title: Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis

status: Public on Jun 21 2019

city: Pittsburgh

first: Tracy

last: Tabib

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: A comprehensive understanding of the changes in gene expression in cell  types involved in idiopathic pulmonary fibrosis (IPF) will shed light on the  mechanisms underlying the loss of alveolar epithelial cells, and  development of honeycomb cysts and fibroblastic foci. We sought to  understand changes in IPF lung cell transcriptomes and gain insight into  innate immune aspects of pathogenesis. We investigated IPF  pathogenesis using single cell RNA-sequencing of fresh lung explants,  comparing human IPF fibrotic lower lobes reflecting late disease, upper  lobes reflecting early disease and normal lungs. IPF lower lobes showed  increased fibroblasts, and basal, ciliated, goblet and club cells, but  decreased alveolar epithelial cells, and marked alterations in  inflammatory cells. We found three discrete macrophage subpopulations  in normal and fibrotic lungs, one expressing monocyte markers, one  highly expressing FABP4 and INHBA (FABP4hi), and one highly  expressing SPP1 and MERTK (SPP1hi). SPP1hi macrophages in fibrotic lower lobes showed highly upregulated SPP1 and MERTK expression. Low-level local proliferation of SPP1hi macrophages in normal lungs was strikingly increased in IPF lungs. Co-localization and causal modeling supported the role for these highly proliferative SPP1hi macrophages in activation of IPF myofibroblasts in lung fibrosis. These data suggest SPP1hi macrophages contribute importantly to lung fibrosis in IPF, and that therapeutic strategies targeting MERTK and macrophage proliferation may show promise for treatment of this disease.

overall_design:
Single cell RNA-Seq 3 Prime gene expression comparison of normal/healthy donor lung tissue with upper IPF lobe tissue and lower IPF lobe tissue.  Single-cell suspensions from three normal control donor lungs and separate upper and lower sections of three lungs from patients with idiopathic pulmonary fibrosis were prepared. Single cell RNA-seq libraries were generated using 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics). For analysis of normal lung composition and cell populations, three additional lungs were included (2 on V1 chemistry, 1 on V2 chemistry).  Brochoalvelolar lavage (BAL) samples were both run on V2 chemistry.  This GEO submission contains only processed data (raw counts in sparse matrix format).

***Please note that the GEO records contain only processed data (raw counts in sparse matrix format) as raw data is unavailable due to patient privacy concerns.

first: Christina

last: Morse

first: John

last: Sembrat

first: Humberto

last: Trejo Bittar

first: Kristina

last: Buschur

first: Eleanor

last: Valenzi

first: Yale

last: Jiang

first: Daniel

last: Kass

last: Gibson

first: Wei

last: Chen

first: Ana

last: Mora

first: Panayiotis

last: Benos

first: Mauricio

last: Rojas

first: Robert

last: Lafyatis


title: The MMTV-Wnt1 murine model produces two phenotypically distinct subtypes of mammary tumors with unique therapeutic responses to an EGFR inhibitor

status: Public on Jun 26 2019

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Antiviral innate immunity of hepatitis C virus-infected stem cell-derived hepatocytes

status: Public on Jun 13 2019

city: Hannover

first: Arnaud

last: Carpentier

address: Twincore, Feodor Lynen-Strasse 7

country: Germany

institute: Twincore

type: Expression profiling by high throughput sequencing

summary: Purpose: RNAseq analysis of hPSC undergoing in vitro hepatic differentiation, to validate proper differentiation at different times of differentiation (D0 to D21)

overall_design:
Differentiated hepatocytes were then subjected to HCV infection (HCV compared to non infected NINF control), with or without various antiviral treatment (TEL) or JAK/STAT pathway inhibitor treatment (JSI), followed by analysis of global gene expression change. Particular emphasize was done on Innate Immune Genes and Interferon Regulated Genes (IRG)
For each sample, individual run.  hPSC undergoing in vitro hepatic differentiation.  Differentiated hepatocytes subjected to HCV infection (HCV compared to non infected NINF control), with or without various antiviral treatment (TEL) or JAK/STAT pathway inhibitor treatment (JSI).

first: Richard

middle: J

last: Brown


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - cell line ATACseq

status: Public on Jun 20 2019

city: Heidelberg

first: Bernhard

last: Radlwimmer

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

institute: Deutsches Krebsforschungszentrum / German National Cancer Research Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Glioblastomas in adult patients are classified into four subtypes, IDH, MES, RTK I, and RTK II, based on DNA-methylation and RNA-expression data. Tumour subtype transitions are common during treatment, and transitions to the mesenchymal (MES) subtype are associated with therapy resistance and adverse prognosis. Here, we present DNA methylome and histone modification data of glioblastoma primary tumours and find that glioblastoma subtypes differ in their enhancer landscapes. Using Core Regulatory Circuitry analysis of chromatin and orthogonal analysis of RNA-derived gene regulatory networks, we identified 38 subtype Master Regulators whose cell population-specific activities we further mapped in single-cell RNA sequencing data. These analyses identified the oligodendrocyte precursor marker and chromatin modifier SRY-Box 10 (SOX10) as a master regulator in RTK I tumours. In vitro functional studies demonstrated that SOX10 loss causes a subtype switch analogous to the proneural-mesenchymal Transition observed in patients at the transcriptomic, epigenetic and phenotypic levels. This subtype transition is dependent on the activity of the SOX10 and enhancer co-factor Bromodomain Containing 4 (BRD4). Sox10 repression in an in vivo syngeneic graft glioblastoma mouse model results in increased tumour invasion, immune cell infiltration and significantly reduced survival, reminiscent of progressive human glioblastoma. These results identify SOX10 as a bona fide master regulator of the RTK I subtype, with both tumour cell-intrinsic and microenvironmental effects, highlighting that both glioblastoma cell plasticity and their tumour-microenvironment interactions are important contributors to tumour phenotypes.

overall_design: Two RTK I-like cell lines were transduced with experimental systems that allow repression of the SOX10 gene: LN229 with CRISPRi, and ZH487 with shRNA. In each case, 3 independent SOX10-targeting reagents were used. In this series, chromatin accessibility was profiled using ATACseq in the two models. For each model, a single SOX10-targeting reagent was used, and ATACseq performed in duplicates for each condition (total 4 samples per model). A consensus peakset was defined per condition and differential regions identified using DiffBind.

first: Carl

last: Herrmann

first: Zuguang

last: Gu

first: Qi

last: Wang

first: Yonghe

last: Wu

first: Michael

middle: C

last: Fletcher


title: Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [scRNA-seq]

status: Public on Mar 01 2019

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: We performed single-cell (sc)RNA-Seq on male donors FACS-sorted “primitive” (CD34+ CD133+ CD90+) and “progenitor” (CD34+ CD133+ CD90-) HSPC cells treated with IL2RG ZFN,  High Specificity (HS), (Low Specificity (LS) or control RNP in a ratio 1 to 1. We also included HS RNP and the cognate repair template containing a GFP expression cassette delivered by AAV6 and sorted for targeted integration (HS/AAV6 GFP+ vs. HS/AAV6 GFP-)

overall_design: We analysed  cells 24h after nucleases delivery. In order to identify cell subpopulations within samples and better enable comparison across datasets, we performed multi-set canonical correlation analysis and segregated cell clusters using the Louvain graph-based clustering approach. We computed the significant components using a supervised approach and we identified 6 clusters, 2 of which were enriched for HSC/MPP marker genes and depleted of lineage-associated markers. The analysis of the transcriptional landscape of cells  indicate that p53 pathway activation and modulation of cell cycle progression genes are consistently observed upon nuclease treatment across different HSPC types/states, including the most primitive subset as putatively identified in our single-cell. analysis

first: Giulia

last: Schiroli

first: Samuele

last: Ferrari

first: Pietro

last: Genovese

first: Luigi

last: Naldini

first: Stefano

last: Beretta


title: Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response


title: Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [bulk RNA-seq]

summary: We evaluated transcriptional changes elicited by targeting AAVS1 and IL2RG genes and we found that the impact of one or few nuclease-induced DNA DSBs is minor and mainly limited to genes belonging to the p53 pathway. The same pathway was elicited by gene editing at two distinct genomic loci and was more pronounced in primitive vs. progenitor cells.

overall_design: We analysed AAVS1 and IL2RG-edited cells 24h upon ZFN nucleases delivery on FACS-sorted “primitive” (CD34+ CD133+ CD90+) and “progenitor” (CD34+ CD133+ CD90-) cells from HSPC derived from 10 different donors. We performed the experiment in 3 biological replicate for a total of 18 samples analyzed. We then devided the samples according to the treatments (control monomers, DSB induced by IL2RG and AAVS1 ZFNs) and cells populations (primitive and progenitors).

first: Anastasia

last: Conti

first: Raffaella

last: Di Micco


title: Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [Clear-seq]

summary: We analysed AAVS1 edited cells in presence and absence of GSE56 (p53 inhibitor) 14 days upon electroporation to evaluate whether p53 transient inhibition by GSE56 could aggravate the genotoxicity risk of the procedure

overall_design: We deep sequenced a panel of 151 cancer-associated genes, including TP53, in cultured HSPC edited with AAVS1 HS RNP in the presence or not of GSE56 from three independent donors. We identified few low-frequency variants in all samples when comparing either editing or control treatment to each other for every donor, without any significant difference in number, type or distribution of nucleotide substitutions in HSPC edited with or without GSE56 or control cells.


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - tumour methylation microarray data

status: Public on Nov 05 2018

type: Methylation profiling by genome tiling array

overall_design:
60 adult GBs were profiled on the Illumina human 450k and EPIC methylation microarrays. A previously used classifier (see Sturm et al., Cancer Cell, 2012; doi: 10.1016/j.ccr.2012.08.024) consisting of 7386 shared probes on both platforms was used to subtype the tumours (IDH: 12; MES: 18; RTK I: 12; RTK II: 18).

Raw data requires controlled access and is deposited at EGA under study EGAS00001003230

middle: N


title: A cellular anatomy of the normal adult human prostate and prostatic urethra

status: Public on Dec 04 2018

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center


title: Genome-wide transcriptional analysis of human iPSC-derived healty control vs. schizophrenia cortical interneurons.

status: Public on Nov 16 2018

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: We report down-regulation of protocadeherins in schizophrenia interneurons by genome-wide transcriptome analysis.

overall_design: RNA sequencing analysis (bulk) of healthy control interneurons vs. schizophrenia interneurons. Four independent iPS lines per group (total 8 iPSC lines) with three independent differentiations

first: Sangmi

last: Chung

first: Simon

last: Xi


title: Bulk RNA-sequencing of cell types isolated by FACS from normal human prostates

summary: Differential expression of prostatic cell types were determined using RNA-sequencing of FACS sorted cell types from normal human prostates. The cell types sequenced were basal epithelia, luminal epithelia, a heterogeneous fibromuscular stroma and a poorly understood "other" epithelial population.

overall_design: Fresh human prostate specimens were digested into single-cell suspensions for flow cytometry, populations of cells were subject to bulk RNA-sequencing.

first: Douglas

middle: W

last: Strand

middle: H

first: Chad

middle: M

last: Vezina


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - cell line gene expression microarray data

first: Bernhard

last: Radlwimmer

overall_design: Two RTK I-like cell lines were transduced with experimental systems that allow  repression of the SOX10 gene: LN229 with CRISPRi, and ZH487 with shRNA. In each case, 3 independent SOX10-targeting reagents were used. In this series, expression microarray profiling was used to compare the transcriptomes of the two models with and without repression of SOX10 expression. To identify SOX10-regulated genes, limma differential expression analysis was performed, comparing the expression of control (mock and NT) to the SOX10-repressed samples.

first: Carl

last: Herrmann

first: Zuguang

last: Gu

first: Qi

last: Wang


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - cell line RNAseq experiments

overall_design:
The RTK I-like glioblastoma cell line model LN229 was transduced with CRISPRi and sgRNAs repressing expression of the SOX10 gene. RNAseq was performed in the control and SOX10 knockdown conditions.

Please note that the processed data files generated from multiple samples are linked as Series supplementary files [2] Raw data requires controlled access and is deposited at EGAS00001003230.

first: Yonghe

last: Wu

first: Michael

last: Fletcher


title: Global analysis of the actively translating portion of the transcriptome of control and YBX1 depleted proliferating epidermal cells by high-resolution RNA-seq analysis

status: Public on May 28 2019

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 99 Brookline Ave

institute: BIDMC

summary: To investigate the mechanisms underlying the effects of YBX1 depletion on epidermal progenitors, we performed deep RNA-seq analysis of control versus YBX1-depleted proliferating epidermal cells. Since YBX1 can affect both transcription and translation, we analyzed both total mRNA and polysomaly associated mRNAs using sucrose density gradient sedimentation. Deep RNA-seq analysis based on duplicate samples showed that 57 genes were significantly modulated in YBX1 siRNA treated cells at the level of total mRNA as compared to control siRNA cells, while 115 genes exhibited changes in polysomal mRNA, respectively. Considering the predominantly cytosolic localization of YBX1 in the epidermis, we hypothesized that most of the observed transcriptional changes are secondary to changes in YBX1 mediated translational regulation of specific mRNA subsets. To identify such translational targets of YBX1, we analyzed transcripts that were equally expressed within total RNA populations of control and YBX1 siRNA cells but were selectively modulated in the polysomal mRNA fractions of YBX1 depleted cells. Further examination revealed that out of the 96 affected polysomaly associated mRNAs, 39 were most discriminatory in expression in polysomal versus total mRNA.

overall_design: Analysis of total mRNA and polysomaly associated mRNAs from epidermal cells transfected with either control or YBX1 siRNAs using sucrose density gradient sedimentation and deep RNA-sequencing.

first: Eunjeong

last: Kwon

first: Anna

last: Mandinova


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - tumour rRNA-depleted total ssRNAseq data

overall_design:
60 adult GBs (by subtype: IDH, 12; MES: 18; RTK I: 12; RTK II: 18) and 4 normal brain regions (frontal, occipital, temporal, parietal) were characterised by rRNA-depleted total ssRNAseq.

Please note that [1] the processed data files generated from multiple samples are linked as Series supplementary files and are indicated in the corresponding sample description field [2] Raw data requires controlled access and is deposited at EGAS00001003230.


title: Single Cell RNA-sequencing of cell types isolated by FACS from normal human prostates

summary: Single-cell RNA-sequencing was conducted on specific cell types and heterogeneous viable cells (sorted by FACS) in order to determine a cellular atlas of the normal human prostate.

overall_design: Fresh human prostate specimens were digested into single-cell suspensions for flow cytometry, populations of cells were subject to single-cell RNA-sequencing using the 10x Genomics platform.


title: A galling insect activates plant reproductive programs during gall development

status: Public on Aug 16 2018

city: Columbia

first: William

middle: G.

last: Spollen

state: MO

address: 113 Bond Life Sciences Center

department: Informatics Research Core Facility

institute: University of Missouri-Columbia

summary: Some insects can redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We addressed this possibility using RNA sequencing (RNAseq) to quantify the transcriptional responses of wild grapevine (Vitis riparia Michx.) leaves to a galling parasite, phylloxera (Daktulosphaira vitifoliae (Fitch 1855)). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology classes were significantly enriched in developing galls, and that expression of many putative genes involved in flower formation was significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall, and perhaps other similar galls, appears to be phenotypically and transcriptionally convergent on the plant carpel.

overall_design: Comparison of 4 gall developmental stages (1-4) with 3 ungalled control leaves (small, medium, large)

first: Jack

last: Schultz

first: Patrick

middle: P

last: Edger

first: Mélanie

last: Body

first: Heidi

last: Appel


title: The m 6 A-methylase complex recruits TREX and regulates mRNA export.

status: Public on Oct 03 2018

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

summary: N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA. This modification has previously been shown to alter the export kinetics for mRNAs though the molecular details surrounding this phenomenon remain poorly understood. Here we show that the m6A complex (WTAP, KIAA1429, METTL3/14) drives recruitment of the TREX mRNA export complex onto m6A modified mRNAs and this process is essential for the efficient export of certain mRNAs. Depletion of the core m6A complex leads to loss of TREX from mRNAs which undergo the m6A modification. We show that TREX stimulates recruitment of the m6A reader protein YTHDC1 to the mRNP and the m6A complex influences the interaction of TREX with YTHDC1. We suggest that m6A acts as a surrogate for other TREX recruitment mechanisms such as splicing and 5’ capping, in long internal and final exons which may otherwise be devoid of this essential complex for mRNA export.

overall_design: mRNA profiles of control and Virilizer/WTAP RNAi samples in cytoplasmic and nuclear cell fractions generated by mRNA-seq in triplicate using HiSeq 2500

first: Simon

last: Lesbirel

first: Nicolas

last: Viphakone

first: Matthew

last: Parker

first: Jacob

first: Catherine

last: Heath

first: Stuart

middle: A

last: Wilson


title: RNA-seq analysis of T cells with persistent Foxp3 transcriptional dynamics using Foxp3-Timer mice (Foxp3-Tocky)

status: Public on Jul 10 2018

city: London

first: Masahiro

last: Ono

address: Sir Alexander Fleming Building

department: Life Sciences

institute: Imperial College London

summary: We grouped Foxp3+ cells from Foxp3 Timer reporter mice into Blue1, Blue2, Red1, and Red2, and sorted these cells according to their Timer fluorescence expression, and analysed the transcriptional profiles of those cells, comparing them with those of effector and naive T cells using RNA-seq. Foxp3 Timer reporter mice were sensitised by a hapten, and 5 days later, the draining LNs of the skin were analysed.

overall_design:
Foxp3Timer mice were sensitised with application of 3% Oxazolone to abdominal skin. 5 days later inguinal and axillary Lymph nodes were harvested and pooled within the 3 biological replicates. The following populations of T-cells were sorted from each mouse:
1. CD44loFoxp3Timer- (Naïve T-cells)
2. CD44hiFoxp3Timer- (Activated effector T-cells)
3. CD4+ Pers1 (BL1, persistent Foxp3 transcription)
4. CD4+ Pers2 (BL2, persistent Foxp3 transcription)
5. CD4+ PAt (RD1, quiescent Treg)
6. CD4+ Arrested (RD2, arrested Foxp3 transcription)
RNA was extracted and RNA-seq data obtained, generating a triplicate dataset for the 6 T-cell populations.

first: David

last: Bending


title: Genome-wide transcriptional analysis of human iPSC-derived healthy control vs. schizophrenia cortical interneurons

status: Public on Oct 18 2018

first: Weihua

last: Huang

summary: We report specific changes in schizophrenia developmental interneurons by genome-wide transcriptome analysis.

overall_design: RNA sequencing analysis (bulk) of healthy control interneurons vs. schizophrenia interneurons. Fourteen independent iPSC lines per group with two independent differentiations

first: Sangmi

last: Chung


title: Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [Amplicon-seq]

first: Ivan

last: Merelli

overall_design: We analysed in vitro bulk population of IL2RG-edited HSPCs in presence or not of the transient expression of the p53 inhibitor GSE56. Cells were harvested 72h after gene editing procedure and processed for genomic DNA extraction and target sequencing of a 180-bp amplicon within the integrated corrective IL2RG cDNA. Similarly, we performed target sequencing by specifically amplifying the same cDNA region from peripheral blood mononuclear cells of immunodeficient NSG mice 21 weeks after transplant of HSPC edited in presence or not of GSE56.

first: Samuele

last: Ferrari

first: Pietro

last: Genovese

first: Stefano

last: Beretta


title: Physiologic expression of Srsf2(P95H) causes myeloid expansion, impaired competitive stem cell function and initiates the myeloproliferative/myelodysplastic syndrome in vivo [RNA-seq2]

status: Public on Jun 18 2018

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

summary: Mutations in the RNA splicing complex member SRSF2 are found frequently in myelodysplastic syndrome and related malignancies such as chronic myelomonocytic leukemia. These mutations cluster on proline 95, with P95H the most frequent. How SRSF2P95H mutations modify hematopoiesis and promote MDS/MPN development is not clear. We have established a conditionally activatable Srsf2P95H/+ knock-in allele which, when expressed within the hematopoietic stem cell populations caused profound myeloid bias, at the expense of erythroid and lymphoid cells, and a reduced frequency and competitive repopulation of HSCs. Long-term aging of Srsf2P95H/+ resulted in the development of MDS/MPN characterised by myeloid dysplasia and monocytosis. Reproducible key phenotypic features make this a mouse model suitable for mechanistic and preclinical MDS sudies.

overall_design: RNAseq of Lin-/cKit+/eYFP+ (Immature haematopoietic multipotent progenitors) sorted from whole bone marrow in vivo tamoxifen treated hScl-CreERT R26eYFP Srsf2 P95H generated by deep sequencing, using Illumina X-ten.

first: Carl

middle: R

last: Walkley

first: Monique

middle: F

last: Smeets

first: Shuh

middle: Y

last: Tan

first: Jane

last: Xu

first: Govardhan

last: Anande

first: Ashwin

last: Unnikrishnan

first: John

middle: E

last: Pimanda

first: Meaghan

last: Wall

first: Louise

last: Purton


title: Physiologic expression of Srsf2(P95H) causes myeloid expansion, impaired competitive stem cell function and initiates the myeloproliferative/myelodysplastic syndrome in vivo [RNA-seq]

overall_design: RNAseq of whole bone marrow in vivo tamoxifen treated R26CreERT2 Srsf2 P95H generated by deep sequencing, using Illumina NextSeq500


title: Gene expression changes induced by LINC00284 (NRAD1) knockdown in MDA-MB-468 cells

status: Public on Jun 12 2019

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 11F11, 5850 College Street

country: Canada

institute: Dalhousie University

summary:
LINC00284 knockdown was achieved by anti-LINC00284 (NRAD1) GapmeR#4 treatment and compared to cells treated with control GapmeR
Knockdown of LINC00284 (NRAD1) was verified by QPCR, microarray gene expression changes were also verified by QPCR

overall_design: RNA was collected from MDA-MB-468 cells 48hours post treatment with the GapmeRs.

first: Dejan

last: Vidovic


title: MicroRNA profiles of 110 primary breast cancer tumors of systemically untreated, lymph node negative and estrogen receptor positive patients

status: Public on Feb 16 2018

city: Odense

first: Ines

last: Block

address: J.B. Winsløws Vej 4

department: Department of Clinical Genetics

country: Denmark

institute: Odense University Hospital

summary:
MicroRNA profiles of 110 primary breast cancer tumors of systematically untreated, lymph node negative and ER positive patients. Half of the patients developed metastasis while 55 patients remained metastasis-free. The miRCURY LNA microRNA array ready-to-spot probe-set was purchased from Exiqon. The set contains capture-probes for 1212 human, 1040 mouse and 679 rat miRNAs based on the miRBase version 16. Probes were spotted in triplets on CodeLink HD (SurModics) activated glass slides and post-processed according to the CodeLink protocol.

SUBMITTER_CITATION: Ines Block, Mark Burton, Kristina P. Sørensen, Lars Andersen, Martin J. Larsen, Martin Bak, Søren Cold, Mads Thomassen, Qihua Tan, Torben A. Kruse. Association of miR-548c-5p, miR-7-5p, miR-210-3p, miR-128-3p with recurrence in systemically untreated breast cancer. Oncotarget 2018 Jan; 9:9030-9042. https://doi.org/10.18632/oncotarget.24088

overall_design: Equal amounts of RNA from all included samples were pooled and used as common reference. The analysis was carried out as two-color microarray analysis. Individual samples were labelled with Hy3 and the common reference sample was labelled with Hy5. Hybridization, washing, and scanning (Agilent G2565CA Microarray scanner) were performed according to the recommendations provided by Exiqon.

first: Mark

last: Burton

first: Kristina

last: Sørensen

first: Lars

last: Andersen

first: Martin

last: Larsen

last: Bak

first: Søren

last: Cold

first: Mads

last: Thomassen

first: Qihua

first: Torben

last: Kruse


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype

first: Bernhard

last: Radlwimmer

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-Seq Analysis of Dose-Dependent TCDD-Elicited Femoral Gene Expression in Male Mice

status: Public on Apr 30 2018

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

institute: Michigan State University

summary: Dose-dependent femoral gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on gene expression in the femur of C57BL/6 male mice.

overall_design: Three biological replicates for each dose (0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30) of TCDD and sesame oil vehicle

first: Kelly

last: Fader

first: Rance

last: Nault


title: Physiologic expression of Srsf2(P95H) causes myeloid expansion, impaired competitive stem cell function and initiates the myeloproliferative/myelodysplastic syndrome in vivo.

first: Alistair

last: Chalk


title: Expression profile of GIST48 cells with siETV1 or siFOXF1 knockdown

status: Public on Feb 01 2018

city: New York

first: Yuedan

last: Chen

state: NY

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary: To study FOXF1 transcriptome and compare that with ETV1 transcriptome, we knocked down ETV1 or FOXF1 with siRNA in GIST48 cells and studied the transcriptome changes

overall_design: 6 samples including 2 controls are included

first: Ping

last: Chi


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - tumour methylation (WGBS) data

summary: Glioblastomas in adult patients are classified into four subtypes, IDH, MES, RTK I, and RTK II, based on DNA-methylation and RNA-expression data. Tumour subtype transitions are common during treatment, and transitions to the mesenchymal (MES) subtype are associated with therapy resistance and adverse prognosis. Here, we present DNA methylome and histone modification data of glioblastoma primary tumours and find that glioblastoma subtypes differ in their enhancer landscapes. Using Core Regulatory Circuitry analysis of chromatin and orthogonal analysis of RNA-derived gene regulatory networks, we identified 38 subtype Master Regulators whose cell population-specific activities we further mapped in single-cell RNA sequencing data. These analyses identified the oligodendrocyte precursor marker and chromatin modifier SRY-Box 10 (SOX10) as a master regulator in RTK I tumours. In vitro functional studies demonstrated that SOX10 loss causes a subtype switch analogous to the proneural-mesenchymal Transition observed in patients at the transcriptomic, epigenetic and phenotypic levels. This subtype transition is dependent on the activity of the SOX10 and enhancer co-factor Bromodomain Containing 4 (BRD4). Sox10 repression in an in vivo syngeneic graft glioblastoma mouse model results in increased tumour invasion, immune cell infiltration and significantly reduced survival, reminiscent of progressive human glioblastoma. These results identify SOX10 as a bona fide master regulator of the RTK I subtype, with both tumour cell-intrinsic and microenvironmental effects, highlighting that both glioblastoma cell plasticity and their tumour-microenvironment interactions are important contributors to tumour phenotypes.

overall_design:
60 adult GBs (by subtype: IDH, 12; MES: 18; RTK I: 12; RTK II: 18) and 4 normal brain regions (frontal, occipital, temporal, parietal) were characterised by WGBS.    The following analyses were performed on the generated data:  - methylation feature calling (DNA methylation valleys; lowly methylated regions; partially methylated domains)  - correlating region analysis (integration of WGBS + ssRNAseq)

Please note that [1] the processed data files generated from multiple samples are linked as Series supplementary files and are indicated in the corresponding sample description field [2] Raw data requires controlled access and is deposited at EGAS00001003230.

first: Carl

last: Herrmann

first: Zuguang

last: Gu

first: Qi

last: Wang

first: Yonghe

last: Wu

first: Michael

last: Fletcher


title: Acute condensin depletion causes genome decompaction without altering the level of global gene expression in Saccharomyces cerevisiae

status: Public on Oct 25 2017

city: New York City

first: Matthew

last: Paul

address: 1230 York Ave

department: Bioinformatics Resource Center

institute: Rockefeller University

summary: Condensins are broadly conserved chromosome organizers that function in chromatin compaction and transcriptional regulation, but to what extent these two functions are linked has remained unclear. Here, we analyzed the effect of condensin inactivation on genome compaction and global gene expression in the yeast Saccharomyces cerevisiae. Spike-in-controlled 3C-seq analysis revealed that acute condensin inactivation led to a global decrease in close-range chromosomal interactions as well as more specific losses of homotypic tRNA gene clustering. In addition, we identified a condensin-rich topologically associated domain between the ribosomal DNA and the centromere on chromosome XII that is lost upon condensin inactivation. Unexpectedly, these large-scale changes in chromosome architecture were not associated with global changes in transcript levels as determined by spike-in-controlled mRNA-seq analysis. Our data suggest that the global transcriptional program of S. cerevisiae is resistant to condensin inactivation and the associated profound changes in genome organization.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Caenorhabditis elegans

overall_design: Examination of 3C-seq and RNA-seq following condnesin perturbation. Condensin (SMC4) ChIP-seq in wild type cells.

first: Tovah

last: Markowitz

first: Andreas

last: Hochwagen

first: Sevinc

last: Ercan


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - cell line ChIPseq experiments

overall_design:
The RTK I-like glioblastoma cell line model LN229 was transduced with CRISPRi and sgRNAs repressing expression of the SOX10 gene. Histone mark ChIPseq (H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K36me3, H3K9me3) was performed in the control and SOX10 knockdown conditions and used to annotate the genome using the Roadmap Epigenome 18-state ChromHMM model.

Please note that [1] the processed data files generated from multiple samples are linked as Series supplementary files and are indicated in the corresponding sample description field [2] Raw data requires controlled access and is deposited at EGAS00001003230.


title: RNA editing is the essential function of ADAR1 and, in the absence of MDA5, is dispensable for normal adult homeostasis

status: Public on Aug 14 2017


title: Physiologic expression of Srsf2(P95H) causes myeloid expansion, impaired competitive stem cell function and initiates the myeloproliferative/myelodysplastic syndrome in vivo [WES]

overall_design:
Whole Exome Sequencing of in vivo tamoxifen treated R26CreERT2 Srsf2 P95H, using Illumina HiSeq X Ten. Exome sequencing data was acquired for 6 samples from 50-60 weeks post tamoxifen treatment (time of euthanasia due to animals becoming moribund). Genomic DNA was isolated from both whole BM and matched ear tissue from three independent animals (two R26-CreERT2 Srsf2P95H/+ and one hScl-CreERT R26eYFP Srsf2P95H/+ ). SRA Study accession: SRP108226.
Please note that, for somatic mutation calling, each processed data file was generated from two samples. For the variant calling, there are multiple files per animal+ tissue depending on the method used.

last: Walkley

first: Monique

last: Smeets

first: Shuh

last: Tan

first: Jane

last: Xu

first: Govardhan

last: Anande

first: Ashwin

last: Unnikrishnan

first: John

last: Pimanda

first: Meaghan

last: Wall

first: Louise

last: Purton


title: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - tumour ChIPseq data

first: Bernhard

last: Radlwimmer

overall_design:
20 GBs (IDH: 6; MES: 4; RTK I and RTK II: 5 each) were characterised by histone mark ChIPseq (H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K36me3, H3K9me3, with WGS as input control).    The following analyses were performed on the above data:  - ChromHMM analysis (using the Roadmap Epigenome 18-state model)  - superenhancer analysis (on H3K27ac data)  - active enhancer analysis (combining H3K27ac, H3K4me1 data)

Please note that [1] the processed data files generated from multiple samples are linked as Series supplementary files and are indicated in the corresponding sample description field [2] Raw data requires controlled access and is deposited at EGAS00001003230.

first: Carl

last: Herrmann

last: Gu


title: RNA editing is the essential function of ADAR1 and, in the absence of MDA5, is dispensable for normal adult homeostasis [RNAseq (Adult Brain)]

first: Alistair

last: Chalk

summary: Adenosine-to-Inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive feature of the epitranscriptome. There are estimated to be over 100 million potential A-to-I editing sites in humans and A-to-I editing can have varying consequences for gene expression. Whilst editing resulting in protein recoding defines the role of ADAR2, ADAR1 has been proposed to have both editing-dependent and -independent functions. The relative contribution of these putative functions to ADAR1 biology is unclear. We demonstrate that the absence of ADAR1-mediated editing is well tolerated when the cytosolic dsRNA sensor MDA5 is deleted. These mice have normal hematopoiesis, tissue patterning and life span. A direct comparison of the complete deletion of ADAR1 and the specific loss of A-to-I editing activity demonstrates that RNA editing is the only essential function of ADAR1 in adult mice. Therefore, preventing MDA5 substrate formation by endogenous RNA is the essential in vivo function of ADAR1-mediated editing.

overall_design: RNAseq of Feotal Brain in a E861A point mutant of ADAR on a MDA5 knockout background generated by deep sequencing, in triplicate using Illumina NextSeq500

first: Jacki

last: Heraud-Farlow

first: Sandra

last: Linder

first: Qin

last: Li

first: Scott

last: Taylor

first: Joshua

last: White

first: Brian

last: Liddicoat

first: Ankita

last: Gupte

first: Jin

middle: B


title: RNA editing is the essential function of ADAR1 and, in the absence of MDA5, is dispensable for normal adult homeostasis [RNAseq (Fetal Brain)]

overall_design: RNAseq of Feotal Brain in a E861A point mutant of ADAR generated by deep sequencing, in duplicate, using Illumina HiSeq 2000

last: Walkley


title: AHR ChIP-Seq of male mouse liver following 2 hour TCDD exposure

status: Public on Apr 12 2017

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

summary: Aryl hydrocarbon receptor ChIP-Seq performed in livers of male mice gavaged with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) for 2hrs

overall_design: Five biological replicates

first: Kelly

last: Fader

first: Shaimaa

last: Ahmed

first: Jason

last: Matthews

first: Timothy

last: Zacharewski


title: RNA editing is the essential function of ADAR1 and, in the absence of MDA5, is dispensable for normal adult homeostasis [mmPCR-seq]

overall_design: Microfluidics-based multiplex PCR and deep sequencing (mmPCR-seq) identification of A-to-I editing sites in 8 tissues from 12 week old mice in a E861A point mutant of ADAR on a MDA5 knockout background


title: LncRNAs specific signature in acute myeloid leukemia with intermediate risk

status: Public on Oct 01 2016

city: TOULOUSE

first: Etienne

last: DE CLARA

address: 2 avenue Hubert Curien

country: France

institute: INSERM

summary: The aim of this study was to investigate the role of lncRNAs in acute myeloid leukemia with normal cytogenetics (NC-AML). To this end, we used RNA-sequencing approach on forty NC-AML to evaluate the lncRNAs expression profile.

overall_design: lncRNAs expression profile of 40 AML patients were generated by RNAsequencing using Illumina HiSeq 2000

first: Marina

last: Bousquet

last: De Clara


title: Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harboring mutations in the GBA1 gene, and from healthy control donors

status: Public on Jun 01 2017

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Retroviral and Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
Proteomic analysis of GBA1 patient-derived dopaminergic neurons reveal impeded neurite outgrowth.

overall_design: human iPSc lines were derived from human dermal fibroblasts from PD patients harboring the mutation N370S in GBA1, and control donors. Gene expression datasets were generated from 5 previously unpublished iPSC clones to assess pluripotency

first: Helle

last: Bogetofte

first: Brent

last: Ryan

first: Pia

last: Jensen

first: Dana

last: Vergoossen

first: Tara

last: Caffrey

first: Lisa

last: Kiani

first: Hugo

last: Fernandez

first: Jane

last: Vowles

first: Morten

last: Meyer

first: Martin

last: Røssel-Larsen

first: Richard

last: Wade-Martins


title: SNP Genotype and Gene Expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harboring mutations in the GBA1 gene, and from healthy control donors

type:
Expression profiling by array
SNP genotyping by SNP array
Genome variation profiling by SNP array


title: RNA editing by ADAR1 is essential for erythropoiesis [array]

status: Public on Jul 24 2016

first: Alistair

last: Chalk

summary: Erythroid progenitors purified from EpoRCreR26eYFPADAR1fl/- and  EpoRCreR26eYFPADAR1fl/+ control mice were compared for global gene array profiles

overall_design: Each sample was purified from one mouse

first: B

last: Liddicoat

first: J

last: Hartner

last: Lu

first: A

first: S

last: Orkin

first: C

last: Walkley


title: RNA-Seq Analysis of Dose-Dependent TCDD-Elicited Gene Expression in Male Mice

status: Public on Feb 28 2017

first: Timothy

last: Zacharewski


title: ADAR1-mediated A-to-I RNA editing is essential for erythropoiesis


title: MIA gene family-related signaling in oral squamous cell carcinoma cells

status: Public on Jul 01 2016

city: Kashihara

first: Tomonori

last: Sasahira

state: Nara

address: 840 Shijocho

department: Molecular Pathology

country: Japan

institute: Nara medical University

summary: Melanoma inhibitory activity (MIA) gene family is novel tumor-associated molecules. Although MIA gene family has several tumor progressive and/or suppressive functions, the detailed relevant signaling partners are unclear and investigated. In this study, we investigated the detailed MIA gene family-associated signaling using human oral squamous cell carcinoma cells.

overall_design: Human oral squamous cell carcinoma-derived HSC3 cells were transfected with　control, MIA, MIA2, TANGO, MATE2, or LEMD1 siRNA. The effect on gene　knockdown was evaluated by cDNA microarray.


title: FOXF1 defines the core-regulatory circuitry in gastrointestinal stromal tumor (GIST)

first: Yuedan

last: Chen


title: Different N-terminal isoforms of Oct-1 control expression of distinct sets of genes and their high level in cancer cells promotes pro-oncogenic processes

status: Public on May 14 2016

city: Moscow

first: Elizaveta

last: Pankratova

address: Vavilova st. 32

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: High level of Oct-1 isoforms in cells promotes pro-oncogenic processes

overall_design: Total RNA obtained from Namalwa cell line stably transfected by Oct-1 isoforms: Oct-1A, or Oct-1L or Oct-1X  compared to untransfected  control Namalwa cells. For each of the experimental conditions, total RNA was extracted from four cell lines using TRIzol Reagent (Invitrogen), followed by clean up on Ambion columns (Illumina Total-Prep RNA Amplification Kit, Ambion). Biotin-labelled cRNA targets were synthesized starting from 1.5 µg of total RNA. Double stranded cDNA synthesis was performed with Illumina TotalPrep RNA Amplification Kit (Ambion), and biotin-UTP-labelled antisense RNA was transcribed in vitro using Ambion’s Kit. All steps of the labelling were performed according to the manufacturer’s protocol. After purification, targets were diluted in hybridization buffer at a concentration of 240 ng/µl, and hybridization was allowed to proceed at 58°C for 20 h. For microarray analysis, the Illumina HumanHT-12 v4 Sentrix Expression BeadChip was used. Hybridization of labelled cRNA to the BeadChip, washing, and scanning were performed according to the Illumina BeadStation 500× manual. The array signal was developed via 10-min incubation with streptavidin-Cy3. The HumanHT-12 v4 Sentrix Expression BeadChip was washed and subsequently dried via centrifugation for 4 min at a setting of 275 xg. The arrays were scanned on the Illumina BeadArray reader, a confocal-type imaging system with 532 (Cy3) nm laser illumination.

first: Alexander

last: Stepchenko

first: Sofia

last: Georgieva


title: RNA Sequencing Quantitative Analysis of cell lines derived from tumours from two mouse models of human osteosarcoma that recapitulate clinically distinct human osteosarcoma subtypes.

status: Public on Jul 06 2015

summary:
Purpose: Osteosarcoma (OS) is the most common primary bone malignancy. OS consists of several subtypes including fibroblastic, osteoblastic and chondroblastic OS. We have developed genetically engineered mouse models of human OS that recapitulate two distinct subtypes, fibroblastic (Osx-CreLox p53-/- Rb-/-) and osteoblastic (Osx-Cre shRNA p53-/-) OS.  The goal of this study was to identify transcriptional differences that distinguish the two subtypes.
Methods: mRNA profiles of cell lines derived from tumours from Osx-Cre p53fl/fl Rbfl/fl (fibroblastic OS) and Osx-Cre shRNA TRE-p53.1224 pRbfl/fl (osteoblastic OS) mouse models were generated by RNA sequencing, in triplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 12,436 transcripts in the tumours of Osx-Cre p53fl/fl Rbfl/fl and 12,074 Osx-Cre shRNA TRE-p53.1224 pRbfl/fl with the TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes.
Conclusions: Our study represents a detailed analysis of OS subtype transcriptomes generated by RNA-seq technology.

overall_design: mRNA profiles of cell lines derived from tumours from two genetically engineered mouse models of human osteosarcoma (Osx-Cre p53fl/fl Rbfl/fl and Osx-Cre shRNA TRE-p53.1224 pRbfl/fl) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Emma

middle: K

last: Baker

first: Carl


title: Gene and microRNA expression changes induced by overexpression of SphK1 in papillary thyroid cancer cells

status: Public on Sep 24 2016

city: Guangzhou

first: Weiwei

last: Liang

address: 58 Zhongshan Road II

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Gene and microRNA expression changes induced by overexpression of SphK1 in papillary thyroid cancer cells [RNA-seq]

summary: The oncogenic roles of Sphingosine kinase 1 (SphK1) in various cancers, including thyroid cancer, have been well demonstrated. However, miRNAs associated with the oncogenic roles of SphK1 remains largely unknown. The goal of this study is to detect the global gene and microRNA (miRNA) expression in response to Sphk1 over-expression and identify potential therapeutic targets. To achieve this, SphK1 was stably overexpressed in papillary thyroid cancer cell line TPC1. Then the mRNA and miRNA expression were quantified using digital gene expression (DGE) analysis and small RNA-seq in TPC1-Vector and TPC1-SphK1 cells, respectively. miRNA-mRNA interactions were explored by microT-CDS and the predicted networks were visualized using CytoScape. In this study, we found that over-expression of SphK1 differentially regulates 46 miRNAs and 506 mRNAs expression in TPC1 cells. Combining bioinformatics prediction of mRNA targets and DGE data on mRNA expressions allowed to identify mRNA targets of deregulated miRNAs. The direct interaction between miR-144-3p and FN1 mRNA, which mediates the pro-invasive role of SphK1 in thyroid cancer cells, was experimentally validated. In general, our results provided a miRNA-mRNA regulatory network in response to SphK1 overexpression in thyroid cancer cells. We also demonstrated a role of miR-144-3p and FN1 in mediating oncogenic function of SphK1, which enhance the understanding of etiology of thyroid cancer.

overall_design: The mRNA profiles of TPC1-Vector and TPC1-SphK1 cells were generated by sequencing, in duplicate, using a Illumina HiSeq 2500.

first: Zhiwei

last: Xie

first: Weiling

last: Cui

first: Yan

last: Guo

first: Lijuan

last: Xu

first: Jueheng

last: Wu

first: Hongyu

last: Guan


title: ADAR1-mediated A-to-I RNA editing is essential for erythropoiesis [RNA-seq]

first: Alistair

last: Chalk

summary:
Purpose: RNA editing by ADAR1 is essential for hematopoietic development. The goals of this study were firstly, to identify ADAR1-specific RNA-editing sites by indentifying A-to-I (G) RNA editing sites in wild type mice that were not edited or reduced in editing frequency in ADAR1 deficient murine erythroid cells. Secondly, to determine the transcription consequence of an absence of ADAR1-mediated A-to-I editing.
Methods: Total RNA from E14.5 fetal liver of embryos with an erythroid restricted deletion of ADAR1 (KO) and littermate controls (WT), in duplicate. cDNA libraries were prepared and RNA sequenced using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. A-to-I (G) RNA editing sites were identified as previously described by Ramaswami G. et al., Nature Methods, 2012 using Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). RNA editing sites were confirmed by Sanger sequencing.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 14,484 transcripts in the fetal livers of WT and ADAR1E861A mice with BWA. RNA-seq data had a goodness of fit (R2) of >0.7, p<0.0001 between biological duplicates per genotype. Clusters of hyper-editing were onserved in long, unannotated 3'UTRs of erythroid specific transcripts. A profound upregulation of interferon stimulated genes were found to be massively upregulated (up to 5 log2FC) in KO fetal liver compared to WT. 11.332 (6,894 novel) A-to-I RNA editing sites were identified when assessing mismatches in RNA-seq data.
Conclusions: Our study represents the first detailed analysis of erythroid transcriptomes and A-to-I RNA editing sites, with biologic replicates, generated by RNA-seq technology. A-to-I RNA editing is the essential function of ADAR1 and is required to prevent sensing of endogenous transcripts, likely via a RIG-I like receptor mediated axis.

overall_design: Fetal liver mRNA profiles of E14.5 wild type (WT) and ADAR Epor-Cre knock out mice were generated by deep sequencing, in duplicate using Illumina HiSeq 2000.

first: Brian

middle: J

last: Liddicoat

first: Jochen

last: Hartner

first: Robert

last: Piskol

first: Gokul

last: Ramaswami

first: Paul

middle: D

last: Kingsley

first: Vijay

middle: G

last: Sankaran

first: Meaghan

last: Wall

first: Louise

last: Purton

first: Miyoko

last: Higuchi

first: Peter

last: Seeburg

first: James

last: Palis

first: Jun

last: Lu

first: Stuart

first: Jin

last: Li


title: Gene and microRNA expression changes induced by overexpression of SphK1 in papillary thyroid cancer cells [miRNA-seq]

first: Weiwei

last: Liang

summary: The oncogenic roles of Sphingosine kinase 1 (SphK1) in various cancers, including thyroid cancer, have been well demonstrated. However, miRNAs associated with the oncogenic roles of SphK1 remains largely unknown. The goal of this study is to detect the global gene and microRNA (miRNA) expression in response to Sphk1 over-expression and identify potential therapeutic targets. To achieve this, SphK1 was stably overexpressed in papillary thyroid cancer cell line TPC1. Then the mRNA and miRNA expression were quantified using digital gene expression (DGE) analysis and small RNA-seq in TPC1-Vector and TPC1-SphK1 cells, respectively. miRNA-mRNA interactions were explored by microT-CDS and the predicted networks were visualized using CytoScape. In this study, we found that over-expression of SphK1 differentially regulates 46 miRNA and 506 mRNAs expression in TPC1 cells. Combining bioinformatics prediction of mRNA targets and DGE data on mRNA expressions allowed to identify mRNA targets of deregulated miRNAs. The direct interaction between miR-144-3p and FN1 mRNA, which mediates the pro-invasive role of SphK1 in thyroid cancer cells, was experimentally validated. In general, our results provided a miRNA-mRNA regulatory network in response to SphK1 overexpression in thyroid cancer cells. We also demonstrated a role of miR-144-3p and FN1 in mediating oncogenic function of SphK1, which enhance the understanding of etiology of thyroid cancer.

overall_design: The miRNA profiles of TPC1-Vector and TPC1-SphK1 cells were generated by sequencing, in duplicate, using a Illumina HiSeq 2500.

first: Zhiwei

last: Xie

first: Weiling

last: Cui

first: Yan

last: Guo

first: Lijuan

last: Xu

first: Jueheng


title: Gene expression profile of two colorectal cancer HT29 and DLD-1 cell lines cultivated in 2-dimensional or 3-dimensional cell culture enriched with laminin rich extracellular matrix proteins

status: Public on Dec 01 2015

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

summary: Conventional monolayer cell cultures used in cancer research accumulated basic knowledge of carcinogenesis which correlates with basic observations in tumor biology. Nevertheless, attempts to transfer accumulated cancer biology knowledge to clinical applications fails in most of the cases. Gathered data suggest that 2D cell culture models lack many features of tumor tissue in vivo. Although it has been demonstrated that cancer cells are generally more resistant to various types of treatments when cultured in extracellular matrix (ECM) based 3D cultures it is not clear if this phenomenon is attributed to the ECM dependent gain of function or the loss of non-physiological cellular state demonstrated while cultured at 2D conditions. To address the question of which universal molecular mechanisms if any are gained/lost in ECM-dependent manner we carried out genome wide gene expression analysis of human colorectal carcinoma DLD-1 and HT-29 cell lines cultured in 2D or ECM based 3D conditions.

overall_design: RNA was isolated 48h after growing in two different cell culture systems

first: V

first: K

last: Suziedelis


title: Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma

status: Public on Jul 01 2015

first: Alistair

last: Chalk

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


title: Mutations in the NOTCH pathway regulator MIB1 cause left ventricular noncompaction cardiomyopathy

status: Public on Aug 10 2015

city: Madrid

first: Jose Luis

last: de la Pompa

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).

summary: Left ventricular noncompaction (LVNC) Causes prominent ventricular trabeculations and reduces cardiac systolic function. The clinical presentation of LVNC ranges from asymptomatic to heart failure. We show that germline mutations in human MIB1 (mindbomb homolog 1), which encodes an E3 ubiquitin ligase that promotes endocytosis of the NOTCH ligands DELTA and JAGGED, cause LVNC in autosomal-dominant pedigrees, with affected individuals showing reduced NOTCH1 activity and reduced expression of target genes. Functional studies in cells and zebrafish embryos and in silico modeling indicate that MIB1 functions as a dimer, which is disrupted by the human mutations. Targeted inactivation of Mib1 in mouse myocardium causes LVNC, a phenotype mimicked by inactivation of myocardial Jagged1 or endocardial Notch1. Myocardial Mib1 mutants show reduced ventricular Notch1 activity, expansion of compact myocardium to proliferative, immature trabeculae and abnormal expression of cardiac development and disease genes. These results implicate NOTCH signaling in LVNC and indicate that MIB1 mutations arrest chamber myocardium development, preventing trabecular maturation and compaction.

overall_design: RNA was isolated from the ventricles of 16 WT and 16 Mib1flox; CTnT-cre hearts at E14.5 and then pooled into four replicates.

first: Guillermo

last: Luxán

first: Jesús

middle: C

last: Casanova

first: Beatriz

last: Martínez-Poveda

first: Belén

last: Prados

first: Gaetano

last: D'Amato

first: Donal

last: MacGrogan

first: Alvaro

last: Gonzalez-Rajal

first: David

last: Dobarro

first: Carlos

last: Torroja

first: Fernando

last: Martinez

first: José

middle: L

last: Izquierdo-García

first: Leticia

last: Fernández-Friera

first: María

last: Sabater-Molina

first: Young-Y

last: Kong

first: Gonzalo

last: Pizarro

first: Borja

last: Ibañez

first: Constancio

last: Medrano

first: Pablo

last: García-Pavía

first: Juan

last: Gimeno

first: Lorenzo

last: Monserrat

first: Luis

last: Jiménez-Borreguero


title: Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma (methylation)

first: Alistair

last: Chalk

summary: Therapeutic targeting of the Wnt pathway is of high clinical interest for treating bone loss disorders such as osteoporosis. These therapies inhibit the action of negative regulators of osteoblastic Wnt signaling. The observation that Wnt inhibitory factor 1 (WNT1) was epigenetic silencing in osteosarcoma (OS) raised concerns for such a treatment approach. In this study, genome-wide methylation profiling of OS derived from mouse models demonstrated Wif1 silencing in OS is not driven by DNA methylation. Treatment of mouse and human OS cells with methylation and HDAC inhibitors showed Wif1 was unresponsive to methylation inhibition but responded robustly to HDAC inhibition. Consistent with an HDAC dependent mechanism of silencing, the Wif1 locus in OS was characterized by low levels of acetylation and a bivalent H3K4/H3K27 trimethylation state. Wif1 expression marked late stages of normal osteoblast development and stratified OS tumours based on differentiation stage across species. Culture of human and mouse OS cells under differentiation inductive conditions increased expression of Wif1 in parallel with known osteoblast differentiation markers. Together these results demonstrate that Wif1 is not targeted for silencing by DNA methylation in OS. The reduced expression of Wif1 in OS cells is in context with their stage in differentiation.

overall_design: 3 cell lines derived  from primary tumors from p53 Rb Osterix-Cre:lox OS model, 3 Osteoblasts (differentiated Kusa4b10 cells (21 days under osteoblastic differentiation conditions)

first: E

last: Baker

first: A

first: S

last: Taylor

last: Gupte

last: Bhattacharya

last: Green

first: T

last: Martin

first: L

last: Purton

first: M

last: Robinson

first: C

last: Walkley


title: Wnt inhibitory factor 1 (WIF1) is not silenced by DNA methylation in osteosarcoma, and instead, represents a marker of osteoblastic differentiation stage (gene expression)

summary: The aim was to identify  pathways and genes that are transcriptionally deregulated in osteosarcoma due to changes in CpG island DNA methylation. In order to identify candidates, we compared low passage cell cultures derived from a mouse model of osteosarcoma to mature osteoblasts derived by in vitro differentiation of the mouse bone marrow stromal cell line, Kusa4b10. Under cell culture osteoblastic differentiating conditions, Kusa4b10 cells acquire a mature osteoblastic phenotype (21 days). A potential role for DNA methylation in directing gene expression changes was established by integrating gene expression data with genome wide DNA methylation maps generated by methyl-DNA binding domain capture and NimbleGen promoter arrays (MBDCap-Chip).


title: PTHR1 knock-down in osteosarcoma cells

summary:
Expression analysis of OS tumors with shRNA knockdown of PTHR1
mouse OS 80 (a Cre:lox OS cell line from Boston) was tagged with firefly luciferase expression construct. They were then infected with either control (renilla luciferase shRNA) or an shRNA that effective knocks-down PTHR1 (PTHR1.358; para-thyroid hormone receptor). The cells were injected with matrigel onto the back flank of Balb/c nu/nu mice and left to grow for 1 month with weekly monitoring of tumour size by in vivo luciferase assay. At 4 weeks the tumours were removed and trizol stored. Whole tumour was ground up and set form micro-array.

overall_design: 6 tumors with shRNA PTHR1 knockdown ; 6 tumors with shRNA control (renilla luciferase shRNA) knockdown

first: Megan

last: Russell

first: Ankita

last: Goraida

first: Patricia

last: Ho

first: Jack

first: Carl


status: Public on Jan 29 2015

summary:
Purpose: We have used microarrays to identify gene expression profiles that distinguish mouse OS cells from normal pre-osteoblast cells and mature osteoblast cells.
Methods: Transcriptional profiles of three cell lines derived from tumors from Osx-Cre p53fl/fl Rbfl/fl (fibroblastic OS) mouse model, and from pre-osteoblast cells (Kusa4b10 mouse bone marrow stromal cell line) and osteoblast cells (derived by in vitro differentiation of the Kusab410 mouse bone marrow stromal cell line)  were generated by microarray analysis, each in triplicate, using Affymetrix mouse Gene1.0ST arrays.

overall_design: Transcriptional profiles were analyzed in cell lines derived from tumors from a genetically engineered mouse model of human osteosarcoma (Osx-Cre p53fl/fl Rbfl/fl) and osteoblast cells derived from the Kusa4b10 mouse bone marrow stromal cell line, in the undifferentiated state (pre-osteoblasts) and differentiated state (osteoblasts).

first: Emma


title: RNA Sequencing Quantitative Analysis and identification of RNA editing sites of Wild Type and ADAR1 editing deficient (ADAR1E861A) murine fetal liver RNA

status: Public on Jul 23 2015

summary:
Purpose: RNA editing by ADAR1 is essential for hematopoietic development. The goals of this study were firstly, to identify ADAR1-specific RNA-editing sites by indentifying A-to-I (G) mismatches in RNA-seq data compared to mm9 reference genome in wild type mice that were not edited or reduced in editing frequency in ADAR1E861A editing deficient mice. Secondly, to determine the transcriptional consequence of an absence of ADAR1-mediated A-to-I editing.
Methods: Fetal liver mRNA profiles of embryonic day 12.5 wild-type (WT) and ADAR1 editing-deficient (ADAR1E861A) mice were generated by RNA sequencing, in triplicate (biological replicates), using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. A-to-I (G) RNA editing sites were identified as previously described by Ramaswami G. et al., Nature Methods, 2012 using Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). RNA editing sites were confirmed by Sanger sequencing.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 14,484 transcripts in the fetal livers of WT and ADAR1E861A mice with BWA. RNA-seq data had a goodness of fit (R2) of >0.94 between biological triplicates per genotype. Approximately 4.4% of the transcripts showed differential expression between the WT and ADAR1E861A fetal liver, with a LogFC≥1.5 and p value <0.05. A profound upregulation of interferon stimulated genes were found to be massively upregulated (up to 11 logFC) in ADAR1E861A fetal liver compared to WT. 6,012 A-to-I RNA editing sites were identified when assessing mismatches in RNA-seq data of WT and ADAR1E861A fetal liver.
Conclusions: Our study represents the first detailed analysis of fetal liver transcriptomes and A-to-I RNA editing sites, with biologic replicates, generated by RNA-seq technology. A-to-I RNA editing is the essential function of ADAR1 and is required to suppress interferon signaling to endogenous RNA.

overall_design: Fetal liver mRNA profiles of E12.5 wild type (WT) and ADAR E861A mutant mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 200.

first: Brian

last: Liddicoat

first: Robert

last: Piskol

first: Miyoko

last: Higuchi

first: Peter

middle: H

last: Seeburg

first: Jin

last: Li

first: Jochen

last: Hartner


title: Transcriptomes of the hybrid mouse diversity panel subjected to Isoproterenol challenge

status: Public on Jul 10 2013

city: Los Angeles

first: Christoph

middle: Daniel

last: Rau

address: 675 Charles E Young Drive S

institute: UCLA

summary: Transcriptomes performed on left ventricular heart samples from mice of the hybrid mouse diversity panel, a set of over a hundred inbred strains of mice.  In this project, the strains were challenged with Isoproterenol, a beta-adrenergic agonist to induce cardiac hypertrophy and failure.  Results are useful for the analysis of heart-related traits in mice

overall_design: Mice were given three weeks of ISO @ 20ug/g/day for three weeks, then sacrificed.  Left ventricles from these mice and matched controls were used for transcripome analysis.

first: Jessica

last: Wang

first: Yibin

first: Aldons

last: Lusis


title: Comprehensive gene expression profile of extrahepatic bile ducts in mice with experimental biliary atresia

status: Public on Jun 01 2013

city: Cincinnati

first: Jorge

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: Newborn Balb/c mice were injected intraperitoneally with 1.5x10^6 fluorescent-forming units (ffu) of type- A Rhesus Rotavirus (RRV) or 0.9% normal saline (NS; control) within 24 hours of birth to induce experimental model of biliary atresia. Extrahepatic bile ducts including gallbladder were microdissected en bloc at 3, 7 and 14 days after RRV or saline injections. GeneChip® Mouse Gene 1.0 ST Array (Affymetrix, CA) were used to screen mRNAs whose expression was differently regulated after RRV challenge compared to normal saline controls.

overall_design: Gene expression profiling:  Each experimental conditon contains 3 sets of samples. Each sample consists of two to six extrahepatic bile ducts pooled prior to isolation of total RNA to ensure generation of adequate mRNA to perform quantitative experiments.

first: Kazuhiko

last: Bessho

first: Reena

last: Mourya

first: Pranavkumar

last: Shivakumar

first: Stephanie

last: Walters

first: John

last: McGee

first: Anil

last: Jegga

first: Marepalli

last: Rao


title: Comprehensive gene expression profile of human livers from patients with biliary atresia at the time of diagnosis and the corresponding disease and normal controls

summary: Liver biopsy samples were obtained from 64 infants with biliary atresia at the time of intraoperative cholangiogram. Liver biopsy samples were obtained from 14 age-matched infants with other causes of intrahepatic cholestasis, and from 7 deceased-donor children. GeneChip® Human Gene 1.0 ST Array (Affymetrix, CA) were used to screen mRNAs whose expression was specifically regulated in the livers from patients with biliary atresia.

overall_design: Gene expression profiling: Liver biopsy samples obtained from infantas with other causes of intrahepatic cholestasis were served as diseased control. Liver tissue obtained from deceased-donor children were served as normal control. A molecular signataure of biliary atresia at the time of diagnosis was identified by comparing hepatic gene expression profile from biliary atresia to those from diseased and normal controls.


title: EphrinB2 Regulation by PTH and PTHrP Revealed by Molecular Profiling in Differentiating Osteoblasts

status: Public on Apr 10 2013

first: Alistair

last: Chalk

summary: With the aim of identifying new pathways and genes regulated by PTH(1-34) and PTH-related protein 1-141 [PTHrP(1-141)] in osteoblasts, this study was carried out using a mouse marrow stromal cell line, Kusa 4b10, that acquires features of the osteoblastic phenotype in long-term culture conditions. After the appearance of functional PTH receptor 1 (PTHR1) in Kusa 4b10 cells, they were treated with either PTH(1-34) or PTHrP(1-141), and RNA was subjected to Affymetrix whole mouse genome array.

overall_design:
Timecourse experiment on Kusa4b10 cell lines, treatment with PTH or PTHrP, collection at 1, 6 and 24 hours

NOTE: This work has been published in 2008 (PMID 18627264); Since the original normalised data for this project is unavailable,  the data has been re-normalised using a standard method for GEO submission in 2013. Therefore, the re-normalized data represented in this records may differ slightly from the original normalized data in the publication.

first: E

last: Allan

first: K

last: Häusler

first: T

last: Wei

first: J

last: Gooi

middle: W

last: Quinn

first: B

last: Crimeen-Irnin

first: S

last: Pompolo

first: N

last: Sims

first: M

middle: T

last: Gillespie

last: Onyia

last: Martin


title: Anti-cancer drug sensitive DNA methylation marker research

status: Public on Dec 31 2011

city: Daejeon

first: Han-Chul

last: Lee

address: 111 Gwahangno, Yuseong-gu

department: Medical Genome Research Center

country: South Korea

institute: KRIBB

summary: Genome wide DNA methylation profiling of normal and colon cancer and assosiation study between anti-cancer drug respond group and non-respond group.  The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 118 paired anti-cancer drug response tested colon cancer and adjacent normal tissues

overall_design: Bisulphite converted DNA from the 248 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: JinCheon

last: Kim


title: Expression Profiling of Adult Male Germ Cell Tumors

status: Public on Nov 10 2005

first: James

last: Korkola

address: 1275 York Ave

department: Cell Biology

institute: Memorial Sloan-Kettering

summary:
Expression profiling of a panel of 101 adult male germ cell tumors and 5 normal testis specimens was performed on Affymetrix U133A and U133B microarrays. This data has been used to:
1) generate a gene classifier that predicts histology (see PMID 15870693).
2) identify candidate target genes on 12p, a region that is gained in almost 100% of germ cell tumors (see PMID 16424014)
3) identify pluripotency associated genes through comparison of pluripotent embryonal carcinoma vs. undifferentiated seminoma.
ONGOING:
4) Identification of genes associated with patient outcome and cisplatin resistance.
Keywords: germ cell tumor, histologic subtypes

overall_design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 1999. The tumor samples consist of 17 seminomas, 15 pure EC, 15 pure T, 10 pure YS, 2 pure CC, and 42 NSGCT with mixed histologies. There were six patients who had each had two tumors per patient that were included in this study (designated with the same number but different letter- e.g. 155A and 155C are from same patient but represent two different tumors, one being the primary testicular lesion, the other being a liver metastasis). Five normal testis specimens (and one pooled sample consisting of equal amounts of the 5 normal testis specimens) from individual of similar ages were used as controls.

first: Jane

last: Houldsworth

first: Rajendrakumar

last: Chadalavada

first: Adam

last: Olshen

first: Debbie

last: Dobrzynski

first: Victor

last: Reuter

first: George

last: Bosl

last: Chaganti


title: Gene expression profiling in HSF1-knockdown human oral squamous cell carcinoma HSC-3 cells

status: Public on May 23 2012

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary: Heat shock transcription factor 1 (HSF1) is recognized as the major regulator of the heat shock transcriptional response, and also plays a central role in the cellular functions of cancer cells. Here, to identify the molecular mechanism by which HSF1 regulates the proliferation of cancer cells, comparative gene expression analysis was performed with mock and HSF1-knockdown cells. Silencing of HSF1 in human oral squamous cell carcinoma HSC-3 cells was carried out by siRNA technology and the expression of HSF1 was confirmed by Western blotting. Gene expression was analyzed using GeneChip oligonucleotide microarrays and computational gene expression analysis tools. HSF1 knockdown significantly decreased the number of viable cells. Of the 54,675 probe sets analyzed, 221 probe sets were up-regulated and 423 probe sets were down-regulated by >2-fold in HSF1-knockdown cells.

overall_design: HSC-3 human oral squamous carcinoma cells were treated with siRNA for HSF1 or luciferase. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Ayako

last: Kariya

first: Tatsuya

last: Yunoki


title: Molecular signature with high accuracy for biliary atresia identifies a role for Interleukin-8 in pathogenesis of disease

first: Jorge

middle: A

last: Bezerra

overall_design: Refer to individual Series


title: Gene expression data from different types of renal tumors and normal kidneys

status: Public on Sep 25 2008

city: Rotterdam

first: Dmitry

last: Zubakov

state: ZH

address: Dr. Molewaterplein, 50

department: FMB

country: Netherlands

institute: Erasmus Medical Centre Rotterdam

summary:
Identification and evaluation of specific molecular markers is of great importance for reliable diagnostics and outcome prediction of renal neoplasms
Using the Affymetrix microarray, we established the gene expression signatures of normal kidneys and different types of renal tumors.
Keywords: Several different biological groups, several samples per group

overall_design: We analysed several arrays per specific type of renal tumor and normal kidney tissues

first: Adrianna

last: Szponar

first: Justyna

last: Pawlak

first: Anna

last: Jauch

first: Gyula

last: Kovacs


title: Expression profiles of esophageal cancer cell lines

status: Public on Dec 01 2008

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

institute: Hiroshima University

summary:
Expression profiles of immortal esophageal squamous cancer cell lines were compared with those of cultured mortal noncancerous esophageal epithelial cells.
Keywords: Cell type comparison

overall_design: We analyzed 20 arrays for human esophageal squamous cancer cell lines and 2 arrays for noncancerous epithelial cells.

first: Eiso

first: Keiji

last: Tanimoto

first: Masahiko

last: Nishiyama