title: Transcriptome changes in the Alzheimer's middle temporal gyrus: importance of RNA metabolism and mitochondria-associated membrane (MAM) genes

status: Public on Jun 19 2019

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

summary: We used Illumina Human HT-12 v4 arrays to compare RNA expression of middle temporal gyrus (MTG; BA21) in Alzheimer’s Disease (AD = 97) and non-demented controls (ND = 98).  A total of 938 transcripts were highly differentially expressed (adj p < 0.01; log2 Fold Change (FC) ≥ |0.500|, with 411 overexpressed and 527 underexpressed in AD.  Our results correlated with expression profiling in neurons from AD and ND obtained by Laser Capture Microscopy in MTG  from an independent dataset (log2 FC correlation: r = 0.504; p = 2.2e-16).  Additionally selected effects were validated by qPCR. ANOVA analysis yielded no difference between genders in response to AD, but some gender specific genes were detected (e.g: IL8 and AGRN in males, and HSPH1 and GRM1 in females).  Several transcripts were associated with Braak Staging (e.g AEBP1 and DNALI1), ante-mortem MMSE (e.g. AEBP1 and GFAP) and Tangle density (eg. RNU1G2, and DNALI1). At the pathway level we detected enrichment of Synaptic Vesicle Processes and GABAergic transmission genes. Finally, applying the Weighted Correlation Network Analysis (WGCNA) we identified 4 expression modules enriched for neuronal and synaptic genes, mitochondria-associated membrane (MAM), chemical stimulus and olfactory receptor and non-coding RNA metabolism genes.    Our results represent an extensive description of MTG mRNA profiling in a large sample of AD and ND.  These data provide a list of genes associated with AD, and correlated to neurofibrillary tangles density. In addition, these data emphasize the importance of mitochondrial membranes and transcripts related to olfactory receptors in AD.

overall_design: We compared RNA expression of middle temporal gyrus (MTG; BA21) between Alzheimer’s Disease (AD = 97) and non-demented controls (ND = 98) using Illumina Human HT-12 v4 arrays

first: Jonida

last: Krate

first: Elaine

last: Delvaux

last: Nolz

first: Diego

last: Mastroeni

first: Antonio

last: Persico

first: Wayne

last: Jepsen

first: Thomas

last: Beach

first: Matthew

last: Huentelman

first: Paul

last: Coleman


title: Sex-specific programming effects of parental obesity in pre-implantation embryonic development

status: Public on Jul 07 2019

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Sex-specific programming effects of parental obesity in pre-implantation embryonic development [RNASeq Data of Oocytes]

summary: Obesity is a global rising problem with epidemiological dimension. Obese parents can have programming effects on their offspring leading to obesity and associated diseases in later life. This constitutes a vicious circle. Epidemiological data and studies in rodents demonstrated differential programming effects in male and female offspring, but the timing of their developmental origin is not known. This study investigated if sex-specific programming effects of parental obesity can already be detected in the pre-implantation period. Diet induced obese male or female mice were mated with normal-weight partners and blastocysts were recovered. Gene expression profiling revealed sex-specific responses of the blastocyst transcriptome to maternal and paternal obesity. The changes in the transcriptome of male blastocysts were more pronounced than those of female blastocysts, with a stronger impact of paternal than of maternal obesity. The sperm of obese mice revealed an increased abundance of several miRNAs compared to lean mice. Our study indicates that sex-specific programming effects of parental obesity already start in the pre‑implantation period and reveals specific alterations of the sperm miRNA profile as mechanistic link to programming effects of paternal obesity.

overall_design: We examined the transcriptome of oocytes of female mice which had previously been set on a high fat diet (HFD) (n=6) and compared it to the transcriptome of oocytes derived from mice which were fed a control diet (CD) (n=6) by RNA-seq.

first: Kathrin

last: Hedegger

first: Julia

last: Philippou-Massier

first: Stefan

last: Krebs

first: Helmut

last: Blum

last: Kunzelmann

first: Klaus

last: Förstemann

first: Martina

last: Gimpfl

first: Adelbert

middle: A

last: Roscher

first: Regina

last: Ensenauer

first: Eckhard

last: Wolf

first: Maik

last: Dahlhoff


title: Sex-specific programming effects of parental obesity in pre-implantation embryonic development [RNASeq Data of Sperm]

overall_design: Investigation of the sperm transcriptome by RNA sequencing of mice which had previously been set on a high fat diet (HFD) for nine weeks (n=8), compared to the transcriptome of sperm of mice which were fed a control diet (CD) (n=8).


title: dCas9 activation of RP11-326A19.4

status: Public on Jun 11 2019

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

summary: Transfection experiments aimed at understanding the impact of upregulation a lncRNA (RP11-326A19.4) on genome-wide transcription

overall_design: HEK293T cells were transfected with dCas9-VP160 alongside either a cgRNA (SG -286) construct expressing either a targeting the promoter region of a lncRNA (RP11-326A19.4) or tracrRNA only for 48 h. Sample RNAs were then analyzed on human Clariom D arrays.

first: Sebastien

last: Soubeyrand


title: A human TH17 population with a tissue-resident signature in healthy and inflamed oral mucosal tissues [Bulk RNA-seq]

status: Public on Dec 08 2019

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

summary: T cells in mucosal tissues fulfill a complex array of duties to ensure maintenance of barrier immunity. In oral mucosa tissue, we found that increased inflammation altered CD4 T cell subsets in a spatially-dependent manner, although it had a modest effect on the frequency of tissue-resident memory T cells (TRM) and the CD4 T cell transcriptome. In contrast, localization to the tissue profoundly altered the transcriptional profile, emphasizing the importance of studying healthy tissue to understand disease-specific changes. Our data revealed the existence of a TH17 cell population that is predominantly found in the tissue-resident, but not transient, CD4 T cell compartment in mucosal tissue.

overall_design: This project contains bulk RNA-seq data from paired oral mucosa tissue and blood CD4 T cell subsets from 10 subjects and 10X genomics sequencing of CD4 T cell subsets from one individual

first: Amanda

middle: S

last: Davis

first: Hayley

middle: N

last: Roozen

middle: J

last: Dufort

first: Hannah

last: DeBerg

first: Martha

last: Delaney

first: Florian

last: Mair

first: Jami

middle: R

last: Erickson

first: Chloe

middle: K

last: Slichter

middle: D

last: Berkson

first: Matthias

last: Mack

first: Yu

last: Lwo

last: Ko

first: Yu-Wen

last: Chiu

first: Jessica

middle: C

last: Hsu

first: Peter

last: Linsley

first: Douglas

last: Dixon

first: Martin

last: Prlic


title: The RNA-Binding Protein DND1 Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming

status: Public on Jun 14 2019

city: Aurora

first: Victor

last: Ruthig

state: CO

department: Pediatrics, Section of Developmental Biology

institute: University of Colorado Anschutz Medical Campus

summary: Analysis of our transcriptome and RNA immunoprecipitation experiments indicate DND1 acts as a positive regulator of chromatin modifiers in male germ cells, linking RNA binding proteins and epigenetic regulation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptome timecourse (E12.5, E13.5 and E14.5) comparing muring male germ cells homozygous for Ter mutation in Dnd1 to wild type male germ cells done in conjunction with in vitro work with HEK293 cells transfected with tagged Dnd1 for digestion optimized RNA immunoprecipitation sequencing (DO-RIP-seq) experiments to identify a RNA recognition element for DND1 as well as transcipt targets of this RNA binding protein.

first: Blanche

last: Capel

first: Jacke

last: Keene

first: Matthew

last: Friedersdorf


title: RNA SEQ NTHi modA10

status: Public on Apr 15 2019

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

country: Australia

institute: Griffith University

summary: Comparison of RNA expression profiles from NTHi strain R2866 expressing methyltransferase ModA10 (ON) or not (LOCK_OFF).

overall_design: RNA isolated from triplicate cultures of each strain (modA10 ON and modA10 LOCK_OFF) grown in sBHI to mid-log; comparison of gene expression profiles by comparing modA10ON vs. modA10 LOCK_OFF to determine differential gene expression influenced by ModA10 methylation differences.

middle: M

first: Michael

middle: P

last: Jennings


title: Selective Disruption of Core Regulatory Transcription [AQuA-HiChIP]

status: Public on Sep 27 2019

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: With emerging methods recently developed to capture protein-anchored 3D epigenome folding we herein report an experimental advance yielding a fundamental and systematic improvement in understanding the 3D genome: integrated normalization of orthologous chromatin for measurement of absolute changes in the landscape. With Absolute Quantification of chromatin Architecture (AQuA-HiChIP) global and local changes in the 3D epigenome can be measured, and the absolute differences in protein-anchored folding can be determined. These changes can be defined in a way that couples the relative occupancy of chromatin regulatory factors or histone marks to absolute quantification of 3D chromatin structure. While our method has intrinsic limitations, including restriction by the scope of available ChIP-grade antibodies with mouse/human cross-reactivity, the approach to measuring absolute components of chromatin folding will enable new insights into the topological determinants of transcriptional control and tissue-specific epigenetic memory.

overall_design: Genome-wide 3D interaction profiles as mediated by H3K27ac histone marks, in Rhabdomyosarcoma (RMS) cell lines before and after HDAC inhibition

first: Berkley

middle: E

last: Gryder

first: Xinyu

last: Wen


title: Selective Disruption of Core Regulatory Transcription

status: Public on May 31 2019


title: Characterisation of the myeloid differentiation process of human hematopoietic stem cells

status: Public on Apr 16 2019

city: Zurich

first: Slavica

last: Dimitrieva Janeva

state: Zurich

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH Zürich / University of Zurich

summary: Hematopoietic stem cells (HSCs) can self-renew and/or differentiate into various functionally divergent progenitor cell types, such as common myeloid progenitors (CMPs), megakaryocyte-erythrocyte progenitors (MEPs) or granulocyte-macrophage progenitors (GMPs). When the process of self-renewal and differentiation is altered, e.g. upon genetic or epigenetic changes in HSCs, abnormal (pre)leukemic stem cell subpopulations may form, eventually resulting in the onset of hematological malignancies. To gain insight into the physiology and subsequent patho-physiology of self-renewal and differentiation, we performed RNA sequencing as well as proteomics analyses of human HSCs and downstream (myeloid) progenitor cells.

overall_design: RNA sequencing as well as quantitative proteomic analysis was performed for highly purified, FACS-sorted hematopoietic stem and progenitor cell subpopulations isolated from five healthy donors.

first: Fabienne

last: Meier-Abt

last: Dimitrieva


title: The role of TEFM in mitochondrial gene expression [smallRNA]

status: Public on Apr 01 2019

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigated the role of TEFM in vivo by creating heart- and skeletal-muscle specific knockout of this gene. We identified that TEFM is required for the processivity of POLRMT and its loss leads to significantly decreased mitochondrial transcription.

overall_design: Small RNA from isolated heart mitochondria from four control mice (L/L) and four Tefm knockout mice (L/L, cre), was sequenced and analysed for differential expression.

first: Aleksandra

last: Filipovska


title: Transcriptomic analysis of topping-induced axillary shoot outgrowth in Nicotiana tabacum

status: Public on Jun 30 2020

city: Qingdao

first: Jing

last: Lv

state: China

address: No.11, Keyuan Jingsi Road, Laoshan District

country: China

institute: CAAS

summary: We applied the Illumina HiSeq™ 2000 platform and analyzed differentially expressed genes (DEGs) from untopped and topped plants to study the global changes in gene expression in response to topping. We found that the number of DEGs varied from 7609 to 18,770 based on the reads per kilobase per million mapped reads (RPKM) values. The Gene Ontology (GO) enrichment analysis revealed that the cellular carbohydrate metabolic process and the disaccharide metabolic process, which may contribute to starch accumulation and stress/defense, were overrepresented terms for the DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that many DEGs were involved in starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, and plant hormone signal transduction, among other processes. The knowledge gained will improve our understanding of the processes of axillary shoot formation and enlargement at the transcriptional level. This study lays a solid foundation for future studies on molecular mechanisms underlying the growth of axillary shoots.

overall_design: The axillary shoot samples  from control (untopped) and topped plants after 1, 3 and 5 days

first: Wei-feng

last: Wang

first: Peng

last: Chen

first: Yu-he

last: Sun


title: A network of transcriptome modules demonstrates mechanistic pathways of both virus induced and non-viral asthma exacerbations in children [nasal]

status: Public on Apr 08 2019

first: Stephanie

last: Osmond

summary: We leverage a systems-scale network analysis approach to demonstrate repertoires of cellular transcriptional pathways underlying loss of asthma control, and show how these pathways differ in viral associated and non-viral exacerbations.

overall_design: 208 children with exacerbation prone asthma were enrolled according to the inclusion criteria. Each child had baseline samples collected and were prospectively monitored for the onset of cold symptoms (Events) during a 6 month period. 106/208 children came in during one or more events and had sufficient samples collected for analysis. Events were grouped as exacerbation associated (Ex+) or not exacerbation associated (Ex-) depending on whether the event lead to clinical symptoms that resulted in systemic corticosteroid use within 10 days of event onset or resolved without treatment with systemic corticosteroids. The primary endpoint compared Ex+ events to Ex- events. Based on nasal virus PCR results, events were further classified as virus associated (V+) or nonviral (V-). The secondary endpoint compared V+Ex+, V+Ex-, V-Ex+, and V-Ex- events.

last: Altman

first: Michelle

last: Gill

first: Elizabeth

last: Whalen

first: Denise

last: Babineau

first: Baomei

last: Shao

first: Andrew

middle: H

last: Liu

first: Brett

last: Jepson

first: Rebecca

last: Gruchalla

first: George

middle: T

last: O'Connor

first: Jackie

last: Pongracic

first: Carolyn

last: Kercsmar

first: Gurjit

last: Khurana Hershey

first: Edward

last: Zoratti

first: Stephen

last: Teach

first: Meyer

last: Kattan

first: Len

middle: B

last: Bacharier

first: Avi

last: Beigelman

first: Steve

last: Sigelman

first: Scott

last: Presnell

first: James

last: Gern

first: Peter

last: Gergen

first: Lisa

last: Wheatley

first: Alkis

last: Togias

first: William

middle: W

last: Busse

first: Daniel

last: Jackson


title: Expression data from human induced pluripotent stem cells

status: Public on Mar 12 2019

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

country: Japan

institute: National Institute of Health and Sciences

summary:
We used microarrays to detail the global gene expression of human induced pluripotent stem cells
We investigated reference gene expression in human iduced pluripotent stem cells.

overall_design: 10 human induced pluripotent stem cell lines (201B7, 253G1, 409B2, HiPS-RIKEN-1A, HiPS-RIKEN-2A, HiPS-RIKEN-12A, Tic, mc-iPS, ATCC-DYR0100hiPSc, ATCC-DYR0103hiPSc)

first: T

first: S

last: Yasuda

first: Y

last: Sato


title: Gene expression altered by HOTAIR knockdown in MCF-7-TNR

status: Public on Jan 11 2019

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

summary: The human HOTAIR-specific siRNA and control siRNA were transfected into MCF-7-TNR cells. RNA was collected at 72 hrs after transfection. RNA-SEQ was carried out to profile the gene expression altered by HOTAIR knockdown.

overall_design: The goal of this experiment was to profile the genes that are regulated by HOTAIR in a human breast cancer cell line. HOTAIR was knockdown by siRNA. Gene expression was probed globally using RNA-SEQ.

first: Simon

last: Alsager


title: Impaired immunosurveillance by the simultaneous loss of both atypical PKCs drives intestinal cancer through the serrated pathway [IECs DKO aPKC]

status: Public on Dec 20 2018

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: The serrated adenocarcinoma subtype accounts for 15-30% of all colorectal cancers (CRCs) and is aggressive and treatment-resistant. it is an alternative mechanism for CRC development characterized by dysregulation of the MAPK pathway. We show that human serrated tumors display reduced expression of PKCz and PKCl/i, and that the simultaneous inactivation of these genes in the mouse intestinal epithelium resulted in spontaneous tumorigenesis through the serrated pathway that progressed to advanced cancer. Whereas epithelial PKCl/i deficiency led to immunogenic cell death that repressed tumor initiation, interferon and CD8+ T cell responses were impaired concomitant with stromal activation and immunosuppression driven by PKCz loss. Thus, PKCz and PKCl/i cooperatively suppress serrated tumorigenesis. Targeting this stromal activation and immunosuppression showed synergistic curative activity.

overall_design: RNA was extracted from small intestinal epithelial cells from WT and intestinal epithelial cell-specific atypical PKC (either one of or both PKClambda/iota and PKCzeta) mice.

first: Yuki

last: Nakanishi

first: Angeles

last: Duran

first: Antoine

last: L’Hermitte

first: Phillip

last: Shelton

first: Naoko

first: Miguel

last: Reina-Campos

first: Jianfeng

last: Huang

first: Ferran

last: Soldevilla

first: Bas

last: Baaten

first: Daniele

last: Tauriello

first: Elias

last: Castilla

first: Munveer

last: Bhangoo

first: Fei

last: Bao

first: Darren

last: Sigal

first: Maria

last: Diaz-Meco


title: Round, columnar and hypertrophic chondrocytes of wild type mice

status: Public on Oct 31 2018

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

institute: Kyoto University

summary:
To survey altered gene expreesion in round, colmnar and hypertrophic chondrocytes of wil type mice, total RNA preparations from round chondrocytes and colmnar/hypertrophic chondrocytes were subjected to
gene microarray analysis. Results provide insight into the transcriptional profile of each chondrocytes and provide further insight into their functions.

overall_design: Total RNA preparations from three cartilage plate portions enriched with round chondrocytes or columnar/hypertrophic chondrocytes were mixed and then subjected to Affymetrix Mus musculus microarrays. Round chondrocytes and columnar/hypertrophic chondrocytes were analyzed.

first: Hiroshi

last: Takeshima


title: Single-cell transcriptomic analysis of mouse neocortical development

status: Public on Jan 14 2019

city: Chapel Hill

first: Mark

last: Zylka

state: NC

address: 5109D Neuroscience Research Building

institute: University of North Carolina - Chapel Hill

summary: The development of the mammalian cerebral cortex depends on careful orchestration of proliferation, maturation, and migration events, ultimately giving rise to a wide variety of neuronal and non-neuronal cell types. To better understand cellular and molecular processes that unfold during late corticogenesis, we perform single-cell RNA-seq on the mouse cerebral cortex at a progenitor driven phase (embryonic day 14.5) and at birth—after neurons from all six cortical layers are born. We identify numerous classes of neurons, progenitors, and glia, their proliferative, migratory, and activation states, and their relatedness within and across age. Using the cell-type-specific expression patterns of genes mutated in neurological and psychiatric diseases, we identify putative disease subtypes that associate with clinical phenotypes. Our study reveals the cellular template of a complex neurodevelopmental process, and provides a window into the cellular origins of brain diseases.

overall_design: 6 biological replicates of E14.5 cortex, 3 biological replicates of P0 cortex. Each replicate contains a pool of cells from male and female littermates

first: Lipin

last: Loo

first: Jeremy

last: Simon


title: The role of TEFM in mitochondrial gene expression

first: Stefan

last: Siira

overall_design: Refer to individual Series


title: Impaired immunosurveillance by the simultaneous loss of both atypical PKCs drives intestinal cancer through the serrated pathway

first: Jorge

last: Moscat


title: The diurnal rhythm of adipose tissue gene expression is reduced in obese patients with type 2 diabetes

status: Public on Jan 24 2019

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

country: Netherlands

institute: Amsterdam University Medical Centers

summary: Animal studies have linked disturbed adipose tissue clock gene rhythms to the pathophysiology of the metabolic syndrome. However, data on molecular clock rhythms in human patients are limited. Therefore, in a standardized real life setting, we compared diurnal gene expression profiles in subcutaneous adipose tissue between obese patients with type 2 diabetes and age-matched healthy lean control subjects, using RNA sequencing. In patients, 1.8% (303 genes) of expressed genes showed significant diurnal rhythms, compared to 8.4% (1421 genes) in healthy controls. In patients, the core clock genes showed reduced amplitude oscillations. Enrichment analysis revealed a loss of rhythm in canonical metabolic pathways including AMPK signaling and cAMP mediated signaling in patients. In conclusion, we provide the first transcriptomics atlas of human adipose tissue diurnal rhythms, and show evidence of decreased diurnal clock and metabolic gene expression rhythms in subcutaneous adipose tissue of obese patients with type 2 diabetes.

overall_design: We provided 6 obese patients with type 2 diabetes and 6 age matched healthy lean control subjects with three identical meals per day at fixed timepoints (Zeitgeber Time (ZT) 0:30, ZT 6:00 and ZT 11:30, with ZT 0:00 representing wake-up time) for three days. Subcutaneous adipose tissue samples from the four peri-umbilical quadrants were obtained at four time points (day 2: ZT 15:30, day 3: ZT 0:15, ZT 5:45 and ZT 11:15).

first: D

last: Stenvers

first: A


title: Transcript levels of genes in both the wild type SN148 and the crz1/crz1 mutant with or without 0.2M CaCl2 treatment

status: Public on Nov 30 2018

city: Zibo

first: Linghuo

last: Jiang

address: 266 West Road Xincun

institute: Shandong University of Technology

summary: We report the expression levels of transcripts for two alleles of 6,211 genes in log-phase growing cells of the wild type SN148 and the crz1/crz1 with or without 0.2M CaCl2 treatment.We find that as compared to the wild type cells without 0.2M CaCl2 treatment, there are 828 genes upregulated in the wild type cells with 0.2M CaCl2 treatment.

overall_design: RNA sequencing of wildtype SN148 and crz1/crz1 mutant with or without 0.2M CaCl2 treatment

first: Malcolm

last: Whiteway

first: Huihui

last: Xu


title: Differential gene expression of TLR7 overexpressing inflammatory hemophagocytes, Ly6Chi Monocytes, and Red Pulp Macrophages

status: Public on Jan 15 2019

first: Stephanie

last: Osmond

summary: We have defined a novel population of monocyte-derived hemophagocytes (inflammatory hemophagocytes (iHPC)) found in situations of inflammation, such as TLR7.1 mice that overexpress TLR7. These iHPC are similar yet distinct from red pulp macrophages (RPM) and differentiate in response to chronic TLR7 signals.  In vivo, iHPC phagocytose red blood cells and platelets causing anemia and thrombocytopenia.  We performed this study to further understand iHPC and their relationship to RPM and monocytes and determine what gene signatures make them unique.

overall_design: We sorted the following populations from spleens of 9-16 week old female WT B6 and TLR7.1 mice: iHPCs (TLR7.1 mice), Ly6Chi monocytes (WT B6 and TLR7.1 mice), and RPM (WT B6 and TLR7.1 mice).  iHPC were identified as Live, CD45.2+, SiglecF-, Ly6G-, Ly6C-, CD31hi,VCAMlow, F4/80low,CD11b+ cells; monocytes were defined as Live, CD45.2+, SiglecF-, Ly6G-, Ly6C+, Ccr2+, CD11b+ cells; and RPM were defined as Live, CD45.2+, SiglecF-, Ly6G-, Ly6C-, CD31low,VCAMhi, F4/80+,CD11b-/int cells. We submitted lysates from 6 samples of each population (a total of 30 samples).

first: Holly

last: Akilesh

first: Matthew

last: Buechler

first: Jeffery

last: Duggan

first: William

middle: O

last: Hahn

first: Bharati

last: Matta

first: Xizhang

last: Sun

first: Griffin

last: Gessay

first: Elizabeth

last: Whalen

first: Michael

last: Mason

first: Scott

last: Presnell

first: Keith

last: Elkon

first: Adam

last: Lacy-Hulbert

first: Betsy

last: Barnes

first: Marion

last: Pepper

first: Jessica

last: Hamerman


title: Comparison of Transcriptomes between A549 and H23 Cells

status: Public on Sep 06 2018

first: Bin

last: Shan

summary: We profiled transcriptomes in human lung cancer cell lines H23 and A549 cells.

overall_design: H23 and A549 were cultured to ~80% confluent. Total cell RNA was extracted using Trizol. Three independent cultures of each cell line were lysed for RNA. The extracted RNA was processed for RNA-SEQ on Illumina HIGHSEQ 2500.

first: Simon

last: Alsager


title: Effects of Bloom RNAi on Transcriptomes in A549 Cells

summary: We profiled transcriptomes in human lung cancer cell line A549 when the expression of Bloom was knockdown by the siRNA specific to Bloom.

overall_design: A549 cells were cultured in DMEM.  Bloom-specific and control siRNAs were transfected into A549 cells using RNAiMAX. Total cell RNA was extracted at 48 hrs after transfection. Three independent transfections were carried out for each siRNA. The extracted RNA was processed for RNA-SEQ on Illumina HIGHSEQ 2500.


title: Impaired immunosurveillance by the simultaneous loss of both atypical PKCs drives serrated intestinal cancer

first: Jorge

last: Moscat

overall_design: RNA was extracted from small intestinal tissues from WT and intestinal epithelial cell-specific atypical PKC (both PKClambda/iota and PKCzeta) mice.

first: Yuki

last: Nakanishi

first: Angeles

last: Duran

first: Antoine

last: L’Hermitte

first: Phillip

last: Shelton

first: Naoko

first: Miguel

last: Reina-Campos

first: Jianfeng

last: Huang

first: Ferran

last: Soldevilla

first: Bas

last: Baaten

first: Daniele

last: Tauriello

first: Elias

last: Castilla

first: Munveer

last: Bhangoo

first: Fei

last: Bao

first: Darren

last: Sigal

first: Maria

last: Diaz-Meco


title: A CRISPR loss-of-function Hepatic progenitor cells expansion screen in liver organoids

status: Public on Aug 27 2018

city: Cambridge

first: Frederic

last: Sigoillot

state: MA

address: 181 Massachusetts Avenue

department: Chemical Biology and Therapeutics

institute: Novartis Institutes for Biomedical Research

summary: Biliary epithelial cells (BECs) form bile ducts in the liver, and are facultative liver stem cells that establish a ductular reaction (DR) to support liver regeneration following injury. Liver damage induces periportal LGR5+ putative liver stem cells which can form BEC-like organoids, suggesting RSPO-LGR4/5-mediated WNT/β-catenin activity is important for a DR. We addressed the roles for this and other signaling pathways in a DR by performing a focused CRISPR-based loss-of-function screen in BEC-like organoids, followed by in vivo validation and single-cell RNA sequencing. We found BECs lack and do not require LGR4/5-mediated WNT/β-Catenin signaling during DR, while YAP and mTORC1 signaling are required for this process. Upregulation of LGR5/AXIN2 is required in hepatocytes to enable their regenerative capacity in response to injury. Together, these data highlight heterogeneity within the BEC pool and delineate signaling pathways involved.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design:
The 1000 element library is a pooled CRISPR library with 1000 unique CRISPR sgRNA.  The take rate library is a DNA barcode library (https://www.cellecta.com/content/uploads/2014/10/Cellecta-PAC-Barcode-Library-13Kx13K-Plasmid-12082901.pdf). The manuscript presents the finding of a pooled CRISPR screen on liver organoid culture system using a 1000 element CRISPR library.  To develop the screening assay, we evaluated the clonal growth kinetics of the liver organoids by infecting the organoids with the take rate library which is composed of DNA barcodes that do not perform genetic perturbation.  The take rate library result confirms that the liver organoids do not display strong clonal growth and thus are suitable for screening.
We use cell survival and proliferation as the measure for identifying signalling pathways regulating HPC expansion in vitro.

first: Lara

last: Planas-Paz

first: Tianliang

last: Sun

first: Monika

last: Pikiolek

first: Nadire

last: Cochran

first: Sebastian

last: Bergling

first: Vanessa

last: Orsini

first: Zinger

last: Yang

first: Jasna

last: Jetzer

first: Maryam

last: Syed

first: Marilisa

last: Neri

first: Sven

last: Schuierer

first: Lapo

last: Morelli

first: Philipp

last: Hoppe

first: Wibke

last: Schwarzer

first: Carlos

last: Cobos

first: John

middle: L

last: Alford

first: Le

last: Zhang

first: Rachel

last: Cuttat

first: Annick

last: Waldt

first: Nicole

last: Carballido-Perrig

first: Florian

last: Nigsch

first: Bernd

last: Kinzel

first: Thomas

last: Nicholson

first: Yi

first: Xiaohong

last: Mao

first: Luigi

last: Terracciano

first: Carsten

last: Russ

last: Reece-Hoyes

first: Caroline

middle: G

last: Keller

first: Andreas

last: Sailer

first: Tewis

last: Bouwmeester

first: Linda

last: Greenbaum

first: Jesse

last: Lugus

first: Feng

last: Cong

first: Gregory

last: McAllister

last: Hoffman

first: Guglielmo

last: Roma

first: Jan


title: A network of transcriptome modules demonstrates mechanistic pathways of both virus induced and non-viral asthma exacerbations in children

first: Stephanie

last: Osmond

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


title: The role of TEFM in mitochondrial gene expression [TruSeq]

first: Stefan

last: Siira

overall_design: Total RNA from isolated heart mitochondria from four control mice (L/L) and four Tefm knockout mice (L/L, cre), was sequenced and analysed for differential expression.

first: Aleksandra

last: Filipovska


title: A network of transcriptome modules demonstrates mechanistic pathways of both virus induced and non-viral asthma exacerbations in children [blood]

first: Matthew

last: Altman

first: Michelle

middle: A

last: Gill

first: Elizabeth

last: Whalen

first: Denise

last: Babineau

first: Baomei

last: Shao

first: Andrew

last: Liu

first: Brett

last: Jepson

first: Rebecca

middle: S

last: Gruchalla

first: George

last: O'Connor

first: Jackie

last: Pongracic

first: Carolyn

last: Kercsmar

first: Gurjit

last: Khurana Hershey

first: Edward

last: Zoratti

first: Stephen

last: Teach

first: Meyer

last: Kattan

first: Len

last: Bacharier

first: Avi

last: Beigelman

first: Steve

last: Sigelman

first: Scott

last: Presnell

first: James

last: Gern

first: Peter

last: Gergen

first: Lisa

last: Wheatley

first: Alkis

last: Togias

first: William

last: Busse

first: Daniel

last: Jackson


title: Genome wide DNA methylation sequencing by XmaI-RRBS resolves breast cancer epigenetic heterogeneity and suggests novel perspectives for personalized therapy

status: Public on Nov 22 2018

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

type: Methylation profiling by high throughput sequencing

summary: Aim: To provide a breast cancer (BC) methylotype classification by genome-wide CpG islands bisulfite DNA sequencing. Results: Overall, 6 distinct BC methylotypes were identified. Of these, BC cell lines constitute a separate group extremely highly methylated at the CpG islands. In turn, primary BC samples segregate into two major subtypes, highly and moderately methylated.

overall_design: XmaI-RRBS DNA methylation sequencing method was used to profile DNA methylation of 111 BC samples and 6 normal breast samples.

first: Alexander

last: Tanas

middle: I


title: Effects of HOTAIR RNAi on Transcriptomes in H23 Cells

first: Bin

last: Shan

summary: We profiled transcriptomes in human lung cancer cell line H23 when the expression of HOTAIR was knockdown by the siRNA specific to an HOTAIR isoform HOTAIR-N (NR_047517).

overall_design: H23 cells were cultured in RPMI1640.  HOTAIR-N-specific and control siRNAs were transfected into H23 cells using RNAiMAX. Total cell RNA was extracted at 48 hrs after transfection. Three independent transfections were carried out for each siRNA. The extracted RNA was processed for RNA-SEQ on Illumina HIGHSEQ 2500.

first: Simon

last: Alsager


title: A Single-Cell Atlas of Cell Types, States, and Other Transcriptional Patterns from Nine Regions of the Adult Mouse Brain

status: Public on Aug 22 2018

city: Boston

first: Arpiar

last: Saunders

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: We report 690K single-cell transcriptomes from nine different brain regions from adult mice (Frontal and Posterior Cortex, Hippocampus, Thalamus, Cerebellum, Striatum, Globus Pallidus externus/Nucleus Basalis, Entopeduncular / Subthalamic Nuclei, & Substantia Nigra / Ventral Tegmental Area).

overall_design: Single-cell suspensions were made from P60-70 C57BL/6 male mice (3-7 replicates / mouse) and sampled with Drop-seq. On average, each cell received 17.4 K Illumina sequencing reads from which we counted 2.2K transcripts and 1.2 K genes. In total, we measure 31.7K unique genes.

last: McCarroll


title: Effects of HOTAIR RNAi on Transcriptomes in T47D Cells

summary: We profiled transcriptomes in human breast cancer cell line T47D when the expression of HOTAIR was knockdown by the siRNA specific to an HOTAIR isoform HOTAIR-N (NR_047517).

overall_design: T47D cells were cultured in RPMI1640.  HOTAIR-N-specific and control siRNAs were transfected into T47D cells using RNAiMAX. Total cell RNA was extracted at 48 hrs after transfection. Three independent transfections were carried out for each siRNA. The extracted RNA was processed for RNA-SEQ on Illumina HIGHSEQ 2500.


title: Concerted regulation of mitochondrial and nuclear non-coding RNAs by a dual-targeted RNase Z [TruSeq]

status: Public on Aug 20 2018

first: Stefan

middle: J

last: Siira

summary: The molecular roles of the dually targeted ElaC domain protein 2 (ELAC2) during nuclear and mitochondrial RNA processing in vivo have not been distinguished. We generated conditional knockout mice of ELAC2 to identify that it is essential for life and its activity is non-redundant. Heart and skeletal muscle-specific loss of ELAC2 causes dilated cardiomyopathy and premature death at 4 weeks. Transcriptome-wide analyses of total RNAs, small RNAs, mitochondrial RNAs and miRNAs identified the nuclear and mitochondrial molecular targets of ELAC2 in vivo. We show that ELAC2 is required for processing of nuclear and mitochondrial tRNAs and for the balanced maintenance of C/D box snoRNAs, a new class of tRNA fragments, and miRNAs. We identify that correct biogenesis of regulatory non-coding RNAs is essential for both cytoplasmic and mitochondrial protein synthesis as well as the assembly of mitochondrial ribosomes and cytoplasmic polysomes. Taken together our data show that nuclear tRNA processing is required for the balanced production of snoRNAs and miRNAs for gene expression and that 3′ tRNA processing follows 5′ tRNA processing but nevertheless is an essential step in the production of all mature mitochondrial RNAs and the majority of nuclear tRNAs.

overall_design:
Total RNA from heart tissue from three control mice (L/L) and three Elac2 knockout mice (L/L, cre), was sequenced with four technical replicates each and analysed for differential expression.
RNA sequencing libraries were constructed using the Illumina TruSeq Sample Prep Kit. Paired end deep sequencing of the mitochondrial RNAs was performed on an Illumina NextSeq 500 according to the manufacturer’s instructions.

first: Aleksandra

last: Filipovska


title: Concerted regulation of mitochondrial and nuclear non-coding RNAs by a dual-targeted RNase Z


title: Concerted regulation of mitochondrial and nuclear non-coding RNAs by a dual-targeted RNase Z [tRF]

overall_design:
Total RNA from heart tissue from three control mice (L/L) and three Elac2 knockout mice (L/L, cre), was sequenced with four technical replicates each and analysed for differential expression.
RNA sequencing libraries were constructed using the Illumina Small RNA Sample Prep Kit, with a size selection step for 15 - 35 nt RNAs. Paired-end deep sequencing of the mitochondrial RNAs was performed on an Illumina NextSeq 500 according to the manufacturer’s instructions.


title: Elevated T cell levels in peripheral blood predict poor clinical response following rituximab treatment in new-onset type 1 diabetes

status: Public on Dec 05 2018

city: Seattle,

first: Stephanie

last: Osmond

institute: Benaroya Research Institute

summary: Peripheral blood samples were collected from subjects enrolled in the TrialNet study TN-05. This was a phase II study of the effects of the anti-CD20 monoclonal antibody rituximab in new-onset T1D. Total RNA was isolated from whole blood samples and then globin-reduced. RNAseq libraries were prepared from the globin-reduced RNA.

overall_design: The rituximab trial was a randomized, double-blind study of patients (N = 87) with newly diagnosed T1D assigned to receive infusions of rituximab or placebo on days 1, 8, 15, and 22 of the study. The primary outcome was the geometric mean area under the curve (AUC) for the serum C-peptide level during the first 2 hours of a mixed-meal tolerance test assessed after 1 year. We obtained RNA-seq data from a subset of subjects in the original trial (N = 56 subjects originally), sampled at different visits (0, 26, 52, 78 and 104 weeks) for a total of 205 samples (mean ~4 samples per patient). Of 205 initial samples, 195 yielded high-quality RNA-seq data consistent with subject annotation, and were used in downstream analyses.

last: Linsley

first: Carla

last: Greenbaum

first: Mario

last: Rosasco

middle: R

first: Kevan

middle: C

last: Herold

first: Matthew

last: Dufort


title: Concerted regulation of mitochondrial and nuclear non-coding RNAs by a dual-targeted RNase Z [sRNA]

overall_design:
Total RNA from heart tissue from three control mice (L/L) and three Elac2 knockout mice (L/L, cre), was sequenced with four technical replicates each and analysed for differential expression.
RNA sequencing libraries were constructed using the Illumina Small RNA Sample Prep Kit, with a size selection step for 15 - 100 nt RNAs. Paired-end deep sequencing of the mitochondrial RNAs was performed on an Illumina NextSeq 500 according to the manufacturer’s instructions.


title: Ulcerative Colitis subjects

status: Public on Apr 01 2018

last: Gordon

address: 1 Portland Street

institute: Pfizer Inc

overall_design: Refer to individual Series


title: UC Colon RNAseq subset analysis

summary: RNAseq was used to confirm findings from microarrays and identify additional genes different between inflamed and non-inflamed tissue

overall_design: Multiple biopsies were taken from UC subjects to better understand the variability of gene expression

middle: M


title: Molecular prediction of adjuvant cisplatin efficacy in Non-Small Cell Lung Cancer (NSCLC) - validation in two independent cohorts

status: Public on Dec 25 2017

city: Hoesholm

first: Anker

last: Hansen

address: Venlighedsvej 1

country: Denmark

institute: Medical Prognosis Institute A/S

summary: Introduction: Effective predictive biomarkers for selection of patients benefiting from adjuvant platinum-based chemotherapy in non-small cell lung cancer (NSCLC) are needed. Based on a previously validated methodology, molecular profiles of predicted sensitivity in two patient cohorts are presented. Methods: The profiles are correlations between in vitro sensitivity to cisplatin and vinorelbine and baseline mRNA expression of the 60 cell lines in the National Cancer Institute panel. An applied clinical samples filter focused the profiles to clinically relevant genes. The profiles were tested on 1) snap-frozen tumors from 133 patients with completely resected stage 1B-2 NSCLC randomized to adjuvant cisplatin and vinorelbine (ACV, n=71) or no adjuvant treatment (OBS, n=62) [GSE14814] and 2) formalin-fixed paraffin-embedded (FFPE) pre-treatment tumors from 95 patients with completely resected stage 1A-3B NSCLC receiving adjuvant cisplatin and vinorelbine. Results: The combined cisplatin and vinorelbine profiles showed: 1) univariate Hazard Ratio (HR) for sensitive versus resistant of 0.265 (95% CI:0.079-0.889, p=0.032) in the ACV cohort and a HR of 0.28 in a multivariate model (95% CI:0.08-1.04, p=0.0573); 2) significant prediction at 3 year survival from surgery in univariate (HR=0.138 (95% CI:0.035-0.537), p=0.004) and multivariate analysis (HR=0.14 (95% CI:0.030-0.6), p=0.0081). No discrimination was found in the OBS cohort (HR=1.328, p=0.60). The cisplatin predictor alone had similar figures with 1) univariate HR of 0.37 (95% CI:0.12-1.15, p=0.09) in the ACV cohort and 2) univariate HR of 0.14 (95% CI:0.03-0.59, p=0.0076) to three years. Functional analysis on the cisplatin profile revealed a group of upregulated genes related to RNA splicing as a part of DNA damage repair and apoptosis. Conclusions: Profiles derived from snap-frozen and FFPE NSCLC tissue were prognostic and predictive in the patients that received cisplatin and vinorelbine but not in the cohort that did not receive adjuvant treatment.

overall_design:
A total of 95 pre-treatment non-small cell lung cancer samples were profiled for gene expression by using Affymetrix U133+2 platform. Raw cel data were preprocessed by RMA.

Data from GSE14814 were used directly, without re-analysis.

first: Ida

middle: K

last: Buhl

first: Eric

last: Santoni-Rugiu

first: Jesper

last: Ravn

first: Ib

last: Christensen

first: Thomas

last: Jensen

first: Bruce

last: Pratt

first: Jon

last: Askaa

first: Peter

first: Steen

last: Knudsen

first: Jens

last: Sørensen


title: Identification of a T cell signature associated with allergic diseases in Human

status: Public on Oct 05 2017

last: Osmond

address: 1201 9th Ave

summary: We wish to show that Th2A cells have a distinct gene expression profile compared to Th2 cells in allergic subjects

overall_design: We sorted conventional Th1 cells (CXCR3+ CCR4- CCR6-), conventional Th17 cells (CCR6+), Th2A cells (CRTH2+ CD161+ CD49d+ CD27- CD45RB-) and conventional Th2+ cells (CRTH2+ CD161-) from the PBMC of 3 subject pools. Each pool consisted of cells from 2-3 allergic donors. Sorted TH subsets were stimulated for 6 hours with anti-CD3/CD28 beads (Life Technologies, STIM samples) or left unstimulated (CTRL samples) prior to extraction of RNA (RNeasy Mini kit; Qiagen).

first: Erik

last: Wambre

first: Veronique

last: Bajzik

first: Jonathan

last: DeLong

first: Archila

last: Diego

first: Kimberly

last: O'Brien

first: Cate

last: Speake

first: Quynh-Anh

last: Nguyen

first: Amedee

last: Renand

first: Vivian

last: Gersuk

first: Chester

last: Ni

first: Sean

last: Bennett

first: Bran

last: Vickery

first: Mary

last: Farrington

first: David

last: Jeong

last: Robinson

first: William

last: Kwok


title: The Adenovirus E1A C Terminus Suppresses a Delayed Antiviral Response and Modulates RAS Signaling [RNA-seq]

status: Public on Dec 13 2017

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: The N-terminal half of adenovirus e1a assembles multimeric complexes with host proteins that repress innate immune responses and force host cells into S-phase. In contrast, the functions of e1a's C-terminal interactions with FOXK, DCAF7, and CtBP are unknown. We found that these interactions modulate RAS signaling, and that a single e1a molecule must bind all three of these host proteins to suppress activation of a subset of IFN-stimulated genes (ISGs). These ISGs were otherwise induced in primary respiratory epithelial cells at 12 hr p.i. This delayed activation of ISGs required IRF3 and coincided with an ∼10-fold increase in IRF3 from protein stabilization. The induced IRF3 bound to chromatin and localized to the promoters of activated ISGs. While IRF3, STAT1/2, and IRF9 all greatly increased in concentration, there were no corresponding mRNA increases, suggesting that e1a regulates the stabilities of these key activators of innate immune responses, as shown directly for IRF3.

overall_design: mRNA-seq

first: Nathan

last: Zemke

first: Arnold

last: Berk


title: The Adenovirus E1A C Terminus Suppresses a Delayed Antiviral Response and Modulates RAS Signaling


title: Effect of group III phospholipase A2 deletion in azoxymethane-induced colon carcinogenesis modeled colon

status: Public on Nov 01 2017

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

summary: Lipid mediators play pivotal roles in colorectal cancer and colitis, but only a limited member of the phospholipase A2 (PLA2) subtypes, which lie upstream of various lipid mediators, have been implicated in the positive or negative regulation of these diseases. Clinical and biochemical evidence suggests that secreted PLA2 group III (sPLA2-III) is associated with colorectal cancer, although its precise role remains obscure. Here we have found that sPLA2-III-null (Pla2g3-/-) mice are highly resistant to colon carcinogenesis. Furthermore, Pla2g3-/- mice are less susceptible to dextran sulfateinduced colitis, implying that the amelioration of colonic inflammation by sPLA2-III ablation may underlie the protective effect against colon cancer. Lipidomics analysis of the colon revealed significant reduction of pro-inflammatory/pro-tumorigenic lysophosholipids as well as unusual elevation of colon-protective fatty acids and their oxygenated metabolites in Pla2g3-/- mice. Overall, our results establish a role of sPLA2-III in the promotion of colorectal inflammation and cancer, expand our understanding of the divergent roles of multiple PLA2 enzymes in the gastrointestinal tract, and point to sPLA2-III as a novel druggable target for colorectal diseases.

overall_design: Model, Azoxymethane-induced carcinogenesis. Mice were intraperitoneally administered azoxymethane once a week for 6 weeks and then sacrificed 28 weeks after the last treatment. Condition, tissues with colorectal cancer (AOM) versus normal (vehicle) colon tissues, and Pla2g3 knockout (–/–) versus Pla2g3 wild-type (+/+); Samples, mixed sample of colon tissues from 3-5 mice, respectively

first: Remi

last: Murase

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: KIF26B promotes proliferation and metastasis by activating the VEGF signaling pathway in gastric cancer

status: Public on Sep 01 2017

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University


title: Identification of differential expression genes in gastric cancer cell SGC7901 with or without knockdown KIF26B.

summary: In the study presented here, differential expression analysis of global gene profiling were performed in gastric cancer cells transfected with siKIF26B or negative control.

overall_design: To characterize the overall cellular response to KIF26B silencing, gene expression microarray profiling was performed in SGC7901 cells.

first: Hui

last: Zhang


title: Gene expression-based identification of differential expression genes on gastric cancer samples with or without lymph node metastasis

summary: In the present study, gene expression microarray was utilized to screen the differentially expressed genes between metastatic and nonmetastatic gastric cancers.

overall_design: In the study presented here, differential expression analysis of global gene profiling were performed in gastric tissues, including 2 cases of nontumorous gastric tissues, 5 cases of primary gastric cancer tissues without lymph node metastasis and 5 cases of primary gastric cancer tissues with lymph node metastasis.


title: ChIP-seq of transcription factors regulating the TLR-induced transcriptional cascades in macrophages

status: Public on Jun 11 2017

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

summary: Toll-like receptors (TLRs) are responsible for sensing pathogen components, initiating cascades of signaling pathways, transcription factors, chromatin regulators, and activating thousands of genes contributing to diverse immune functions in macrophages. Conventional system approaches have been used to analyze TLR-induced transcriptional cascades. However, commonly used approaches possess a number of limitations, including a bias toward weakly induced genes, which are far more prevalent than strongly induced genes, and an inability to distinguish functionally important protein-DNA interactions identified by ChIP-seq from interactions that may be functionally insignificant. To develop a better understanding of a TLR-induced transcriptional cascade, we used more stringent criteria to analyze RNA-seq, ChIP-seq, and transcription factor binding motif data sets. Our analysis provided a number of insights into the regulation of an inducible transcriptional cascade. This stringent and quantitative strategy can effectively reveal gene-specific regulatory mechanisms from genome-wide studies.

overall_design: Bone marrow-derived macrophages from wild type or knockout mice were stimulated with 100ng/ml lipid A for 0, 15, 30, 60, and 120 min. Sonicated chromatin samples were incubated with antibodies for Brg1, CEBPβ, CEBPδ, Fos, JunB, JunD, ATF3, CREB, and RelA.

first: Xin

last: Liu


title: Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense

status: Public on Jun 06 2017

summary: Successful host defense against pathogens requires innate immune recognition of the correct pathogen associated molecular patterns (PAMPs) by pathogen recognition receptors (PRRs) to trigger the appropriate gene program tailored to the pathogen. While many PRR pathways have been shown to contribute to the innate immune response to specific pathogens, the relative importance of each pathway for the complete transcriptional program elicited has not been examined in detail. Herein, we used RNA-sequencing with wildtype and mutant macrophages to delineate the innate immune pathways responsible for the early transcriptional response to Staphylococcus aureus, a ubiquitous microorganism that can activate a wide variety of PRRs. Unexpectedly, only two PRR pathways – the Toll-like receptor (TLR) and Stimulator of Interferon Gene (STING) pathways - were identified as dominant regulators of approximately 95% of the genes that were potently induced within the first four hours of macrophage infection with live S. aureus.  TLR signaling predominantly activated an inflammatory program, STING signaling activated an antiviral/type I interferon response, and both pathways contributed to a program linking innate and adaptive immunity. Only a small number of genes were induced in the absence of TLR or STING signaling, and these genes possessed a strong hypoxia signature. STING pathway activation required live S. aureus and was largely dependent on the DNA sensor cyclic guanosine-adenosine synthase (cGAS) recognition of S. aureus DNA. Interestingly, using a cutaneous infection model, we found that the TLR and STING pathways played opposite roles in host defense to S. aureus, with TLR signaling being required for protective interleukin (IL)-1 and neutrophil recruitment and STING signaling having an opposite effect. These results provide novel insights into the complex interplay of innate immune signaling pathways triggered byS. aureus and uncover opposing roles of TLR and STING in cutaneous host defense to S. aureus.

overall_design: Files are labeled according to the figures  in which they were used. Note, that many data files were used in multiple figures or figure panels. Files are labeled by genotype of macrophages (WT=wildtype; KO= StingGt/Gt; DKO=MyD88-/-TRIF-/-) and whether the macrophages were treated with live (Live) or heat killed (HK) or uninfected (zero hour). Labeling of time points is in the order of "minutes_replicate #." For example, "WT_HK_30_2" indicates that this is wild type mouse macrophages stimulated with heat killed bacteria at the 30-minute time point and is replicate number 2. Reads were converted into RPKM, and the RPKM for all replicates listed for a given time point were averaged to obtain the average RPKM that was used for figures and analyses. For samples listed as contributing to either figure 3 or supplemental figure 2, the replicates that do NOT end in either KO_analysis nor DKO analysis were used to determine induced genes in wild type macrophages. In contrast, the replicates that end in KO_analysis or DKO_analysis were used to determine dependence on either STING signaling or MyD88/TRIF signaling, respectively. If a replicate was used in the STING or MyD88/TRIF dependence analysis for both live and heat-killed S. aureus, "live_and_hk" was added after the dependence analysis it contributed to. Some 0h samples were used in both live and heat-killed analyses.

first: Philip

last: Scumpia

first: Joshua

last: Norman


title: Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (bulk RNA-seq of T-cell clone)

status: Public on Jun 08 2017

first: Stephanie

last: Osmond

summary: Islet-reactive T cells found in peripheral blood of type 1 diabetes (T1D) subjects are thought to be involved in disease pathogenesis, but full understanding of their role is complicated by their presence also in blood of in healthy subjects. To elucidate their role in T1D, we have combined flow cytometry and single cell RNA sequencing (RNA-seq) techniques to link prior antigen exposure, inferred from expanded TCR clonotypes, and functional capacities of islet antigen-reactive CD4+ memory T cells. We find that cells activated by pooled peptides from immunodominant islet antigens showed significantly higher clonotype sharing within recent onset T1D subjects than in healthy individuals, consistent with in vivo T cell expansion during disease progression. There was no clonotype sharing between donors, indicating a predominance of TCRs with distinct or “private” specificities. Expanded clonotypes could be stable, as one was detected at repeat visits by spanning more than a year by one subject. We identified distinct IGRP peptides as the targets of expanded TCR clonotypes from two T1D subjects, thereby implicating this molecule as a trigger for CD4+ T cell expansion during T1D. Transcriptome profiles of cells from T1D and healthy subjects differed, particularly in cells having the most highly expanded TCR clonotypes. As a group, cells with the most highly expanded TCR clonotypes showed Th2-like phenotypes, but at the single cell level there was phenotypic heterogeneity within and between donors. Our findings demonstrate unique specificities and phenotypes of individual islet-reactive CD4+ memory T cells that have expanded during disease progression.

overall_design: This project contains RNA-seq files from four cell types: 1) T cell clone (N=149 single cell profiles); 2) T cell clone (N=9 bulk cell profiles); 3) CD8+ influenza-reactive T cells (N=45 single cell profiles); and 4) CD4+ pooled islet antigen-reactive T cells (N=246 single cell profiles).

first: Karen

last: Cerosaletti

first: Fariba

last: Whitman

first: Junbao

last: Yang

first: Hannah

last: DeBerg

first: Elisabeth

last: Israelsson

first: Cate

last: Speake

first: Vivian

last: Gersuk

first: James

last: Eddy

first: Helena

last: Reijonen

first: Carla

last: Greenbaum

first: Martin

last: Prilic

first: Erik

last: Wambre

first: Raphael

last: Gottardo

first: Gerald

last: Nepom

first: Peter

last: Linsley


title: Gene expression markers differentiating between malignant and benign follicular thyroid tumors

status: Public on Jun 03 2017

city: Gliwice

first: Aleksandra

last: Pfeifer

address: Wybrzeze Armii Krajowej 15

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology

summary: Differential diagnosis between malignant follicular thyroid cancer (FTC) and benign follicular thyroid adenoma (FTA) is a great challenge for even an experienced pathologist and requires special effort. Molecular markers may potentially support a differential diagnosis between FTC and FTA in postoperative specimens. The purpose of this study was to derive molecular support for the differential diagnosis, in the form of a simple multigene mRNA-based classifier that would differentiate between FTC and FTA tissue samples.

overall_design: Gene expression profiling was performed in 27 follicular thyroid cancers and 25 follicular thyroid adenomas.

first: Bartosz

last: Wojtas

first: Malgorzata

last: Oczko-Wojciechowska

last: Kukulska

first: Agnieszka

last: Czarniecka

first: Markus

last: Eszlinger

first: Thomas

last: Musholt

first: Tomasz

last: Stokowy

first: Michal

last: Swierniak

first: Ewa

last: Stobiecka

first: Dagmara

last: Rusinek

last: Tyszkiewicz

first: Monika

last: Kowal

first: Jolanta

last: Krajewska

first: Steffen

last: Hauptmann

first: Dariusz

last: Lange

last: Jarzab

first: Ralf

last: Paschke

first: Barbara


title: Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes

first: Stephanie

last: Osmond

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


title: Expression profiling of Cellvibrio japonicus using either glucose or cellobiose

status: Public on Jan 01 2017

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes, many of which have been categorized as functionally redundant. Here we present data that suggests that carbohydrate active enzymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted b-glucosidases is required in a physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual b-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Our approach for parsing related carbohydrate active enzymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.

overall_design: Two carbon conditions (glucose, cellobiose); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 12 samples


title: Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of CD8+ influenza-reactive T cells)

first: Karen

last: Cerosaletti

first: Fariba

last: Whitman

first: Junbao

last: Yang

first: Hannah

last: DeBerg

first: Elisabeth

last: Israelsson

first: Cate

last: Speake

first: Vivian

last: Gersuk

first: James

last: Eddy

first: Helena

last: Reijonen

first: Carla

last: Greenbaum

first: William

last: Kwok

first: Martin

last: Prilic

first: Erik

last: Wambre

first: Raphael

last: Gottardo

first: Gerald

last: Nepom

first: Peter

last: Linsley


title: Defects in mitochondrial RNA processing in disease

status: Public on Mar 23 2017

city: Perth

first: Stefan

last: Siira

address: 15 Hospital Ave, Nedlands

institute: The Kids Research Institute Australia

summary: The expression of mitochondrially-encoded genes requires the efficient processing of long precursor RNAs at the 5´ and 3´ ends of tRNAs, a process which, when disrupted, results in disease. Two such mutations reside within mt-tRNALeu(UUR); a m.3243A>G transition, which is the most common cause of MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes), and m.3302A>G which often causes mitochondrial myopathy (MM). We used parallel analysis of RNA ends (PARE) that captures the 5´ terminal end of 5´-monophosphorylated mitochondrial RNAs to compare the effects of the m.3243A>G and m.3302A>G mutations on mitochondrial tRNA processing. We confirmed previously identified RNA processing defects, identified common internal cleavage sites and new sites unique to the m.3243A>G mutants that do not correspond to transcript ends. These sites occur in regions of predicted RNA secondary structure, or are in close proximity to such regions, and may identify regions of importance to the processing of mtRNAs.

overall_design: Mitochondrial RNA 5’ end profiles were generated using PARE for 143B cybrid cells containing mtDNA harbouring m.3243A>G and m.3302A>G mutations.

first: Aleksandra

last: Filipovska


title: Gene expression profile of NPTr cells infected with swine H1N1/2009 influenza A virus

status: Public on Mar 24 2017

city: Wuhan

first: Shishuo

last: Zhang

address: Shizishan Street

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

summary: In order to identify the swine genes which play roles in the regulation of swine influenza A virus replication, the gene microarray was performed to explore the systematical host response to the swine H1N1/2009 influenza A virus infection in porcine cells.

overall_design: Two pools of total RNA were extracted from the swine H1N1/2009 influenza A virus infected or uninfected NPTr cells and hybrided on Affymetrix  Porcine genome array Array.

first: Hongbo

last: Zhou


title: Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of T-cell clone)

first: Stephanie

last: Osmond

first: Karen

last: Cerosaletti

first: Fariba

last: Whitman

first: Junbao

last: Yang

first: Hannah

last: DeBerg


title: Dysregulated TLR7 signaling drives anemia via development of unique hemophagocyte

status: Public on Jul 29 2018


title: Allergen-induced activation of NK cell genes represents an early life immune response in development of allergic asthma

status: Public on Mar 27 2018

summary: Peripheral blood samples from children enrolled in the URECA cohort were collected at age 2. In short, at each URECA research center, within 16 hours of blood collection, mononuclear cells were separated and incubated (48 hours, 37C, 5% CO2) in the presence of German cockroach extract (10mg/mL; CR), dust mite extract (Dermatophagoides pteronyssinus, 10mg/mL; DM), tetanus toxoid (5mg/mL; TT), or medium alone (NS).

overall_design: For the initial case-control cohort (cohort 1), cases (n=21) were URECA participants who met the following inclusion criteria: a) ≥2 aeroallergen sensitizations at age 3, 5, and 7 including sensitization to DM and/or CR at each age, b) a diagnosis of asthma at age 7, and c) had PBMC RNA samples collected at age 2. Controls (n=30) were URECA participants with: a) no aeroallergen sensitization through age 7, b) did not have asthma at age 7, and c) had PBMC RNA samples collected at age 2. Controls were selected to match to cases on at least a bivariate level according to the following variables: gender, race, URECA site, birth season, and levels of Bla g 1, Der f 1, and Def p 1 measured in the home 3 months after birth. All available NS, CR, DM, and TT stimulation PBMC samples from these 51 individuals were selected for RNA-sequencing. For cohort 2, seven additional URECA participants were selected who met the following inclusion criteria: a) ≥1 aeroallergen sensitization by age 7 including CR sensitization, b) a diagnosis of asthma at age 7, and c) PBMC RNA samples collected at age 2. Fourteen additional controls were selected to match these cases by the same criteria as the controls of cohort 1. Furthermore, all URECA participants with PBMC RNA samples collected at age 2 and who had sufficient year 7 outcome data for group classification were added to the sequencing run to allow a 4 group comparison based on CR sensitization (age 3, yes/no) and asthma (age 7, yes/no). For the latter analyses, only NS and CR stimulation PBMC samples were used for RNA-sequencing.

first: Matthew

last: Altman

first: Elizabeth

last: Whalen

first: Alkis

last: Togas

first: George

last: O'Connor

first: Leonard

last: Bacharier

first: Gordon

last: Bloomberg

first: Meyer

last: Kattan

first: Robert

last: Wood

first: Scott

last: Presnell

first: Petra

last: Le Beau

first: Katy

last: Jaffee

first: Cynthia

last: Visness

last: Busse

first: James

middle: E

last: Gern


title: Response of peripheral blood mononuclear cells from  20 healthy donor and 15 patients with type 1 diabetes to type 1 diabetogenic protein (IGRP, PPI) derived peptide stimulation.

status: Public on Aug 15 2016

first: Stephanie

last: Osmond

summary: CD4 T cell responses are characterized based on a limited number of molecular markers selected from exisiting knowledge. The goal of the experiment was to assess antigenic-peptide specific T-cell responses in vitro without bias using microarrays.

overall_design: PBMCs were isolated from 20 healthy donors and 15 patients with type 1 diabetes. The cells were stimulated with peptides derived from type 1 diabetogenic protein (IGRP, PPI) for 24 hours. Unstimulated cells were cultured without the peptides for 24 hours.

first: Shinobu

last: Yamamoto

first: Daisuke

last: Chujo

first: Durgha

last: Nattamai

first: Nicole

last: Baldwin

first: Kimberly

last: O'Brien

first: Quynh-Anh

last: Nguyen

first: Vivan

last: Gersuk

first: Esperanza

last: Anguiano

first: William

last: Kwok

first: Jacques

last: Banchereau

first: Gerald

middle: T

last: Nepom

first: Hideki

last: Ueno

first: Damien

last: Chaussabel


title: Rb and p53 cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance

status: Public on Feb 24 2017

city: Buffalo

first: David

last: Goodrich

address: Elm and Carlton

department: Pharmacology&Therapeutics

institute: Roswell Park Cancer Institute

summary: Prostate cancer relapsing from antiandrogen therapies can exhibit variant histology with altered lineage marker expression, suggesting lineage plasticity facilitates therapeutic resistance. Mechanisms underlying prostate cancer lineage plasticity are unknown, and relevant experimental models are needed. We demonstrate Rb1 loss facilitates lineage plasticity and metastasis of prostate adenocarcinoma initiated by Pten mutation in the mouse. Additional loss of Trp53 causes resistance to antiandrogen therapy. Gene expression profiling indicates mouse tumors are comparable to human prostate cancer neuroendocrine variants; both mouse and human tumors exhibit increased expression of epigenetic reprogramming factors like Ezh2 and Sox2. Clinically relevant Ezh2 inhibitors restore androgen receptor expression and sensitivity to antiandrogen therapy. These findings uncover genetic mutations enabling prostate cancer progression, identify mouse models for studying prostate cancer lineage plasticity, and suggest an epigenetic approach for extending clinical responses to antiandrogen therapy.

overall_design: 27 mouse samples; 4 wild type and 23 with floxed alleles. The purpose of the experiment was to compare the gene expression profile of prostate tumors from mice with different genotypes. The genotypes compared include PBCre4:Ptenfl/fl, PBCre4:Ptenfl/fl:Rb1fl/fl, and PBCre4:Ptenfl/fl:Rb1fl/fl:Trp53fl/fl where fl=floxed alleles of the indicated genes. Tumors, either primary or metastatic, from individual mice  were dissected, RNA extracted, and RNA analyzed by RNA-seq. Castrate recurrent tumors were dissected from mice that had been surgically castrated at 30 weeks of age, and tumors collected at relapse as mice became moribund.

first: Sheng

middle: Y

last: Ku

first: Spencer

last: Rosario

first: Yanqing

last: Wang

first: Ping

last: Mu

first: Mukund

last: Seshadri

first: Zachary

first: Maxwell

middle: P

last: Labbe

first: Eduardo

last: Cortes

first: Jianmin

first: Henry

last: Long

first: Bo

last: Xu

first: Myles

last: Brown

first: Massimo

last: Loda

first: Charles

last: Sawyers

first: Leigh

last: Ellis


title: Response of peripheral blood mononuclear cells to peptide stimuli

first: Stephanie

last: Osmond

overall_design: Refer to individual Series


title: Response of peripheral blood mononuclear cells to west nile virus (E, NS2a) and type 1 diabetogenic antigens (GAD65, ZnT8) derived peptide stimulation.

overall_design: PBMCs were isolated from 3 healthy donors. The cells were stimulated with peptides derived from west nile virus (E, NS2a), type 1 diabetogenic antigens (GAD65, ZnT8) for 24 hours. Unstimulated cells were cultured without the peptides for 24 hours.

first: Shinobu

last: Yamamoto

first: Elizabeth

last: Whalen

first: Daisuke

last: Chujo

first: Durgha

last: Nattamai

first: Nicole

last: Baldwin

first: Kimberly

last: O'Brien

first: Quynh-Anh

last: Nguyen

first: Vivan

last: Gersuk

first: Esperanza

last: Anguiano

first: Junbao

last: Yang

first: William

last: Kwok

first: Jacques

last: Banchereau

first: Gerald

last: Nepom

first: Hideki

last: Ueno

first: Damien


title: Response of peripheral blood mononuclear cells from  15 healthy donor and 15 patients with type 1 diabetes to type 1 diabetogenic protein (GAD65, IGRP, PPI, ZnT8) and influenza virus M derived peptide stimulation.

overall_design: PBMCs were isolated from 15 healthy donors and 15 patients with type 1 diabetes. The cells were stimulated with peptides derived from type 1 diabetogenic protein (GAD65, IGRP, PPI, ZnT8) and influenza virus M for 24 hours. Unstimulated cells were cultured without the peptides for 24 hours.

last: Chaussabel


title: Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of CD4+ pooled islet antigen-reactive T cells)

first: Karen

last: Cerosaletti

first: Fariba

last: Whitman

first: Hannah

last: DeBerg

first: Elisabeth

last: Israelsson

first: Cate

last: Speake

first: Vivian

first: James

last: Eddy

first: Helena

last: Reijonen

first: Carla

last: Greenbaum

middle: W

first: Martin

last: Prilic

first: Erik

last: Wambre

first: Raphael

last: Gottardo

first: Peter

last: Linsley


title: Response of peripheral blood mononuclear cells from patients with allergy to cat and silver birch wood derived antigenic peptide stimulation.

first: Stephanie

last: Osmond

overall_design: PBMCs were isolated from 2 donors with allergy. The cells were stimulated with antigenic peptides derived from silver birch wood and cat for 24 hours. Unstimulated cells were cultured without the peptides for 24 hours.

first: Shinobu

last: Yamamoto

first: Elizabeth

last: Whalen

first: Daisuke

last: Chujo

first: Durgha

last: Nattamai

first: Nicole

last: Baldwin

first: Kimberly

last: O'Brien

first: Quynh-Anh

last: Nguyen

first: Vivan

last: Gersuk

first: Esperanza

last: Anguiano

first: Junbao

last: Yang

first: William

last: Kwok

first: Jacques


title: Response of peripheral blood mononuclear cells from young (≤ 45 years old) and old (>60 years old) healthy donors to influenza virus derived peptide stimulation.

overall_design: PBMCs were isolated from 11 young (≤ 45 years old) and old (> 60 years old) healthy donors. The cells were stimulated with peptides derived from influenza virus for 24 hours. Unstimulated cells were cultured without the peptides for 24 hours.

last: Banchereau

first: Gerald

last: Nepom

first: Hideki

last: Ueno

first: Damien

last: Chaussabel


title: Ionic immune suppression within the tumour microenvironment limits T cell effector function

status: Public on Aug 13 2016

city: Bethesda

first: Suman Kumar

last: Vodnala

address: 10 Center Drive

department: Surgery Branch

institute: NCI

summary: Tumours progress despite being infiltrated by effector T cells. Tumour necrosis is associated with poor survival in a variety of cancers. Here, we report that that necrosis causes release of an intracellular ion, potassium, into the extracellular fluid of human and mouse tumours. Surprisingly, elevated extracellular potassium ([K+]e) was sufficient to profoundly suppress mouse and human T cell anti-tumour function. Elevations in [K+]e acted to acutely impair T cell receptor (TCR) dependent Akt-mTOR phosphorylation and effector function. Potassium mediated suppression of Akt-mTOR signalling and T cell effector function required intact activity of PP2A, a serine/threonine phosphatase. The suppressive effect mediated by elevated [K+]e required a T cell-intrinsic increase in intracellular potassium ([K+]i) and was independent of changes in plasma membrane potential (Vm). Finally, ionic reprogramming of tumour-specific T cells via over-expression of the voltage-gated potassium channel Kv1.3 lowered [K+]i and improved effector functions in vitro and in vivo, with this gain of function being dependent on intact channel function. Consequently, Kv1.3 T cell expression enhanced tumour clearance and the survival of melanoma-bearing mice. These results uncover a previously undescribed ionic checkpoint against T cell function within tumours and identify new strategies for cancer immunotherapy.

overall_design: RNA expression was measured by RNA-Seq on day 5 of cultures, maintained in individual biologial triplicates which were stimulated with immobilized anti-CD3/28 antibodies or kept in complete media (no stim) - with equivalent conditions treated with isotonic media containing elevated potassium.

first: Robert

last: Eil

first: Suman

first: David

last: Clever

first: Christopher

last: Klebanoff

first: Madhusudhanan

last: Sukumar

first: Jenny

middle: H

last: Pan

first: Douglas

last: Palmer

first: Alena

last: Gros

first: Tori

middle: N

first: Shashank

last: Patel

first: Geoff

last: Guittard

first: Zhiya

last: Yu

first: Valentina

last: Carbonaro

first: Klaus

last: Okkenhaug

last: Schrump

first: W

last: Linehan

first: Rahul

last: Roychoudhuri

first: Nicholas

last: Restifo


title: The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis

status: Public on May 03 2017

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary:
Check Web Link for HMMs(11 States) for Retina hg19 and mm9

https://pecan.stjude.cloud/proteinpaint/study/retina_hic_2018


title: Next generation sequencing of human immune cell subsets across diseases

status: Public on Jan 06 2015

first: Stephanie

last: Osmond

state: WA

summary: This study compared whole transcriptome signatures of 6 immune cell subsets and whole blood from patients with an array of immune-associated diseases. Fresh blood samples were collected from healthy subjects and subjects diagnosed type 1 diabetes, amyotrophic lateral sclerosis, and sepsis, as well as multiple sclerosis patients before and 24 hours after the first treatment with IFN-beta. At the time of blood draw, an aliquot of whole blood was collected into a Tempus tube (Invitrogen), while the remainder of the primary fresh blood sample was processed to highly pure populations of neutrophils, monocytes, B cells, CD4 T cells, CD8 T cells, and natural killer cells. RNA was extracted from each of these cell subsets, as well as the whole blood samples, and processed into RNA sequencing (RNAseq) libraries (Illumina TruSeq). Sequencing libraries were analyzed on an Illumina HiScan, with a target read depth of ~20M reads. Reads were demultiplexed, mapped to human gene models (ENSEMBL), and tabulated using HTSeq. Read count data were normalized by the TMM procedure (edgeR package).

overall_design: We performed whole genome RNAseq profiling of immune cell subsets and whole blood from subjects with an array of immune-associated diseases.

first: Cate

last: Speake

first: Peter

last: Linsley

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel

first: Scott

last: Presnell

first: Michael

last: Mason

first: Vivian

last: Gersuk

first: Kimm

last: O'Brien

first: Quynh-Anh

last: Nguyen

first: Carla

last: Greenbaum

first: Jane

last: Buckner

first: Uma

last: Malhotra


title: Response of IRF7-deficient peripheral blood mononuclear cells to pH1N1 influenza virus infection

status: Public on Apr 07 2015

summary: IRF7 plays a critical role in the production and amplification of the antiviral type I and III interferon response. Autosomal recessive IRF7-deficiency resulted in life-threatening influenza disease in a 3-year-old child. We studied the impact of IRF7-deficiency in non-hematopoietic tissues (fibroblasts and lung epithelial cells) as well in hematopoietic cells (peripheral blood mononuclear cells (PBMCs)). Genome-wide gene expression analysis demonstrated a profound loss of type I and III IFNs in PBMCs infected with influenza virus.

overall_design: PBMCs were isolated from 4 healthy donors and patients with deficiencies for IRF7 and UNC93B. The cells were infected with influenza virus A/CA/4/2009 at a multiplicity of infection (MOI) of 2 for 8 and 16 hours. Uninfected cells were cultured for 16 hours.

last: Ciancanelli

first: Sarah

middle: X

last: Huang

first: Priya

last: Luthra

first: Hannah

last: Garner

first: Yuval

last: Itan

first: Stefano

last: Volpi

first: Fabien

middle: G

last: Lafaille

first: Celine

last: Trouillet

first: Mirco

last: Schmolke

first: Randy

middle: A

last: Albrecht

first: Elisabeth

last: Israelsson

first: HyeKyung

last: Lim

first: Melina

last: Casadio

first: Tamar

last: Hermesh

first: Lazaro

last: Lorenzo

first: Lawrence

last: Leung

first: Vincent

last: Pedergnana

first: Bertrand

last: Boisson

first: Satoshi

last: Okada

first: Capucine

last: Picard

first: Benedicte

last: Ringuier

first: Francoise

last: Troussier

first: Laurent

last: Abel

first: Isabelle

last: Pellier

first: Luigi

middle: D

last: Notarangelo

first: Adolfo

last: Garcia-Sastre

first: Christopher

middle: F

last: Basler

first: Frederic

last: Geissmann

first: Shen-Ying

last: Zhang

first: Hans-Willem

last: Snoeck

first: Jean-Laurent

last: Casanova


title: DNA methylation-based classification of human central nervous system tumors [reference set]

status: Public on Jan 14 2018

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: Background: Modern neuropathology is challenged by an increasing number of clinically-relevant CNS tumor subgroups that require assessment of a multitude of molecular markers for classification, as well a highly trained medical staff. Failure to meet this challenge leads to tumor misclassification, which can have severe consequences for affected patients.  Methods: We compiled a cohort of genome-wide DNA methylation profiles of 2,682 tumors from 82 histologically and/or molecularly distinct CNS tumor classes across all ages and histologies that served as reference for a Random Forest-based diagnostic classifier. This classifier was used to prospectively investigate a further 1,104 CNS tumor samples in order to determine its clinical utility.  Results: The classifier was able to reliably assign tumor samples to a given diagnostic category with a misclassification rate of less than 2%. The system functioned robustly across laboratories and using different DNA methylation profiling techniques. Prospective application to clinical samples resulted in a reclassification of 12% of tumors compared with standard practice alone. A further 12% could not be classified by methylation profiling – this subset was highly enriched for unusual syndrome-associated tumors and likely novel entities.  Conclusion: This study represents a proof-of-concept for the application of machine learning approaches in molecular diagnostics using a single, easy-to-use assay. The reference cohort and Random Forest-based classifier are available online as a valuable community tool for improving precision in brain tumor diagnostics. We expect that approaches similar to the one presented herein will rapidly restructure diagnostic practice in neurooncology and across tumor pathology.

overall_design: The Illumina Infinium HumanMethylation450 array (Illumina, San Diego, USA) data from n=2801 patients were used to obtain genome-wide assessment of DNA methylation, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) as described previously (Sturm et al. Cancer Cell. 2012 Oct 16;22(4):425-37)

first: David

last: Capper

last: Jones

first: Volker

last: Hovestadt

first: Andreas

last: von Deimling

first: Stefan

last: Pfister


title: Quantitative Analysis of Transcription Dynamics in Pluripotent and Differentiated Cells

status: Public on Sep 19 2014

first: Stephen

last: Smale

summary: Cellular identity is a direct consequence of the transcriptional output for any given cell type. Understanding the regulatory properties of the genes that define each cell type is of fundamental importance. In this study, we performed a detailed characterization of the gene expression profiles in embryonic stem cells (ESC) and three terminally differentiated primary cell types. Using deep chromatin RNA sequencing (~500 million mapped reads), we were able to accurately quantify transcripts for genes expressed at very low levels. This provides us with the ability to distinguish genes that exhibit a broad dynamic range among cell types from those whose dynamic range of expression is more limited.

overall_design: Strand specific sequencing of chromatin associated transcripts in Embryonic Stem cells and three primary cell types; E14.5 Cortial Neurons, CD4+ CD8+ Thymocytes and Bone Marrow Derived Macrophages

first: M

middle: V

last: Edwards

first: S


title: LAA expression profiles on LSC compared to other tissues

status: Public on Apr 23 2015

city: Ulm

first: Jochen

last: Greiner

address: Helmholzstrasse 10

department: Internal Medicine III

institute: University Clinic Ulm

summary:
Leukemic stem cells (LSC) might be the source for leukemic disease self-renewal and account for disease relapse after treatment, which makes them a critical target for further therapeutic options. Leukemia associated antigens (LAA) might be suitable structures to be attacked by immunotherapeutic agents.   We performed primary AML sample enrichment and microarray studies to define LAA expression levels in AML.   We compared the LAA expression in the enriched CD34+CD38- AML fraction to that of enriched HSC of healthy donors and AML bulk cells (CD34+CD38+, CD34-CD38+ and CD34-CD38). Furthermore, we investigated the expression patterns of co-stimulatory molecules in LSC, bulk AML cells and enriched HSC,   Conclusion: We demonstrated the differential expression of several LAA in LSC, and their suitability as target structures.
We enriched primary AML samples using CD34 and CD38 as markers to compare LAA expression levels of LSC, HSC and AML bulk.

overall_design:
LAA expression profiles comparing LSC, HSC and leukemic bulk AML

citation: Leukemic progenitor cells are susceptible to targeting by stimulated cytotoxic T cells against immunogenic leukemia-associated antigens
Vanessa Schneider, Lu Zhang, Markus Rojewski, Natalie Fekete, Hubert Schrezenmeier, Alexander Erle, Lars Bullinger, Susanne Hofmann, Marlies Götz, Konstanze Döhner, Susann Ihme, Hartmut Döhner, Christian Buske, Michaela Feuring-Buske, Jochen Greiner

first: Vanessa

last: Schneider


title: Effect of group X phospholipase A2 deletion in dextran sulfate sodium-induced colitis modeled colon

status: Public on Feb 01 2016

first: Yoshitaka

last: Taketomi

summary: Within the secreted phospholipase A2 (sPLA2) family, group X sPLA2 (sPLA2-X) has the highest capacity to hydrolyze cellular membranes and has long been thought to promote inflammation by releasing arachidonic acid (AA), a precursor of pro-inflammatory eicosanoids. Unexpectedly, we found that transgenic mice globally overexpressing human sPLA2-X (PLA2G10-Tg) displayed striking immunosuppressive and lean phenotypes with lymphopenia and increased M2-like macrophages, accompanied by marked elevation of free omega-3 polyunsaturated fatty acids (PUFAs) and their metabolites. Studies using Pla2g10-deficient mice revealed that endogenous sPLA2-X, which is highly expressed in the colon epithelium and spermatozoa, mobilized omega-3 PUFAs or their metabolites to protect against dextran sulfate sodium (DSS)-induced colitis and to promote fertilization, respectively. In colitis, sPLA2-X deficiency increased colorectal expression of Th17 cytokines, and omega-3 PUFAs attenuated their production by lamina propria cells partly through the fatty acid receptor GPR120. In comparison, cytosolic phospholipase A2 (cPLA2alpha) protects from colitis by mobilizing omega-6 AA metabolites including prostaglandin E2. Thus, our results underscore a previously unrecognized role of sPLA2-X as an omega-3 PUFA mobilizer in vivo, segregated mobilization of omega-3 and omega-6 PUFA metabolites by sPLA2-X and cPLA2alpha, respectively, in protection against colitis, and the novel role of a particular sPLA2-X-driven PUFA in fertilization.

overall_design: Model, DSS-induced colitis. Mice were orally administrated 1% DSS.; Condition, 4 condition experiments: DSS-induced colitis (day 7) versus control, and Pla2g10 knockout (–/–) versus Pla2g10 wild-type (+/+); Samples, mixed sample of colon tissues from 3 mice, respectively

first: Remi

last: Murase

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: Comparative Analysis of Transcriptional Responses in Monocytes from Human Neonates, Adults, and Older Adults

status: Public on Aug 09 2014

summary: Human neonates and older adults frequently exhibit a reduced capacity to control microbial infections. A variety of mechanisms involving both the innate and adaptive immune systems have been proposed to contribute to these deficiencies. The emergence of RNA sequencing (RNA-seq) as an accurate and quantitative method for examining mRNA levels provides an opportunity to compare transcriptional responses to a stimulus at a global scale in neonates, adults, and older adults. An examination of ex vivo monocyte responses to lipopolysaccharide stimulation or Listeria monocytogenes infection (with cord blood monocytes representing neonatal monocytes) revealed extensive similarities between all three age groups, with only a small number of genes exhibiting statistically significant differences. Using transcription factor motif analyses and RNA-seq data sets from a variety of mouse mutants, the most significant neonatal deficiencies corresponded to genes that require interferon response factor-3 or type 1 interferon signaling for their activation. In older adults, the most striking difference was broad, low-level activation of inflammatory genes prior to stimulation, consistent with prior evidence of a chronic inflammatory state in older adults. These results demonstrate the value of quantitative RNA-seq analyses and the feasibility of cross-species comparisons between well-defined mouse networks and human data sets.

overall_design: RNA-seq of primary cells from three independent donors in three different age-groups across 3 time-points stimulated with either LPS or Listeria monocytogenes.

first: Michelle

last: Lissner


title: Expression data from mouse tissue Angiotensin II treated for 0,1,3,7days

status: Public on Jul 16 2014

city: beijing

first: zhang

middle: yun

last: long

state: beijing

address: No.10 Xitoutiao, You An Men

department: Department of Physiology and Pathophysiology,

institute: School of Basic Medical Sciences, Capital Medical University

summary:
Angiotensin II (Ang II) mediated signaling plays a key role in the development of hypertension associated target organ damages. However, the gene expression changes regulated by Ang II in the early stage of acute cerebral, cardiac, renal, vascular injury remain unclear.
we investigated Ang II–mediated gene expression alteration associated with the development of early cerebral, cardiac, renal, vascular injury by microarray assay in a mouse model.

overall_design: All mice were euthanized by an overdose of pentobarbital on days 1, 3 and 7 of  Angiotensin II  treatment. Total RNA was isolated with TRIzol (Invitrogen) from brains, hearts, kidneys and vessels (n=1-3 per group) at each time point according to manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA). On the GeneChip Mouse Genome 430 2.0 Array, over 45,000 probe sets analyze the expression level of over 39,000 transcripts and variants from over 34,000 well characterized mouse genes.

first: Hui-Hua

last: Li

first: Yun-Long

last: Zhang


title: Functional analysis of the TRIB1 associated locus (TRIBAL) linked to plasma triglycerides and coronary artery disease

status: Public on Feb 14 2014

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

institute: UOHI

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


title: TRIBAL overexpression in HepG2 cells

summary:
Objective - The TRIB1 locus has been linked to hepatic triglyceride metabolism in mice and to plasma triglycerides and coronary artery disease (CAD) in humans.  The lipid associated SNPs identified by genome-wide association studies (GWAS) are located ~ 30 kb downstream from TRIB1 suggesting complex regulatory effects on genes or pathways relevant to hepatic triglyceride metabolism.   The goal of this study was to investigate the functional relationship between common SNPs at the TRIB1 locus and plasma lipid traits.
Methods & Results - Characterization of the risk locus reveals that it encompasses a gene, TRIB1 associated locus (TRIBAL) comprised of a well conserved promoter region and an alternatively spliced transcript.  Bioinformatic analysis and re-sequencing identified a single nucleotide polymorphism (SNP), rs2001844, within the promoter region that associates with increased plasma triglycerides, reduced HDL-C and CAD risk.  Furthermore, we show that rs2001844 is an expression trait locus (eQTL) for TRIB1 expression in blood and alters TRIBAL promoter activity in a reporter assay model.  The TRIBAL transcript has features typical of long noncoding RNAs (lncRNA), including poor sequence conservation.  Modulation of TRIBAL expression had limited impact on either TRIB1 or lipid regulatory genes mRNA levels in human hepatocyte models.  In contrast, TRIB1 knockdown markedly increased TRIBAL expression in HepG2 cells and primary human hepatocytes.
Conclusions - These studies demonstrate an interplay between a novel locus,TRIBAL, and TRIB1.  TRIBAL is located in the GWAS identified risk locus, responds to altered expression of TRIB1, harbors a risk SNP that is an eQTL for TRIB1 expression and associates with plasma triglyceride concentrations.

overall_design: HepG2 hepatoma cells were stably infected with TRIBAL1 or no insert carrying lentiviruses

first: A

last: Douvris

last: Soubeyrand


title: Gene expression profiles of white adipose tissues from C57BL/6 mice in the effect of high fat diet

status: Public on Mar 20 2014

summary: Metabolic disorders including obesity and insulin resistance have their basis in dysregulated lipid metabolism and low-grade inflammation. In a microarray search of unique lipase-related genes whose expressions are associated with obesity, we found that two secreted phospholipase A2s (sPLA2s), PLA2G5 and PLA2G2E, were robustly induced in adipocytes of obese mice. Analyses of Pla2g5-/- and Pla2g2e-/- mice revealed distinct and previously unrecognized roles of these sPLA2s in diet-induced obesity. PLA2G5 hydrolyzed phosphatidylcholine in fat-overladen low-density lipoprotein to release unsaturated fatty acids, which prevented palmitate-induced M1 macrophage polarization. As such, PLA2G5 tipped the immune balance toward an M2 state, thereby counteracting adipose tissue inflammation, insulin resistance, hyperlipidemia and obesiy. PLA2G2E altered minor lipoprotein phospholipids, phosphatidylserine and phosphatidylethanolamine, and moderately facilitated lipid accumulation in adipose tissue and liver. Collectively, the identification of metabolic sPLA2s adds this gene family to a growing list of lipolytic enzymes that act as metabolic coordinators.

overall_design: Model, high fat diet-induced obesity; Condition, two condition experiments: high fat diet versus low fat diet feeding for 18 weeks; Samples, 2 replicates of mixed sample of adipose tissues from 3 mice (C57BL/6 strain), respectively

first: Hiroyasu

last: Sato


title: Response of fresh or frozen peripheral blood mononuclear cells from 1 healthy donor to influenza virus derived peptide stimulation.

city: Seattle,

first: Stephanie

last: Osmond

institute: Benaroya Research Institute

overall_design: PBMCs were isolated from 1 healthy donor. The fresh cells or cells thawed from cryopresevation (frozen) were stimulated with peptides derived from influenza virus for 24 hours. Unstimulated cells were cultured without the peptides for 24 hours. Experiments were done in triplicate.

first: Shinobu

last: Yamamoto

first: Elizabeth

last: Whalen

first: Daisuke

last: Chujo

first: Durgha

last: Nattamai

first: Nicole

last: Baldwin

first: Kimberly

last: O'Brien

first: Quynh-Anh

last: Nguyen

first: Vivan

last: Gersuk

first: Esperanza

last: Anguiano

first: Junbao

last: Yang

first: William

last: Kwok

first: Jacques

last: Banchereau

first: Gerald

last: Nepom

first: Hideki

last: Ueno

first: Damien

last: Chaussabel