title: DNA methylation and copy number profiling in polymicrogyria

status: Public on Nov 18 2020

city: Erlangen

first: Katja

last: Kobow

state: Deutschland

address: Schwabachanlage 6

department: Neuropathology

country: Germany

institute: Universitätsklinikum Erlangen

summary: Polymicrogyria (PMG) is a developmental cortical malformation characterized by an excess of small and frustrane gyration and abnormal cortical lamination. PMG frequently associates with seizures. The molecular pathomechanisms underlying PMG development are not yet understood. About 40 genes have been associated with PMG, and small copy number variations have also been described in selected patients. We recently provided evidence that epilepsy-associated structural brain lesions can be classified based on genomic DNA methylation patterns. Here we analyzed 27 PMG patients employing array-based DNA-methylation profiling on formalin-fixed paraffin-embedded material. A series of 63 well-characterized non-PMG cortical malformations (focal cortical dysplasia type 2a/b and hemimegalencephaly), temporal lobe epilepsy, and non-epilepsy autopsy controls was used as reference cohort. Unsupervised dimensionality reduction and hierarchical cluster analysis of DNA methylation profiles showed that PMG formed a distinct DNA methylation class. Copy number profiling from DNA methylation data identified a uniform duplication spanning the entire long arm of chromosome 1 in 7 out of 27 PMG patients, which was verified by additional fluorescence in situ hybridization analysis. In respective cases about 50% of nuclei in the center of the PMG lesion were 1q triploid. No chromosomal imbalance was seen in adjacent, architecturally normal-appearing tissue indicating mosaicism. Clinically, PMG 1q patients presented with a unilateral frontal or hemispheric PMG without hemimegalencephaly, a severe form of intractable epilepsy with seizure onset in the first months of life, and severe developmental delay. Our results show that PMG can be classified among other structural brain lesions according to their DNA methylation profile. One subset of PMG with distinct clinical features exhibits a duplication of chromosomal arm 1q.

overall_design: Bisulphite converted DNA from 96 samples was hybridised to Illumina Infinium 850k Human Methylation Beadchip arrays

first: Samir

last: Jabari

first: Tom

last: Pieper

first: Manfred

last: Kudernatsch

first: Tilman

last: Polster

first: Friedrich

last: Woermann

first: Thilo

last: Kalbhenn

first: Hajo

last: Hamer

first: Karl

last: Rössler

first: Angelika

last: Mühlebner

first: W

last: Spliet

first: Martha

last: Feucht

first: Yanghao

last: Hou

first: Damian

last: Stichel

first: Andrey

last: Korshunov

first: Felix

last: Sahm

first: Roland

last: Coras

first: Ingmar

last: Blümcke

first: Andreas

last: von Deimling


title: Age-Related Injury Responses of Human Oligodendrocytes to Metabolic Insults: Link to BCL-2 and Autophagy Pathways [RNA-seq]

status: Public on Dec 31 2020

city: Montreal

first: Jack

last: Antel

state: Quebec

address: 3801 University, Montreal Neurological Institut

country: Canada

institute: Montreal Neurological Institute

type: Expression profiling by high throughput sequencing

summary: Myelin destruction and oligodendrocyte (OL) death consequent to metabolic stress is a feature of CNS disorders across the age spectrum. Using cells derived from surgically resected tissue, we demonstrate that young (<age 5) pediatric-aged sample OLs are more resistant to in-vitro metabolic injury than fetal O4+ progenitor cells, but more susceptible to cell death and apoptosis than adult-derived OLs. Pediatric but not adult OLs show measurable levels of TUNEL+ cells, a feature of the fetal cell response. The ratio of anti- versus pro-apoptotic BCL-2 family genes are increased in adult versus pediatric (<age 5) mature OLs and in more mature OL lineage cells. Lysosomal gene expression was increased in adult and pediatric compared to fetal OL lineage cells. Cell death of OLs was increased by inhibiting pro-apoptotic BCL-2 gene and autophagy activity. These distinct age-related injury responses should be considered in designing therapies aimed at reducing myelin injury.

overall_design: Comparison of autophagy and BCL2 family gene expression in oligodendrocyte-lineage cells derived from single-cell RNA sequencing of human tissue from 15 donors across 3 different age groups (fetal, pediatric, adult)

first: Milton

middle: G

last: Fernandes

first: Julia

middle: X

last: Luo

first: Qiao-Ling

last: Cui

first: Kelly

last: Perlman

first: Florian

last: Pernin

first: Moein

last: Yaqubi

first: Jeffrey

middle: A

last: Hall

first: Roy

last: Dudley

first: Myriam

last: Srour

first: Charles

middle: P

last: Couturier

first: Kevin

last: Petrecca

first: Catherine

last: Larochelle

first: Luke

middle: M

last: Healy

first: Jo-Anne

last: Stratton

first: Timothy

middle: E

last: Kennedy


title: A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

status: Public on Nov 20 2020

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of characterization in microbes other than Escherichia coli. Here, we have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (TraDIS), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrated a virulence and motility defect of a Salmonella ΔmgrB mutant and revealed an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Overall, our study highlights the power of interpreting available “omics” datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: A Salmonella transposon mutant pool was generated and used for macrophages infection. Abundance of each mutant was quantified before and after infection and used to assess the requirement for virulence of the disrupted genes.


title: The lncRNA and gene expression profiles during the early stages of mice thymic involution

status: Public on Nov 28 2020

city: Guangzhou

first: Yugu

last: Li

address: Wushan street

country: China

institute: South China Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we collected mice thymus at the age of 1 month, 3 months, and 6 months for sequencing to observe the lncRNA and gene expression profiles in the early stage of thymic involution. RNA-sequencing showed that 340 and 152 differentially expressed genes (DEGs) overlapped at 3- and 6-month-old groups compared with 1-month-old group in males and females, respectively. GO analysis showed that DEGs were significantly enriched in immune response activation, cell proliferation, and fatty acid metabolic process, etc. Next, we identified 15 causal transcription factors. Meanwhile, we identified 16 key DEGs and 29 differentially expressed lncRNAs (DEL), which overlapped both in the male and female groups of 3 months and 6 months for further analysis. Finally, we identified a novel lncRNA–miRNA–mRNA network related to adipocyte deposition using Cytoscape. In summary, this study systematically identified and analyzed the expression profiles of lncRNAs and genes during the early stages of thymic involution, which provided valuable data reference for further exploring the roles of lncRNAs in thymic involution.

overall_design: Identification and analysis of lncRNA and gene expression profiles in the thymus of BALB/c mice at the age of 1 month, 3 months and 6 months

first: Bingxin

first: Yaqiong

last: Ye

first: Qingru

last: Wu


status: Public on Nov 22 2020

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

institute: Institute for Molecular Infection Biology

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Salmonella cells (WT or delta_mgrB) were grown in minimal medium. Total RNA was extracted and sequenced for two biological replicates.

first: Elisa

last: Venturini


status: Public on Nov 17 2020

city: Freiburg

first: Florian

last: Eggenhofer

address: Georges Köhler Allee 106

department: Institute for Informatics

institute: University of Freiburg

summary: Our study highlights the power of interpreting available “omics” datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.

overall_design: Ribosome profiling analysis of the Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 translatome paired with transcriptome sequencing

first: Sarah

middle: L

last: Svensson

first: Cynthia

last: Sharma


title: Systems biology demonstrates the predominant role of circulating interferon-alpha in primary Sjögren's syndrome and a genetic association with the class II HLA DQ locus

status: Public on Nov 04 2020

city: Strasbourg

first: Jacques-Eric

last: Gottenberg

address: 15 Renee Descartes Street

country: France

institute: Institut de Biologie Moleculaire et Cellulaire

summary: Primary Sjögren’s syndrome (pSS) is the second most frequent systemic autoimmune disease, affecting 0.1% of the general population. No specific immunomodulatory drug has demonstrated efficacy for this disease, and no biomarker is available to identify patients at risk of developing systemic complications. To characterize the molecular and clinical variability across pSS patients, we integrated transcriptomic, proteomic, cellular and genetic data with clinical phenotypes in a cohort of 351 pSS patients. Unbiased global transcriptomic analysis revealed an IFN gene signature as the strongest driver of transcriptomic variability. The resulting stratification was replicated in three independent cohorts. As transcriptomic analysis did not discriminate between type I and II interferons, we applied digital ELISA to find that the IFN transcriptomic signature was driven by circulating IFNɑ protein levels. This cytokine, detectable in 75% of patients, was significantly associated with clinical and immunological features of disease activity at enrollment, and with increased frequency of systemic complications during the 5-year follow-up. Genetic analysis revealed a significant association between IFNɑ protein levels and an MHC-II HLA-DQ locus and anti-SSA antibody. Additional cellular analysis revealed that the polymorphism acts through upregulation of HLA II molecules on conventional DCs. Our unbiased analysis thus identified the predominance of IFNα as driver of pSS variability, and revealed an association with HLA gene polymorphisms.

overall_design: Whole blood transcriptome from 351 primary Sjögren’s syndrome patients was studied using Affymetrix chip. Resulting data were used to study the biological heterogeneity among patients and to link it to clinical heterogeneity.


title: Leukemia-on-a-Chip: Dissecting the chemo-resistance mechanisms in B-cell acute lymphoblastic leukemia (B-ALL) bone marrow niche

status: Public on Oct 31 2020

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

summary: B-cell acute lymphoblastic leukemia (B-ALL) blasts hijack the bone marrow (BM) microenvironment to form chemo-protective leukemic BM ‘niches’, facilitating chemo-resistance and, ultimately, disease relapse. However, the ability to dissect these evolving, complex interactions among distinct B-ALL subtypes and their varying BM niches is limited with current in vivo methods. Herein, we reconstituted an in vitro three-dimensional (3D) organotypic leukemic BM niche model using a ‘Leukemia-on-a-Chip’ platform and comparatively studied the spatial and genetic heterogeneity of the BM niche in regulating B-ALL chemotherapy resistance. By emulating the leukemia BM anatomy in vitro, we determined that the perivascular and endosteal niches, through providing cytokine (e.g. CXCL12) and adhesive (e.g. VCAM-1/OPN) signals, differentially enhance downstream leukemia-intrinsic NF-κB signaling to support B-ALL survival and regulate cell cycle-related signaling to promote dormancy, which following demonstrated the pre-clinical utility of this microphysiological system to screen concomitant niche-directed therapies. Furthermore, we revealed the heterogeneity across different B-ALL subtypes by mapping subtype-specific leukemia and niche signals with application of single-cell RNA sequencing and analysis, which may contribute to chemotherapy resistance and disease relapse. Together, these results validate that our Leukemia-on-a-Chip allows for real-time and controllable dissection of the dynamic and heterotypic interactions between leukemia blasts and their BM microenvironment, which may translate to personalized therapeutics screening and disease management.

overall_design: Single-cell RNA-sequencing libraries of the retrived cells form the ex vivo human bone marrow niche models. Human REH B-ALL cells, Human SUP-B15, Human umbilical vein cells (HUVECs, Lonza), Human mesenchymal stem cells (hMSC, Lonza) and Human osteoblasts (hFOB 1.19, ATCC) were also sequenced as controls

first: Matthew

middle: T

last: Witkowski

first: Iannis

last: Aifantis

first: Chao

last: Ma

first: Weiqiang

last: Chen


title: RNA-Seq analysis of liver and peripheral nervous tissues from cynos treated with GS-8873.

status: Public on Oct 30 2020

city: Foster City

first: Ricardo

last: Ramirez

state: CA

address: 333 Lakeside Drive

institute: Gilead Sciences, Inc.

summary: GS-8873, an HBV RNA transcript suppressor involving the TENT4A/B RNA stabilization complex was evaluated in 13‑week toxicity studies with 8 weeks of recovery. Cynomolgus monkeys were orally dosed by gavage at 0, 0.5, 1.5, 3 and 6 mg/kg/day. Neuroelectrophysiology testing was conducted at weeks 4 and 13 of dosing and at week 4 and 8 post-recovery. Adverse electrophysiology effects occurred by week 13 in both species with a dose response compared to controls. The mean latency percent change values were increased (>10%) by week 4 in the monkey cauda equina. Monkey 13 week latency values increased by 24% and 31% in the sural nerves and cauda equina respectively with reductions in NCV. The electrophysiology values did not return to vehicle control group levels after 8 weeks of recovery, although some reversal was evident.  Monkey lumbar dorsal root ganglia samples from the 6 mg/kg/day dose group were evaluated by RNA-Seq and revealed 102 differentially expressed genes enriched for neuronal disease pathway associations compared to the controls.

overall_design: 8 animals were used for oral dosing by gavage: 4 with 6 mg/kg/day and 4 with 0 mg/kg/day of HBV mRNA transcript inhibitor GS-8873 for 13-weeks. At the time of sacrifice, samples were collected from liver, spinal cord and dorsal root ganglia of each animal. Three spinal cord samples were obtained from each animal from cervical, thoracic and lumbar regions. Two Dorsal root ganglia samples were obtained from each animal from cervical and lumbar regions.

first: April

middle: D

last: Lake-O'Connell

first: Kevin

last: Holsapple

first: Tanya

last: McDonnell

first: Joseph

middle: C

last: Arezzo

first: Lindsay

last: Gamelin

first: Mei

last: Yu

first: Dylan

last: Glatt

first: Ryan

last: Dick

first: Xiaodong

last: Xie

first: Regina

last: Choy

first: Guofeng

last: Cheng

first: Chin

middle: H

last: Tay

first: Anne

last: Chester

first: Darryl

last: Kato

first: Leigh

last: Burns-Naas


title: Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer's disease

status: Public on Sep 28 2020

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

summary: Alzheimer’s disease (AD) is the most common form of dementia but has no effective treatment. A comprehensive investigation of cell-type-specific responses and cellular heterogeneity in AD is required to provide precise molecular and cellular targets for therapeutic development. Accordingly, we perform single-nucleus transcriptome analysis of 169,496 nuclei from the prefrontal cortical samples of AD patients and normal control (NC) subjects. Differential analysis shows that the cell-type-specific transcriptomic changes in AD are associated with the disruption of biological processes including angiogenesis, immune activation, synaptic signaling, and myelination. Subcluster analysis reveals that compared to NC brains, AD brains contain fewer neuroprotective astrocytes and oligodendrocytes. Importantly, our findings show that a subpopulation of angiogenic endothelial cells is induced in the brain in patients with AD. These angiogenic endothelial cells exhibit increased expression of angiogenic growth factors and their receptors (i.e., EGFL7, FLT1, and VWF) and antigen-presentation machinery (i.e., B2M and HLA-E). This suggests that these endothelial cells contribute to angiogenesis and immune response in AD pathogenesis. Thus, our comprehensive molecular profiling of brain samples from patients with AD reveals previously unknown molecular changes as well as cellular targets that potentially underlie the functional dysregulation of endothelial cells, astrocytes, and oligodendrocytes in AD, providing important insights for therapeutic development.

overall_design:
Single-nucleus RNA-sequencing of prefrotnal cortex from AD patients and healthy control.

NOTE: Endothelial cells cluster, originally described in the publication, contains other vascular cell types including pericytes, smooth muscle cells, and fibroblasts (See Sun et al., Nature Neuroscience, 2023).

first: N

last: Ip N

first: S

middle: F

last: Lau


title: Gene expression during synaptic regeneration between cochlear hair cells and neurons

status: Public on Sep 14 2020

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Significant changes in the expression of synaptic and inflammatory genes were observed early after damage, during regeneration of the fibers and synapses, and after completion of in vitro regeneration between afferent neurons and cochlear hair cells.

overall_design: Explants of the cochlea from early postnatal mice were exposed to kainate to induce glutamate toxicity. The organ of Corti (OC), housing the hair cells, and spiral ganglion (SG), containing the afferent neurons, were separated by dissection and mRNA analyzed by Illumina hybridization.

first: Chen-Chi

last: Wu

first: Aurore

last: Brugeaud

first: Ariel

last: Yeh

first: Marco

last: Petrillo

first: Albert

middle: S

last: Edge

first: Konstantina

last: Stankovic


title: Directionality of developing skeletal muscles is set by mechanical forces

status: Public on Oct 27 2020

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

summary: Formation of oriented myofibrils is a key event in the development of a functional musculoskeletal system. However, the mechanisms that control orientation of myocytes, their fusion and the resulting directionality of adult muscles remain enigmatic. Here, we utilized in vivo and in vitro live imaging, CAS9/CRISPR-mediated mutagenesis in fish, genetic experiments in mice and single cell transcriptomics to demonstrate that individual myocyte polarization and subsequent orientation depend on cell stretch imposed by skeletal expansion. Our data revealed that upon migration, individual facial myocytes form unpolarized clusters corresponding to future muscle groups. These clusters undergo oriented stretch and alignment during embryonic growth. Experimental in vivo perturbations of cartilage shape, size and distribution caused disruptions in directionality and number of myofibrils. Controlled in vitro 2D and 3D experiments applying continuous tension via artificial attachment points demonstrated a sufficiency for mechanical forces to instruct coherent polarization of myocyte populations. Consistently, perturbations of cartilage extension revealed a role of the developing skeleton in the directional outgrowth of non-muscle soft tissues during limb and facial morphogenesis.

overall_design: We performed single cell transcriptomic analysis of cells collected daily from soft and hard culture conditions (Fig. 7b). cDNA libraries were prepared and sequenced from 2000 cells from each condition via 10X Genomics Chromium platform

first: Kazunori

last: Sunadome

first: Delf

last: Kah

first: Ben

last: Fabry

first: Csaba

last: Adori

first: Alek

last: Erickson

first: Polina

last: Kameneva

first: Shigeaki

last: Kanatani

first: Marketa

last: Kaucka

first: Ivar

last: Dehnisch

last: Tesarova

first: Tomáš

last: Zikmund

first: Jozef

last: Kaiser

first: Steven

last: Edwards

first: Kaj

last: Fried

first: Igor

last: Adameyko


title: Mycobacterium abscessus -bronchial epithelial cells cross-talk through Type I interferon signaling

status: Public on Aug 16 2020

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Manipulating niche composition limits damage to haematopoietic stem cells during Plasmodium infection

status: Public on Sep 10 2020

city: Cambridge

first: Sam

last: Watcham

address: Jeffery Cheah Biomedical Centre

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: Severe infections are a major stress on haematopoiesis, where the consequences for haematopoietic stem cells (HSCs) have only recently started to emerge. HSC function critically depends on the integrity of complex bone marrow (BM) niches, however whether the BM microenvironment plays a role in mediating the effects of infection on HSCs remains an open question. Here, using a murine model of malaria and combining single cell RNA sequencing, mathematical modelling, transplantation assays and intravital microscopy, we show that haematopoiesis is reprogrammed upon infection, whereby the HSC compartment turns over significantly faster than in steady-state and HSC function is drastically affected as a result. Interferon is found to affect both haematopoietic and mesenchymal BM cells and we specifically identify a dramatic loss of osteoblasts and alterations in endothelial cell function. Osteo-active parathyroid hormone treatment abolishes infection-triggered HSC proliferation and, coupled with Reactive Oxygen Species quenching, enables partial rescuing of HSC function.

overall_design: LK blood progenitor cells from 2 WT and 2 Malaria-infected mice were sequenced by 10X Genomics and compared across genotypes

first: Myriam

last: Haltalli

first: Nicola

last: Wilson

first: Bertie

last: Gottgens

first: Cristina

last: Lo Celso


title: Multi-model preclinical platform predicts clinical response of melanoma to immunotherapy

status: Public on Jun 01 2020

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary: Although immunotherapy has revolutionized cancer treatment, only a subset of patients demonstrates durable clinical benefit. Definitive predictive biomarkers and targets to overcome resistance remain unidentified, underscoring the urgency to develop reliable immunocompetent models for mechanistic assessment. Here we characterize a panel of syngeneic mouse models representing a variety of molecular and phenotypic subtypes of human melanomas and exhibiting their diverse range of responses to Immune Checkpoint Blockade (ICB). Comparative analysis of genomic, transcriptomic and tumor-infiltrating immune cell profiles demonstrated alignment with clinical observations and validated the correlation of T-cell dysfunction and exclusion programs with resistance. Notably, genome-wide expression analysis uncovered a Melanocytic Plasticity Signature (MPS) predictive of patient outcome in response to ICB, suggesting that the multipotency and differentiation status of melanoma can determine ICB benefit. Our comparative preclinical platform recapitulates melanoma clinical behavior and can be employed to identify new mechanisms and treatment strategies to improve patient care.

overall_design: The cell lines and GEM-derived allografts from the four models were harvested and DNA was extracted for whole exome sequencing. 1.0x106 melanoma cells (Cell line-derived allografts) from each model were implanted subcutaneously (s.c.) into C57BL/6N mice. When the tumors reached in average 75mm3, mice were randomized and treated with mouse aCTLA-4 (BioXCell, BP0164, clone 9D9) or mouse IgG2b as isotype control (BioXcell, BP0086). Antibodies were administered intravenously (i.v.) at a final dose of 10mg/Kg twice per week for a total of 4 doses. Tumors were harvested at endpoint and RNA extracted for sequencing.

first: Eva

last: Pérez-Guijarro

first: Howard

last: Yang

first: Romina

last: Araya

first: Rajaa

last: El Meskini

first: Helen

last: Michael

first: Suman

middle: K

last: Vodnala

first: Kerrie

last: Marie

first: Cari

last: Smith

first: Sung

last: Chin

first: Khiem

last: Lam

first: Andres

last: Thorkelsson

middle: J

last: Iacovelli

first: Alan

last: Kulaga

first: Anyen

last: Fon

first: Aleksandra

last: Michalowski

first: Willy

last: Hugo

first: Roger

last: Lo

first: Nicholas

last: Restifo

first: Shyam

last: Sharan

first: Terry

last: Van Dyke

last: Goldszmid

first: Zoe

last: Weaver Ohler

first: Chi-Ping

last: Day

first: Glenn

last: Merlino


title: Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

status: Public on Jun 14 2020

first: Qian

last: Yang

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We profiled fresh-frozen esophageal tumor and normal samples and cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs was investigated by ChIP-Seq, RNASeq, 4C-Seq and luciferase assay. Biological functions of candidate factors were evaluated by measuring cell proliferation, colony formation, cell apoptosis and xenograft growth. Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. Here, we aim to compare of Eso26 cells knock down HNF4A with siRNA and control transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. We also report the application of circular chromatin conformation capture (4C) sequencing technology for studying master transcription factor (HNF4A) in human esophageal adenocarcinoma cancer cell lines (Eso26).

overall_design: Esophageal Cancer and normal cell lines and fresh-frozen tissues were harvested, and ChIPseq was performed using H3K27Ac and transcription factor antibodies. Eso26 cells knock down HNF4A with siRNA and control were generated by deep sequencing, in triplicate, using Illumina GAIIx. 4C sequencing analysis in espohageal adenocarcinoma cell line.

first: Jian

last: Pan

first: Tiago

last: Silva

first: Nicole

last: Gull

first: Jasmine

last: Plummer

first: Stephanie

last: Chen

first: Kenji

last: Daigo

first: Takao

last: Hamakubo

first: Ling-Wen

last: Ding

first: Samuel

last: Klempner

first: Benjamin

last: Berman

first: H

last: Koeffler

first: De-Chen

last: Lin


title: Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters

status: Public on Apr 30 2020

first: Weiya

middle: Stephanie

last: Ni

state: California

address: 1450 Biggy Street

institute: University of Southern California

summary: Our study focuses on a family of ubiquitously expressed human C2H2 zinc finger proteins comprised of ZFX, ZFY, and ZNF711. Although their protein structure suggests that ZFX, ZFY, and ZNF711 are transcriptional regulators, the mechanisms by which they influence transcription have not yet been elucidated. We used CRISPR-mediated deletion to create bi-allelic knockouts of ZFX and/or ZNF711 in female HEK293T cells (which naturally lack ZFY). We found that loss of either ZFX or ZNF711 reduced cell growth and that the double knockout cells have major defects in proliferation. RNA-seq analysis revealed that thousands of genes showed altered expression in the double knockout clones, suggesting that these TFs are critical regulators of the transcriptome. To gain insight into how these TFs regulate transcription, we created mutant ZFX proteins and analyzed them for DNA binding and transactivation capability. We found that zinc fingers 11-13 are necessary and sufficient for DNA binding and, in combination with the N terminal region, constitute a functional transactivator. Our functional analyses of the ZFX family provides important new insights into transcriptional regulation in human cells by members of the large, but under-studied family of C2H2 zinc finger proteins.

overall_design: RNA-seq, ChIP-seq, ChIP-exo, (and EPIC array (GSE148960)) in HEK293T kidney cells and 22Rv1 prostate cells


title: Trajectory Mapping of the Early Drosophila Germline Reveals Controls of Zygotic Activation and Sex Differentiation

city: Kweishan, Taoyuan

first: Shu Yuan

address: Wenhua 1st Rd, No. 259

country: Taiwan

institute: Chang Gung University

summary: We report single-cell RNA-sequencing data for sexed D. melanogaster germ cells from 0-8h embryos. We find in this time window that the transcriptome of male and female germ cells diverge and this coincides with the activation of the zygotic germline genome.

overall_design: Three datasets were collected to provide comprehensive coverage of the early germline: 0-8h unsexed germ cells, 5-8h male germ cells, 5-8h female germ cells


title: The spatial landscape of gene expression isoforms in tissue sections

status: Public on Aug 26 2020

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Mouse brain 10x Genomics Visium Spatial Transcriptomics profiles sequence either with Illumina for standard profiling and Nanopore promethION long read sequencer for full-length profiling.

overall_design: Visium Spatial Transcriptomics profiles of 2 mouse hippocampal samples (CBS1, CBS2) and 1 mouse olfactory bulk sample (MOB) sequence with short (illumina) and long (Nanopore) reads.

first: Joseph

last: Bergenstråhle

first: Kim

last: Thrane

first: Pascal

last: Babry

first: Rainer

last: Waldmann

first: Joakim

last: Lundeberg


title: RNA-seq analysis of differentially expressed genes as a function of initial cell-population density during lineage-commitment in mouse embryonic stem cells

status: Public on Sep 09 2020

city: Delft

first: Hirad

last: Daneshpour

address: Van der Maasweg 9

country: Netherlands

institute: TU Delft

summary: We examined all transcriptome-level expressions in three initial cell-population densities (862, 1724 and 5172 cells/cm2) in the first two days of differentiation in N2B27. We collected cells in 10-mL tubes and centrifuged them using a pre-cooled centrifuge. We then extracted RNA from each cell-pellet using the PureLink RNA Mini Kit (Ambion, Life Technologies) according to its protocol. We next prepared the cDNA library with the 3′ mRNASeq library preparation kit (Quant-Seq, Lexogen) according to its protocol. We then loaded the cDNA library onto an Illumina MiSeq system using the MiSeq Reagent Kit v3 (Illumina) according to its protocol. We analyzed the resulting RNA-seq data as previously described (Trapnell et al., Nat Protoc 2012). We performed the read alignment using TopHat, read assembly using Cufflinks and analyses of differential gene expression data using Cuffdiff. We used the reference genome for Mus musculus from UCSC (mm10). We performed enrichment analysis of genes based on their FPKM values (e.g., more than 2-fold expressed when two initial population densities are compared) by using GO-terms from PANTHER (Mi et al., Nucl Acids Res 2019) and custom MATLAB script (MathWorks). We visualized results of pre-sorted, Yap1-related genes (LeBlanc et al., Elife 2018; Mugahid et al., Elife 2020; Yu et al., Oncogene 2018; Huh et al., Cells 2019; Zhu et al., Nature Sci Rep 2018; Zhou et al., Int J Mol Sci 2016; Vigneron & Vousden, EMBO J 2012; Kim et al., Cell 2015) into heat maps that displays the normalized expression value (row Z-score) for each gene and each condition.

overall_design: We analyzed a total of 7 samples (see listed below). Each sample is represented by 3 biological replicates that were acquired from 3 independent experiments.

first: Pim

last: van den Bersselaar

first: Hyun

last: Youk


title: The midbody acts as a translationally active membraneless organelle

status: Public on Jul 18 2020

city: Boston

first: Michael

middle: Demian

last: Blower

state: MA

address: 185 Cambridge St CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

summary: mRNAs associated with microtubules during interphase, metaphase and the midbody stage of cytokinesis were sequenced. Selective midbody-localized RNAs were identified and their translational characteristics were studied.

overall_design: poly-A+ RNAs were purified and sequenced from microtubules purified during interphase, metaphase or midbodies.

first: Ahna

last: Skop


title: Small RNA transcriptome analysis by parallel single cell small RNA sequencing (PSCSR-seq)

status: Public on Jul 07 2020

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute Of Biological Sciences, Beijing (NIBS)

summary: miRNA and other forms of small RNA are now known to regulate many biological processes, and miRNA profiling is already used biomedically for cancer diagnosis, staging, progression, prognosis, and to evaluate responsivity to treatment. However, there is no robust analytical method capable of dissecting the individual miRNA expression profiles from the highly heterogeneous cells comprising tumor samples. Here, we developed parallel single cell small RNA sequencing (PSCSR-seq), which enables highly sensitive and high-throughput miRNA expression profiling of individual cells. We applied PSCSR-seq to examine the small RNA profiles from large numbers of cultured cancer cells, human PBMCs, and from a tumor in a melanoma mouse model. We anticipate that PSCSR-seq can be broadly applied for small RNA analysis in cancer research and more generally in life science.

overall_design: small RNA transcriptome analysis in cancer cell lines, PBMCs, tumor tissue

first: Jia

last: Li


title: Analysis of RNA-TAG labeling in HeLa lysates

status: Public on Apr 25 2020

city: La Jolla

first: Neal

last: Devaraj

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: UCSD

summary: We report the application of RNA-sequencing to streptavidin-affinity purified RNA transcripts from HeLa cell lysates. RNA was biotinylated using the enzymatic RNA-TAG methodology using two variants of E. Coli TGT, the wild type enzyme and an obligate dimeric form of the enzyme for comparison of selectivity. From this analysis, it was determined that the obligate dimer enabled affinity purification of the desired transcript with much greater selectivity.

overall_design: Examination of 2 different RNA labeling conditions in HeLa cell lysates

first: Kayla

middle: N

last: Busby

first: Dongyang

last: Zhang


title: Single Cell Transcriptional Analysis of Donor and Recipient Immune Cell Chimerism in the Rejecting Kidney Transplant

status: Public on Jul 22 2020

city: st louis

first: andrew

last: malone

state: MO

address: 4525 laclede ave

institute: Washington University

type: Genome variation profiling by high throughput sequencing

summary: We analyzed the transcriptomes from 81139 cells from 5 kidney transplant biopsies. We sequenced the germline coding sequence from donor and recipient pairs corresponding to each biopsy as a reference to determine donor host chimerism in each kidney.

overall_design: 10X Chromium and NGS used for single cell RNA-seq and Whole-exome sequencing respectfully.

first: Andrew

last: Malone


title: Naproxen Chemoprevention Promotes Immune Activation In Lynch Syndrome Colorectal Mucosa

status: Public on Jun 25 2020

city: Houston

first: Eduardo

last: Vilar

state: Texas

address: 1155 Pressler Street

department: Department of Clinical Cancer Prevention

institute: The University of Texas MD Anderson Cancer Center

summary: Lynch syndrome (LS) patients are at markedly increased risk for colorectal cancer. It is being increasingly recognized that the immune system plays an essential role in LS tumor development. Therefore, immune interception strategies are emerging as a novel way to prevent cancer in LS. This phase Ib, placebo-controlled, randomized clinical trial and a co-clinical trial using a LS mouse model and patient-derived organoids aims to evaluate the safety and tolerability as well as to discover novel molecular pathways involved in the activity of Naproxen as chemoprevention in LS patients.

overall_design: This is a phase Ib, placebo-controlled, randomized clinical trial of two doses (440mg and 220mg) of Naproxen administered daily over a period of 6 months from January 2014 to October 2017, and a co-clinical trial using a LS mouse model and patient-derived organoids to validate the biomarker results. There are 21 pre- and 21 paired post-treatment mRNAseq samples in human placebo group (PL), 14 pre- and 14 paired post-treatment mRNAseq samples in human low-dose (220mg) naproxen group (LD),  15  pre- and paired post-treatment mRNAseq samples in human high-dose (440mg) naproxen group (HD),  6 mRNAseq samples in patient-derived organoids control group and 6 paired mRNAseq samples in patient-derived organoids naproxen group,  3 independent mRNAseq samples in LS mouse model control group and 3 independent mRNAseq samples in LS mouse model naproxen group. All samples were sequenced by Illumina HiSeq4000 instrument that generated paired-end 75 or 76-base pair (bp) reads.


title: A Transcriptional Regulatory Loop of Master Regulator Transcription Factors, PPARG, and Fatty Acid Synthesis Promotes Esophageal Adenocarcinoma

status: Public on Jun 06 2020

first: Qian

last: Yang

summary: We profiled esophageal adenocarcinoma cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs was investigated by ChIP-Seq, RNA-Seq, 4C-Seq and luciferase assay. Biological functions of candidate factors were evaluated by measuring cell proliferation, colony formation, cell apoptosis and xenograft growth. Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. Here, we aim to compare of Eso26 or OE33 cells knock down PPARG with siRNA and control transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. We also report the application of ChIP sequencing technology for studying master transcription factor (PPARG) in human esophageal adenocarcinoma cancer cell lines (Eso26 and OE33).

overall_design: Esophageal Cancer cell lines were harvested, and ChIPseq was performed using transcription factor antibodies. Eso26 and OE33 cells knock down PPARG with siRNA and control were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Sai

last: Ma

first: Bo

last: Zhou

first: Yunzhi

last: Pan

first: Wei

first: Stephen

last: Freedland

first: Ling-Wen

last: Ding

middle: R

last: Freeman

first: Joshua

last: Breunig

first: Jian

first: H

last: Koeffler

first: De-Chen

last: Lin


title: Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens

status: Public on May 21 2020

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätsstraße 150

department: Microbial Biology

institute: Ruhr University Bochum

summary: The genome of Agrobacterium tumefaciens C58 harbors three genes encoding small proteins (<50 aa) with a domain of unknown function DUF1127 (ATU_RS08170, ATU_RS08175, ATU_RS21905). To investigate their function we created a triple-deletion mutant lacking those genes. Total RNA was isolated from A. tumefaciens wild type and from the triple mutant (∆∆∆) at optical densities (OD) of 0.5 and 1.5, and after 24 h of growth (30 °C in YEB medium at 180 rpm) and sequenced on an Illumina platform.  For data analysis, 672 small regulatory RNA (sRNA) genes annotated by Wilms et al. (1), Lee et al. (2) and Möller et al. (3) were added to the genome. At OD 0.5 a total of 76 genes showed significantly altered expression in ΔΔΔ. The number increased to 896 and 2,575 genes at OD 1.5 and after 24 h, respectively. 15 genes were upregulated in all three growth phases in ΔΔΔ. At ODs 0.5 and 1.5 numerous genes associated with glycine/serine synthesis were upregulated in the mutant. Additionally, phosphorus starvation and denitrification genes were highly induced at OD 1.5, whereas almost all sugar ABC-transporter genes were downregulated. Overall, the results demonstrate a great impact of DUF1127 proteins on the transcriptome of A. tumefaciens.      1.  Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F. 2012. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol 9:446–57.  2.  Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K. 2013. A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens. PLoS One 8:e70720.  3.  Möller P, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F. 2014. Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PLoS One 9:e110427.

overall_design: Illumina RNA sequencing of the transcriptomes of Agrobacterium fabrum C58 wild type and a triple deletion mutant ∆L4 (∆ATU_RS21905) ∆atu1667 (∆ATU_RS08170) ∆atu8161 (∆ATU_RS08175) lacking all three short DUF1127 proteins.

first: Alexander

last: Kraus

first: Mareen

last: Weskamp

first: Jennifer

last: Zierles

first: Miriam

last: Balzer

first: Ramona

last: Busch

first: Jessica

last: Eisfeld

first: Jan

last: Lambertz

first: Marc

last: Nowaczyk


title: Comprehensive Analyses of 723 Transcriptomes Enhance GWAS Biological Interpretation and Genomic Prediction for Complex Traits in Cattle

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

summary: In this study, we generated 94 RNA-seq data that were colloced from different tissues in Hereford cow (L1 Dominette 01449) and its relatives. By combining these RNA-seq data with our other data and published data, we uniformly assembled and analyzed a total of 723 transcriptomes from 91 tissues and cell types in cattle, to identify tissue-specific genes with the highest specific expression. We then detected the trait-relevant tissues and cell types, and improved genomic prediction for milk production traits.

overall_design: All the tissues were collocted in a previous study (Harhay et al. 2010). total RNA was extracted from snap frozen tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. The quantity and purity of RNA were measured using a NanoDrop 8000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer System (Agilent, Santa Clara, CA, USA).

first: Lingzhao

last: Fang


title: Malignant melanotic Xp11 neoplasms exhibit a clinicopathological spectrum and gene expression profiling akin to alveolar soft part sarcoma: a proposal for reclassification

status: Public on May 14 2020

city: Nanjing

first: xiaotong

last: Wang

state: Jiangsu

address: Zhongshan East Road 305

department: Pathology

institute: Nanjing Jinlin Hospital

summary: We employed RNA sequencing-based clustering analysis to better understand the relationship of this unique entity to its closest histopathologic and immunophenotypic counterparts, including ASPS, conventional PEComa, and Xp11 translocation RCC

overall_design: Gene expression profiling analysis in 4 tumor types.

first: Xiaotong

first: Qiu

last: Rao


title: Single-cell transcriptomics during different phases post cardiac ischemia reveals secreted B2M to regulate fibroblast activation

status: Public on Mar 04 2020

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: The efficiency of the repair process following ischemic cardiac injury is a crucial determinant for the progression into heart failure and is controlled by both intra- and intercellular signaling within the heart. An enhanced understanding of this complex interplay will enable better exploitation of these mechanisms for therapeutic use. We used single-cell transcriptomics to collect gene expression data of all main cardiac cell types at different time-points after ischemic injury.

overall_design: Single-cell transcriptomes were generated at several timepoints after ischemia-reperfusion injury in adult mice. Also, single-cell transcriptomes were generated 3 days after myocardial infarct surgery.

first: Bas

last: Molenaar

first: Louk

last: Timmer

first: Marjolein

last: Droog

first: Monika

last: Gladka

first: Ilaria

last: Perini

first: Danielle

last: Versteeg

first: Lieneke

last: Kooijman

first: Hesther

last: de Ruiter


title: Bisulfite (methylome) sequencing of msh1 memory line and non-memory (normal looking) sibling plants with isogenic Col-0 wild-type control in Arabidopsis [generation 2 to 6]

status: Public on Apr 03 2020

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

type: Methylation profiling by high throughput sequencing

summary: Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent  generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype. Memory plants were self pollinated for six generations and plants from each generations were Bisulfite sequenced.

overall_design: Four to Five memory plants and fiver Col-0 wild-type plants from generation 2 to 6  were sequenced. The first generation data from the same project were submitted under different GEO number:GSE118874

first: Xiaodong

last: Yang

first: Sally

last: Mackenzie


title: MicroRNA expression in Snd1 KO mouse liver

status: Public on Jan 28 2020

city: Helsinki

first: Juha

middle: Mikael

last: Saarikettu

address: Viikinkari 1

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: The RNA-binding protein Snd1 can regulate gene expression through various mechanisms, including microRNA decay. Here we have investigated microRNA expression in livers of WT and Snd1 knockout (KO) mice

overall_design: Total RNA obtained from 8-12 week-old mice. Biological quadruplicates (4WT + 4KO)


title: Gene expression in Snd1 KO mouse spleen

status: Public on Jan 25 2020

summary: Analysis of gene expression in spleens of WT and Snd1 knockout (KO) mice

overall_design: Total RNA obtained from 8-12 week-old mice. Biological duplicates (2WT + 2KO)

middle: M


title: TGFβ-activated kinase 1-dependent microglial and macrophage responses aggravate long-term outcomes after ischemic stroke

status: Public on Mar 10 2020

city: Pittsburgh

first: Yejie

last: Shi

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

summary: Microglia/macrophages (Mi/MΦ) can profoundly influence stroke outcomes by acquiring functionally dominant phenotypes (pro-inflammatory or anti-inflammatory; neurotoxic or neuroprotective). Identification of the molecular mechanisms that dictate the functional status of Mi/MΦ after brain ischemia/reperfusion may reveal novel therapeutic targets for stroke. We hypothesized that activation of TGFβ-activated kinase 1 (TAK1), a key MAP3K upstream of multiple inflammation-regulating pathways, drives Mi/MΦ towards a pro-inflammatory phenotype and potentiates ischemia/reperfusion brain injury. Young adult mice were subjected to 1 h of middle cerebral artery occlusion (MCAO) followed by reperfusion. TAK1 was targeted by tamoxifen-induced Mi/MΦ-specific knockout (mKO).  Mi/MΦ functional status and brain inflammatory profiles were assessed 3 days after MCAO by RNA-seq of flow cytometry-sorted brain Mi/MΦ. The results showed that TAK1 promotes ischemia/reperfusion-induced inflammation, brain injury, and maladaptive behavior by enhancing pro-inflammatory and neurotoxic Mi/MΦ responses.

overall_design: TAK1 mKO mice were generated by crossing the Cx3cr1 CreER mice and Map3k7 flox mice for 2 generations. Both strains were on a C57BL/6 background. The full genotype for the TAK1 mKO mice was Cx3cr1(CreER/wt);Map3k7(flox/flox). Hemizygous Cx3cr1 CreER mice served as age- and sex-matched wild-type (WT) controls (genotype Cx3cr1(CreER/wt);Map3k7(wt/wt)). TAK1 mKO mice and WT control mice received intraperitoneal injections of tamoxifen (75 mg/kg/day for 4 days) to induce TAK1 knockout.  Forteen days after the initial tamoxifen injection, TAK1 mKO mice and WT control mice (8-10 weeks old, male) were subjected to transient focal cerebral ischemia induced by occlusion of the left middle cerebral artery for 1 hour, followed by reperfusion. The CD11b+CD45low (microglia) and CD11b+CD45high (macrophage) cell populations were collected by fluorescence-activated cell sorting from the left (ipsilesional) brain hemisphere 3 days after ischemic stroke. There were 4 groups: WT microglia, WT macrophage, TAK1 mKO microglia, and TAK1 mKO macrophage. In each group there were 2-3 biological replicates. For microglia, each sample was from 1 mouse brain. For macrophages, each sample was pooled from 3 brains to obtain enough cells. The sorted cells were subjected to mRNA sequencing.

first: Jun

last: Chen


title: Single-cell RNA sequencing of adult Drosophila ovary identifies transcriptional programs governing oogenesis

status: Public on Mar 27 2020

city: New Orleans

first: Wu-Min

last: Deng

state: LA

address: 1700 Tulane Avenue

department: School of Medicine, Department of Biochemistry

institute: Tulane University

summary: Using single-cell RNA sequencing technology, we have built a comprehensive transcriptomic dataset for the adult Drosophila ovary and connected tissues. A total of 429,855,892 reads were obtained with 28,995 mean reads per cell for the final dataset of 7,053 high-quality cells containing an overall 11,782 genes. Using this dataset, we identified the transcriptional trajectory of the entire follicle cell population over the course of their development from stem cells to the oogenesis-to-ovulation transitioning phase in the Corpus luteum. We further identify expression patterns during essential developmental events which take place in somatic and germline cell types such as differentiation, cell-cycle switching, migration, symmetry breaking, nurse cell engulfment, egg-shell formation, and corpus luteum signaling. Extensive experimental validation of unique expression patterns in both ovarian and non-ovarian cells also led to the identification of many new markers specific to cell-type and stage. The inclusion of several nearby tissue types in this dataset also led to our identification of functional convergence in expression between distantly related cell types such as the immune-related genes which were similarly expressed in immune cells (hemocytes) and ovarian somatic cells (stretched cells) during their brief phagocytic role in nurse cell engulfment. Taken together, these findings provide new insight into the temporal regulation of genes in a cell-type specific manner during oogenesis and begin to reveal the relatedness in expression between cell and tissues types.

overall_design: scRNA-seq (10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry and Illumina NovaSeq 6000) of adult ovaries from female Drosophila melanogaster flies.

first: Deeptiman

last: Chatterjee

first: Allison

last: Jevitt


title: Mapping pulmonary endothelial cell heterogeneity at homeostasis and during tissue regeneration

status: Public on Feb 27 2020

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Pulmonary endothelial cells are an essential component of the lung alveolus, where they assist in integrating this niche with the cardiovascular system to perform gas exchange with the external environment. Despite its importance, the extent and function of endothelial cell heterogeneity within the lung remains incompletely understood. Using single-cell analytics, we show that multiple vascular endothelial cell populations exist in the mouse lung, including macrovascular endothelium (maECs), microvascular endothelium (miECs), and a new population we have termed regulator endothelium (RECs). RECs express a unique gene signature including elevated expression of Cd34 (Cd34high), Vegfr2 (Kdr), Ednrb, and Car4. The location of RECs within the lung is similar to other miECs at homeostasis, but they appear to preferentially invest regions of regenerating lung tissue after acute lung injury. Receptor-ligand analysis indicates that RECs are primed to receive reparative signals from alveolar type I cells through Vegfa-Vegfr2. Interestingly, influenza infection reveals the emergence of a highly proliferative endothelial cell population (PECs) that likely contributes to revascularization of the alveolar space after injury and may arise from Cd34low miECs. These studies map endothelial cell heterogeneity in the adult lung and characterize the preferential response of novel endothelial cell subpopulations required for proper tissue regeneration after acute lung injury.

overall_design: All experiments used C57BL/6 female mice aged 6-8 weeks old. Single-cell suspensions were prepared from whole mouse lungs. DAPI-negative, CD45-negative and CD31-positive cells were sorted to obtain heterogeneous pulmonary endothelium. For whole-lung scRNA-seq analysis, DAPI-negative, CD45-negative cells were sorted to obtain all non-immune lung cells. Single-cell barcoded droplets were produced using 10X Single Cell 3’ v2 chemistry. Libraries generated were sequenced using the HiSeq Rapid SBS kit. For the heterogeneous pulmonary endothelium samples, the resulting libraries were sequenced across two lanes of an Illumina HiSeq2500 instrument in High-output mode. For the whole lung samples, the resulting libraries were sequenced across a single lane of an Illumina HiSeq2500 instrument in Rapid Run mode. Reads were aligned and gene level unique molecular identifier (UMI) counts were obtained using the Cell Ranger pipeline.

first: Terren

last: Niethamer

first: Collin

last: Stabler

middle: P

first: Edward

middle: E

last: Morrisey


title: Gene expression profiling after cetuximab treatment of HNSCC tumors

status: Public on Jan 17 2020

city: Brussels

first: Sandra

last: Schmitz

address: Avenue Hippocrate, 54

department: Medical Oncology

country: Belgium

institute: Universite catholique de louvain

type: Expression profiling by genome tiling array

summary:
To investigate if cetuximab induces epithelial to mesenchymal transition (EMT) and activation of cancer associated fibroblast (CAF) in the tumors of patients with squamous cell carcinoma of the head and neck (SCCHN).
Cetuximab was administered for two weeks prior to surgery to 20 treatment-naïve patients (CHIRON study). Five untreated patients were included as controls. Tumor biopsies were performed at baseline and before surgery. Gene expression profiles and quantitative real-time PCR (qRT-PCR) analysis of the pre-and post-treatment biopsies were compared. To further investigate EMT and CAF, correlations between previously described EMT and CAF markers and our microarray data set were calculated.

overall_design: 19 samples before cetuximab, 15 samples after treatment.


title: Somatic reprogramming of pteropus bat cells provides new insights in bat antiviral response

status: Public on Jan 01 2020

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

institute: U1208, INSERM

summary: Bats are natural reservoirs for a large range of emerging viruses that cause lethal diseases in humans and domestic animals, but remain asymptomatic in bats. Understanding the host-pathogen interactions relies on the availability of relevant models including susceptible cells, derived from viral target tissues. To obtain bat cell types pertinent for the study of viral infection, we applied somatic reprogramming approach to Pteropus primary cells as initial substrates. Using the novel combination of three transcription factors: ESRRB, CDX2 and c-MYC, we generated reprogrammed cells exhibiting stem cells features.

overall_design: Pteropus somatic cells from trachea and two different isolates of reprogrammed cells derived from those primary cells were analysed, each in triplicates.

first: Noemie

last: Aurine

first: Christian

last: Jean

first: Camille

last: Baquerre

first: Branka

last: Horvat

last: Pain


title: Transcriptional regulation in MCF-7 breast cancer cells treated with proteasome inhibitor MG132 [rna_polii_chIP-seq]

status: Public on Jan 07 2020

city: RTP

first: Trevor

last: Archer

address: 111 TW Alexander

institute: NIH

summary: We report whole genome chromatin immunoprecipitation followed by sequencing (ChIP-seq) of 3 different RNA Pol II CTD modifications in MCF-7 breast cancer cells treated with vehicle (UNTR) or the proteasome inhibitor MG132 for 4 (MG4H) or 24 (MG24H) hours. We find the non-phosphorylated form of RNA Pol II CTD accumulates at TSS of all expressed genes in proteasome inhibited cells, particularly after 24H of MG132 treatment.  Proteasome inhibition enhances Ser5-P and Ser2-P binding at TSS of genes induced by MG132.  We note that proteasome inhibition establishes unique Ser2-P 5’ to 3’ gene profiles at induced compared to repressed genes.  Overall proteasome inhibition enhances RNA Pol II processivity and expression of gene networks relevant to breast cancer. The study provides a comprehensive resource of RNA Pol II binding in proteasome inhibited cells.

overall_design: Examining whole genome RNA Pol II binding in proteasome inhibited  MCF-7 breast cancer cells


title: Chromatin state of MCF-7 breast cancer cells treated with proteasome inhibitor MG132 [histone_mod_chip_seq]

summary: We report whole genome chromatin immunoprecipitation followed by sequencing (ChIP-seq) of histone modifications in MCF-7 breast cancer cells treated with vehicle (UNTR) or the proteasome inhibitor MG132 for 4 (MG4H) or 24 (MG24H) hours. We find that MG132 treatment results in the spreading of the H3-trimethyl lysine 4 mark into gene bodies of a subset of induced genes in MCF-7 cells. The spreading of the H3K4me3 is concomitant with hyperacetylation (H3K27ac, K122ac and K9/14ac) of the corresponding gene TSS.  H3 Lysine 36 trimethylation mark is enriched at genes that are induced by MG132.  Finally, we show that proteasome inhibition establishes a chromatin state that enhances antiproliferative, while dampening cell proliferative gene expression programs relevant to breast cancer. The study provides a comprehensive resource of histone modifications in proteasome inhibited cells.

overall_design: Examination of 5 different histone modifications and total H3 in proteasome inhibited  MCF-7 breast cancer cells


title: Telomeres suppress the activity of retrotransposons in pluripotent stem cells

status: Public on Dec 31 2019

city: Tianjin

first: Sha

last: Zhou

address: Nankai University

department: The State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

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

overall_design: Refer to individual Series


title: Cetuximab treatment of HNSCC

type: Methylation profiling by genome tiling array


title: TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

status: Public on Nov 19 2019

city: Cambridge

first: Ang

middle: Andy

last: Tu

address: 500 Main Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: High-throughput 3′ single-cell RNA-sequencing (scRNA-seq) allows cost-effective, detailed characterization of individual immune cells from tissues. Current techniques, however, are limited in their ability to elucidate essential immune cell features, including variable sequences of T cell antigen receptors (TCRs) that confer antigen specificity. Here, we present a strategy that enables simultaneous analysis of TCR sequences and corresponding full transcriptomes from 3′-barcoded scRNA-seq samples. This approach is compatible with common 3′ scRNA-seq methods, and adaptable to processed samples post hoc. We applied the technique to identify transcriptional signatures associated with T cells sharing common TCRs from immunized mice and from patients with food allergy. We observed preferential phenotypes among subsets of expanded clonotypes, including type 2 helper CD4+ T cell (TH2) states associated with food allergy. These results demonstrate the utility of our method when studying diseases in which clonotype-driven responses are critical to understanding the underlying biology.

overall_design: Single-cell RNA-Sequencing of murine samples via Seq-Well. Mouse 1-4 was sorted against HPV-E7 peptide (RAHYNIVTF) MHC-tetramer. OT1 (spiked into wild-type BL6 murine T cells) samples were enriched for T cells using magnetic beads enrichment, without MHC-tetramer sorting. See DOI: 10.1038/s41590-019-0544-5.

middle: A

first: Todd

last: Gierahn

first: Brinda

last: Monian

first: Duncan

last: Morgan

first: Naveen

last: Mehta

first: Bert

last: Ruiter

first: Wayne

middle: G

last: Shreffler

first: Alex

last: Shalek

first: J

middle: C

last: Love


title: Telomeres suppress the activity of retrotransposons in pluripotent stem cells [exp2]

summary: Telomeres, which locate at the end of chromosomes protect chromosomes from fusion and deterioration. This is essential for cells to maintain genome staibility. We applied RNA-seq, to identify the impact of Terc knockout on the expression of retrotransposons in embryonic stem cells.

overall_design: RNA-seq  analysis of wild type, Terc knockout ESCs

first: Yongwang

last: Zhang

first: Xinyi

last: Lu


title: The Hippo pathway kinase LATS1 scaffolds Beclin1 in autophagy regulation in hepatocellular carcinoma

status: Public on Nov 13 2019

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

summary: Autophagy perturbation represents an emerging therapeutic strategy in cancer. The mammalian Hippo pathway is an evolutionary conserved tumor suppressive network, where the kinases LATS1/2 phosphorylate and inactivate oncogenic YAP/TAZ. Here, we demonstrated a pro-survival role of LATS1, but not LATS2, in hepatocellular carcinoma cells in response to sorafenib, a standard care of advanced HCC. Transcriptomic analysis revealed a restrictive role of LATS1 in autophagy regulation in HCC cells. Further, we found that the autophagy regulation by LATS1 was independent of its kinase activity. Instead, LATS1 stabilized autophagy core-machinery component Beclin 1 via promoting a non-canonical form of K27-linked ubiquitination, and consequently, inactive Beclin 1 self-dimer, in a E3 ligase NEDD4 dependent manner. Our study highlights a functional diversity between LATS1 and LATS2 and uncovers a scaffolding role of LATS1 in mediating a cross-talk between Hippo signalling and autophagy in HCC and therapy response.

overall_design: We performed RNA-sequencing of 3 replicates of 3 different cell lines.

first: Fengyuan

last: Tang

first: Ravi

middle: K

last: Kalathur

first: Gerhard

last: Christofori


title: β-Catenin mutations as  determinants of hepatoblastoma phenotypes in mice

status: Public on Oct 09 2019

first: Edward

middle: V

last: Prochownik

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

summary: Hepatoblastoma (HB) is the most common pediatric liver cancer. While long-term survival is generally favorable, it is dependent upon clinical stage, tumor histology and a variety of biochemical and molecular features.  HB appears almost exclusively before the age of three years, is represented by seven histologic subtypes and is usually associated with highly heterogeneous somatic mutations in the CTNNB1 gene, which encodes b-catenin, a Wnt ligand-responsive transcriptional co-factor. Numerous recurrent b-catenin mutations, not previously documented in HB, have also been identified in various other pediatric and adult cancer types. Little is known regarding the underlying factors that determine the above HB features and behaviors or whether non-HB-associated b-catenin mutations are tumorigenic when expressed in hepatocytes. Here, we investigated the oncogenic properties of 14 different HB- and non-HB-associated b-catenin mutants encoded by Sleeping Beauty vectors following their delivery into the liver by hydrodynamic tail vein injection. We show that all b-catenin mutations, as well as wild-type b-catenin are tumorigenic when co-expressed with a mutant form of yes-associated protein. However, tumor growth rates, histologies, nuclear:cytoplasmic partitioning and metabolic and transcriptional landscapes were strongly influenced by the identities of the b-catenin mutations. These findings provide a context for understanding at the molecular level the notable biological diversity of this important pediatric cancer.

overall_design: RNA purification from five representative tumors of each group was performed using Qiagen RNAeasy columns (Qiagen, Inc., Valencia, CA) followed by DNase digestion. Sample integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).  All samples had RIN values of 8.5-10 prior to any further processing.  Samples for sequencing were prepared using an NEB NEBNext Ultra Directional RNA Library Prep kit according to the directions provided by the vendor (New England Biolab, Beverly, MA) and sequencing was performed on a NovaSeq 6000 Instrument (Illumina, Inc., San Diego, CA) by Novagene, Inc. (Sacramento, CA).

first: Huabo

last: Wang


title: The potential role of long noncoding RNAs in primary open angle glaucoma

status: Public on Sep 28 2019

city: Changsha

first: Feng

state: Hunan

address: 139 Renmin Middle Road, Furong District

institute: The Second Xiangya Hospital

summary: Long non-coding RNAs were associated with the development and progression of glaucoma. Our study aim to identify the potential genes in human trabecular meshwork related to primary open-angle glaucoma (POAG).

overall_design: LncRNAs and mRNAs expression profiles in trabecular meshwork from 4 normal controls and 4 POAG patients were determined through microarray analysis

first: Xuanchu

last: Duan


title: Single-cell, multi-omic analysis identifies regulatory programs in mixed phenotype acute leukemia

status: Public on Oct 25 2019

city: Stanford

first: Jeffrey

middle: Michael

last: Granja

address: 87 Hulme Ct Apt 101

department: Genetics

institute: Stanford University

summary: We present a single-cell framework that integrates highly multiplexed protein quantification, transcriptome profiling, and chromatin accessibility analysis. Using this approach, we establish a normal epigenetic baseline for healthy blood development, which we then use to deconvolve aberrant molecular features within blood from mixed-phenotype acute leukemia (MPAL) patients.

overall_design: scATAC-seq and CITE-seq performed on healthy bone marrow, CD34+ bone marrow, peripheral blood, and MPAL donors


title: Dysregulation of host gene expression by mouse papillomavirus type 1 (MmuPV1) infection

status: Public on Aug 30 2019

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

summary: We performed comprehensive analysis of host gene expression in MmuPV1 infected ear tissues with tumor (T) or without (I) visible warts. The ear tissues from mock-infected (control, C) animals were used as negative control. Total RNA from the collected tissues of 3 animals from each group was subjected to Illumina RNA-seq. After mapping to mouse genome, the genes with dysregulated expression in infected or tumor samples were identified based on comparison to mock-infected contol samples.

overall_design: Gene expression profiling of ear tissues from athymic BALB/c Fox1 nu/nu mice with MmuPV1 or mock infection using Illumina total RNA-seq.

first: Vladimir

last: Majerciak

first: Alexei

last: Lobanov

first: Aayushi

last: Uberoi

first: Paul

middle: F

last: Lambert


title: Ketogenesis activates metabolically protective γδ T cells in visceral adipose tissue [scRNA-Seq]

status: Public on Sep 10 2019

city: New Haven

first: Emily

middle: L

last: Goldberg

state: CT

address: 310 Cedar Street

institute: Yale

summary: Ketone bodies are essential alternative fuels that allow humans to survive periods of glucose scarcity induced by starvation and prolonged exercise. A widely used ketogenic diet (KD), that is extremely high in fat with very-low carbohydrates, drives the host into using β-hydroxybutyrate (BHB) for the production of ATP and lowers NLRP3-mediated inflammation. However, the extremely high fat composition of KD raises the question of how ketogenesis impacts adipose tissue to control inflammation and energy homeostasis. Using single-cell RNA sequencing of adipose tissue-resident immune cells, we identified that KD expands metabolically protective γδ T cells that restrain inflammation. However, a long-term KD caused obesity, impaired metabolic health and depleted the adipose resident γδ T cells. Moreover, mice lacking γδ T cells have impaired glucose homeostasis. We conclude that γδ T cells are mediators of protective immunometabolic responses that link fatty acid driven fuel utilization to reduced adipose tissue inflammation.

overall_design: Mice were fed a chow vs KD for one week. The adipose tissue-resident immune compartment was idenitifed by iv labeling and then assessed by scRNAseq.

first: Irina

last: Shchukina

first: Jennifer

last: Asher

first: Sviatoslav

last: Sidorov

first: Maxim

middle: N

last: Artyomov

first: Vishwa

middle: D

last: Dixit


title: Ketogenesis activates metabolically protective γδ T cells in visceral adipose tissue [bulk RNA-Seq]

overall_design: Mice were fed a chow vs KD for one week. The adipose tissue-resident immune compartment was idenitifed by iv labeling and then assessed by scRNAseq. Visceral adipose tissue gamma delta T cells were sorted and examined by bulk RNA sequencing to identify their role in adipose tissue.


title: Gene expression in Snd1 KO mouse liver

status: Public on Jan 23 2020

first: Juha

middle: Mikael

last: Saarikettu

summary: Analysis of gene expression in livers of WT and Snd1 knockout (KO) mice.

overall_design: Total RNA obtained from 8-12 week-old mice. Biological quadruplicates (4WT + 4KO) were used.


title: Comprehensive transcriptomic profiling of breast cancer patients in SweBCG 91-RT

status: Public on Sep 26 2019

city: Vancouver

first: Laura

last: Chang

state: BC

address: 1152 Mainland St, Suite 430

institute: PFS Genomics

summary:
We performed a retrospective analysis of the SweBCG 91-RT trial, which randomized women with node-negative stage I-IIA breast cancer to whole breast radiotherapy or no radiotherapy following breast-conserving surgery with minimal use of adjuvant systemic treatment.
Primary tumors were profiled with the GeneChip Human Exon 1.0 ST microarray.

overall_design: RNA was isolated from FFPE tissue specimens of the SweBCG 91-RT trial and whole transcriptome profiling was performed. Profiling was successful for 765 patients.

first: Martin

last: Sjöström

first: S

first: Nick

last: Fishbane

first: Elai

last: Davicioni

first: Linda

last: Hartman

first: Erik

last: Holmberg

first: Felix

middle: Y

last: Feng

first: Corey

middle: W

last: Speers

first: Lori

middle: J

last: Pierce

first: Per

last: Malmström

first: Mårten

last: Fernö

last: Karlsson


title: Ketogenesis activates metabolically protective γδ T cells in visceral adipose tissue

first: Emily

last: Goldberg


title: Transcriptome profiling data of urothelial cell carcinoma (UCC) persistently infected with oncolytic Newcastle disease virus

status: Public on Nov 25 2019

city: Serdang

first: Abhimanyu

last: Veerakumarasivam

state: Selangor

address: Jalan Puchong

department: Biomedical Science

country: Malaysia

institute: Universiti Putra Malaysia

summary: Newcastle disease virus (NDV) is an avian virus that selectively replicates and kills many different types of cancer cells and is being developed for cancer treatment. Our aim was to establish persistent infection in EJ28 and TCCSUP bladder cancer cells and identify the dysregulated genes and disrupted molecular pathways associated with persistent infection.

overall_design: mRNA transcriptome profiles of bladder cancer cell lines persistently infected with oncolytic Newcastle disease virus (NDV) AF2240 strain (EJ28Pi and TCCSUPPi) and uninfected (control) EJ28 and TCCSUP bladder cancer cell lines were generated in triplicate by deep sequencing using Illumina HiSeq 2000.

first: Umar

last: Ahmad

first: Chan

middle: S

last: Choy

first: Chau

last: De Ming

first: Syahril

last: Abdullah

first: Khatijah

last: Yusoff


title: Molecular topography of an entire nervous system

status: Public on Aug 21 2019

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Ave South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Nervous systems are constructed from a deep repertoire of neuron types but the underlying gene expression programs that specify individual neuron identities are poorly understood. To address this deficit, we have produced an expression profile of all 302 neurons of the C. elegans nervous system that matches the single cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses unique codes of ~23 neuropeptide-encoding genes and ~36 neuropeptide receptors thus pointing to an expansive "wireless" signaling network. To demonstrate the utility of this uniquely comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression across the nervous system and (2) reveal adhesion proteins with potential roles in synaptic specificity and process placement. These data are available at cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity and function throughout the C. elegans nervous system.

overall_design: Single-cell RNA-sequencing profiles from L4 C. elegans larvae from strains labeling subgroups of neuron types.

first: Seth

middle: R

last: Taylor

middle: M


title: Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons [10X]

status: Public on Aug 23 2019

city: Genève 4

first: Quentin

last: Lo Giudice

state: switzerland

address: 1 rue Michel Servet

department: Department of Basic Neurosciences

institute: University of Geneva

summary: Application of single-cell sequencing technology "10X" to obtain neural retinal transcriptomes. This resource highlight transcriptional sequences that establish the hierarchical ordering of early cell fate specification in the retina.

overall_design: Examination of two batches for a total of 5347 single-cell transcriptomes from E15.5 C57Bl/6 developing retinas.

first: Marion

last: Leuleu

first: Pierre

last: Fabre


title: Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons


title: Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [ATAC-Seq]

status: Public on Jun 13 2019

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

summary: High numbers of tissue-resident memory T (TRM) cells have been associated with better clinical outcomes in cancer patients. However, the molecular characteristics that drive their efficient immune response to tumors are poorly understood. Here, using single-cell and bulk transcriptomic analysis of purified populations of TRM   and non-TRM cells we characterise these populations

overall_design: Population and single cell profiling of subtypes of CD8 cells isolated from human lung and lung tumour samples with flow cytometry

first: James

last: Clarke

first: Bharat

last: Panwar

first: Ariel

last: Madrigal

first: Divya

last: Singh

first: Oliver

last: Wood

first: Serena

last: Chee

first: Amiera

last: Awad

first: Emma

last: King

first: Edwin

last: Woo

first: Aiman

last: Alzetani

first: Grégory

last: Seumois

first: Gareth

last: Thomas

first: Anusha-Preethi

last: Ganesan

first: Peter

last: Friedmann

first: Tilman

last: Sanchez-Elsner

first: Ferhat

last: Ay

first: Christian

last: Ottensmeier


title: Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer.

first: Pandurangan

last: Vijayanand


title: Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [ 10x genomics]

first: James

last: Clarke

first: Bharat

last: Panwar


title: Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [TCR-seq]

first: Ariel

last: Madrigal

first: Divya

last: Singh


title: Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [ bulk RNA-seq]

first: Oliver

last: Wood

first: Serena

last: Chee


title: Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [scRNA-seq]

first: Amiera

last: Awad

first: Emma

last: King


title: Meta-organization of Translation Centers Revealed by Proximity Mapping of Endoplasmic Reticulum Ribosome Interactors

status: Public on Apr 18 2019

city: Durham

first: Christopher

middle: Vincent

last: Nicchitta

state: NC

department: Department of Cell Biology

institute: Duke University School of Medicine

summary: We report a method to use BioID proximity labeling to map the sub-organization of translating mRNAs on the endoplasmic reticulum.  This method first isolates membrane bound polysomes using a Sephacryl 400 resin-based enrichment followed by isolation of biotin labeled polysomes by streptavidin beads and high-throughput sequencing of the bound polysomes.  We find that, for the two pools of polysomes labeled by either LRRC59 or Sec61beta BioID reporters, there is an interesting divergence in specific mRNAs that are entering into the secretory pathway such that secreted proteins are much more enriched towards the LRRC59 reporter with Sec61beta serving a more varied role in mRNA translation.

overall_design: Examination of mRNA from membrane bound polysomes labeled by BioID reporters of Sec61beta and LRRC59 compared to a null cell line as biological replicates.

first: Alyson

last: Hoffman


title: TBX5 Adult Knockout Left Atrial Gene Expression

status: Public on Apr 09 2019

city: Chicago

first: Xinan

middle: Holly

last: Yang

state: IL

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

summary: TBX5 removed from adult mice with R26CreERt2, left and right atrial RNA extracted and sequenced.

overall_design: To define the downstream gene expression changes that occur in the adult atria after removal of TBX5, we compared control left atrium (LA) with Tbx5 knockout LA.

middle: H

first: Rajiv

last: Nadadur

first: Ivan

last: Moskowitz


title: Microarray analysis of the effect of shRNA-mediated HAVCR2 knock-down (KD) in TIM-3-positive AML cell line, KASUMI-3

status: Public on Apr 26 2019

city: Fukuoka

first: Teppei

last: Sakoda

address: 3-1-1, Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

summary:
Purpose: To clarify the function of TIM-3 signaling in AML cells.
Analysis of lentiviral shRNA-mediated knockdown of TIM-3 in TIM-3+ acute myeloid leukemia (AML) cell line, KASUMI-3. Consistent with our previous study (Kikushige et al., Cell Stem Cell 2015) revealing the presence of TIM-3/galectin-9 autocrine loop and its constitutive signaling in AML, KD of receptor,TIM-3, alone significantly impaired the proliferation of KASUMI-3 in vitro and in vivo.

overall_design: To cralify the effect of TIM-3 signaling in AML cells, we compared transcriptome datas of TIM-3 KD KASUMI-3 cells by 2 kinds of shRNA with those of scrambled control KASUMI-3 cells. Microarray experiment was performed with duplicate samples.

first: Yoshikane

last: Kikushige


title: Epithelial retinoic acid receptor beta regulates serum amyloid A expression and vitamin A-dependent intestinal immunity

status: Public on Feb 28 2019

city: Pittsburgh

first: Zheng

last: Kuang

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

summary: Retinoic acid receptor beta regulates intestinal immune transcriptional programs

overall_design: Ileal transcriptomes from 3 RARb floxed mice (wildtype) and 3 RARb (intestinal epithelial cell specific-)KO mice

first: Sureka

last: Gattu

first: Yeji

last: Bang

first: Andrew

last: Chara

first: Tamia

last: Harris

first: Kelly

last: Ruhn

first: Shanthini

last: Sockanathan

first: Lora

last: Hooper


title: RNA Seq of P. aeruginosa clinical isolate collection

status: Public on Apr 08 2019

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

summary:
Purpose : The goal of this study was to use RNA Seq to explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as antimicrobial resistance, biofilm formation or virulence
Methods : mRNA profiles were generated for Pseudomonas aerugionsa clinical samples derived from various geographical locations by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with defaut settings.

overall_design: mRNA profiles from Pseudomonas aeruginosa derived from liquid LB cultures grown to an OD600 = 2  and deep sequenced using Illumina HiSeq 2500.

first: Adrian

last: Kordes

first: Ariane

last: Khaledi

first: Monika

last: Schniederjans


title: GOYA DLBCL clinical trial - RNASeq dataset

status: Public on Feb 01 2019

city: SOUTH SAN FRANCISCO

first: Christopher

middle: Ryan

last: Bolen

state: CA

address: One DNA way

institute: Genentech

summary: This dataset contains collected RNASeq data of 552 samples from the GOYA clinical trial.

overall_design: The GOYA trial tested the efficacy of Gazyva (GA101) compared with Rituxan (Rituximab) in first line, untreated DLBCL patients. Patients were randomized 1:1 to either G or R combined with a CHOP chemotherapy backbone. Tumor samples were collected at baseline, RNA was isolated using RNA-Access, and RNASeq was run with TruSeq (Illumina) RNASeq.

first: Ronald

last: McCord

first: Jeffrey

last: Venstrom


title: Bisulfite (methylome) sequencing of msh1 memory line and non-memory (normal looking) sibling plants with isogenic Col-0 wild-type control in Arabidopsis

status: Public on Aug 06 2019

city: University Park

first: Hardik

last: Kundariya

address: 361 N. Frear

institute: The Pennsylvania State University

summary: Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent  generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype. While rest transgene null plants displayed normal phenotype termed as non-memory.

overall_design: Five memory plants, four non-memory plants, and four Col-0 wild-type plants were sequenced.

first: Xiaodong

last: Yang

first: Sally

last: Mackenzie


title: Expression data (A2058) after treatment with MAPKi, HDACi or both

status: Public on Jan 25 2019

city: Boston

first: Ryan

middle: P

last: Kuzmickas

state: MA

address: 77 Avenue Louis Pasteur, NRB458B

institute: Brigham and Women's Hospital

summary: Transcriptional profiles were examined in A2058 melanoma cells treated with vehicle (DMSO), dabrafenib+trametinib (DT, MAPKi), entinostat (E, HDACi) or all 3 agents (DTE) at 24 hours, prior to the commencement of cell death, to investigate the molecular mechamism by which these drugs and their combinations are functioning.

overall_design: RNA was isolated from A2058 cells 24 hours after treatment with the indicated drugs (3 technical triplicates per treatment arm)

first: Ophélia

last: Maertens


title: Expression data from different levels of anti-CD4 in HIV+ people

status: Public on Jan 01 2019

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

summary:
HIV-infected subjects were stratified to two groups
high IgG anti-CD4 antibodies and low IgG anti-CD4 antibodies on day 14 (D14) after (“high” ≥ 2-fold increase from baseline; “low” < 2-fold increase)

overall_design: HIV+ subject received the influenza vaccine, we draw the blood at the D0 and D7 of vaccination. Total RNA from purified B cells of PBMC was extracted using RNeasy Micro kit . Affymetrix Human GeneChip U133 Plus 2.0 Array was used for RNA hybridization and labeling assay.

first: Wei

last: Jiang


title: Expression data of 3 melanoma cell lines after treatment with MAPKi, HDACi or both

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

overall_design: Refer to individual Series


title: Adipose-Derived Lipocalin-2 Causes Metabolic Dysfunction Only in Female Mice

status: Public on Oct 11 2018

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Lipocalin-2 (LCN2) is a secreted protein involved in innate immunity and also has been associated with several cardiometabolic traits. We examined LCN2 expression in a panel of diverse inbred mouse strains and observed a striking sex difference. Adipose LCN2 was associated with obesity, insulin resistance, dyslipidemia, and hepatic steatosis in females but not males. We expressed LCN2 either in adipose or liver in a tissue specific manner on the background of a whole-body knockout mouse. Adipose LCN2 expression, acting in an autocrine/paracrine manner, promoted metabolic disturbances in females but not males, whereas liver LCN2 expression had no impact on the traits examined. The adipose expression was accompanied by adipose inflammation, fibrosis, and mitochondrial dysfunction, contributing in part to the metabolic disorders. We also show that LCN2 inversely regulates its receptor, LRP2 (or megalin), in a sex-specific manner. Our results demonstrate striking sex- and tissue- specific functions of LCN2.

overall_design: Eight-weeks old female Lcn2-null mice (B6.129P2- Lcn2tm1Aade/AkiJ) on C57BL/6J background were randomly injected intravenously with adeno-associated viral 8 (AAV8) vectors containing either lipocalin-2 (LCN2) or green fluorescent protein (GFP) constructs under an adiponectin promoter (10^12 titer). To increase the adipose tissue specificity of expression, this construct contains a microRNA122 target sequence at the 3’ resulting in selective degradation if expressed in the liver. The animals were then maintained on a HF/HS diet (Research Diets D12266B) until 16 weeks of age. Gonadal and subcutaneous fat samples (n = 4 per group) were taken for RNASeq expression profiling.

first: A

last: Lusis

first: K

middle: C

last: Krishnan


title: Transcriptomic analysis of different human cardiac cell types produced in vitro from human pluripotent stem cells or derived from patients.

status: Public on May 13 2019

city: Great Chesterford

first: Nicolas

last: Gambardella

state: Essex

address: Lewis House, Great Chesterford Court

institute: aSciStance Ltd

summary: The epicardium, an epithelium covering the heart, is essential for cardiac development. During embryogenesis, the epicardium provides instructive signals for the growth and maturation of cardiomyocytes and for coronary angiogenesis. We generated an in vitro model of human embryonic epicardium derived from human pluripotent stem cells (hPSC-epi). These cells were able to differentiate into cardiac fibroblasts (cf) and smooth muscle cells (smc) in vitro (hPSC-epi-cf and hPSC-epi-smc respectively). Furthermore, we showed that they improved maturation of hPSC-derived cardiomyocytes (hPSC-cardio) in vitro while neural crest cells derived from hPSC (hPSC-NC) could not. Furthermore, they improved survival of hPSC-cardio and stimulated angiogenesis when injected in a rat model of myocardium infarction. We performed mRNA sequencing of the hPSC-epi, hPSC-epi-cf, hPSC-smc and hPSC-NC in order to identify the secreted molecules specifically produced by the hPSC-epi and/or its derivatives in comparison with the hPSC-NC. Vascular smooth muscle cells have different embryonic origins and different properties depending on their location in the body. The coronary smooth muscle cells come from the epicardium while the aortic ones come from the mesoderm or the neural crest. We performed mRNA sequencing of human coronary artery smc and human aortic smc to identify a specific signature of the coronary smc. We also compared the genes expressed in the hPSC-epi-smc and the smc derived from hPSC-derived lateral plate mesoderm.

overall_design: For hPSC-derived samples the three replicates are coming from three different in vitro differentiations from H9. For the human primary cells, the triplicates are technical replicates (three different wells from the same culture at the same passage)

first: Laure

last: Le Novère

first: Johannes

last: Bargehr

first: Dharini

last: Iyer

first: Sanjay

last: Sinha


title: RNA-Seq of sorted human  cord-blood derived hematopoietic cell populations

status: Public on Jan 19 2019

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

summary: The goal was to compare the transcriptome profiling of different human hematopoietic stem and progenitor populations to uncover the molecular mechanism involved in stemnes maintenance.

overall_design:
We isolated by flow cytomtery 5 highly purified populations (long term hematopoietic stem cells (LT-HSCs), short term hematopoietic stem cells (ST-HSCs), multipotent progenitors (MPPs), common myeloid progenitor (CMPs), granulocyte and monocyte progenitors (GMPs), multilymphoid progenitors (MLPs)) from 3 to 4 cord blood pools. We extracted RNA from all these populations and performed RNA-sequencing.
Raw data files will be uploaded to EGA.

first: Laura

last: Garcia Prat

first: Shinichiro

last: Takayana

first: Michelle

last: Chan-Seng-Yue


title: Expression data (SKMEL2) after treatment with MAPKi, HDACi or both

summary: Transcriptional profiles were examined in SKMEL2 melanoma cells treated with vehicle (DMSO), dabrafenib+trametinib (DT, MAPKi), entinostat (E, HDACi) or all 3 agents (DTE) at 24 hours, prior to the commencement of cell death, to investigate the molecular mechamism by which these drugs and their combinations are functioning.

overall_design: RNA was isolated from SKMEL2 cells 24 hours after treatment with the indicated drugs (3 technical triplicates per treatment arm)


title: mRNA Expression Data from Murine Hearts of Shiftwork MI, Normal MI and Sham Wildtype Mice at 24-hours Post-MI

status: Public on Nov 30 2018

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

institute: University of Guelph

summary:
Male C57Bl/6 mice were randomized to undergo 5 days of i) a shiftwork protocol (10-hour light: 10-hour dark cycle) before myocardial infarction (MI) surgery, ii) a normal 12-hour light: 12-hour dark environment before MI surgery, iii) a normal 12-hour light: 12-hour dark environment and used as sham controls, or iv) a shiftwork protocol (10-hour light: 10-hour dark cycle) and used as sham controls. MI surgery was performed on the 5th day, after which all mice were returned to a normal 12-hour light: 12-hour dark cycle. Hearts were collected 24-hours post-MI at ZT06.
The microarray approach allows the investigation of transcriptome-wide gene expression changes in hearts from mice on a shiftwork cycle or on a regular light:dark cycle before MI.

overall_design: There are a total of 16 samples, 3 from wildtype mice shiftworked for 5 days before MI, 3 from wildtype mice on a normal light:dark cycle before MI, 5 sham controls on a normal light:dark cycle, and 5 sham controls shiftworked for 5 days. Animals were sacrificed at 6 hours into the light phase.

first: Tami

middle: A


status: Public on Nov 06 2018

city: chongqing

first: bin

last: tang

state: chongqing

address: Southwest Hospital &College of Medical Laboratory Science; Third Military Medical University

department: Department of Clinical Microbiology and Immunology

summary:
Expression data of miRNA profile from colorectal cancer and the adjacent normal tissues infected with F. nucleatum.  Colorectal cancer(CRC) is among the most common cancer types in the world and one of the most lethal cancers. Fusobacterium nucleatum (F. nucleatum) plays an etiologic role in the development of colorectal cancer, but specific tumor molecules involved in the progression of CRC induced by F. nucleatum is not clear. This study investigated some miRNAs and the genes involved in the progression of F. nucleatum-induced colorectal cancer by Affymetrix miRNA microarray technology.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes between Colorectal cancer and the adjacent normal tissues (CONTROL) infected without F. nucleatum . The miRNA array was performed using the affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, California, United States). The chip was processed using a commercial Affymetrix array service (GeneTech Biotechnology Limited Company, Shanghai, China). The affymetrix GeneChip® miRNA 3.0 Array contains 2,999 probe sets unique to human, mouse and rat pre-miRNA hairpin sequences, 2,216 human snoRNA and scaRNA probe sets and covers 153 organisms (19,724 probe sets). Raw data sets were extracted from all Cel files (raw intensity file) after scanning of slides. These raw data sets were separately analyzed using Expression Console and GeneSpring GX12.5 software followed by differential miRNA expression, fold change & cluster analysis.

overall_design: Affymetrix GeneChip® miRNA 3.0 Array  were used to analysis 25 specimens (15  F. nucleatum-induced colorectal cancer, 10 F. nucleatum-induced control).

first: Bin

last: Tang