last: Kastenmüller

first: Konrad

last: Knöpper


title: RNA-seq of wild type and Slc25a3-deficient CD8 T cells

summary: RNA-sequencing and analysis of in vitro differentiated CD8 T cells isolated from WT and Slc25a3-fl/fl Cd4-cre mice.

overall_design: Naive T cells were isolated (d0) or activated for 2 days in vitro by anti-CD3 and anti-CD8 antibodies (d2) or followed with 4 days resting in 10 ng/ml IL-2 after activation (d6). Total RNA was harvestred as subjected to bulk RNA-sequncing analysis.

last: Väth


title: Single-cell RNA-Seq reveals novel myofibroblast charactering epithelial features in the mammary gland of dairy cows

status: Public on Sep 16 2023

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

summary: Our study is the first one to investigate the heterogeneity of bovine mammary gland (MG) and to construct a bovine MG cell atlas by using scRNA-Seq. Our findings provide novel insights into lactation biology of bovine MG. We identified and validated three mature luminal epithelial cells that are involved in the different lactation processes as well as in the immune response. In addition, a novel myofibroblast showing potential differentiation into luminal epithelial cells was identified. The IGF pathway system signal may play an important role in the F13-L5 transition, and the hormone sensing luminal cell (L1), luminal progenitor cells (L2, L3) and immune-sensing luminal cell are correlated with the process.

overall_design: Single-cell RNA sequencing was applied to investigate the transcriptome of 24,472 high-quality MG cells isolated from newborn and adult cows.

first: Fengfei

last: Gu

first: Hui-Zeng


title: Evolution of neuronal cell classes and types in the vertebrate retina [Tree_Shrew]

last: Hahn

last: Monavarfeshani

last: Qiao

first: Allison

last: Kao

first: Yvonne

last: Kölsch

first: Ayush

last: Kumar

first: Ashley

last: Rasys

first: Rose

last: Richardson

first: Herwig

last: Baier

first: Robert

first: Wei

last: Li

first: Markus

last: Sanes

last: Shekhar


title: Gene expression profile at single cell level of alloantigen-specific TEa CD4+ T cells after heart transplantation

status: Public on Sep 28 2023

city: Houston

first: Dawei

last: Zou

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

summary: Alloreactive CD4+ T cells play a central role in allograft rejection, We used single cell RNA sequencing (scRNA-seq) to analyze the cell states of alloreactive CD4+ T cells in periphery and allografts to better understand how alloreactive CD4+ T cells drive allograft rejection.

overall_design: C57BL/6 (B6) mice received adoptive transfer of congenically marked naïve WT or Ldha-/- TEa (TCR transgenic) CD4+ T cells, specifically recognizing the BALB/c I-EÎ± major alloantigen. Subsequently, these mice underwent transplantation of BALB/c hearts. After 7 days post-transplantation, we isolated WT TEa cells from both spleens and heart allografts, along with Ldha-/- TEa cells from the spleens, for single-cell RNA sequencing (scRNA-seq) analysis.

first: Guohua

last: Wang

first: Yin

last: Zheng

first: Wenhao

last: Chen


title: spatiotemporal single-cell transcriptomics in mouse and human to investigate TAM evolution during GBM progression

status: Public on Sep 06 2023

first: Ailiang

last: Zeng

address: 12515 stoney creek dr

department: Cancer Biology

institute: MD Anderson Cancer Center

summary: Glioblastoma (GBM) is the most common and malignant primary brain tumor. Although immunotherapy has shown promise in certain cancer types, it has not been effective against GBM, largely due to its highly immunosuppressive tumor microenvironment (TMEs), which is rich in tumor-associated macrophages/microglia (TAMs). TAMs in late-stage GBM contribute to T-cell exhaustion and worsen prognosis, but the role of TAMs in earlier stages of tumor development is unclear. By employing genetically engineered mouse models and human samples, we used spatiotemporal single-cell transcriptomics to investigate TAM evolution during GBM progression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
1,Single immune cell (CD45+) sequencing of spatial sampling (paired Periphery, Border and Core) in 3 implanted QPP#7 mouse GBMs,  and in 3 human GBM masses (Emory Cohort). 2,Single immune cell sequencing of Mg-TAMs and Mo-TAMs

UPDATE: [Apr-17-2026] The processed data files for Samples GSM7714298, GSM7714300, GSM7714301, which were originally mislabeled and incorrectly associated, have been corrected.
GSM7714298: Correct files were previously mislabeled as files for GSM7714300.
GSM7714300: Correct files were previously mislabeled as files for GSM7714301.
GSM7714301: Correct files were previously mislabeled as files for GSM7714298.

first: Jian

last: Hu

first: Mingxin

first: Kristin

last: Huntoon

first: Chen

last: Ju

first: Bo

last: Zhao


title: Single-cell sequecing of LCMV-specific WT and HIF-1a-deficient CD8 T cells isolated from LCMV-Clone13 infected host mice

first: Hao

last: Wu

summary: To determine the role of hypoxia-inducible factor 1 alpha (HIF-1a) in exhausted T cells, we crossed Hif1a-fl/fl Cd4-Cre mice to tdTomato+ P14 animals and adoptively co-transferred equal numbers of WT and HIF-1a-deficient P14 CD8+ T cells into chronically infected WT host mice. 21 days post infection, we retrieved GFP+ (WT) and tdTomato+ (HIF-1a-deficient) donor P14 T cells by FACS sorting and subjected CITE-seq antibody-barcoded WT and HIF-1a-deficient CD8+ P14 T cells to multiplexed scRNA sequencing analysis.

overall_design: CD8+ tdTomato+ (HIF-1a-deficient) and CD8+ tdTomato+ GFP+ (WT) P14 T cells were FACS-sorted from the spleen and LNs of chronically infected mice using a FACSAria III cell sorter (BD Biosciences). To multiplex different samples for scRNA sequencing, single-cell suspensions after FACS sorting were labelled with different TotalSeqA antibodies (Biolegend). Each sample was labelled with one specific hashtag (1:400 dilution) and CITE-seq antibodies (1:800 dilution, all Biolegend). After labelling for 30 min at 4 °C, samples were washed three times and multiplexed in equal cell numbers at a density of 106 cells/ml.

first: Martin

last: Vaeth


title: Evaluation of breast cancer PDX tumor heterogeneity

status: Public on Jul 18 2023

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

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


title: High-resolution spatial transcriptomics of hormone-induced ovulation in mice

status: Public on Aug 21 2023

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: The rupture of ovarian follicles during ovulation is a crucial and intricate process essential for procreation, yet the molecular mechanisms behind this process are not fully understood. Here, we use high-resolution spatial transcriptomics to reveal the spatiotemporal regulation of cell-type-specific molecular programs driving follicle maturation and rupture during hormone-induced ovulation.

overall_design: High-resolution spatial transcriptomics of immature and preovulatory murine ovaries

first: Madhav

last: Mantri

first: Hanxue

last: Zhang

first: Manny

last: Spanos

first: Yi

last: Ren


title: Evaluation of breast cancer PDX tumor heterogeneity at single cell resolution [scRNA-seq]

summary: Breast cancer is the most commonly diagnosed cancer among women. PDXs (patient-derived xenografts) are similar to cancer cell lines but differ in that they are maintained in a physiological setting as soon as they are isolated from the patient and for subsequent passages. These models are valuable for preclinical trials because PDX models have been shown to closely match their patient counterparts, both in genomic profile and response to treatment. One challenge to treatment development is tumor heterogeneity. In this study, we profiled ER+ and triple negative breast cancer PDX models using single-cell RNA-sequencing. This data may help identify populations of cells which are susceptible to certain treatments in order to improve clinical outcomes for breast cancer patients.

overall_design: ER+ and triple-negative mammary tumors were subjected to single-cell RNA sequencing with the goal of identifying and profiling sub-populations within models to improve outcomes of targeted treatments.

first: J

last: Harrell

first: Amy

middle: L

last: Olex

first: Mikhail

last: Dozmorov

first: Julia

last: Altman

first: David

last: Boyd

first: Emily

last: Zboril


title: Evolution of neuronal cell classes and types in the vertebrate retina

first: Joshua

last: Hahn

sample_organism:
Danio rerio
Didelphis marsupialis
Callithrix jacchus
Homo sapiens
Mustela putorius furo
Sus scrofa domesticus
Bos taurus
Ovis aries
Peromyscus maniculatus
Anolis sagrei
Ictidomys tridecemlineatus
Rhabdomys pumilio
Tupaia chinensis

overall_design: Refer to individual Series


title: Infection phase-dependent dynamics of the viral and host N6-methyladenosine epitranscriptome in the lifecycle of an oncogenic virus in vivo

status: Public on Jul 19 2023

city: ZHENG ZHOU

first: shuai

last: zhang

address: China Henan Zhengzhou Agricultural Road No. 63 (450002)

institute: Henan Agricultural University

type: Methylation profiling by high throughput sequencing

summary: Dynamic alteration of the epitranscriptome exerts regulatory effects on the lifecycle of oncogenic viruses in vitro. However, little is known about these effects in vivo because of the general lack of suitable animal infection models of these viruses. Using a model of rapid-onset Marek’s disease lymphoma in chickens, we investigated changes in viral and host mRNA N6-methyladenosine (m6A) modification during Marek’s disease virus (MDV) infection in vivo. We found that the expression of major epitranscriptomic proteins varies among viral infection phases, reprograming both the viral and the host epitranscriptomes.Specifically, the METTL3/14 complex was suppressed during the lytic and reactivation phases of the MDV lifecycle, whereas its expression was increased during the latent phase and in MDV-induced tumors. METTL3/14 overexpression inhibits, whereas METTL3/14 knockdown enhances, MDV gene expression and replication. These findings reveal the dynamic features of the mRNA m6A modification program during viral replication in vivo, especially in relation to key pathways involved in tumorigenesis.

first: Guoqing

last: Zhuang

first: Aijun

last: Sun


title: Non-alcoholic steatohepatitis disrupts diurnal liver transcriptome rhythms in mice

status: Public on Jun 16 2023

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

institute: University of Lübeck

summary: Circadian profiling improves target gene detection and pathway characterization in mouse models of NASH. Fatty livers show 3-hour advances in metabolic and clock gene transcript rhythms. Circadian profiling further reveals temporal changes in lipid, carbohydrate, and cholesterol metabolic transcripts.

overall_design: Mice were fed with choline free methionine low high fat diet (cdHFD) or normal chow during 2 weeks. Mice were then sacrificed every 6 h and liver was collected. Rnaseq was then performed and data analyzed using different methods.

first: Henrik

last: Oster


title: Single cell sequencing of WT and hb-egfaKO zebrafish spinal cord, at 1 week after sham or transection injury.

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

summary: We identified hb-egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb-egfa mechanism of action, we perforemd single cell sequencing of WT and hb-egfaKO zebrafish spinal cord.

overall_design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 week post injury. Spinal cord of sham-injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing (4 samples in total, WT 1 wpi, WT sham, hb-egfaKO 1 wpi, hb-egfaKO sham).

first: Valentina

last: Cigliola

first: Adam

last: Shoffner

first: Nutishia

last: Lee

first: Clay

last: Becker

first: Jiaul

last: Hoque

first: Trevor

last: Gonzalez

first: Yanchao

last: Han

first: Grace

last: Sheng

first: Timothy

last: Faw

first: Muhammad

last: Abd-El-Barr

first: Shyni

last: Varghese

first: Aravind

last: Asokan

first: Kenneth

middle: D

last: Poss


title: Evolution of neuronal cell classes and types in the vertebrate retina [human]

first: Joshua

last: Hahn

first: Aboozar

last: Monavarfeshani

first: Mu

last: Qiao

first: Allison

last: Kao

first: Yvonne

last: Kölsch

first: Ayush

last: Kumar

first: Ashley

last: Rasys

first: Rose

last: Richardson

first: Herwig

last: Baier

first: Robert

last: Lucas

first: Wei

last: Li

first: Markus

last: Meister

last: Trachtenberg

first: Wenjun

last: Yan

first: Yi-Rong

last: Peng

last: Sanes

first: Karthik

last: Shekhar


title: A Novel Single Vector Intersectional AAV Strategy for Interrogating Cellular Diversity and Brain Function

status: Public on Jun 07 2023

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: As the discovery of cellular diversity in the brain accelerates, so does the need for functional tools that target cells based on multiple features, such as gene expression and projection target. By selectively driving recombinase expression in a feature-specific manner, one can utilize intersectional strategies to conditionally promote payload expression only where multiple features overlap. We developed Conditional Viral Expression by Ribozyme Guided Degradation (ConVERGD), a single-construct intersectional targeting strategy that combines a self-cleaving ribozyme with traditional FLEx switches. ConVERGD offers benefits over existing platforms, such as expanded intersectionality, the ability to accommodate larger and more complex payloads, and a vector design that is easily modified to better facilitate rapid toolkit expansion. To demonstrate its utility for interrogating neural circuitry, we employed ConVERGD to target an unexplored subpopulation of norepinephrine (NE)-producing neurons within the rodent locus coeruleus (LC) identified via single-cell transcriptomic profiling to co-express the stress-related endogenous opioid gene prodynorphin (Pdyn). These studies showcase ConVERGD as a versatile tool for targeting diverse cell types and reveal Pdyn-expressing NE+ LC neurons as a small neuronal subpopulation capable of driving anxiogenic behavioral responses in rodents.

overall_design: Smart-seq were used to profile DBH positive rodent locus coeruleus (LC) neurons

first: Alex

last: Hughes

first: Brittany

last: Pollard

first: Jesse

last: Gammons

first: Phillip

last: Chapman

first: Jay

last: Bikoff

first: Lindsay

last: Schwarz


title: Single-cell transcriptional analysis of CD45+ cells in the rhesus brain during acute SIV infection.

status: Public on Aug 26 2023

city: Davis

first: Chase

middle: Elliott

last: Hawes

state: CA

address: 2005, CIID, County Rd 98 & Hutchinson Drive

department: Center for Immunology and Infectious Diseases

institute: University of California, Davis

summary: People living with HIV are particularly vulnerable to developing a spectrum of neurocognitive abnormalities referred to as HIV-associated neurocognitive disorders. These disorders have been linked to neurological impairment driven by inflammation within areas of the brain controlling cognition. Current data suggest that HIV establishment within the central nervous system (CNS) occurs within the first weeks following infection and drives subsequent neuroinflammatory processes. Various studies have implicated HIV-target cells (i.e., monocytes, macrophages, and CD4 T cells) as key facilitators of HIV CNS establishment via a “trojan horse” mechanism, in which infected cells cross CNS barrier tissues and contribute to viral seeding.   Cellular entry is mediated by integrins, specifically α4 integrins, which are expressed at the blood brain barrier and blood cerebrospinal fluid barrier and allow circulating immune cells to enter the CNS. To investigate the contribution of CNS infiltrating cells to early neurological disease, we utilized an acute rhesus macaque SIVmac251 infection model, where animals were treated with an anti-a4 integrin monoclonal antibody to inhibit immune cell trafficking to the CNS.     To gain insights into neuro inflammatory transcriptional programs induced following SIV infection and how this might be modulated by a4 integrin blockade, we utilized single cell (sc) RNA sequencing of FACS sorted CD45+ cells isolated from brain and spleen.

overall_design: Rhesus macaques were infected intravenously with (10^4 TCID50) SIVmac251 and euthanized at three weeks post-infection. Infected animals were divided into two cohorts and treated with either: (1) 25mg/kg rhesus IgG1 anti-a4 integrin blocking monoclonal antibody or (2) 25mg/kg rhesus IgG1 control antibody (specific for Desipramine). The antibody course was initiated 1 week prior to infection and approximately every 10 days subsequently over the course of the study. Furthermore, a cohort of age matched, untreated, uninfected animals were included as additional controls. At three weeks post-infection, animals were euthanized, and mononuclear cells were collected from the spleen and the right brain hemisphere. Once mononuclear cells were isolated, they were cryopreserved in DMSO and 10% FBS. Cells were subsequently thawed and CD45+ cells enriched using Miltenyi Biotec CD45 Microbeads for non-human primates. Live CD45+ cells were further enriched by fluorescent activated cell sorting for subsequent single cell RNA-seq analyses.

first: Smita

last: Iyer


title: Lurbinectedin is an effective therapeutic target for de novo and transformed small cell lung cancer and modulates EMT and NOTCH signaling pathways.

status: Public on Jun 08 2023

city: New York

first: Triparna

last: Sen

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Small cell lung cancer (SCLC) is a high-grade neuroendocrine tumor with a dismal prognosis and limited treatment options. Lurbinectedin, approved as a second-line treatment for metastatic SCLC, showed only a partial response in clinical trials highlighting the need to develop improved mechanistic insight and predictive biomarkers of response. In this study, we determine the preclinical efficacy of lurbinectedin in a comprehensive panel of SCLC cell lines and patient-derived xenografts of SCLC. Furthermore, we demonstrate that lurbinectedin, either as a single agent or in combination with osimertinib, causes remarkable anti-tumor response in multiple models of SCLC transformation. Transcriptomic analysis identified induction of apoptosis, repression EMT and modulation of PI3K/AKT, NOTCH signalling pathway being associated with lurbinectedin response in de novo and transformed SCLC models. We provide a mechanistic insight of lurbinectedin response in SCLC and is the first demonstration that lurbinectedin is a potential therapeutic target after SCLC transformation.

overall_design: RNA.seq analysis data of small cell lung cancer  of 3 patient derived xenograft models of de-novo small cell lung cancer (LX110, LX33 and LX1322) in lurbinectedin treated and vehicle treated group. Data also include RNA seq analysis of 2 patient derived xenograft models of transformed SCLC , LX1042 and LX831b comparing vehicle, only osimertinib, only lurbinectedin and lurbinectedin+osimertinib combination treatment groups.

first: Dan

last: Hasson

first: Subhamoy

last: Chakraborty

first: Deniz

last: Demircioglu

first: Charles

last: Coleman


title: Histone deacetylation and cytosine methylation are required for the normal compartmentalization of heterochromatin in the genome organization of Neurospora crassa [ChIP-Seq]

status: Public on Jul 03 2023

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes: in the fungus Neurospora crassa, chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures that are anchored by heterochromatic region aggregates. However, insufficient information exists on how histone post-translational modifications, including acetylation, impact genome organization. In Neurospora, the HCHC (HDA-1, CDP-2, HP1, CHAP) complex deacetylates heterochromatic regions including centromeres: loss of individual HCHC members increases centromeric acetylation and cytosine methylation. Here, we evaluate the role of the HCHC complex on genome organization using chromosome conformation capture with high-throughput sequencing (Hi-C) in Δcdp-2 or Δchap deletion strains. CDP-2 loss increases interactions between intra- and inter-chromosomal heterochromatic regions, while removal of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different histone PTM patterns genome-wide: in Dcdp-2, heterochromatic H4K16 acetylation is increased, yet some heterochromatic regions lose H3K9 trimethylation, which locally increases inter-heterochromatin contacts; CHAP loss produces minimal acetylation changes but increases H3K9me3 enrichment in heterochromatin. Furthermore, deletion of the DIM-2 DNA methyltransferase in a Δcdp-2 background causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how enhanced cytosine methylation ensures heterochromatic compartmentalization when silenced regions are acetylated.

overall_design: We analyzed genome organization of mutants of a heterochromatin-specific histone deacetylase complex (the HCHC complex) found in the filamentous fungus Neurospora crassa by chromosome conformation capture by paired-end high-throughput sequencing (Hi-C); Hi-C libraries were generated with the four-base cutters DpnII and MseI, which monitor euchromatic and heterochromatic regions of the Neurospora genome, respectively, due to the location of the recognition sequences of these restriction enzymes. All HCHC mutant Hi-C data was compared to wild type Hi-C data, previously reported in Rodriguez et al. (Pubmed ID: 35244156). We also examined the histone post-translational modification enrichment of wild type and HCHC mutant strains, specifically looking at the acetylation of lysine 9 on histone H3, the acetylation of lysine 16 on histone H4, and the trimethylation of lysine 9 on histone H3.

first: Ashley

middle: W

last: Scadden

first: Alayne

last: Graybill

first: Clayton

last: Hull-Crew

first: Tiffany

last: Lundberg

first: Nickolas

last: Lande


title: The MeRIP-seq and RNA-Seq of SiHa and H8 cells

status: Public on Jun 01 2023

city: Shenzhen

first: sheng

last: zhong

address: The Xinhu Road 1333

institute: The Sourthern Medical University

summary: To investigate the different gens expression and RNA methylation degree in the cervical immortalized cervical cells and cervical cancer cells，

overall_design: We then performed gene expression profiling analysis using data obtained from MeRIP-seq of 2 different cells.

first: Xia

last: Guo

first: Xiaona

last: Chen


title: Functional chromatin signatures premark future lineage-specific enhancers [ChIP-Seq]

first: Julian

last: Pulecio

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: It remains unknown whether early embryonic cells harbor a blueprint for future enhancers that regulate the expression of lineage-specific genes in adult tissues. Here, we demonstrate that embryonic stem cells (ESCs) have transcriptionally competent chromatin regions (CCRs) prepared to induce the expression of lineage genes prior to differentiation. CCRs represent activatable pre-enhancers within the topological chromatin domains of lineage genes, marked by chromatin signatures distinguishable from primed/poised enhancers, enabling their genome-wide identification. The pioneer transcription factor (TF) FOXA2 preferentially binds CCRs during early lineage specification, promoting their conversion into active enhancers. CCRs can be harnessed to boost the expression of master TFs and promote the direct reprogramming of ESCs into differentiated cells, showcasing their potential for practical applications. Our findings identify a mechanism by which ESCs rapidly establish enhancer activity during early lineage differentiation and expand our understanding of the epigenetic features supporting transcriptional regulation and cellular plasticity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K27ac, and the transcription factors FOXA2 (upon CRISPR activation via targeting the promoter region of the FOXA2 gene),OCT4, NANOG and SOX2 in hESCs. All the experiments were performed with n=2 biological replicates.

first: Danwei

last: Huangfu

first: Hyein

last: Cho

first: Jielin

last: Yan


title: Time course transcriptomic analysis of cabbage (Brassica oleracea ssp. capitala L.) during vernalization

status: Public on Apr 17 2023

city: Anseong-si, Gyeonggi-do

first: Heewon

last: Moon

address: 4726,Seodong-daero, Daedeok-myeon

country: South Korea

institute: Chung-ang university

summary: We report here NGS RNA-seqencing datasets for three different vernalization time course of Brassica oleracea plants

overall_design: Three different veranlization treatment to B. oleracea whole plants: NV; non-vernalization under long day photoperiod (16h light/8h dark) for two weeks, V40; vernalization in refrigerator (4°C) under short day photoperiod (8h light/16h dark) for 40 days, AV; after 40days of cold exposure, the samples were returned back to a warm termperature under long day photoperiod (16h light/8h dark) for 7 days

first: Dong

last: Kim


title: Establishment of breast cancer PDX RNA-sequencing data library [bulk RNA-seq]

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: Breast cancer is the most commonly diagnosed cancer among women. PDXs (patient-derived xenografts) are similar to cancer cell lines but differ in that they are maintained in a physiological setting as soon as they are isolated from the patient and for subsequent passages. These models are valuable for preclinical trials because PDX models have been shown to closely match their patient counterparts, both in genomic profile and response to treatment. Collection of RNA-expression data from multiple PDX models was performed to generate a library of RNA-sequencing data which may be utilized to compare tumors from different subtypes or treatment groups.

overall_design: ER+ and triple negative mammary tumors were grown orthopedically in mice for 8 weeks. Tumor cells from each PDX were profiled by bulk RNA-sequencing to determine differentially expressed genes and gene signatures between models with the goal of furthering the fields of oncogenesis, metastasis and drug resistance.

first: J

last: Harrell

first: Amy

last: Olex

first: Mikhail

last: Dozmorov

first: Julia

last: Altman

first: David

last: Boyd

first: Emily

last: Zboril


title: ΔNp63 controls stemness and inflammation in the adult epidermis

status: Public on Mar 31 2023

city: Stony Brook

first: Jinyu

last: Li

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

summary: The p63 transcription factor is critical for epidermis formation in embryonic development, but its role in the adult epidermis is barely investigated. Here we show that acute genetic ablation of ΔNp63, the main p63 isoform, in the adult epidermis disrupts keratinocyte proliferation and self-maintenance and, unexpectedly, triggers an inflammatory psoriasis-like condition. Mechanistically, single-cell RNA sequencing revealed down-regulation of the cell cycle genes, up-regulation of differentiation markers, and induction of several pro-inflammatory pathways in ΔNp63-ablated keratinocytes. Intriguingly, ΔNp63-ablated cells disappear three weeks post-ablation, at the expense of the remaining non-ablated cells. This was not associated with active cell death mechanisms, but rather with reduced stemness and self-maintenance capacity. Indeed, in vivo wound healing assay, a physiological readout of the epidermal stem cell function, was largely impaired in the ablated skin. We found that the Wnt signaling pathway (Wnt5a, Wnt10a, Fzd6, Fzd10) and Col17a1 are the likely ΔNp63 effectors responsible for keratinocyte proliferation and stemness, while AP1 factors are responsible for excessive differentiation, and Il-1a, Il-18, Il-24 and Il-36γ for the suppression of inflammation. These data implicate ΔNp63 as a critical node that coordinates balanced epidermal homeostasis and suppression of inflammation in the adult epidermis, upstream of known regulatory pathways.

overall_design: ScRNA-seq of control or ΔNp63 epidermis at 1 day and 1 week

first: Evguenia

last: Alexandrova

first: Christopher

middle: E

last: Eyermann


title: Molecular subphenotyping using placental transcriptomics in early-onset preeclampsia and fetal growth restriction

status: Public on Aug 25 2023

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

summary: Placental disorders contribute to pregnancy complications including preeclampsia (PE) and fetal growth restriction (FGR), but debate regarding their specific pathobiology persists. Our objective was to apply transcriptomics with weighted gene correlation network analysis (WGCNA) to further clarify the placental dysfunction in these conditions.

overall_design: We performed RNA sequencing (RNA-seq) with WGNCA using 30 human placental samples, separated into villous tissue (VT) and decidua basalis (DB) and clinically grouped as follows: (1) early-onset PE (EOPE, n=8); (2) EOPE+FGR (n=7); normotensive, nonanomalous preterm FGR (n=5); idiopathic preterm birth (iPTB, n=5); and uncomplicated term births (TB, n=5).

first: Irina

middle: A

last: Buhimschi

first: Catalin


title: Zebrafish spinal cord tissue at 1 week post injury

first: Jianhong

last: Ou


title: Functional chromatin signatures premark future lineage-specific enhancers

first: Julian

last: Pulecio

first: Danwei

last: Huangfu


title: Functional chromatin signatures premark future lineage-specific enhancers [4C]

overall_design: 4C using as viewpoints the GATA6, EOMES, PDX1 and SOX17 loci in hESCs. Each 4C experiment had n=2 biological replicates.

first: Wilfred

last: Wong

first: Dylan

last: Murphy

first: Jielin

last: Yan

first: Renhe

last: Luo


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

status: Public on Mar 21 2023

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

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

last: Kim


title: Inhibition of BRD4 Rescues Cardiac phenotype in Myocyte-Specific Lamin A/C Null Mice

status: Public on Mar 19 2023

city: Houaton

first: Ali

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

summary: Deletion of Lmna, encoding nuclear membrane protein LMNA, specifically in mouse cardiac myocytes activates BRD4 and leads to heart failure, arrhythmias, myocardial fibrosis, apoptosis, and premature death, which were partially rescued upon inhibition of BRD4.

overall_design: RNA-seq from Cardiac myocytes from 4 control  (WT) and 4 Myh6-cre:LmnaF/F vehicle treated and 4 Myh6-cre:LmnaF/F JQ1 treated

first: Gaelle

last: Auguste

first: Leila

last: Rouhi

first: Scot

last: Matkovich

first: Cristian

last: Coarfa

first: Matthew

last: Robertson

first: Grazyna

last: Czernuszewicz

first: Priyatansh

last: Gurha


title: An injury responsive enhancer promotes heart regeneration in zebrafish

status: Public on Jul 24 2023

first: Jianhong

last: Ou

summary: we profiled chromatin accessibility of zebrafish endothelial cells after amputation injury and identify an mmp14b endothelial enhancer induced by heart injury in zebrafish. We show that the enhancer is required for mmp14b expression and regeneration in response to heart injury. Moreover, the enhancer depends on a consensus TEAD-binding motif, suggesting a role for Hippo signaling upstream of mmp14b.

overall_design: After cardiac injury, Fli1+ cells are purified for ATAC-seq profiling.

first: Fei

last: Sun

first: Alexis

last: Safi

first: Gregory

last: Crowford

first: Kenneth

last: Poss


title: Functional chromatin signatures premark future lineage-specific enhancers [PRO-Seq]

first: Julian

last: Pulecio

overall_design: Precision Nuclear Run On PRO-seq in hESCs.

first: Danwei

last: Huangfu

first: Hyunwoo

last: Cho

first: Wenbo

last: Li


title: Chromatin profiling of zebrafish spinal cord tissue at 1 week post injury

summary: To identify regulatory tissue regeneration enhancer elements (TREEs) relevant during spinal cord regeneration, we  performed ATAC sequencing datasets of zebrafish spinal cord at 1 week after sham injury and after transection.

overall_design: Spinal cord chromatin profiles 1week after spinal cord transection and in sham injured controls.

first: Valentina

last: Cigliola

first: Adam

last: Shoffner

first: Nutishia

last: Lee

first: Clay

last: Becker

first: Jiaul

last: Hoque

first: Trevor

last: Gonzalez

first: Yanchao

last: Han

first: Grace

last: Sheng

first: Timothy

last: Faw

first: Muhammad

last: Abd-El-Barr

first: Shyni

last: Varghese

first: Aravind

last: Asokan


title: WWOX-dependent gene expression profiling of glioblastoma

status: Public on Apr 11 2023

city: Lodz

first: Żaneta

last: Kałuzińska-Kołat

address: Zeligowskiego St. 7/9

department: Deparment of Molecular Carcinogenesis

country: Poland

institute: Medical University of Lodz

summary: In the current study we employed the CAGE-Seq method and investigated the four glioblastoma cell lines in which two variants through stable transduction were established, i.e., with overexpression of WWOX gene and control variant.

overall_design:
The study was based on four glioblastoma cell lines, i.e., DBTRG-05MG, T98G, U87MG, and U251MG, for which overexpression of gene encoding WWOX was induced by lentiviral transduction. For each cell line, investigated variants included the Control variant (treated with Puro-Blank Lentivirus; abbreviated "vec") and WWOX overexpression variant (treated with GIPZ™ lentiviral system; abbreviated "WWOX"). Each variant was represented by three biological replicates per cell line.

Grant number: 2021/41/N/NZ2/01375
Grant title: WWOX gene as a modulator of the structure and function of the cytoskeleton and intercellular communication in glioblastoma
Funding source: National Science Centre, Poland

first: Damian

last: Kołat

first: Katarzyna

last: Kośla

first: Elżbieta

last: Płuciennik

first: Andrzej

middle: K

last: Bednarek


title: Erythropoietin re-wires cognition-associated transcriptional networks

city: Göttingen

first: Hannelore

last: Ehrenreich

address: Hermann-Rein-Str 3

department: Clinical Neuroscience

institute: Max Planck Institute for Multidisciplinary Sciences

summary: Recombinant human erythropoietin (rhEPO) has potent procognitive effects, likely hematopoiesis-independent, but underlying mechanisms and physiological role of brain-expressed EPO remained obscure. Here, we provide transcriptional hippocampal profiling of male mice treated with rhEPO. Based on ~108,000 single nuclei, we unmask multiple pyramidal lineages with their comprehensive molecular signatures. By temporal profiling and gene regulatory analysis, we build developmental trajectory of CA1 pyramidal neurons derived from multiple predecessor lineages and elucidate gene regulatory networks underlying their fate determination. With EPO as ꞌtoolꞌ, we discover populations of newly differentiating pyramidal neurons, overpopulating to ~200% upon rhEPO with upregulation of genes crucial for neurodifferentiation, dendrite growth, synaptogenesis, memory formation, and cognition. Using a Cre-based approach to visually distinguish pre-existing from newly formed pyramidal neurons for patch-clamp recordings, we learn that rhEPO treatment differentially affects excitatory and inhibitory inputs. Our findings provide mechanistic insight into how EPO modulates neuronal functions and networks.

overall_design: C57BL6/N (WT) male mice received 5000 IU/kg i.p. EPO (12 mice) or solvent control (12 mice). Injections go from age P28 to P48, performed every other day for a total of 11 times. Mice are sacrificed 24 h after the last injection, on P49.

first: Manvendra

last: Singh

first: Ying

last: Zhao

first: Vinicius

last: Daguano Gastaldi

first: Sonja

last: Wojcik

first: Yasmina

last: Curto

first: Riki

last: Kawaguchi

first: Ricardo

middle: M

last: Merino

first: Laura

last: Fernandez Garcia-Agudo

first: Holger

last: Taschenberger

first: Nils

last: Brose

first: Daniel

last: Geschwind

first: Klaus-Armin

last: Nave


title: Chromatin profiling of zebrafish spinal cord tissue at 2 week post injury

first: Jianhong

last: Ou

summary: To identify regulatory tissue regeneration enhancer elements (TREEs) relevant during spinal cord regeneration, we  performed ATAC sequencing datasets of zebrafish spinal cord at 2 weeks after sham injury and after transection.

first: Valentina

last: Cigliola

first: Adam

last: Shoffner

first: Nutishia

last: Lee

first: Clay

last: Becker

first: Jiaul

last: Hoque

first: Trevor

last: Gonzalez

first: Yanchao

last: Han

first: Grace

last: Sheng

first: Timothy

last: Faw

first: Muhammad

last: Abd-El-Barr

first: Shyni

last: Varghese

first: Aravind

last: Asokan

first: Kenneth

last: Poss


title: RNA sequencing of zebrafish spinal cord tissue at 1 week post injury

summary: To identify regulators of spinal cord regeneration, we  performed RNA sequencing of zebrafish spinal cord at 1 week after sham injury and after transection.

overall_design: Spinal cord RNA profiles 1week after spinal cord transection and in sham injured controls.


title: Effect of Sphingomyelin d18:1/14:0 (S14) on gene expression in macrophages

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: We compared the effect of Sphingomyelin d18:1/14:0 (S14) and Lipopolysaccharide (LPS) on the gene expression in mouse macrophages at different timepoints

overall_design: RNA-Seq analysis was performed on bone marrow-derived macrophages (isolated from C57BL/6J wild-type mice; n=4) stimulated for 3 h or 18 h with S14 or LPS or left untreated as control.

first: Friederike

last: Gorki


title: Histone deacetylation and cytosine methylation are required for the normal compartmentalization of heterochromatin in the genome organization of Neurospora crassa

first: Andrew

last: Klocko

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

overall_design: Refer to individual Series


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

first: Musun

last: Park


title: Effect of vaccination, marketing strategy, and bovine respiratory disease development on at arrival transcriptomes of recently weaned beef cattle

status: Public on Mar 09 2023

city: Canyon

first: Matthew

last: Scott

address: 3201 Russell Long Blvd

institute: Texas A&M University

summary: Jugular whole blood samples (Tempus Blood RNA tubes) were collected and utilized from 43 cattle, specifically from all cattle diagnosed with bovine respiratory disease (BRD) during Texas backgrounding (n=32) and randomly selected cattle never treated for BRD (n=11). Total RNA was isolated from blood samples, and were library prepared and sequenced via Illumina NovaSeq 6000 S4 chemistry. Samples were bioinformatically processed in a HISAT2/StringTie2 pipeline, and stratified based on BRD diagnosis and marketing strategy (Auction versus Direct marketing and transport). Differential expression analysis was conducted in R, utilizing an additive, multifactor generalized linear model and blocking for Mississippi pasture and vaccination status. Genes were considered differentially expressed with an FDR cutoff of 0.05. The objective of this study was to identify differentially expressed genes and mechanisms within and across marketing cohorts with and without BRD.

overall_design: Fourty-three whole blood RNA samples selecting for mRNA sequencing (TruSeq Stranded mRNA) taken upon arrival to a Texas backgrounding facility.


title: Psoriasis Improvements and Inflammatory Biomarker Normalization With Secukinumab: The Randomized ObePso-S Study

status: Public on Mar 24 2023

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: To investigate treatment effects of secukinumab on clinical signs and psoriatic inflammation markers over 52 weeks in patients with psoriasis.

overall_design: Patients with psoriasis were randomized 2:1 to receive secukinumab 300 mg (n=54) or placebo (n=28), stratified by body weight (<90 or ≥90 kg), for 52 weeks. At Week 12, patients receiving placebo were switched to secukinumab. Gene expression profiles were evaluated in lesional and non-lesional skin biopsies collected at baseline, Week 12, and Week 52.

middle: G

last: Blauvelt

first: Sandra

last: Garcet


title: Transcriptome-wide profiling of Yeast Phosphofructokinase 1 and 2 RNA targets

status: Public on Jan 31 2023

city: Guildford

first: Waleed

last: Albihlal

state: Surrey

address: Stag Hill Campus

department: Microbial Sciences

country: United Kingdom

institute: University of Surrey

summary: The RNA targets of the yeast Pfk1 and Pfk2 were mapped on a transcriptome scale using formaldehyde-assisted crosslinking and RNA-protein immunoprecipitation followed by high throuput sequencing (fRIP-seq). Tandem affinity purification (TAP) tagged Pfk1 and Pfk2 were usesd to capture the transcritps bound by Pfk1 and Pfk2. We also included a mock IP control i.e. wild type treated exactly the same way as the fRIP-seq samples to account for non-specific RNA interactions with the beads. Moreover, we ran total RNA-seq on wild type control for data normalization. We found that Pfk1 and Pfk2 bind mainly to mRNAs that code for proteins invovled in distinct functions . Our data suggests that, besides their well-characterized functions as glycolytic enzymes, they perfom additional functions as RNA-binding involved in posttranscriptional regulation of gene expression.

overall_design: Our aim was to map transcripts bound by the yeast Pfk1 and Pfk2 to explore their RNA-bining functions and to obtain and insight into their potential secondary function as posttranscriptional regulators of gene expression. We performed formaldehyde assisted crosslinking followed by RNA-protein immuniprecipitation (fRIP-seq) to identify RNAs bound by Pfk1 and Pfk2 under normal physiological conditon. Diploid yeast cells expressing either Pfk1 or Pfk2 with Tandem Affinity purification (TAP) tags as well as dipliod wild type cells for mock IP control were grown in rich YPD media to mid-log phase (OD600 = 0.6) then crosslinked with low concentration of formaldehyde to a final concentration of 0.3% followed by quenching of crosslinking using glycine (final concentration 125 mM). Cells were pelleted then washed three times with 1X PBS then flash frozen in liquid nitroen. Frozen cell pellets were ground under cryogenic conditions using mortar and pestel to fine powders then powders were resuspended in fRIP lysis buffer. Pfk1:TAP-RNA and Pfk2:TAP-RNA were captured using Pan mouse IgG beads. Crosslinking was reveresed followd by proteinase K digestion of proteins then RNA was extracted using standard acidic phenol method. RNA was then converted to cDNA followed by second strand synthesis then double-stranded cDNA was sheared using sonication. Sequencing libraries were constructed using Bioline JetSeq libraray preparation kit as described in product manual. We also perfomed total RNA-seq from wild type diploid cells for data normalization. Samples were sequenced on Illumina HiSeq2500 with minimum of 5 million reads per library. Our data showed that both Pfk1 and Pfk2 bind to hunderds on mRNAs coding for proteins involved in various cellular functions. Interestingly, our data suggests that Pfk1 and Pfk2 bind to mRNAs coding for proteins involved in distinct functions indicating that the two proteins are involved in different cellular functions as posttranscriptional regulators.

first: W

first: A

middle: P

last: Gerber


title: A panel of TDP-43-regulated splicing events verifies loss of TDP-43 function in amyotrophic lateral sclerosis brain tissue

status: Public on Feb 02 2023

city: Auckland

first: Maize

last: Cao

address: 3A Symonds Street

country: New Zealand

institute: University of Auckland

summary: To investigate differential exon usage/ cryptic exon events that occur with TDP-43 depletion using human brain-derived pericytes

overall_design: Differential exon usage analysis was performed on bulk RNA-seq data of 9 donor lines  (6 from motor cortex, 3 from middle temporal gyrus) treated with either scrambled siRNA (scr) or siRNA against TARDBP (siTDP)

middle: C

first: Emma

last: Scotter


title: Expression data from rodents following ischemic injury, permanent middle cerebral artery occlusion (MCAO) Neuregulin-1 treatment.

status: Public on Dec 31 2022

city: Riverside

first: Byron

last: Ford

address: 900 University Ave

institute: University of California-Riverside

summary: We used gene expression profiling to understand the early cellular and molecular mechanisms of NRG1’s effects after the induction of ischemia.

overall_design: Cortical brain tissues were collected three hours following MCAO and NRG1 treatment, RNA extracted and hybrdized to an Affymetrix microarray chip.

first: Monique

last: Surles-Zeigler

first: Yonggang

last: Li


title: Transcriptome profiling of bladders of CYP-treated C57BL6/J mice (male and female)

status: Public on Mar 17 2023

city: Ljubljana

first: Dominika

last: Peskar

address: Vrazov trg 2

department: Institute for Cell Biology

country: Slovenia

institute: Faculty of Medicine

summary: In the present study, we aimed to identify a complete transcriptome profile of the bladders of CYP-treated mice, a commonly used animal model of IC/BPS disease. Our study represents a reference database for the understanding of the mouse model, which is crucial for the more successful translation of the data obtained on this model to human patients.

overall_design: Comparative gene expression analysis of RNA-seq data for C57BL6/J mice (Ctrl males/Females vs CYP Males/Females, CYP mice vs Ctrl mice, Ctrl males vs Ctrl females; 3 animals per group)

first: Tadeja

last: Kuret

first: Katja

last: Lakota

first: Andreja

last: Erman


title: Expression data of liver resident cells from C57BL/6 mouse

status: Public on Feb 27 2023

city: Kunming

first: Xiaolong

last: Zhang

state: Yunnan

address: 935 Jiaoling road

institute: Peking Union Medical College

summary:
The liver is composed of various resident cells, including hepatocytes, Kupffer cells, liver sinusoidal endothelial cells (LSEC), and hepatic stellate cells (HSC). Hepatocytes are the primary type of liver cells, constituting 80% of the liver's mass, and are responsible for tasks such as protein and lipid synthesis, detoxification, and bile secretion. Kupffer cells, on the other hand, are liver-resident macrophages that play a crucial role in detecting foreign antigens and danger signals within the liver, as well as clearing apoptotic cells. LSEC is in charge of blood vessel formation in the liver and is responsible for eliminating cell debris. In the quiescent state, HSC stores vitamin A and is essential in liver fibrosis when activated. Freshly isolated HSCs undergo automatic activation upon culture.
In this study, we present microarray data for freshly isolated mouse hepatocytes, Kupffer cells and LSEC, along with HSCs that have been cultured for 1, 7 or 14 days.

overall_design: Freshly sorted hepatocytes, Kupffer cells, LSECs and culture-activated HSCs were used to obtain microarray data. To culture-activate HSC, the cells were maintained in DMEM supplemented with 10% FBS in a 37°C, 5% CO2 humid incubator for 1, 7, or 14 days. All cells were isolated from naïve C57BL/6 mice. For hepatocytes, Kupffer cells, and LSEC, three biological replicates were included, while one-day cultured HSC had two replicates.

first: Florian

last: Winau


title: GDF15 neutralization restores muscle function and physical performance in a mouse model of cancer cachexia

status: Public on Jan 11 2023

city: Boston

first: Evanthia

last: Pashos

state: MA

address: 1 Portland St

institute: Pfizer Inc

summary: Cancer cachexia is a disorder characterized by both involuntary weight loss and impaired physical performance. Decline in physical performance of patients with cachexia is associated with poor quality of life, and currently there are no effective pharmacological interventions that restore physical performance. Here we examined the effect of GDF15 neutralization in a mouse model of cancer-induced cachexia (TOV21G) that manifested weight loss and muscle function impairments. With comprehensive assessments, our results demonstrated that cachectic mice treated with the anti-GDF15 antibody mAB2 exhibited body weight gain with near-complete restoration of muscle mass and markedly improved muscle function and physical performance. Mechanistically, the improvements induced by GDF15 neutralization were primarily attributed to increased caloric intake, while altered gene expressions in cachectic muscles were restored in both caloric intake-dependent and -independent manners. The findings implicate the potential of GDF15 neutralization as an effective therapy to enhance physical performance of patients with cachexia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of gastrocnemius muscle from non-tumor bearing, IgG control or anti-GDF15 antibody mAB2 in the TOV21G model of cancer cachexia


title: Emergent dynamics of adult stem cell lineages from single cell RNA-Seq of Drosophila testes

status: Public on Jan 10 2023

city: Cambridge

first: Amelie

last: Raz

state: Ma

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

summary: Here we provide a single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq . Proper differentiation of sperm from germline stem cells, essential for production of the next generation, requires dramatic changes in gene expression that drive remodeling of almost all cellular components, from chromatin to organelles to cell shape itself.  Here we provide a single nucleus and single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq (snRNA-seq) data from the Fly Cell Atlas (FCA) study (Li et al., 2022).  With over 44,000 nuclei and 6,000 cells analyzed, the data provide identification of rare cell types, mapping of intermediate steps in differentiation, and the potential to identify new factors impacting fertility or controlling differentiation of germline and supporting somatic cells.  We justify assignment of key germline and somatic cell types using combinations of known markers, in situ hybridization, and analysis of extant protein traps.  Comparison of single cell and single nucleus datasets proved particularly revealing of dynamic developmental transitions in germline differentiation.  To complement the web-based portals for data analysis hosted by the FCA, we provide datasets compatible with commonly used software such as Seurat and Monocle.  The foundation provided here will enable communities studying spermatogenesis to interrogate the datasets to identify candidate genes to test for function in vivo.

overall_design: This dataset was collected from testes of adult Drosophila males.

first: Yukiko

last: Yamashita

first: Margaret

last: Fuller

first: Stephen

last: Dinardo


title: Small RNA sequencing of term whole placenta from normal weight and obese pregnancies

status: Public on Mar 01 2023

first: Perrie

last: O’Tierney-Ginn

address: 800 Washington Street #394

department: Mother Infant Research Institute

institute: Tufts Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Context: An increase in maternal insulin resistance (IR) during pregnancy is essential for normal fetal growth. The mechanisms underlying this metabolic adaptation to pregnancy are poorly understood. Placenta factors are believed to instigate and maintain these metabolic changes, as IR decreases shortly after delivery. Methylation of placental gene loci that are common targets for miRNAs, are associated with maternal IR.   Objective: We hypothesized that placental miRNAs targeting methylated loci are associated with maternal IR during late pregnancy.   Methods: Placental miRNA expression was measured via small RNA-sequencing in a subset of 40 placentas selected by maternal pre-gravid BMI and neonatal adiposity.   Results: Median maternal age was 27.5 years, with a median pre-pregnancy BMI of 24.7 kg/m2, and median HOMA-IR of 2.9. Among the five selected miRNA, near delivery maternal HOMA-IR correlated with the placental expression of miRNA-371b-3p (r=0.25; p=0.008) and miRNA-3940-3p (r=0.32; p=0.0004) across the 132 individuals. After adjustment for confounding variables, placental miRNA-3940-3p expression remained significantly associated with HOMA-IR (β=0.16; p=0.03).   Conclusion: Placental miRNA may have an autocrine or paracrine effect - regulating placental genes which play a role in modulating maternal IR.

overall_design: Whole placenta miRNA profiles at full-term elective ceasarean delivery in women with and without obesity with high and low adiposity neonates. Neonatal % body fat was measured within 48 hrs of delivery. Maternal self-reported race (African American (AA), White (cauc)) and neonatal sex was recorded.

middle: F

last: O'Tierney-Ginn

first: Tianjiao

last: Chu

first: Yoel

last: Sadovsky

first: Patrick

last: Catalano


title: Early-life bacterial exposure affects lung surfactant gene-expression, surfactant function and respiratory rate compared to germ-free mice

status: Public on Jan 01 2023

city: Rockville

first: Julian

last: Lui

state: MD

address: 605 WATTS BRANCH PKWY, 10 Center Drive

institute: NICHD

summary: Mouse lung tissue transcriptome at postnatal day 10. Samples include 9 germ-free, 9 monocultured Bifidobacterium innoculated, and 9 full caecium microbiota innoculated. Plus 5 adult lung tissue as reference.

overall_design: Pregnant BALB/c germ-free mice were kept in separate germ-free isolators until either (a) no exposure (GF), (b) exposure to either Bifidobacterium animalis ssp. Lactis (BI04) or to (c) full cecum content harvested from female SPF mice (Cecum). Subsequently, perinatally exposed offspring were used for the analyses. Lung tissue transcriptomics analysis was done at postnatal day 10 (PNday10) at first phase of lung alveolar development. RNA were extracted for bulk RNA-sequencing.

first: Kenneth

last: Klingenberg Barfod

first: James

last: Iben


title: Transcriptomic profiling of the adult reptilian dentition sheds light on the genes regulating indefinite tooth replacement [scRNA-seq]

status: Public on Dec 24 2022

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

summary: The aim of this study is to discover new genes and cells involved in life-long tooth replacement. Here we study the adult dentition of the leopard gecko (Eublepharis macularius). Single cell RNA-seq was carried out on jaw segments containing the dental forming tissues. One week prior to isolating the cells from the two animals, the developing, unerupted teeth were plucked out of the connective tissue in one part of the jaw. Other regions of the jaw were left intact and are considered controls. The scRNA-seq experiment successfully isolated dental mesenchyme and dental epithelial clusters. There were differences between the conditions when the two animals were combined. The data showed fewer differentiated cell types remain after plucking. We have validated a subset of the genes. This work will lead to discovery of genes and cell populations that may been lost in mammals. The profiling of adult, tissue-resident dental stem cells is likely to inform future tooth regeneration strategies for humans with tooth agenesis.

overall_design:
scRNA-seq

UPDATE: [Apr-17-2026] The processed data files were replaced because a new genome assembly (GCA_028583425.1 MPM_Emac_v1.0) was used. The original (version 1) files are available in GSE221110_version1_processed_data.tar.gz.

first: Joaquin

middle: I

last: Henriquez

first: Katherine

last: Fu

first: Edward

middle: Z

last: Li

first: Joy

last: Richman


title: Effect of Snhg11 knockdown on gene expression in the murine adult dorsal hippocampus

status: Public on Oct 31 2022

city: Barcelona

first: Cesar

last: Sierra

address: C/ Dr Aiguader 88

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: To investigate the role of Snhg11 in brain gene expression regulation, we injected the dorsal DG of adult mice either with an ASO targeting Snhg11 or with a control ASO. RNA extraction of the dorsal hippocampus was done 3 days after injection

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 dorsal hippocampi injected with a Control-ASO and 3 dorsal hippocampi injected with an ASO targeting Snhg11

first: Mara

last: Dierssen


title: Mechanisms and function of de novo DNA methylation in placental development [snRNA-seq]

status: Public on Dec 15 2022

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: DNA methylation is a repressive epigenetic modification that is essential for development, exemplified by the embryonic and perinatal lethality observed in mice lacking de novo DNA methyltransferases (DNMTs). Here we characterise the role for DNMT3A, 3B and 3L in gene regulation and development of the mouse placenta. We demonstrate that each of the DNMTs is required to establish the placental methylome and is distinctly targeted to genome based on underlying chromatin features. Loss of Dnmt3b results in de-repression of germline genes in trophoblast lineages and impaired development of the placental maternal-foetal interface. Critically, loss of DNA methylation in the placenta did not lead to abnormalities in lineage specification or cell identity, but to defective formation and vascularisation of the placental labyrinth. Using Sox2-Cre to delete Dnmt3b in the embryo, leaving expression intact in placental trophoblast cells, we were able to rescue the placental phenotype and, consequently, the embryonic lethality, as Dnmt3b null embryos could now survive to birth. We conclude that the principal function of DNA methylation during embryogenesis is to regulate placental function, which in turn is critical for embryo survival.

overall_design: Using low-input RNA-seq and post bisulphite adaptor tagging (PBAT), we then assayed gene expression and genome-wide DNA methylation in E7.5 ExE and epiblast from Dnmt3a KO, Dnmt3b KO, Dnmt3a/b double KO (DKO), Dnmt3l KO and wildtype (WT) controls.  The de novo DNMT enzymes have been shown to interact with modified histone tails, which modulates their catalytic activity and genome localisation in vitro. Thus, we generated ultra-low input ChIP-seq data for H3K4me1 and H3K27ac to combine with published datasets for H3K4me3, H3K27me3 and H3K36me3 in E6.5 ExE, immediately preceding the completion of de novo DNA methylation.  To investigate the placental phenotype of Dnmt3b KO at the molecular level, we generated single nuclei RNA sequencing data from E12.5 placentas from a Dnmt3b KO and WT control.

first: Courtney

last: Hanna

first: Simon

last: Andrews


title: Defining the spatial-molecular map of fibrotic tendon healing and the drivers of Scleraxis-lineage cell fate and function

status: Public on Oct 25 2022

city: Rocheser

first: Jessica

last: Ackerman

state: NY

address: 665 Elmwood Ave

institute: University of Rochester

summary: Spatial transcriptomic analysis of murine FDL tendons following acute injury and repair to evaluate spatiotemporal programming of tendon healing

overall_design: Hindpaws from Scx-Ai9 mice (Scx-lin+ cells labeled with tdTomato fluorescence prior to surgery) were collected at D0, 14, 21, and 28 post-injury (in duplicate) for ST analysis of healing tendons using the 10X Visium platform

last: Best

first: Samantha

last: Muscat

first: Anne

last: Nichols

first: Elizabeth

last: Pritchett

first: Chia-Lung

last: Wu

first: Alayna

last: Loiselle


title: Mechanisms and function of de novo DNA methylation in placental development [RNA-Seq]


title: Molecular Profiling of Odontoclasts during Physiological Tooth Replacement

last: Flibotte

summary: The odontoclast is a rarely studied cell type that is overly active in many dental pathologies, leading to tooth loss. It is difficult to find diphyodont mammals in which either physiological or pathological root resorption can be studied. Here we use the adult leopard gecko, which has repeated cycles of physiological tooth resorption and shedding. RNA-seq was carried out to compare gene expression profiles of functional teeth to developing teeth. Genes more highly expressed in bell-stage developing teeth were related to morphogenesis (PTHLH, SFRP2, SHH, EDAR). Some genes expressed in osteoclasts (ACP5, CTSK, CSF1R) were relatively more abundant in functional teeth compared with developing teeth. There was, however, no differential expression of RANKL (TNFSF11) in the 2 tooth types. In addition, functional teeth expressed proteolysis genes not found in osteoclasts (ADAMTS2, 3, 4, 14; CTSA, CTSH, CTSS). We used tartrate acid resistant phosphatase and cathepsin K (CTSK) staining to identify odontoclasts in and around the gecko dentition. There were 3 populations of CTSK cells: (1) large, functional multinucleated odontoclasts in the crown of the tooth with a ruffled border inside resorption pits; (2) smaller, precursor cells in the pulp with fewer nuclei; and (3) flattened external precursor cells next to the root and bone of attachment. We found a positive relationship between developing teeth and the population of CTSK+ cells on the root surface. We tested a candidate signal that may be involved in CTSK+ cell presence. An antagonist of CSF1R was delivered to developing teeth in vivo, which resulted in a significant decrease in CTSK and CSF1R compared with DMSO controls. Thus, the CSF1 signaling pathway is upstream of CTSK in teeth. This is the first work to detail the molecular characteristics of odontoclasts during physiological tooth shedding and to demonstrate that in vivo, local drug delivery is possible in the gecko model.

overall_design:
Comparative gene expression profiling analysis of bulk RNA-seq data for functional and developing teeth in adult leopard geckos.

UPDATE: [Apr 08, 2026] The title and summary were updated.


title: Mechanisms and function of de novo DNA methylation in placental development [ChIP-seq]


title: Ambient RNA analysis of single-nuclei RNA-Seq data from the frontal cortex of C57BL/6J mice

status: Public on Oct 19 2022

city: Los Angeles

first: Genevieve

last: Konopka

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

summary: Contamination of ambient RNA was found in single-nuclei RNA-Seq data of mouse frontal cortex. CellBender plus subcluster cleaning selectively removed ambient RNA signature from glial cell types.

overall_design: P56 wildtype mice were harvested rostral part of the frontal cortex which is corresponding to the cortex part of Coronal level 22-36 in Allen Brain Atlas: Reference Atlas, Version 2 (2011), and extracted single nuclei for sequencing.

first: Joseph

middle: S

last: Takahashi

first: Yuxiang

last: Liu

first: Ashwinikumar

last: Kulkarni

first: Miles

last: Fontenot


title: APOE4 drives transcriptional heterogeneity and maladaptive immunometabolic responses of astrocytes (Spatial)

status: Public on Oct 20 2022

city: Lexington

first: Joshua

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

summary: Apolipoprotein 4 (APOE4), is the strongest genetic risk allele associated with the development of late onset Alzheimer’s disease (AD). Across the CNS, astrocytes are the predominant expressor of Apoe while also being critical mediators of neuroinflammation and cerebral metabolism. APOE4 has been consistently linked with dysfunctional neuro-immunometabolism, however insights into the molecular constituents driving these responses remain unclear. Utilizing complimentary approaches across humanized ApoE expressing mice and isogenic IPS astrocytes, we demonstrate that harboring ApoE4 alters astrocyte immunometabolic response to pro-inflammatory stimuli. Our findings demonstrate that ApoE4-expressing astrocytes acquire distinct transcriptional repertoires at the single-cell and spatially-resolved domains, which driven, in-part, by preferential utilization of the cRel transcription factor. Further, inhibiting cRel translocation abrogated inflammatory-induced glycolytic shift and ultimately resulted in significantly dampened glycolysis-associated metabolites in tandem with mitigating production of multiple pro-inflammatory cytokines. Altogether, our findings elucidate novel cellular underpinnings by which ApoE4 drives maladaptive immunometabolic responses of astrocytes.

overall_design: Male, targeted replacement humanized APOE33 and APOE44 mice were used for these studies. 5mg/kg LPS was administered systemically via IP injection and mice were euthanized 24hrs later.


title: Mechanisms and function of de novo DNA methylation in placental development

last: Biggins

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

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: Refer to individual Series


title: Mechanisms and function of de novo DNA methylation in placental development [PBAT]

last: Hanna


title: APOE4 drives transcriptional heterogeneity and maladaptive immunometabolic responses of astrocytes (scRNA-Seq)


title: APOE4 drives transcriptional heterogeneity and maladaptive immunometabolic responses of astrocytes


title: Single-cell RNA sequencing reveals distinct transcriptional features of the purinergic signaling in mouse trigeminal ganglion

status: Public on Oct 12 2022

city: GuangZhou

first: Jia

last: Shilin

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Institute of Stomatological Research, Sun Yat-sen University

summary: Trigeminal ganglion (TG) is the first station of sensory pathways in the orofacial region. The TG neurons communicate with satellite glial cells (SGCs), macrophages and other cells forming a functional unit that is responsible for processing of orofacial sensory information. Purinergic signaling, one of the most widespread autocrine and paracrine pathways, plays a crucial role in intercellular communication. The multidirectional action of purinergic signaling in different cell types contributes to the neuromodulation and orofacial sensation. To fully understand the purinergic signaling in these processes, it is essential to determine the shared and unique expression patterns of genes associated with purinergic signaling in different cell types. Here, we performed single-cell RNA sequencing of 22,969 cells isolated from normal mouse TGs. We identified 18 distinct cell populations, including 6 neuron subpopulations, 3 glial subpopulations, 7 immune cell subpopulations, fibroblasts, and endothelial cells. We also revealed the transcriptional features of genes associated with purinergic signaling, including purinergic receptors, extracellular adenosine triphosphate (eATP) release channels, eATP metabolism-associated enzymes, and eATP transporters) in each cell type. Our results have important implications for understanding and predicting the cell type-specific roles of the purinergic signaling in orofacial signal processing in the trigeminal primary sensory system.

overall_design: Bilateral TGs of 5 normal mouse were harvested (n=10) and performed scRNA-seq. We aimed to identify distinct cellular populations in TG and describe the transcriptional features of the genes associated with the purinergic signaling in each cell type using scRNA-seq.

first: Lijia

last: Mai

first: Shilin

last: Jia

first: Qing

first: Yanhao

last: Chu

first: Jinyue

first: Shengyan

last: Yang

first: Fang

last: Huang

first: Hongwen

last: He

first: Wenguo

last: Fan


title: Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice

first: Cesar

last: Sierra

summary: In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn

overall_design: Neuronal hippocampal population from adult (4 month old) mice was isolated by  Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq.

first: Mara

last: Dierssen


title: Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system

status: Public on Oct 05 2022

city: Atlanta

first: Eliver

last: Ghosn

state: GA

address: 1760 Haygood Dr NE

department: Lowance Center for Human Immunology

institute: Emory University School of Medicine

summary: Single-cell transcriptomics enables the definition of diverse human immune cell types across multiple tissue and disease contexts. Still, deeper biological understanding requires comprehensive integration of multiple single-cell -omics (transcriptomic, proteomic, and cell receptor repertoire). To improve the identification of diverse cell types and the accuracy of cell-type classification in our datasets, we developed SuPERR-seq, a novel analysis workflow to increase the resolution and accuracy of clustering and allow for the discovery and characterization of previously hidden cell subsets. We show that by incorporating information from cell-surface proteins and immunoglobulin transcript counts, we accurately remove cell doublets, and prevent widespread cell-type misclassification. This approach uniquely improves identification of heterogenous cell types in the human immune system, including a novel subset of antibody-secreting cells in the bone marrow.

overall_design:
scRNA-seq of the gene expression profile, surface-protein expression profile and the V(D)J profile of 3 Peripheral blood mononuclear cell (PBMC) and 2 Bone marrow (BM) from healthy donors.
Please note that processed data was generated from all GEX, ADT and V(D)J raw data and is linked to the corresponding *[GEX] sample records.

first: Congmin

last: Xu

first: Junkai

first: Astrid

last: Kosters

first: Benjamin

last: Babcock

first: Peng

last: Qiu


title: Trophoblast induced reprogramming of the decidualization program

status: Public on Sep 28 2022

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: Transcriptional effect of trophoblast-decidual interactions.

overall_design: Sequencing of endometrial fibroblasts before and after decidualization, and before and after co-culture with HTR8 and Bewo.

first: Kshitiz

last: Gupta