title: Transcriptional responses in whole blood of healthy adult volunteers experimentally challenged with S. Paratyphi

status: Public on Sep 02 2019

city: Oxford

first: Amber

last: Barton

address: Centre for Clinical Vaccinology and Tropical Medicine

institute: Oxford Vaccine Group

summary: This studies describes the transcriptional response in whole blood derived from healthy adult volunteers experimentally infected with S. Paratyphi A. Samples were collected at pre-challenge baseline (Group: CTRL), at day 7 after challenge in those participants who stayed well over 14 days following challenge (Group: suspected Enteric Fever - sEF). Participants who developed signs of enteric fever were sampled at the time of inititiation of antibiotics (Group: EF).In this group diagnosis was confirmed by blood culture positive for S. Paratyphi (SPT). Antibiotic therapy commenced at time of diagnosis or at day 14 after challenge in those who did not develop symptoms. The clinical results of this study have been published in: Dobinson et al. Evaluation of the Clinical and Microbiological Response to Salmonella Paratyphi A Infection in the First Paratyphoid Human Challenge Model. Clin Infect Dis. 2017 Apr 15;64(8):1066-1073.

overall_design: Dose escalation human challenge model.

first: Christoph

last: Blohmke

first: Andrew

last: Pollard

first: Julius

last: Muller


title: Quantitative Analysis of Musashi2-reporter positive and Musashi2-reporter negative KPf/fC pancreatic cancer cell transcriptomes

status: Public on Jun 18 2019

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this study is to compare the transcriptome of pancreatic cancer stem cells (Musashi2-reporter positive) to pancreatic cancer non-stem cells (Musashi2-reporter negative).
Methods: Musashi2-reporter mice contain a GFP-cassette knocked into the first exon of the endogenous Musashi2 locus; heterozygous mice are used to track cells expressing Musashi2. These mice were crossed to the KPf/fC (Ptf1a-Cre; KrasG12D; p53f/f) mouse model of pancreatic cancer. Tumors from endstage Musashi2-reporter KPf/fC mice were dissociated and FACS sorted for EpCAM+/GFP+ (Musashi2+ stem cells) and EpCAM+/GFP- (Musashi2- non-stem cells). For sequencing, mRNA libraries were generated from total RNA and sequenced with 50 basepair (bp) single end reads (SR50) to a depth of approximately 30 million reads per sample on an Illumina HiSeq2500 using V4 sequencing chemistry.
Conclusions: Our study provides comparative transcriptomic data from primary isolated pancreatic cancer stem and non-stem cells in biologic replicates.

overall_design: KPf/fC pancreatic cancer stem (Musashi2+) and non-stem (Musashi2-) cell mRNA profiles from late-stage primary tumors were generated by deep-sequencing biological triplicates using Illumina HiSeq2500.

first: Nikki

middle: K

last: Lytle

first: Tannishtha

last: Reya


title: Transcriptional responses in whole blood of febrile individuals in Nepal

summary: In this study, whole blood samples were used to determine the gene expression of febrile culture confirmed enteric fever cases (ST = S. Typhi; SPT = S. Paratyphi), febrile culture negative individuals presenting to hospital in Kathamandu (sEF = suspected enteric fever),  and healthy community controls (CTRL).

overall_design: Prospective diagnostic study.

middle: J


title: Single-cell profiling of cutaneous T-cell lymphoma after treatment with vorinostat and photophoresis.

status: Public on Jun 25 2019

city: Iowa City

first: Ali

last: Jabbari

state: Iowa

address: 200 Hawkins Drive

department: Dermatology

country: USA

institute: University of Iowa

summary: Cutaneous T cell lymphomas (CTCL), encompassing a spectrum of T-cell lymphoproliferative disorders involving the skin, have collectively increased in incidence over the last 40 years. Sézary syndrome (SS) is an aggressive form of CTCL characterized by significant presence of malignant cells in both the blood and skin. The guarded prognosis for SS reflects a lack of reliably effective therapy, due in part to an incomplete understanding of disease pathogenesis. Using single-cell sequencing of RNA at the induction of vorinostat and photopherisis treatment (GSE122703) and at the progression on therapy. We identifed thea decrease conventional SS cell markers on therapy and an increase in the number of cells expressing FOXP3+.

overall_design: Single-cell RNA sequencing was performed on CD4+ T cells isolated from the blood of a patient with Sezary Syndrome using the 10x genomics 5-prime expression profiling kits. The peripheral blood sample was separated into cancerous (P4, CD3+CD4+CD5brightSSChi) and noncancerous (P5, CD3+CD4+CD5intSSCint).

first: Nicholas

last: Borcherding


title: Full-length mRNA sequencing reveals principles of poly(A) tail length control

status: Public on Jun 04 2019

city: Berlin

first: Ivano

last: Legnini

state: Germany

address: Robert-Rössle-Straße 10, Haus 87

department: BIMSB

country: Germany

institute: MDC

summary: We report FLAM-seq, a cDNA library preparation method coupled to PacBio single-molecule sequencing for profiling full-length mRNAs including their poly(A) tail.

sample_organism:
Caenorhabditis elegans
Homo sapiens
synthetic construct
synthetic RNA

overall_design: FLAM-seq data for 2 replicates of HeLa S3 cells, iPSCs, cerebral organoids, C. elegans L4 and adult, and one replicate for synthetic RNA and cDNA standards.

first: Jonathan

last: Alles

first: Nikos

last: Karaiskos

first: Salah

last: Ayoub

first: Nikolaus

last: Rajewsky


title: Transcriptional responses in whole blood of healthy adult volunteers experimentally challenged with S. Typhi

summary: In this study, whole blood samples were used to determine the gene expression of healthy adult volunteers experimentally challenged with S. Typhi Quailes strain. Samples were collected at baseline (pre-challenge; Group: CTRL) and 7 days after challenge (Group: sEF) in individuals who did not reach diagnostic criteria. In those reaching the diagnostic endpoint (typhoid fever; Group: EF) the sample on the day of diagnosis when antibiotic treatment commenced was taken. These samples were derived from the placebo arm of a recent a Single Centre, Randomised, Doubleblind, Placebo Controlled Study to Evaluate M01ZH09 in a Healthy Adult Challenge Model, Using Ty21a Vaccine as a Positive Control. Darton et al. PMID: 27533046.

overall_design: Human challenge model.


title: Diagnostic host gene signature for distinguishing enteric fever from other febrile diseases

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

overall_design: Refer to individual Series


title: Endothelial cell subtypes co-opt a TGFb/miR-30c-driven fibrinolytic pathway that supports tumor growth

status: Public on May 14 2019

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: In tumors, extravascular fibrin forms provisional scaffolds for angiogenesis but is degraded by fibrinolysis and replaced with collagen in a process that resembles wound healing. We report that fibrin-mediated angiogenesis is inhibited and tumor growth is delayed following postnatal deletion of TGFβR2 in the endothelium (TGFβR2iECKO). TGFβR2iECKO endothelial cells (ECs) fail to up-regulate the fibrinolysis inhibitor Serpine1/PAI-1 due, in part, to uncoupled TGFβ-mediated suppression of miR-30c. Bypassing TGFβR signaling with vascular tropic nanoparticles that deliver miR-30c AntagomiRs is sufficient to promote PAI-1-dependent tumor growth and increase fibrin abundance whereas miR-30c Mimics inhibit tumor growth and promote vascular-directed fibrinolysis in vivo. Using single cell RNA sequencing, we also show that subtypes of ECs in tumors show a spectrum of Serpine1 and uPar (urokinase receptor) expression suggesting functional diversity in ECs at the level of individual cells; furthermore, fresh EC isolates from lung and mammary tumor models have differential abilities to degrade fibrin and launch new vessel sprouts which is linked to their inverse expression patterns of miR-30c and Serpine1 (i.e. miR-30chiSerpine1lo ECs are poorly angiogenic and miR-30cloSerpine1hi ECs are highly angiogenic). Thus, EC subtypes co-opt physiological processes such as wound healing by subverting a previously uncharacterized vascular-directed fibrinolytic pathway that supports tumor growth.

overall_design:
Single-cell RNA-sequencing of tumor and normal endothelial cells

Researchers may wish to include the data series from GSE186467 which will increase the numbers of endothelial cells for analysis.

first: James

middle: V

last: McCann

middle: D

last: Dudley


title: Deletion of Cdkn1b in ACI rats perturbs mammary progenitor cell proliferation and differentiation through non-cell-autonomous mechanisms

status: Public on Feb 11 2019

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Emerging data indicate that breast epithelial stem cells and progenitors, particularly those in the luminal epithelial cell lineage, are the cells-of-origin of breast carcinomas, and factors that influence breast cancer risk may alter the number and/or properties of these cells. We hypothesize that a subset of p27+ cells represent hormone-responsive progenitors that are quiescent due to the high activity of TGFβ signaling in these cells. The Estrogen-induced mammary tumor model in ACI inbred rats is physiologically relevant rodent model of breast cancer. In the present study we successfully generated Cdkn1b knockout ACI rats and performed comprehensive phenotypic assessment and RNAseq profiling using FACS sorted basal (CD24+CD29high) and luminal (CD24+CD29low) cell populations to characterize Cdkn1b+/+ and Cdkn1b-/- females in prepubertal and adult cohorts. We found that p27KO rats exhibited mammary differentiation phenotype and reduced numbers of mammary epithelial progenitor pool, Interestingly, p27 ablation has the most pronounced effect on luminal progenitor cell gene expression, and milk protein genes and pStat5 were dramatically upregulated, while PR and FoxA1 were greatly downregulated in Cdkn1b-/- luminal cells. Further characterization of mammary glands of prepubertal Cdkn1b knockout rats by fat pad transplantation illustrated p27 deletion in the mammary cancer susceptible ACI rat strain induced mammary epithelial cell differentiation through cell non-autonomous mechanisms.

overall_design:
KO strain nomenclature: ACI.Cg.-Cdkn1bem1Musc (DEL-32) and ACI.Cg.-Cdkn1bem4 (DEL-65). Data was generated with an equal contribution of em1 and em4 for both genotypes (+/+ and -/-, littermates selected from HET crosses, unless indicated otherwise. All KO animals for em1 and em4 had cataracts from birth
 Bulk RNA-Seq: RNA-Seq of both Cdkn1b knockout and wild type ACI rat mammary glands, at various ages, and various FACS sorted cell types.
ChIP-seq: ChIP-seq for PR of both Cdkn1b knockout and wild type 9 week old ACI rat mammary glands, with basal/myoepithelial and luminal FACS sorted cell types. Anti-PR antibody (H-190, Santa Cruz, cat# sc-7208).
Bulk RNA-Seq: RNA-Seq of ACI and BN rats treated with and without E2, sorted for luminal and basal fractions of the mammary gland.

first: Lina

last: Ding

first: Lauren

middle: B

last: Shunkwiler

middle: W

last: Harper

first: Kunihiko

last: Hinohara

first: Sung

last: Huh

first: Yang

last: Zhao

first: Muhammad

last: Ekram

first: Jan

last: Guz

first: Michael

last: Kern

first: Alexander

last: Awgulewitsch

last: Shull

first: Bart

middle: M

last: Smits


title: Effect of the BET inhibitor, JQ1, on gene expression in triple-negative breast cancer cell lines

status: Public on Mar 16 2019

city: Cleveland

first: Gurkan

last: Bebek

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Univ.

summary:
To study the effect of BET inhibition on gene expression in triple-negative breast cancer cells, we treated MDA-MB-231 and HCC70 cells with vehicle or the prototypical BET inhibitor, JQ1, for 72 hours. By comparing the expression profiles of vehicle-treated versus JQ1-treated cells, we can identify genes that respond to BET inhibition.
The Affymetrix Human Gene 2.0. St Microarray were processed with RMA (robust multichip average algorithm) as implemented in Bioconductor package oligo, where background subtraction, quantile normalization and summarization (via median-polish) was accomplished. The top differentially expressed genes were identified using empirical Bayesian procedure of limma package. FDR method was selected to adjust the p-values for multiple testing.

overall_design: MDA-MB-231 and HCC70 cells were treated with 0.1% DMSO or 500 nM JQ1 for 72 hours followed by RNA isolation

first: Jennifer

last: Sahni

first: Sylvia

middle: S

last: Gayle

first: Ruth

last: Keri


title: Transcriptional signatures associated with in vivo growth of lung cancer cells

status: Public on May 23 2019

city: Aurora

first: Joanna

last: Poczobutt

department: Medicine

institute: University of Colorado Denver

summary: Interactions between cancer cells and the host cells in the tumor microenvironment (TME) are critical for tumor growth and metastasis. While the host cells have been widely studied within the TME, cancer cell have been mostly studied in vitro. We hypothesized that the growth of cancer cells in vivo results in specific changes in cancer cells’ transcriptome that reflect specific interactions between cancer cell and the TME. To begin to define the changes in cancer cells growing in vivo, we performed RNA-seq transcriptome analysis of cancer cells isolated from murine tumors and compared them to transcriptomes of cells growing in vitro. In this study we used two murine lung cancer cell lines, both derived from a spontaneous lung adenocarcinoma in C57BL/6 mouse: (1) Lewis Lung carcinoma (LLC) and (2) CMT167(CMT). We first harvested RNA from these 2 cell lines cultured in vitro. To assess the transcriptome of cells growing in vivo, we employed an orthotopic immunocompetent model of lung adenocarcinoma in which murine lung cancer cells are directly implanted into the left lobe of syngeneic mice. LLC or CMT cells were injected into the lung of GFP-expressing mice of C57BL/6 strain. Resulting tumors were harvested, processed into single cell suspension, and cancer cells were isolated from host cells by flow cytometry, sorting for GFP-negative cells. RNA was extracted from freshly isolated cells. Furthermore, to assess if the changes associated with in vivo growth are permanent, we re-plated the cells isolated from mice, cultured them further in vitro, and extracted their RNA. Our RNA-seq analysis has shown that both cell lines undergo robust specific changes in transcriptional profile when growing in vivo as compared to cells cultured in vitro. Majority of these signatures were reversed in cells that were replated and further cultured in vitro after isolation from mice.

overall_design: The following conditions were analyzed: (1)LLC In Vitro. RNA was extracted from LLC cells cultured in vitro. This condition has 5 independently cultured and harvested replicates.(2) LLC In Vivo. RNA was extracted from LLC cells that were injected into mice, formed a tumor, and cancer cells were isolated by flow cytometry. This condition has 5 independently injected and harvested replicates. Each replicate is a pool of 3-5 mice.(3) LLC Pass. A sample of LLC cells isolated from tumors was replated and further cultured in vitro. This condition has 5 independent replicates.(4) CMT In Vitro. RNA was extracted from CMT cells cultured in vitro. This condition has 3 independently cultured and harvested replicates.(5) CMT In Vivo. RNA was extracted from CMT cells that were injected into mice, formed a tumor, and cancer cells were isolated by flow cytometry. This condition has 3 independently injected and harvested replicates. Each replicate is a pool of 3-5 mice.(6) CMT Pass. A sample of LLC cells isolated from tumors was replated and further cultured in vitro. This condition has 3 independent replicates.

first: Howard

last: Li

first: Maria

last: McSharry

first: Subhajyoti

last: De

first: Vinod

last: Yadav

first: Jeff

last: Kwak

first: Bonnie

last: Bullock

first: Trisha

middle: R

last: Sippel

first: Teresa

middle: T

last: Nguyen

first: Dwight

last: Hanson

first: Mary

middle: C

last: Weiser-Evans

first: Raphael

last: Nemenoff


title: Single-cell profiling of cutaneous T-cell lymphoma reveals underlying heterogeneity predicting with disease progression.

status: Public on Mar 22 2019

first: Ali

last: Jabbari

summary: Cutaneous T cell lymphomas (CTCL), encompassing a spectrum of T-cell lymphoproliferative disorders involving the skin, have collectively increased in incidence over the last 40 years. Sézary syndrome (SS) is an aggressive form of CTCL characterized by significant presence of malignant cells in both the blood and skin. The guarded prognosis for SS reflects a lack of reliably effective therapy, due in part to an incomplete understanding of disease pathogenesis. Using single-cell sequencing of RNA, we confirm that SS is a clonal disease, but we further define a more complex model featuring distinct transcriptomic states within SS. Our analysis showed the involvement of FOXP3+ malignant T cells during clonal evolution, transitioning from FOXP3+ T cells to GATA3+ or IKZF2+ (HELIOS) tumor cells. Transcriptomic diversities in a clonal tumor can be used to predict disease stage, and we were able to characterize a gene signature that predicts disease stage with close to 80% accuracy. Supporting the critical role of FOXP3+ T cell involvement during clonal evolution, FOXP3 was found to be the most important factor to predict early disease in SS, along with another 19 genes used to predict CTCL stage. This work offers insight into the heterogeneity of SS, providing better understanding of the transcriptomic diversities within a clonal tumor, which can predict tumor stage and thereby offer guidance of therapy.

overall_design: Single-cell RNA sequencing was performed on CD4+ T cells isolated from the blood of a patient with Sezary Syndrome using the 10x genomics 5-prime expression profiling kits. The peripheral blood sample was separated into malignant (P4, CD3+CD4+CD5brightSSChi) and nonmalignant (P5, (CD3+CD4+CD5intSSCint).

first: Nicholas

last: Borcherding


title: Gene expression profiling of adult chondrocyte populations

status: Public on Apr 23 2019

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: We profiled gene expression of purified cell types isolated from 5 musculoskeletal tissues: tendon, bone, muscle, cartilage and ligament. We then performed WGCNA to identify tissue-specific transcription factors, signaling pathways and cell surface receptors. The sequencing data for muscle cells is made available here.

overall_design: 3 biological replicates from pig samples

first: Gabriel

last: Ferguson

first: Ben

last: Van Handel


title: RNA-Seq profiling of 29 immune cell types and peripheral blood mononuclear cells

status: Public on Feb 06 2019

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

institute: Freiburg Medical Center

summary: We performed RNA-Seq transcriptome profiling on 29 immune cell types consituting peripheral blood mononuclear cells (PBMCs) sorted from 4 Singaporean-Chinese individuals (S4 cohort). We also performed RNA-Seq and microarray transcriptome profiling of PBMCs from an extended cohort of 13 individuals (S13 cohort). The data was used first to characterize the transcriptomic signatures and relationships among the 29 immune cell types. Then we explored the difference in mRNA composition in terms of transcripts proportions and abundance. Lastly, we performed deep deconvolution for both microarray and RNA-Seq technologies.

overall_design: Total RNA of 29 immune cell types (from 4 individuals) and peripheral blood mononuclear cells (PBMCs, from 13 individuals) was extracted for gene expression profiling. The 13 PBMCs samples were processed with both microarray and RNA-Seq platforms.

first: Bernett

last: Lee

first: Weili

last: Xu

first: You

last: Hwang

first: Michael

last: Poidinger

first: João

last: de Magalhães

first: Anis

last: Larbi


title: Single-cell profiling of cutaneous T-cell lymphoma

status: Public on Mar 25 2019


title: Isolating the Escherichia coli transcriptomic responses to superoxide generation and stress from cadmium chalcogenide quantum dots

status: Public on Feb 02 2019

city: Boulder

first: Thomas

last: Aunins

state: CO

address: 3460 Colorado Ave, B5

institute: University of Colorado Boulder

summary: In this study we investigate the transcriptomic response of Escherichia coli to CdTe-2.4 and benign CdSe-2.4 quantum dots, each with and without illumination to elucidate the phototherapeutic effect of CdTe-2.4. Our analysis sought to separate the transcriptomic responses of E. coli to the presence of superoxide and the presence of cadmium chalcogenide nanoparticles. We found eight genes to be consistently differentially expressed as a response to superoxide generation, and these genes demonstrate a consistent association with the DNA damage response and deactivation of iron-sulfur clusters, characteristic of a superoxide response. We found eighteen genes associated the presence of cadmium-based quantum dots, in isolation from the superoxide effect. In further analysis of these genes, we performed both amino acid supplementation and gene knockout experiments, identifying the importance of leucyl-tRNA downregulation as a cadmium-based QD response, as well as reinforcing the relationship between CdTe-2.4 stress and iron-sulfur clusters through the gene tusA. This study demonstrates the transcriptomic response of E. coli to CdTe-2.4 and CdSe-2.4 quantum dots and parses the different effects of superoxide versus material effects on the bacteria. Our findings may provide useful information towards the development of quantum dot-based antibacterial therapy in the future.

overall_design: Examination of differential expression of genes between CdTe and CdSe conditions both with and without illumination, as compared to a no treatment control.

first: Kristen

last: Eller


title: Identification of flowering time genes associated with vernalization in Chinese cabbage and their differential expression in radish

status: Public on Nov 02 2018

city: Deajeon

first: Won Yong

last: Jung

state: N/A = Not Applicable

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute Bioscience and Biotechnology(KRIBB)

summary: We conducted genome-wide transcriptome analysis using the inbred Chinese cabbage line, ‘4004’, which displayed early flowering in response to vernalization. A total of 1,677 differentially-expressed genes (DEGs) were identified with and without vernalization. Transcriptome analysis identified 223 homologs of Arabidopsis Ft genes in Chinese cabbage, and 50 of these genes responded to vernalization. RT-qPCR analysis of major Ft genes showed that the majority of flowering enhancers were up-regulated in response to vernalization, whereas most flowering repressors were down-regulated in response to vernalization. Among the major Ft genes, the expression of BrCOL1-2, BrFT1/2, BrSOC1/2/3, BrFLC1/2/3/5, and BrMAF was strongly affected by vernalization.

overall_design: Examination of vernalization in 4004 inbred lines. Shoots mRNA profiles of 0 and 35day old Chinese cabbage were generated by deep sequencing, in replicate, using Illumina hiseq2000.

first: Hye

last: Cho

first: Won

first: Areum

first: Youn-Sung

last: Kim


title: RNA-seq showed suppressed immune-related profile rescue pregnancy in an abotion mouse model

status: Public on Oct 01 2018

city: Guangzhou

first: Yi

last: Xiaochun

state: Guangdong

address: No. 107  West Road along the river, Yuexiu District

country: China

institute: Sun Yat-sen Memorial Hospital of the Sun Yat-sen University

summary:
Purpose:We hypothesize that there were some beneficial effects in survive fetal and protected fetal from demise in placenta. Here we use RNA-seq to characterize the transcriptome changes of placenta tissue and pay more attention to immune-related genes.
Methods: Female CBA/J mice were randomly allocated into two groups , abortion-prone group(A) and normal pregnance group(N), which mated with DBA/2J and BALB/c respectively. Male and female mice were mated 2∶1 at 18:00 and checked for vaginal plugs at 8:00 next day. Females with vaginal plugs were segregated and defined day 0.5 of gestation.Mice were killed by neck dislocation on day 13.5 of gestation and placentas were excised and immediately snap-frozen in liquid nitrogen before being stored at −80°C for subsequent analysis. Placental mRNA profiles were generated by deep sequencing using Illumina seq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: we mapped about 55 million sequence reads per sample to the mouse genome (build mm8) and 23995 transcripts with TopHat workflow.   523 genes were differentially expressed at a significance level of P-value < 0.005 and a fold-change ≥ 2 with two group both FPKM ≤1.5 ignored. We found 24 genes contribute to suppressing immune system and 6 are against it.
Conclusions: Our study represents the first detailed analysis of transcriptomes in placenta in the abotion model and immunosuppression can rescue pregnancy loss.

overall_design: 6 samples


title: Polychromic reporter mice reveal unappreciated innate lymphoid cell progenitor heterogeneity and elusive ILC3 progenitors in bone marrow

status: Public on May 11 2019

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

summary: Innate lymphoid cells (ILCs) play strategic roles in tissue homeostasis and immunity. ILCs arise from lymphoid progenitors undergoing lineage restriction leading to the development of specialised ILC subsets.  We generated ‘5x polychromILC’ compound transcription factor reporter mice to delineate ILC precursor states by revealing the multifaceted expression of key ILC-associated transcription factors (Id2, Bcl11b, Gata3, Rorc(γt) and Rora) during ILC development in the bone marrow.  This approach allowed previously unattained enrichment of rare progenitor subsets and revealed hitherto unappreciated ILC precursor heterogeneity.  In vivo and in vitro assays identified novel precursors with potential to generate all ILC subsets and natural killer cells, and also permitted discrimination of elusive ILC3 bone marrow antecedents.  Single cell gene expression analysis identified a discrete ILC2-committed population and delineated transition states between early progenitors and a highly heterogeneous ILC1/3/NK precursor cell cluster.  This diversity may facilitate greater lineage potential upon progenitor recruitment to peripheral tissues.

overall_design: Bone marrow was removed from femurs, tibiae and hips by flushing with PBS + 2% FCS, or by centrifuging briefly at 6000 x g.  Red blood cells were removed by incubation with RBC lysis solution (140 mM NH4Cl, 17 mM Tris; pH 7.2). Single cell suspensions were incubated with fluorochrome-, or biotin-, conjugated antibodies in the presence of anti-CD16/CD32 antibody (Fc block, clone 2.4G2), followed by fluorochrome-conjugated streptavidin. We purified individual Lin–Id2+ bone marrow cells (a small number of Lin–Id2– cells were also sampled for comparison) and performed single cell (sc)RNA-seq to profile progenitor cell gene expression.  Subsequently, in order to obtain sufficient representation of the less frequent subsets we purified bone marrow progenitors based on the transcription factor and surface marker expression profiles that defined the subpopulations outlined above and summarised in Table 1.

first: Jennifer

last: Walker

first: Paula

last: Clark

first: Jillian

middle: L

last: Barlow

first: Aydan

last: Szeto

first: Ana

last: Ferreira

first: Batika

last: Rana

first: Helen

middle: E

last: Jolin

first: Noe

last: Rodriguez

first: Meera

last: Sivasubramaniam

first: Richard

last: Pannell

first: James

last: Cruickshank

first: Maria

last: Daly

first: Liora

last: Haim-Vilmovsky

first: Sarah

last: Teichmann

first: Andrew

middle: N

last: McKenzie


title: Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation.

status: Public on Jan 15 2019

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

institute: University of Freiburg

summary:
Purpose: Find out the consequences of Pou5f3/Oct4 and Nanog binding to the nucleosome distribution before and after Zygotic Genome Activation
Methods: MNase-seq of the wild-type(WT), Pou5f3 (MZspg) and Nanog (MZnanog) mutant zebrafish embryos at 512-cell stage and dome stage.
Results: Nanog, Sox19b and Pou5f3 bind to the High Nucleosome Affinity Regions (HNARs). HNARs are spanning over 600 bp, featuring high in vivo and predicted in vitro nucleosome occupancy and high predicted propeller twist DNA shape value. We suggest a two-step model, where the same intrinsic DNA properties of HNAR promote both high nucleosome occupancy and differential binding of TFs. In the first step, already prior to ZGA, Pou5f3 and Nanog reduce nucleosome occupancy on HNARs genome-wide. In the second step, Nanog and Pou5f3/SoxB1 complex maintain open chromatin state on the subset of HNARs, acting synergistically. Nanog binds to the HNAR center, while the Pou5f3/SoxB1 complex stabilizes the flanks.

overall_design: Genome-wide nucleosome occupancy in 512-cell and dome staged wild-type (WT), MZspg (Pou5f3) and MZnanog (Nanog) zebrafish mutant embryos was assayed by MNase treatment followed by deep sequencing (MNase-seq), using Illumina HiSeq 2500.

first: Marina

last: Veil

first: Lev

last: Yampolsky

first: Björn

last: Grüning


title: Environmental Pollutant Induced Epigenetic Predisposition to Developmental Defects and Cancer Phenotypes in the Progeny

status: Public on Jan 01 2019

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

summary: Hexavalent Chromium, Cr(VI), exposure is known to cause cancer and is a significant human health concern. While the effect of Cr(VI) exposure on exposed individuals is well studied, long-term effects of the same on the progeny of exposed individual are not known. In this study, using Drosophila model system, we show that Cr(VI) exposure of mothers leads to phenotypic variations in the progeny who have never been exposed to Cr(VI). These phenotypic variations arise due to epigenetic instability in the somatic tissues of the progeny rather than novel genetic mutations. Using a Drosophila cancer model system, we also show that maternal Cr(VI) exposure can lead to cancer phenotypes in the progeny and the propensity to cause cancer phenotypes in the progeny is fixed in the population for at least three generations. Thus, we show for the first time that effects of Cr(VI) exposure can last for several generations. This study also lays the foundation to use Drosophila model system to provide novel insights into Cr(VI) and other heavy metal toxicity.

overall_design: Total mRNA profiles of ovaries from heads of Kr[If-1] flies with and without phenotypes.


title: High-Depth Transcriptomic Profiling Reveals the Temporal Gene Signature of Mesenchymal Stem Cells During Chondrogenesis

status: Public on Jul 11 2018

city: St Louis

first: Farshid

last: Guilak

state: Missouri

address: Couch Building, 3rd Floor, #3213

department: Orthopaedics

institute: Washington University in St Louis

summary:
Cartilage tissue engineering seeks to replace degenerated or damaged cartilage following disease or injury. Mesenchymal stem/stromal cells (MSCs) provide an attractive cell source for cartilage repair; however, the underlying molecular pathways that drive chondrogenesis of these pools of adult stem cells remains poorly understood. Here, we generated a rich data set of high throughput RNA sequencing of human MSCs throughout chondrogenesis at six different time points. Our data is consisted of 18 libraries with three individual donors as biological replicates, each library possessing a sequencing depth of 100 million reads. We also performed flow cytometric, histological, and biochemical analyses in parallel to validate the quality of our in vitro engineered cartilage. Differential gene expression and gene ontology analyses identified dynamic changes in multiple biological pathways, namely downregulation in cell cycle and proliferation, and upregulation in extracellular matrix synthesis. Weighted gene correlation network analysis also identified an important chondrogenic gene subset, whose functional characterization promises to further harness the potential of MSCs for cartilage tissue engineering. Furthermore, we created a graphic user interface encyclopedia built with the goal of producing an open resource of transcriptomic regulation for additional data-mining and pathway analysis of the process of MSC chondrogenesis.
The tool can be accessed at: http://msc-browser.guilaklab.com

overall_design: High throughput RNA sequencing following mesenchymal stem cells throughout chondrogenesis at six different time points with 3 donors as biological replicates

first: Nguyen

middle: P

last: Huynh

first: Bo

last: Zhang


title: Single-cell mapping of lineage and identity in direct reprogramming

status: Public on Sep 25 2018

first: Samantha

last: Morris

address: Department of Developmental Biology, Washington University School of

summary: Direct lineage reprogramming involves the conversion of cellular identity. Single-cell technologies are useful for deconstructing the considerable heterogeneity that emerges during lineage conversion. However, lineage relationships are typically lost during cell processing, complicating trajectory reconstruction. Here we present ‘CellTagging’, a combinatorial cell-indexing methodology that enables parallel capture of clonal history and cell identity, in which sequential rounds of cell labelling enable the construction of multi-level lineage trees. CellTagging and longitudinal tracking of fibroblast to induced endoderm progenitor reprogramming reveals two distinct trajectories: one leading to successfully reprogrammed cells, and one leading to a ‘dead-end’ state, paths determined in the earliest stages of lineage conversion. We find that expression of a putative methyltransferase, Mettl7a1, is associated with the successful reprogramming trajectory; adding Mettl7a1 to the reprogramming cocktail increases the yield of induced endoderm progenitors. Together, these results demonstrate the utility of our lineage-tracing method for revealing the dynamics of direct reprogramming.

overall_design: This dataset consists of 10 Drop-seq libraries and 18 10x Genomics libraries, including 4 biological replicates of reprogramming timecourse experiments

first: Brent

last: Biddy


title: Dysregulation of long non-coding RNA genes during ZIka virus Infection

status: Public on Jun 30 2018

first: vineela

last: gangalapudi

state: CALIFORNIA

address: 8723 Alden drive

department: Biomedical sciences

institute: Cedars- sinai Medical center

summary: We utilized an unbiased RNA sequencing approach to profile the lncRNA transcriptome in ZIKV infected Vero cells.We identified a total of 121 lncRNA genes that are differentially regulated at 48 hours post infection (hpi).Protein-lncRNA interaction maps revealed that MALAT1 and NEAT1 share common interacting partners. ZIKV mediated dysregulation of these two regulatory lncRNAs can alter the expression of respective downstream target genes and associated biological functions, importantly cell division. In conclusion, this investigation is the first to provide insight into the biological connection of lncRNAs and Zika virus which can be further explored for developing antiviral therapy.

overall_design: Examination of the biological connection between zika virus and LincRNAs.

first: Deisy

last: Contreras

first: Vineela

last: Gangalapudi

first: Masumi

last: Padhye

first: Arunachalam

last: Ramaiah

first: Jie

last: Tang

first: Vaithilingaraja

last: Arumugaswami


title: Cocaine self-administration alters transcriptome-wide responses in the brain's reward circuitry

status: Public on Aug 22 2018

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Global changes in gene expression that underlie the circuit and behavioral dysregulation associated with cocaine addiction remain incompletely understood. Here, we determined how a history of cocaine self-administration (SA) “re-programs” transcriptome-wide responses at baseline and in response to cocaine re-exposure after prolonged withdrawal (WD). We assigned male mice to one of six groups: saline or cocaine SA + 24 hr WD; or saline/cocaine SA + 30 d WD + an acute saline/cocaine challenge within the previous drug-paired context. RNA-seq was then conducted on six interconnected brain reward regions. We focused on patterns of gene expression that were altered by cocaine SA, in particular, molecular targets that show priming or desensitization upon re-exposure to cocaine. Genes that were affected uniquely by acute cocaine after cocaine SA+WD displayed region-specific regulation. The greatest number of regulated genes were seen in nucleus accumbens, dorsal striatum, and basolateral amygdala. Further analysis revealed several transcription factors as key upstream regulators in these three regions, including several not previously implicated in cocaine action. Regulation of subsets of these primed and desensitized genes correlated robustly with SA behavior displayed by individual mice. For example, analysis of transcriptome-wide expression changes revealed that genes associated with cocaine intake respond to contextual information in a region-specific manner. This comprehensive picture of transcriptome-wide regulation by cocaine SA and WD throughout the brain’s reward circuitry provides new insight into the molecular basis of cocaine addiction, which will guide future studies of the key molecular pathways involved.

overall_design: Understanding global changes in gene expression underlying behavioral dysregulation associated with cocaine addiction

first: Deena

last: Walker

first: Hannah

last: Cates

first: Yong-Hwee

last: Loh

first: Immanuel

last: Purushothaman

first: Li

last: Shen

first: Eric

last: Nestler


title: RNA-sequencing (RNA-seq) in BxPC-3 and S2-007 cell lines

status: Public on Apr 18 2018

city: Brighton

first: Leandro

last: Castellano

address: Falmer, JMS Building

institute: University of Sussex

summary: RNA sequencing technology has been carried out in order to compare mRNA expression changes in epithelial BxPC-3 versus mesenchymal S2-007 cells.

overall_design: To evaluate the changes in gene expression in BxPC-3 and S2-007 cells we have performed RNA-seq in cells growing in standard condition. Three biological replicates for each cell lines were used for expression analysis (6 samples in total).

first: Silvia

last: Ottaviani


title: Identification of miR-100 and miR-125b targets by AGO2 RIP-seq and RNA-seq after ectopic expression of miR-100 or miR-125b and evaluation of the TGFb expression signature in PANC-1 cells by RNA-seq

summary: To identify targets post-transcriptionally regulated by miR-100 and miR-125b, we have performed AGO2 RIP-seq and RNA-seq following overexpression of the two miRNAs in PANC-1 cells.  In addition, we have carried out RNA-seq following TGFb stimulus to evaluate changes in gene expression driven by TGFb.

overall_design: For AGO2 RIP-seq and RNA-seq PANC-1 cells were transfected with precursor miRNA mimics for miR-100, miR-125b and negative control (0.5nM) for 24h. The experiment was performedin two biological replicates. For evaluation of changes in gene expression driven by TGFb PANC-1 cells were treated with TGFb (5nM) or vehicle control for 72h. Three biological replicates for each condition were used for expression analysis.


title: SMAD2/3 chromatin immunoprecipitation and sequencing (ChIP-seq) in PANC-1 cells following TGFb treatment

summary: ChiP-seq has been carried out in order to evaluate SMAD2/3 target genes after TGFb treatment in PANC-1 cells.

overall_design: To assess the global SMAD2/3 in PANC-1 cells in the context of TGFb, we performed ChIP-seq in cells treated with TGFb (5nM) for 1 h. The experiment was performed using two biological replicates for SMAD2/3 ChIP samples and one single replicate for the input sample.


title: miRNA expression profiling in PANC-1 cells treated with TGFb and additional PDAC lines

summary: miRNAs are known to be involved in PDAC tumourigenesis. However, not many have been investigated in the context of TGFb-induced EMT. To identify novel miRNAs involved in this response, we performed a miRNA profiling study in PANC-1 cells treated with TGFb and additional PDAC lines with epithelial or mesenchymal characteristics.

overall_design: miRNA expression profiling was performed using a panel of 4 increasingly mesenchymal cell lines: BxPC-3 cells, PANC-1 cells treated with vehicle or TGFb (5nM) for 72h and S2-007 cells. Three biological replicates for each condition were used for expression analysis.


title: Genome-wide transcriptome analysis of the ovaries in different sheep

status: Public on Feb 13 2018

city: Beijing

first: Xiangyang

last: Miao

state: Beijing

address: 2 Yuanmingyuan West Road,Nongda South, Haidian

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

summary: We performed a genome-wide analysis of mRNAs and lncRNAs from Small Tail Han sheep of genotypes FecBBFecBB (Han BB) and FecB+ FecB+ (Han++) and from Dorset sheep (Dorset) to identify potential regulators of fecundity. An integrated analysis revealed significantly correlated patterns of expression. Dramatic changes of mRNAs and lncRNAs suggest their critical roles in sheep fecundity. This study provides a novel view of the regulatory mechanisms involved in sheep fecundity.

overall_design: Ovary transcritomic profiles of  different sheep were generated by RNA-Seq, in triplicate, using Illumina HiSeq 2000.

first: Qingmiao

last: Luo

first: Xiaoyu

last: Qin


title: DNA methylome analysis of the ovaries in different sheep

type: Methylation profiling by high throughput sequencing

summary: we constructed a methylated DNA immunoprecipitation combined with high throughput sequencing (MeDIP-seq) strategy to investigate the differentially methylated genes between the Dorset, HanBB and Han++ sheep ovaries. Our findings suggest the genes involved in immune response, branched-chain amino acid metabolism, cell growth and cell junction were differentially methylated in or around the gene body regions. These findings provide prospective insights on the epigenetic basis of sheep fecundity.

overall_design: Construction of a methylated DNA immunoprecipitation combined with high throughput sequencing (MeDIP-seq) strategy to investigate the differentially methylated genes in the ovaries between Dorset, HanBB and Han++ sheep.

first: Lingli

last: Xie

first: Ai

last: Li


title: Analysis of gene expression changes in B cells upon Csnk2b conditional deletion

status: Public on Dec 31 2017

city: Verona

first: Nicola

last: Vitulo

state: Verona

address: Ca' Vignal 1, Strada Le Grazie 15

department: Department Biotechnology

country: Italy

institute: University of Verona

summary: Protein kinase CK2, a tetrameric enzyme composed by 2 catalitic alpha and 2 regulatory beta subunits, supports malignant B cell lymphocyte growth, however, its physiological role in B lymphopoiesis is still unknown. With this analysis we intended to assess if CK2 plays a role in peripheral B cell development and to do this we compared the mRNA from Csnk2b+/+ (WT) and Csnk2b-/- (KO) purified splenic B cells. Here we report a list of all genes identified as differentially expressed between WT and KO B cells.

overall_design: Examination of splenic B cell mRNA profiles of 8-weeks-old Csnk2b+/+ (n=3) and Csnk2b-/- (n=3) mice generated with …

first: Elisa

last: Mandato

first: Fortunato

last: Zaffino

first: Alessandro

last: Casellato

first: Marco

last: Pizzi

first: Paolo

last: Macaccaro

first: Sara

last: Canovas Nunes

first: Laura

last: Quotti Tubi

last: Zumerle

first: Sabrina

last: Manni

first: Odile

last: Filhol-Cochet

first: Brigitte

last: Boldyreff

first: Christian

last: Siebel

first: Antonella

last: Viola

first: Livio

last: Trentin

first: Giorgio

last: Valle

first: Gianpietro

last: Semenzato

first: Francesco

last: Piazza


title: The renoprotective effects of soy protein in the aging kidney.

status: Public on Oct 02 2017

city: Columbia

first: Alan

last: Parrish

address: MA415 MSB, 1 Hospital Drive

department: Medical Pharmacology & Physiology

institute: University of Missouri

summary: Late-life intervention with a soy-enriched diet attenuated age-dependent changes in renal structure and dysfunction in male Fischer 344 rats.

overall_design: Examination of a 14% soy diet vs. a control diet on the attenuation of chronic kidney disease in aged F344 rats

first: Elizabeth

last: Grunz-Borgmann

first: LaNita

last: Nichols


title: A context-specific cardiac Beta-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart

status: Public on Jan 23 2018

city: Goettingen

last: Zelarayan

state: Lower Saxony

address: Robert-Koch Strasse 40

department: Institute of Pharmacology and Toxicology

institute: University Medical Center, Goettingen

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

overall_design: Refer to individual Series


title: Transcriptional responses to oral live attenuated typhoid vaccines

status: Public on Oct 12 2017

city: Oxford

first: Amber

last: Barton

address: Centre for Clinical Vaccinology and Tropical Medicine

institute: Oxford Vaccine Group

summary: Enteric fever is a major public health problem and causes numerous deaths annually. Ty21a is the only efficacious oral, live attenuated typhoid vaccine currently licensed for use, however, its mechanism of protection is poorly understood. To address this knowledge gap, we interrogated transcriptional profiles following vaccination with Ty21a and an immunogenic experimental oral live attenuated vaccine, M01ZH09, and related these findings to immunogenicity, and incubation period and disease severity following challenge with Salmonella Typhi four weeks after vaccination. Despite originating from the same parent strain (Ty2), we detected marked differences in the gene expression between both vaccines. Analysis of the transcriptome 7 days after M01ZH09 vaccination implicated transcriptional patterns associated with the cell cycle correlated significantly with humoral immunogenicity 28 days after vaccination. In contrast, significantly induced T and NK cell responses were associated with Ty21a vaccination, and integrative analysis indicated signatures reflecting amino acid metabolism with delayed onset of disease. Stimulation of PBMCs collected from participants prior to and following vaccination with the two vaccine strains in vitro confirmed the superior capacity of Ty21a to induce NK cells, validating gene expression results. These data provide insight into the effects of oral live attenuated typhoid vaccines on the human molecular immune response and underline the involvement of T cell response signatures with protection following challenge.

overall_design: A Single Centre, Randomised, Doubleblind, Placebo Controlled Study to Evaluate M01ZH09 in a Healthy Adult Challenge Model, Using Ty21a Vaccine as a Positive Control. In total, 161 samples were analysed, including paired pre-vaccination control samples. Several post-vaccination time points were included, for details please refer to Figure 1A&B, Supplementary Figure 1A in the manuscript Differential induction of cell cycle and NK cell responses by two live-attenuated oral vaccines against typhoid fever.

first: Christoph

last: Blohmke

first: Andrew

last: Pollard


title: Multivalent binding of PWWP2A to H2A.Z-marked transcriptional active chromatin regulates mitosis and organ development

status: Public on May 31 2017

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich


title: A context-specific cardiac Beta-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart [ChIP-seq]

first: Laura

summary: Activation of the evolutionarily conserved, developmental Wnt pathway has been reported during maladaptive cardiac remodeling. Although the function of Wnt-transcriptional activation in development is well described, the consequences of Wnt pathway activation, as well as its cardiac-specific regulatory role in the adult heart, is largely unknown. We show that β-catenin and Transcription factor 7-like 2 (TCF7L2), the main nuclear components of the Wnt-transcriptional cascade, and their transcriptional activity are increased upon pathological remodeling in both murine and human hearts. To understand the consequences of increased Wnt signaling pathway activity, we utilized an in vivo mouse model in which β-catenin is acutely stabilized in adult cardiomyocytes (CM), leading to increased ventricular TCF7L2 expression and activation of its target genes. Mice with stabilized β-catenin displayed cardiac hypertrophy, increased mortality, reduced cardiac function and altered calcium homeostasis, similar to experimentally induced hypertrophy. Moreover, we observed a re-activation of Wnt-dependent developmental gene programs including activation of the Wnt/β-catenin-independent pathway, increased CM cell cycling with poly-nucleation and cytoskeletal disorganization, underscoring a central role in adult tissue remodeling. By integrating transcriptome analyses and genome-wide occupancy (ChIP-seq) of the endogenous ventricular TCF7L2, we show that upon aberrant Wnt activation, TCF7L2 induces context and Wnt-specific gene regulation in pathological remodeling. Interestingly, β-catenin stabilized ventricles showed increased histone H3 lysine 27 acetylation (H3K27ac) and TCF7L2 recruitment to novel disease-associated gene-specific enhancers. Importantly, using integrative motif analyses and experimental evidences, our data uncovered a role for GATA4 as a cardiogenic regulator of TCF7L2/β-catenin complex and established a paradigm for cell-specific effects of Wnt signaling. Altogether, our studies unraveled the nuclear Wnt-TCF7L2-associated chromatin landscape and its role in adult tissue remodeling leading to heart failure.

overall_design: Genome-wide TCF7L2 and H3K27ac binding profiles in wild type and β-catenin stabilized murine adult cardiac ventricles

first: Lavanya

last: Iyer


title: Multivalent binding of PWWP2A to H2A.Z-marked transcriptional active chromatin regulates mitosis and organ development [RNA-seq]

summary: The essential histone variant H2A.Z affects various DNA-based biological processes by so far not well understood mechanisms. Using a comprehensive label-free quantitative mass spectrometry-based approach we identified the human H2A.Z nucleosome interactome providing further insights into H2A.Z’s regulatory functions. Besides histone modification writer, eraser and reader complexes we identified PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A binds unprecedented strong to chromatin through a concerted multivalent binding mode. Two internal protein regions separately allow H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain mediates direct DNA binding. PWWP2A is found at euchromatic regions where it preferable binds to the H2A.Z-nucleosome-containing transcriptional start sites of transcribed genes. Cellular depletion of PWWP2A results in impaired proliferation caused by a mitotic delay likely due to deregulation of involved target genes. According with the strong cellular phenotype, knockdown of frog PWWP2A leads to severe developmental cranial facial defects arising from neural crest cell differentiation and migration problems. Together, this study identifies PWWP2A as an H2A.Z-specific multivalent chromatin binder and provides a novel link between H2A.Z, chromosome segregation and organ development.

overall_design: RNASeq of HeLa cells treated with control or PWWP siRNA

first: Sebastian

last: Pünzeler

first: Gabriele

last: Wagner

first: Eva

last: Keilhauer

first: Nina

last: Wommelsdorf

first: Susanne

last: Leidescher

first: Stephanie

last: Link

first: Yolanda

last: Markaki

first: Catherine

last: Regnard

first: Andrea

last: Schmid

first: Katrin

last: Schneider

first: Ramona

last: Spitzer

first: Chiara

last: Vardabasso

first: Lisa

last: Zink

first: Emily

last: Bernstein

first: Heinrich

last: Leonhardt

first: Matthias

last: Mann

first: Ralph

last: Rupp

first: Sandra

last: Hake


title: Aedes aegypti strain:LVP_AGWG (yellow fever mosquito)

status: Public on Aug 23 2018

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Aedes aegypti mosquitoes infect hundreds of millions of people each year with dangerous viral pathogens including dengue, yellow fever, Zika, and chikungunya. Progress in understanding the biology of this insect, and developing tools to fight it, depends on the availablity of a high-quality genome assembly. Here we use DNA proximity ligaton (Hi-C) and Pacific Biosciences long reads to create AaegL5 - a highly contiguous A. aegypti reference.

overall_design:
We use DNA proximity ligation (Hi-C) to create a chromosome-length genome assembly for the mosquito Aedes aegypti.
Please note that the majority of the processed data files have been generated using merged data from all three experiments. The files that were limited to a particular sample are indicated in each sample description field.
contributor: Aiden Lab


title: Transcriptional landscape of different brain regions in a Rett syndrome mouse model

status: Public on Sep 30 2018

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

summary: We propose to investigate differential gene expression in Hippocampus and Frontal cortex of MeCP2 knock-out to gain more resolution on transcriptomic changes that occur in the Rett syndrome mouse model

overall_design: Sequencing of RNA from Hippocampus and Frontal Cortex pool samples of MeCP2 knock-out and wild-type mice

first: Paolo

last: Petazzi


title: Identification of CREBBP bound genes in germinal center B cells

status: Public on Jan 11 2017

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

summary: Inactivating mutations of the gene encoding for the CREBBP acetyltransferase are highly frequent in diffuse large B cell lymphoma (DLBCL, 30% of cases) and follicular lymphoma (FL, 60% of cases), the two most common cancers derived from the germinal-center (GC). However, the role of CREBBP inactivation in lymphomagenesis remains unclear. Using functional epigenomics and mouse genetics, here we define the program modulated by CREBBP in primary human GC B cells and show that CREBBP regulates enhancer/super-enhancer networks, with specific roles in GC/post-GC cell fate decisions. Conditional GC-specific deletion of Crebbp in the mouse perturbs the expression of a limited set of genes involved in the regulation of signal transduction (BCR, TLR and CD40), lineage specification (NF-κB and BCL6) and terminal B cell differentiation (PRDM1, IRF4). Consistently, Crebbp-deficient B cells exhibit proliferative advantage and show impaired plasma cell differentiation. While GC-specific loss of Crebbp was not sufficient to initiate malignant transformation, compound Crebbp-haploinsufficient/BCL2-transgenic mice, mimicking the genetics ofFL and DLBCL, display an increased incidence of clonal lymphoid malignancies recapitulating the features of the human diseases. These findings establish CREBBPas a haploinsufficient tumor suppressor gene in GC B cells and provide insights into the mechanisms and targets by which loss of CREBBP contributes to lymphomagenesis.

overall_design: ChIP-seq analysis of CREBBP bound regions and H3K27Ac in purified human germinal center B cells.

first: Antony

last: Holmes

first: Riccardo

last: Dalla-Favera


title: Gene expression profile analysis of germinal center B cells from conditional Crebbp knockout mice and littermate controls

summary: Inactivating mutations of the gene encoding for the CREBBP acetyltransferase are highly frequent in diffuse large B cell lymphoma (DLBCL, 30% of cases) and follicular lymphoma (FL, 60% of cases), the two most common cancers derived from thegerminal-center (GC). However, the role of CREBBP inactivation in lymphomagenesisremains unclear. Using functional epigenomics and mouse genetics, here we definethe program modulated by CREBBP in primary human GC B cells and show thatCREBBP regulates enhancer/super-enhancer networks, with specific roles in GC/post-GC cell fate decisions. Conditional GC-specific deletion of Crebbp in the mouseperturbs the expression of a limited set of genes involved in the regulation of signaltransduction (BCR, TLR and CD40), lineage specification (NF-κB and BCL6) andterminal B cell differentiation (PRDM1, IRF4). Consistently, Crebbp-deficient B cellsexhibit proliferative advantage and show impaired plasma cell differentiation. WhileGC-specific loss of Crebbp was not sufficient to initiate malignant transformation,compound Crebbp-haploinsufficient/BCL2-transgenic mice, mimicking the genetics ofFL and DLBCL, display an increased incidence of clonal lymphoid malignanciesrecapitulating the features of the human diseases. These findings establish CREBBPas a haploinsufficient tumor suppressor gene in GC B cells and provide insights intothe mechanisms and targes by which loss of CREBBP contributes to lymphomagenesis.

overall_design: Murine germinal center B cells (B220+CD95+PNA+) were sorted from the spleen of conditional Crebbp knock-out, Crebbp heterozygous and Crebbp wild type mice (crossed with the Cg1-Cre deletor strain) and sacrificed at day 12 after immunization with sheep red blood cells (SRBC)(n=4WT, 5HET and 5KO). Total RNA was extracted from single cell suspensions and processed according to the Ovation RNA Amplification System and Encore® Biotin Module protocols (both from NuGEN). Samples were analyzed on Affymetrix Mouse Genome 430 2.0 arrays.

last: Baden Holmes


title: Gene bivalency at Polycomb domains regulates cranial neural crest positional identity [ChIP-seq]

status: Public on Mar 31 2017

city: Basel

first: Filippo

middle: M.

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: The cranial neural crest cells are pluripotent cells that provide head skeletogenic mesenchyme and are crucial for craniofacial patterning. Here, we analyzed the in vivo chromatin landscapes of mouse cranial neural crest subpopulations. Early postmigratory neural crest subpopulations contributing to distinct mouse craniofacial structures displayed similar chromatin accessibility patterns, yet differed transcriptionally. Accessible promoters and enhancers of differentially silenced genes carried H3K27me3/H3K4me2 bivalent chromatin marks embedded in large Ezh2-dependent Polycomb domains, indicating transcriptional poising. These postmigratory bivalent regions were already present in neural crest premigratory progenitors. At Polycomb domains, H3K27me3 antagonized H3K4me2 deposition, which was restricted to accessible sites. Thus, bivalent Polycomb domains provide a chromatin template for the regulation of cranial neural crest cell positional identity in vivo contributing novel insights into the epigenetic regulation of face morphogenesis.

overall_design: RNAseq, ChIPseq (single H3K27me3, H3K4me2 and H3K27ac ChIPseq; sequential H3K27me3/H3K4me2 ChIPseq) and ATACseq profiling of cranial neural crest cell (NCC) progenitors (E8.5) and postmigratory subpopulations (FNP, Mx, Md, PA2; E10.5 and E11.5) of wildtype, Ezh2-conditional knockout, Hoxa2-temporal knockout and Hoxa2-overexpression genotypes.

first: Maryline

last: Minoux

first: Sjoerd

last: Holwerda

first: Antonio

last: Vitobello

first: Taro

last: Kitazawa

first: Hubertus

last: Kohler

first: Michael

last: Stadler

last: Rijli


title: TGF-β regulation of miRNA expression in pancreatic cancer

first: Leandro

last: Castellano

first: Silvia

last: Ottaviani


title: Rac1 controls both the secretory function of the mammary gland and its remodelling for successive gestations

status: Public on Nov 01 2016

city: Sheffield

first: Nasreen

last: Akhtar

address: Beech Hill Rd

institute: University of Sheffield

summary: To study the effects of Rac1 gene deletion on development and function of the mammary gland.

overall_design: The microarray was conducted from RNA isolated from mouse mammary glands harvested from Involution day 2 mice.  Cre-mediated specific Rac1 gene deletion in luminal mammary epithelial cells was achieved by crossing Rac1fx/fxRosaYFP mice with WAPiCreTg/• mice to produce Rac1fx/fxYFP ;WAPiCreTg/• (Rac1-/-) mice. Rac1fx/fxYFP mice that lacked the Cre gene were used as wild type (WT) controls.  The RNA was isolated from the inguinal gland 4 for each mouse.

first: Weiping

last: Li

first: Aleksander

last: Mironov

first: Charles

last: Streuli


title: Intra-individual tumoral heterogeneity of ovarian serous adenocarcinomas [Illumina]

status: Public on Aug 09 2016

city: Seoul

first: Je-Keun

last: Rhee

address: 222 Banpo-daero, Seocho-Gu

institute: Catholic Univ. of Korea

type: Methylation profiling by genome tiling array

summary: Intra-individual tumoral heterogeneity (ITH) is a hallmark of solid tumors and impedes accurate genomic diagnosis and selection of proper therapy. The purpose of this study was to identify ITH of ovarian serous adenocarcinomas (OSAs) and to determine the utility of ascitic cancer cells as a resource for mutation profiling in spite of ITH. We performed whole-exome sequencing, copy number profiling, and DNA methylation profiling of four OSA genomes using multiregional biopsies from 13 intraovarian lesions, 12 extraovarian tumor lesions (omentum/peritoneum), and ascitic cells. We observed substantial levels of heterogeneity in mutations and copy number alterations (CNAs) of the OSAs. We categorized the mutations into 'common', 'shared' and 'private' according to the regional distribution. Six common, 8 shared, and 24 private mutations were observed in known cancer-related genes,. but common mutations had a higher mutant allele frequency and included TP53 mutations in all four OSAs. Region-specific chromosomal amplifications and deletions involving BRCA1, PIK3CA, and RB1 were also identified. Of note, the mutations detected in ascitic cancer cells represented 92.3-100% of overall somatic mutations in the given case. Phylogenetic analyses of ascitic genomes predicted a polyseeding origin of somatic mutations in ascitic cells. Our results demonstrate that despite ITH, somatic mutations, CNAs, and DNA methylations in both “common” category and cancer-related genes were highly conserved in ascitic cells of OSAs, highlighting the clinical relevance of genome analysis of ascitic cells. Ascitic tumor cells may serve as a potential resource to discover somatic mutations of primary OSA with diagnostic and therapeutic relevance.

overall_design:
Genome wide DNA methylation profiling of ascitic cells as well as biopsies from ovarian serous adenocarcinomas cases obtained by Illumina Infinium 450k Human DNA methylation Beadchip
Bisulphite converted DNA from the 16 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Tae-Min

last: Kim

first: Sug-Hyung

last: Lee


title: A context-specific cardiac Beta-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart [RNA-eq]

first: Laura

last: Zelarayan

summary:
Summary: Activation of the evolutionarily conserved, developmental Wnt pathway has been reported during maladaptive cardiac remodeling. Although the function of Wnt-transcriptional activation in development is well described, the consequences of Wnt pathway activation, as well as its cardiac-specific regulatory role in the adult heart, is largely unknown. We show that β-catenin and Transcription factor 7-like 2 (TCF7L2), the main nuclear components of the Wnt-transcriptional cascade, and their transcriptional activity are increased upon pathological remodeling in both murine and human hearts. To understand the consequences of increased Wnt signaling pathway activity, we utilized an in vivo mouse model in which β-catenin is acutely stabilized in adult cardiomyocytes (CM), leading to increased ventricular TCF7L2 expression and activation of its target genes. Mice with stabilized β-catenin displayed cardiac hypertrophy, increased mortality, reduced cardiac function and altered calcium homeostasis, similar to experimentally induced hypertrophy. Moreover, we observed a re-activation of Wnt-dependent developmental gene programs including activation of the Wnt/β-catenin-independent pathway, increased CM cell cycling with poly-nucleation and cytoskeletal disorganization, underscoring a central role in adult tissue remodeling. By integrating transcriptome analyses and genome-wide occupancy (ChIP-seq) of the endogenous ventricular TCF7L2, we show that upon aberrant Wnt activation, TCF7L2 induces context and Wnt-specific gene regulation in pathological remodeling. Interestingly, β-catenin stabilized ventricles showed increased histone H3 lysine 27 acetylation (H3K27ac) and TCF7L2 recruitment to novel disease-associated gene-specific enhancers. Importantly, using integrative motif analyses and experimental evidences, our data uncovered a role for GATA4 as a cardiogenic regulator of TCF7L2/β-catenin complex and established a paradigm for cell-specific effects of Wnt signaling. Altogether, our studies unraveled the nuclear Wnt-TCF7L2-associated chromatin landscape and its role in adult tissue remodeling leading to heart failure.
Purpose: The aim of this study was to compare transcriptome profiles (RNA-seq) of normal (containing a Cre recombinase positive locus- Cre "positive" control with a WT β-catenin locus; to eliminate effects of Cre-mediated cardiac toxicity) and β-catenin stabilized murine adult cardiac ventricles.
Methods: Adult cardiac tissue mRNA profiles for normal and Wnt-activated mice were obtained using deep sequencing, in triplicates, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by DESeq2. qPCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Our study represents the first detailed analysis of the processes triggered upon Wnt activation in the adult heart, which was so far, not investigated. We report that this Wnt activation in the adult heart maintains its developmental function; however due to the lack of adequate developmental plasticity in the adult heart, culminates in pathological remodeling.

overall_design: Gene expression profiling from cardiac ventricles of 15 weeks-old mice with wild type and β-catenin stabilized mice

first: Lavanya

last: Iyer


title: Intra-individual genomic heterogeneity of ovarian serous adenocarcinoma [Agilent]

type: Genome variation profiling by genome tiling array

overall_design:
The purpose of this study was to identify intra-individual tumor heterogenety of ovarian serous adenocarcinomas
Four to nine different ovarian cancer areas from intraovarian and extra-ovarian lesions that were at least 1cm apart as well as 50 ml ascites were collected from the four OSA patients. Genomic DNA from tumor and matched normal samples were simultaneously hybridized onto the array. Total 29 array experiments were conducted.


title: RNA-sequencing (RNA-seq) in breast cancer cell lines after ectopic manipulation of miR-26a expression

status: Public on Jun 30 2016

summary: RNA sequencing technology has been carried out in order to evaluate mRNA expression changes after manipulation of miR-26a in both MCF-7 and MDA-MB-231 breast cancer cell lines.

overall_design: To evaluate the entire set of genes modulated by miR-26a in breast cancer, we performed RNA-seq after ectopic manipulation of this miRNA. We over-expressed miR-26a in MCF-7 epithelial cancer cell lines and also reduced its activity by stably transfecting MDA-MB-231 mesenchymal-like cancer cell lines with a specific sponge vector. GO terms and pathway enriched analysis of the transcripts that significantly change upon miR-26 ectopic manipulation implicates miR-26ab in cell cycle, apoptosis, cell spreading and cell adhesion in breast cancer


title: Intra-individual tumoral heterogeneity of ovarian serous adenocarcinomas


title: Silencing of GATA3 defines a novel stem cell like subgroup of ETP-ALL

status: Public on Feb 26 2016

city: Berlin

first: Lars

last: Fransecky

address: Hindenburgdamm 30

department: Hematology and Oncology

institute: Charité University Hospital Berlin

summary: Genome wide expression profiling was used to detect cases of adult T-ALL lacking GATA3 expression. GATA3low T-ALL exhibited enrichment of myeloid/lymphoid progenitor (MLP) and granulocyte/monocyte progenitor (GMP) genes, while T-cell specific signatures were downregulated. Among upregulated genes FLT3 was identified and mutational analyses revealed a high rate of FLT3 mutations.

overall_design: Analysis of 83 samples of bone marrow mononuclear cells (39x HGU-133 2.0 plus chip; 44x HGU-133 A&B Set) from adult patients with acute T-cell lymphoblastic leukemia (T-ALL)

first: Martin

last: Neumann

first: Sandra

last: Heesch

first: Lorenz

last: Bastian

first: Karsten

last: Spiekermann

first: Tobias

last: Herold

first: Claudia

last: Baldus


title: Genetic and epigenetic profiles of elderly AML

status: Public on Jan 01 2018

first: Patricia

last: Silva

department: Campus Benjamin Franklin, Hematology

institute: Charité Berlin

summary:
Since characterization of molecular alterations in elderly acute myeloid leukemia (AML) patients using comprehensive studies are lacking, we investigated genetic and epigenetic alterations to unravel the specific background of this unfavorable disease.
We studied AML patients by sequencing 555 genes on an Illumina HiSeq2000 platform and investigated DNA methylation profiles using the Illumina 450K array.

overall_design: Bisulfit converted genomic DNA samples extracted from bone marrow of elderly AML (n=79) were hybridized onto an Illumina Infinium HumanMethylation450 Beadchip.

last: Neuman

first: Michael

last: Schroeder

first: Sebastian

last: Vosberg

first: Cornelia

last: Schlee

first: Konstandina

last: Isaakidis

first: Jutta

middle: O

last: Tánchez

first: Teresa

last: Hartung

first: Seval

last: Türkmen

first: Alexander

last: Graf

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Carsten

last: Müller-Tidow

first: Christian

last: Thiede

first: Gerhard

last: Ehninger

first: Hubert

last: Serve

first: Jochen

last: Hecht

first: Wolfgang

last: Berdel

first: Philipp

middle: A

last: Greif

first: Christoph

last: Röllig


title: Identification of KMT2D regulated genes in germinal center B cells

status: Public on Sep 10 2015

first: Laura

last: Pasqualucci

summary: Somatic mutations of the KMT2D methyltransferase gene represent a common genetic lesion in multiple cancer types. In diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL), these mutations are highly recurrent and occur early during tumorigenesis, suggesting a central role in transformation. Here we show that FL/DLBCL-associated KMT2D mutations impair its enzymatic activity and lead to diminished global H3K4 methylation in germinal center (GC) B cells and DLBCL, consistent with the enrichment of KMT2D binding at enhancer and promoter regions marked by mono- and tri-methylation. Conditional deletion of Kmt2d early during B cell development, but not after initiation of the GC reaction, leads to an increase in GC B cells, whose transcriptional profile is enriched in cell-cycle regulatory and B-cell receptor signaling genes. Consistently, Kmt2d-deficient B cells exhibit proliferative advantage ex vivo. Loss of Kmt2d combined with BCL2 deregulation, mimicking FL/DLBCL pathogenesis, leads to an increased incidence of clonal lymphoproliferations resembling the features of the human tumors. These findings suggest that early KMT2D loss facilitates lymphomagenesis by remodeling the epigenetic landscape of the cancer precursor cells. Eradication of KMT2D-deficient cells may represent a rational therapeutic approach targeting early tumorigenic events.

overall_design: ChIP-seq analysis of KMT2D bound regions and histone methylation (H3K4me3, H3K4me1) in normal human germinal center B cells.

first: Antony

last: Holmes

first: Katia

last: Basso

first: Riccardo

last: Dalla-Favera


title: Multivalent binding of PWWP2A to H2A.Z-marked transcriptional active chromatin regulates mitosis and organ development [ChIP-seq]

first: Tobias

last: Straub

overall_design: ChIP-Seq of GFP-tagged H2A.Z.1, H2A.Z.2, PWWP2A and H3K4me3 in HeLa cells

first: Sebastian

last: Pünzeler

first: Gabriele

last: Wagner

first: Eva

last: Keilhauer

first: Nina

last: Wommelsdorf

first: Susanne

last: Leidescher

first: Stephanie

last: Link

first: Yolanda

last: Markaki

first: Catherine

last: Regnard

first: Andrea

last: Schmid

first: Katrin

last: Schneider

first: Ramona

last: Spitzer

first: Chiara

last: Vardabasso

first: Lisa

last: Zink

first: Emily

last: Bernstein

first: Heinrich

last: Leonhardt

first: Matthias

last: Mann

first: Ralph

last: Rupp

first: Sandra

last: Hake


title: Experiment 4: Klf4, FoxD3, FoxD5 and combined FoxD3 and FoxD5  loss-of-function experiments at 30% epiboly Wild Type zebrafish embryos

status: Public on Dec 31 2013

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

institute: University of Freiburg

summary: Morpholino injections were performed to investigate transcriptional targets of Klf4, FoxD3 and FoxD5  in the blastula stage embryos (4,7 hours postfertilization) of wild type zebrafish embryos.

overall_design: Experiments were performed in biological duplicates or triplicates. Cy3 and Cy5 channels were splitted in Genedata Analyst software, quantile normalised and used for independent comparisons.

first: Kay

last: Kotkamp

first: D

first: W

last: Driever


title: Experiment 2: Klf2a, Klf2b and FoxD3 overexpression experiments at 30% epiboly MZspg and WT embryos with or without protein synthesis inhibition

summary: Overexpression experiments with or without protein synthesis inhibition were performed to investigate transcriptional targets of Klf2a, Klf2b and FoxD3 in the blastula stage embryos (4,7 hours postfertilization) of wild type or MZspg backgroumd

overall_design: Experiments were performed in biological duplicates. Cy3 and Cy5 channels were splitted in Genedata Analyst software, quantile normalised and used for independent comparisons.


title: Experiment 2: Pou5f1 and Sox2 overexpression experiments with or without protein synthesis inhibition

status: Public on Mar 01 2010

summary: Pou5f1 and Sox2 overexpression experiments with and without protein synthesis inhibitor were performed to investigate direct transcriptional targets of Pou5f1 and Sox2

overall_design: Experiments were performed in biological triplicates.  Cy3 and Cy5 chnnels were splitted in Genedata Analyst software, quantile normalised and used for independent comparisons.

first: Wolfgang


title: Experiment 2: Pou5f1 and Sox2 overexpression experiments protein synthesis inhibition

status: Public on Jul 31 2013

summary: Pou5f1 and Sox2 overexpression experiments with protein synthesis inhibitor were performed to investigate direct transcriptional targets of Pou5f1 and Sox2

overall_design: Experiments were performed in biological triplicates. Cy3 and Cy5 channels were split and analyzed separately using Genedata Analyst software, quantile normalised and used for independent comparisons.


title: Rocaglates convert DEAD-box protein eIF4A into a sequence-selective  translational repressor

status: Public on Jun 15 2016

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

summary: Rocaglamide A (RocA) typifies a class of protein synthesis inhibitors that selectively kill aneuploid tumor cells and repress translation of specific mRNAs. RocA targets eukaryotic initiation factor 4A (eIF4A), an ATP-dependent DEAD-box RNA helicase; its mRNA selectivity is proposed to reflect highly structured 5′ UTRs that depend strongly on eIF4A-mediated unwinding. However, rocaglate treatment may not phenocopy the loss of eIF4A activity, as these drugs actually increase the affinity between eIF4A and RNA. Here, we show that secondary structure in 5′ UTRs is only a minor determinant for RocA selectivity and RocA does not repress translation by reducing eIF4A availability. Rather, in vitro and in cells, RocA specifically clamps eIF4A onto polypurine sequences in an ATP-independent manner. This artificially clamped eIF4A blocks 43S scanning, leading to premature, upstream translation initiation and reducing protein expression from transcripts bearing the RocA-eIF4A target sequence. In elucidating the mechanism of selective translation repression by this lead anti-cancer compound, we provide an example of a drug stabilizing sequence-selective RNA-protein interactions.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Bind-n-Seq and iCLIP-Seq

first: Stephen

last: Floor

first: Nicholas

last: Ingolia


title: Experiment 3: Comparison of MZspg and Mspg transcriptomes

summary: Comparison of Mspg and MZspg mutants at two stages, zebrafish

overall_design: Experiments were performed in biological triplicates.  Cy3 and Cy5 channels were splitted in Genedata Analyst software, quantile normalised and used for  comparisons.


title: Host gene expression signatures of H1N1, H3N2, HRV, RSV virus infection in adults

status: Public on Jun 22 2016

city: Ann Arbor

first: Alfred

last: Hero

state: MI

address: 1301 Beal Avenue

institute: University of Michigan

summary: Consider the problem of designing a panel of complex biomarkers to predict a patient's health or disease state when one can pair his or her current test sample, called a target sample, with the patient's previously acquired healthy sample, called a reference sample. As contrasted to a population averaged reference, this reference sample is individualized. Automated predictor algorithms that compare and contrast the paired samples to each other could result in a new generation of test panels that compare to a person's healthy reference to enhance predictive accuracy. This study develops such an individualized predictor and illustrates the added value of including the healthy reference for design of predictive gene expression panels. The objective is to predict each subject's state of infection, e.g., neither exposed nor infected, exposed but not infected, pre-acute phase of infection, acute phase of infection, post-acute phase of infection. Using gene microarray data collected in a large-scale serially sampled respiratory virus challenge study, we quantify the diagnostic advantage of pairing a person's baseline reference with his or her target sample.

overall_design:
The data was collected over 7 different challenge studies performed by Duke University under a contract awarded by the DARPA Predicting Health and Disease program. These 7 challenge studies are referred to as RSV DEE1, H3N2 DEE2, H1N1 DEE3, H1N1 DEE4, H3N2 DEE5, HRV UVA, and HRV DUKE. These studies consist of 2886 microarray chips assaying 12,023 genes of 148 human volunteer subjects under 4 different inoculation regimes (HRV, RSV, H1N1, H3N2).

[1] RSV DEE1 consists of 420 microarray chips assaying 12,023 genes of 20 human volunteer subjects.

[2] H3N2 DEE2 consists of 355 microarray chips assaying 12,023 genes of 17 human volunteer subjects.

[3] H1N1 DEE3 consists of 477 microarray chips assaying 12,023 genes of 24 human volunteer subjects.

[4] H1N1 DEE4 consists of 386 microarray chips assaying 12,023 genes of 19 human volunteer subjects.

[5] H3N2 DEE5 consists of 482 microarray chips assaying 12,023 genes of 21 human volunteer subjects.

[6] HRV UVA consists of 295 microarray chips assaying 12,023 genes of 20 human volunteer subjects.

[7] HRV DUKE consists of 471 microarray chips assaying 12,023 genes of 27 human volunteer subjects.

During each challenge study, subjects had peripheral blood taken prior to inoculation with virus (baseline), immediately prior to inoculation (pre-challenge) and at set intervals following challenge. RNA was extracted at Expression Analysis (Durham, NC) from whole blood using the PAXgene™ 96 Blood RNA Kit (PreAnalytiX, Valencia, CA) employing the manufacturer's recommended protocol. While whole blood RNA is initially extracted, a secondary procedure (B-globin reduction) was then employed to remove the contribution of red blood cell (RBC) RNA to the total RNA. A set of four peptide nucleic acid (PNA) oligomers whose sequences are complementary to the 3' portions of the alpha and beta hemoglobin RNA transcripts were added to reduce globin RNA transcription due to RBC. The inhibition of globin cDNA synthesis dramatically reduces the relative amount of anti-sense, biotin-labeled cRNA corresponding to the hemoglobin transcripts. Hybridization and microarray data collection were performed using the Human Genome U133A 2.0 Array (Affymetrix, Santa Clara, CA) and expression profiles were pre-processed using robust multi-array (RMA) method.

The subject designations including symptom status, infection/shedding status, infection onset and offset time can be found at the web link.

first: Geoffrey

last: Ginsburg


title: Adipose tissue remodeling during drastic weight loss

status: Public on Aug 19 2015

city: paris

first: veronique

last: PELLOUX

address: 50-52 bld Vincent Auriol

department: UMR 1166 eq 6

country: France

institute: INSERM

summary: The main aim of this experiment was to investigate gene expression on human subcutaneous adipose tissue following bariatric surgery. Our questions consisted in understanding how gene expression was linked to clinical parameters of obese patients and whether this drastic weight loss was discriminated this data.

overall_design: Total RNA obtained from isolated human subcutaneous adipose tissue of 42 subjects at 2 different time points (0, 1 year), after bariatric surgery.

first: Veronique

last: Pelloux

first: Yuejun

last: Liu


title: Experiment 1: Developmental time curve in wild-type and MZspg embryos

summary:
Developmental curve of zebrafish MZ spg mutants compared to WT, 10 timepoints from 0 to 8 hours post fertilization
transcriptome changes by microarray analysis at ten distinct time-points during development, from ovaries to late gastrulation, in MZ spg and WT zebrafish

overall_design: Experiments were performed in biological triplicates, except  at 1 hr timepoint, which was performed in duplicate. Cy3 and Cy5 channels were splitted in the Genedata software and  normalized using quantile normalization (Genedata) and used for comparison  betwen MZspg and WT gene expression levels at each stage(Stage specific gene sets), as well as for comparison of expresion levels of the same genotype at different timepoints ( temporal profiles)


title: Molecular signatures in peripheral T-cell lymphoma (PTCL)

status: Public on Feb 08 2010

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary: Molecular signatures to improve diagnosis in PTCL and prognostication in angioimmunoblastic T-cell lymphoma (AITL). Gene expression profiling of PTCL patient samples was performed to investigate whether molecular signatures can be used to identify distinct entities of PTCL.

overall_design: Gene expression profiling was performed  on PTCL and natural-killer cell lymphoma (NKCL) to define molecular classifiers for the more common entities of PTCL, to identify unique entities within PTCL-U, to elucidate unique tumor and microenvironmental interactions and oncogenic pathways in AITL, and to construct a molecular prognosticator for AITL.


title: Gene expression signatures delineate biological and prognostic subgroups in peripheral T-cell lymphoma

status: Public on Jun 01 2015

summary: Peripheral T-cell lymphoma (PTCL) encompasses a heterogeneous group of neoplasms with generally poor clinical outcome. Currently 50% of PTCL cases are not classifiable: PTCL-not otherwise specified (NOS). Gene-expression profiles on 372 PTCL cases were analyzed and robust molecular classifiers and oncogenic pathways that reflect the pathobiology of tumor cells and their microenvironment were identified for major PTCL-entities, including 114 angioimmunoblastic T-cell lymphoma (AITL), 31 anaplastic lymphoma kinase (ALK)-positive and 48 ALK-negative anaplastic large cell lymphoma, 14 adult T-cell leukemia/lymphoma and 44 extranodal NK/T-cell lymphoma that were further separated into NK-cell and gdT-cell lymphomas. Thirty-seven percent of morphologically diagnosed PTCL-NOS cases were reclassified into other specific subtypes by molecular signatures. Reexamination, immunohistochemistry, and IDH2 mutation analysis in reclassified cases supported the validity of the reclassification. Two major molecular subgroups can be identified in the remaining PTCL-NOS cases characterized by high expression of either GATA3 (33%; 40/121) or TBX21 (49%; 59/121). The GATA3 subgroup was significantly associated with poor overall survival (P=.01). High expression of cytotoxic genesignaturewithin the TBX21 subgroup also showed poor clinical outcome (P=.05). InAITL, high expression of several signatures associated with the tumor microenvironment was significantly associated with outcome. A combined prognostic score was predictive of survival in an independent cohort (P=.004).

overall_design: Gene expression profiling (GEP) was performed on 193 cryopreserved pretreatment biopsy specimens from newly diagnosed PTCL patients from institutes in the Lymphoma Leukemia Molecular Profiling Project (LLMPP), Singapore, and International (I)-PTCL group consortiums.


title: Genome-wide analysis of skeletal muscle gene expression in mice with C26 tumor-induced muscle wasting and cachexia

status: Public on Aug 30 2011

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

summary: Analysis of gene expression in CD2F1 mice with cancer cachexia due to implantation of C26 colon carcinoma cells.

overall_design: Total RNA obtained from quadriceps muscle of female CD2F1 mice with early weight loss (10%) or severe weight loss (15%) due to intrascapular subcutaneous implantation of one million C26 colon adenocarcinoma cells.

first: Tufan

last: Aydogdu

first: Leonidas

middle: G

last: Koniaris

first: Denis

last: Guttridge

first: Sawsan

last: Khuri

first: Noelia

middle: J

last: Kunzevitzky


title: RNA-seq in breast cancer cell lines after manipulation of miR-23b expression

status: Public on May 01 2013

city: Brighton

first: Leandro

last: Castellano

address: Falmer, JMS Building

institute: University of Sussex

summary: RNA sequencing technology has been carried out in order to evaluate mRNA expression changes after manipulation of miR-23b in both MCF-7 and MDA-MB-231 breast cancer cell lines

overall_design:
Our study implicates miR-23b in cytoskeletal remodeling in breast cancer.
To evaluate the entire set of genes modulated by miR-23b we performed RNA-seq after ectopic manipulation of this miRNA in breast cancer cell lines.
We over-expressed this miRNA in MCF-7 epithelial cancer cell lines and also reduced its activity by stably transfecting MDA-MB-231 mesenchymal-like cancer cell lines with a specific sponge vector. RNA-seq analysis revealed a number of candidate targets of this miRNA.

first: Loredana

last: Pellegrino


title: Pou5f1 transcription targets in zebrafish

first: Daria

last: Onichtchouk

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

overall_design: Refer to individual Series


title: Experiment 4: Affymetrix validation array

summary:
Zebrafish embryo were analyzed at 30 and 60 % epiboly for changes in transcriptome of wild-type and MTspg mutant embryos
The Data are used as an independent experimental validation of data obtained for the same stages by Agilent arrays in the main experiments (especially Exp. 1)

overall_design: Experiments were performed in biological duplicate.  Genedata Expressionist Analyst was used for comparison  betwen MZspg and WT gene expression levels at each stage

first: Wolfgang

last: Driever


title: Experiment 3: Klf2a and  Klf2b  loss-of-function experiments at 30% epiboly Wild Type zebrafish embryos

summary: Morpholino injections were performed to investigate transcriptional targets of Klf2a, and Klf2b  in the blastula stage embryos (4,7 hours postfertilization) of wild type zebrafish embryos.

first: Kay

last: Kotkamp

first: D

first: W


title: Transcriptional targets of Pou5f1 in Zebrafish (Danio Rerio)


title: Transcriptomics and methylomics of human monocytes [transcriptome]

status: Public on Nov 24 2014

city: Winston-Salem

first: Yongmei

state: NC

address: Medical Center Blvd.

institute: Wake Forest School of Medicine

summary:
The MESA Epigenomics and Transcriptomics Study has been launched to investigate potential gene expression regulatory methylation sites in humans by examining the association between CpG methylation and gene expression in purified human monocytes from a large study population (community-dwelling participants in the Multi-Ethnic Study of Atherosclerosis (MESA)).
The MESA Epigenomics and Transcriptomics Study was funded by a National Heart, Lung and Blood Institute grant (R01HL101250) through the NIH Roadmap Epigenomics Program in 2009.

overall_design:
The current study is particularly focused on the relationships between transcriptomics and methylomics with age.
Data includes transcriptomic and methylomic data from CD14+ samples, collected from 1,202 individuals ranging 44 - 83 years of age (Exam 1).  Peripheral monocytes were isolated from blood (Exam 5) with anti-CD14 coated magnetic beads, and the Illumina HumanHT-12 v4 Expression BeadChip and the Illumina HumanMethylation450 BeadChip were used to provide genome-wide coverage of mRNA expression and DNA methylation, respectively.  This data enabled us to identify CpG loci whose degree of methylation was associated with age (age-DMR),and identify age- and expression-associated methylation sites (age-eMS), whose degree of methylation was associated with age and cis-gene expression (+/- 1Mb), after adjusting for other covariates such as race, gender, study site, and sample contaimination with B-cells, T-cells, natural killer cells, and neutrophils.

To estimate residual sample contamination for monocyte data analysis, separate enrichment scores for neutrophils, B cells, T cells, and natural killer cells were calculated and provided as sample characteristics.
The participant race, gender, and study site were provided as 'raceGenderSite variable' which represents a combination of those factors.

A detailed description of each sample characteristics is included in the 'README.txt'.


title: Experiment 1: Overexpression experiments at 30% epiboly MZspg and WT embryos with or without protein synthesis inhibition

summary: Overexpression experiments with or without protein synthesis inhibition were performed to investigate transcriptional targets of Klf4, FoxD3, and Nanog-like in the blastula stage embryos (4.7 hours postfertilization) of wild type or MZspg background.

overall_design: Experiments were performed in biological triplicates. Cy3 and Cy5 channels were splitted in Genedata Expressionist and Analyst software, quantile normalised and used for independent comparisons.


title: Transcriptomics and methylomics of human monocytes


title: Genome-wide ChIP-chip analysis of the binding targets of the naïve and activated aryl hydrocarbon receptor

status: Public on Apr 17 2009

first: Maureen

last: Sartor

address: 2017 Palmer Commons-100 Washtenaw Ave.

type: Genome binding/occupancy profiling by genome tiling array

summary:
Knowledge of the range of genes directly regulated by the Ah receptor would facilitate integration of the complex physiologic mechanisms that regulate the response to its toxic ligands at a systems biology level.  In this report, we have combined multiple technologies and knowledge-bases to conduct an integrative genome-wide analysis of Ah receptor gene targets, and interpret the results to elucidate the underlying physiological functions of the AHR in mammals.  Specifically, we used chromatin immunoprecipitation and hybridization to promoter tiling arrays to map constitutive, B[a]P- and TCDD-induced Ah receptor binding sites in a mouse hepatoma cell line, incorporating gene expression data and information from predicted cis-binding elements and overlapping molecular concept signatures.

Keywords: ChIP-chip; treatment response; genotype

overall_design: In the study presented here, mouse hepa-1c1c7 cells and c35 mutant hepa-1c1c7 derived cells with AHR unable to bind DNA, were used to predict AHR binding targets.  Two biological replicates were performed each condition (the naïve state, treated with B[a]P, and treated with TCDD).  Four replicate chips were performed for non-specific IgG.

first: Michael

last: Schnekenburger

first: Jennifer

last: Marlowe

first: John

middle: F

last: Reichard

first: Ying

last: Wang

first: Yunxia

last: Fan

first: Ci

last: Ma

first: Saikumar

last: Karyala

first: Danielle

last: Halbleib

first: Xiangdong

first: Mario

last: Medvedovic

first: Alvaro

last: Puga