title: CSF pQTL study in the Japanese population [genotyping Q35]

first: Daimei

last: Sasayama

first: Kotaro

last: Hattori

first: Shintaro

last: Ogawa

first: Yuki

last: Yokota

first: Ryo

last: Matsumura

first: Toshiya

last: Teraishi

first: Hiroaki

last: Hori

first: Miho

last: Ota

first: Sumiko

last: Yoshida

first: Hiroshi

last: Kunugi


title: RNA-Seq and miRNA-Seq of human placenta: spontaneous preterm birth in the presence of intra-amniotic infection/inflammation and controls

status: Public on Jun 14 2016

city: Columbus

first: William

middle: Edward

last: Ackerman IV

state: Ohio

address: N521 Doan Hall, 410 West 10th Avenue

department: Obstetrics and Gynecology

country: USA

institute: The Ohio State University

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression-based drug screening of neural progenitor cells from individuals with schizophrenia

status: Public on Oct 31 2018

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

overall_design:
Refer to individual Series

Please note that each of the MSAnnn array datasets represents a separate 348-well plate, which were all processed independently (e.g. each plate included its own within-plate vehicle controls).


title: RNA polymerase in pre-B-ALL cell lines

status: Public on Jul 05 2016

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
[Gro-seq] Precursor B acute leukemia cells measured using global nuclear run-on sequencing
[ChIP-Seq] The genome-wide occupancy of ser2 and ser5 phosphorylated RNA pol2 and H3K4me3 was measured in precursor B acute leukemia cells measured using chip-seq.

overall_design:
[Gro-seq] Nascent RNA expression profiles were generated at cells in various basal culture conditions.
[ChIP-Seq] Performed from REH and Nalm6 cells cultured under basal culture conditions. Mnase digestion was used for DNA fragmentation. Antibodies against Ser2 and Ser5 phosphorylated RNA polymerase and H3K4me3 compared to input.
******************************
This study includes reanalysis of Samples in Series GSE39878 (GSM980645, GSM980644), GSE60454 (GSM1480326), and GSE41009 (GSM1006728, GSM100672). The processed data files for the reanalyses are linked to GSE67540 as supplementary files (see the GSE67540_README.txt file for additional information).

first: Susanna

last: Teppo

first: Minna

middle: U

last: Kaikkonen

first: Maria

last: Bouvy-Liivrand

first: Olli

last: Lohi


title: RNA-Seq of human placenta: spontaneous preterm birth in the presence of intra-amniotic infection/inflammation and controls

summary: Using RNA-sequencing (RNA-Seq and miRNA-Seq), we analyzed paired villous trophoblast and decidual basalis transcriptomes of 15 women pregnant with singleton gestations grouped as follows: (1) spontaneous preterm birth (PTB) in the setting of amniocentesis-proven intra-amniotic infection (IAI) and histological chorioamnionits (n=5; GA median [range]: 26 [25-31] weeks); (2) spontaneous idiopathic preterm birth (iPTB, n=5, GA: 32 [30-33] weeks); and (3) term normal pregnancy, that delivered a heathy infant by cesarean section in the absence of labor (n=5; GA: 39 [38-39] weeks).

overall_design:
The primary goal of this study was to identify differentially expressed transcripts and illuminate molecular mechanisms distinguishing IAI-associated PTBs from spontaneous PTBs in the absence of IAI. We further compared iPTB specimens to term specimens to determine genes differentially regulated with advancing gestational age and following spontaneous PTB without IAI. Finally, we determined transcripts selectively expressed in either the villous trophoblast or decidua basalis in each clinical context.

Raw data for this study are not available because consent forms do not allow for public access to raw data.

middle: E

last: Ackerman

first: Catalin

middle: S

last: Buhimschi


title: Gene expression data from SW1990 cells stably expressing Fbw7

status: Public on Dec 31 2015

city: Shanghai

first: Yi

last: Qin

address: Dongan Road

country: China

institute: SHCA

summary: Fbw7 plays a negative role in pancreatic cancer tumorigenesis and progression. To further clarify the function and mechanism that Fbw7 plays in pancreatic cancer,mRNA microarray assays were performed to identify the genes and signaling pathways that were changed upon Fbw7 overexpression.

overall_design: Fbw7 overexpressing SW1990 cells were cultured for RNA extraction and hybridization on Affymetrix mRNA microarrays. These were compared against the control,which were infected by empty control lentiviral particles.

first: Xianjun

last: Yu

first: Shunrong

last: Ji

first: Chen

last: Liang


title: Expression data from murine fibrotic liver tissues and normal liver tissues

status: Public on Apr 25 2016

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

summary:
Long noncoding RNAs (lncRNAs) play important roles in various biological processes; however, few have been identified that regulate hepatic stellate cells (HSCs) activation and the progression of liver fibrosis. To identify the possible roles of lncRNAs in regulating liver fiboris and the potential of lncRNAs as molecular markers for liver fiboris, we systematically analyzed the regulation of lncRNAs and mRNAs in a mouse model of carbon tetrachloride (CCl4)-induced liver fibrogenesis by microarray analysis, which revealed a panel of lncRNAs and mRNAs that were specifically regulated in livers of mice undergoing hepatic fibrosis.
To identify the possible roles of lncRNAs in regulating liver fiboris and the potential of lncRNAs as molecular markers for liver fiboris,we determined the lncRNA and mRNA expression profiles in the livers of fibrotic mice and normal mice by lncRNA and mRNA microarrays.

overall_design: The lncRNA expression profile along with mRNA expression profile of five liver tissues from Balb/c mice treated with CCl4 for 6 weeks and five liver tissues from Balb/c mice treated with oil for 6 weeks were analyzed by Affymetrix GeneChip Mouse Exon 1.0 ST Array.

first: Wei

last: Hong

first: Tao

last: Han


title: Transcriptomic analysis of aggressive meningiomas identifies PTTG1 and LEPR1 as prognostic biomarkers independent of WHO grade

status: Public on Feb 15 2016

city: Heidelberg

first: Christel

last: Herold-Mende

address: Im Neuenheimer Feld 400

department: Department of Neurosurgery

country: Germany

institute: Heidelberg University Hospital

summary: Meningiomas are frequent central nervous system tumors. Although most meningiomas are benign (WHO grade I) and curable by surgery, WHO grade II and III tumors remain therapeutically challenging due to frequent recurrence. Interestingly, relapse also occurs in some WHO grade I meningiomas. Hence, we investigated the transcriptional features defining aggressive (recurrent, malignantly progressing or WHO grade III) meningiomas in 144 cases. Meningiomas were categorized into non-recurrent (NR), recurrent (R), and tumors undergoing malignant progression (M) in addition to their WHO grade. Unsupervised transcriptomic analysis in 62 meningiomas revealed transcriptional profiles lining up according to WHO grade and clinical subgroup. Notably aggressive subgroups (R+M tumors and WHO grade III) shared a large set of differentially expressed genes (n=332; p<0.01, FC>1.25). In an independent multicenter validation set (n=82), differential expression of 10 genes between WHO grades was confirmed. Additionally, among WHO grade I tumors differential expression between NR and aggressive R+M tumors was af rmed for PTTG1, AURKB, ECT2, UBE2C and PRC1, while MN1 and LEPR discriminated between NR and R+M WHO grade II tumors. Univariate survival analysis revealed a significant association with progression-free survival for PTTG1, LEPR, MN1, ECT2, PRC1, COX10, UBE2C expression, while multivariate analysis identified a prediction for PTTG1 and LEPR mRNA expression independent of gender, WHO grade and extent of resection. Finally, stainings of PTTG1 and LEPR confirmed malignancy-associated protein expression changes. In conclusion, based on the so far largest study sample of WHO grade III and recurrent meningiomas we report a comprehensive transcriptional landscape and two prognostic markers.

overall_design: Comparative transcriptomic analysis of 62 low- and high-grade meningiomas

first: Andreas

last: Mock

first: Melissa

last: Schmidt


title: Expression data from OMD- or PRELP-knockdown 5637 cells, and OMD- or PRELP-overexpression T-REx 293 cells

status: Public on Apr 30 2016

city: Chicago

first: Ryuji

last: Hamamoto

state: IL

address: 5835 S. Cottage Grove Ave.

department: Department of Medicine

institute: The University of Chicago

summary:
We knockdowned OMD and PRELP expression by specific siRNAs in 5637 bladder carcinoma cells and conducted expression profile analysis.
We also overexpressed OMD and PRELP in T-REx 293 cells and conducted expression profile analysis.

overall_design: Specific siRNAs targeting OMD and PRELP or control siRNAs (siEGFP and siFFLuc) were transfected into 5637 cells, total RNA was extracted 24 h after transfection. We also extracted total RNA from control T-Rex 293 cells, CAT-overexpressing T-REx cells, OMD-overexpressing T-REx and PRELP-overexpressing T-REx 293 cells.


title: Genome-wide localisation of the bromodomain protein PfBDP1 in the malaria parasite P. falciparum

status: Public on Mar 22 2016

city: Melbourne

first: Michaela

last: Petter

state: VIC

address: 792 Elizabeth Street

department: Peter Doherty Institute

country: Australia

institute: University of Melbourne

summary: During red-blood-cell-stage infection of Plasmodium falciparum, the parasite undergoes repeated rounds of replication, egress, and invasion. Erythrocyte invasion involves specific interactions between host cell receptors and parasite ligands and coordinated expression of genes specific to this step of the life cycle. We show that a parasite-specific bromodomain protein, PfBDP1, binds to chromatin at transcriptional start sites of invasion-related genes and directly controls their expression. Conditional PfBDP1 knockdown causes a dramatic defect in parasite invasion and growth and results in transcriptional downregulation of multiple invasion-related genes at a time point critical for invasion. Conversely, PfBDP1 overexpression enhances expression of these same invasion-related genes. PfBDP1 binds to acetylated histone H3 and a second bromodomain protein, PfBDP2, suggesting a potential mechanism for gene recognition and control. Collectively, these findings show that PfBDP1 critically coordinates expression of invasion genes and indicate that targeting PfBDP1 could be an invaluable tool in malaria eradication.

overall_design: ChIPseq mapping of the genome wide enrichment profile of the P. falciparum bromodomain protein PfBDP1 in two parasite stages and correlation with RNAseq expression data

first: Michael

middle: F

last: Duffy


title: Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2

status: Public on Nov 12 2015

city: Urbana

first: Jongsook

middle: Kim

last: Kemper

state: Illinois

address: 524 Burrill Hall  407 S. Goodwin Ave

department: Department of Molecular & Integrative Physiology

institute: University of Illinois at Champaign-Urbana

summary:
Background: Fibroblast growth factor-19 (FGF19) is an intestinal hormone that mediates postprandial metabolic responses in the liver. The unusual orphan nuclear receptor, Small Heterodimer Partner (SHP), acts as a co-repressor for many transcriptional factors and has been implicated in diverse biological pathways including FGF19-mediated repression of bile acid synthesis. To explore global functions of SHP in mediating FGF19 action, we identify genome-wide SHP binding sites in hepatic chromatin in mice treated with vehicle or FGF19 by ChIP-seq analysis.
Results: The overall pattern of SHP binding sites between these two groups is similar, but SHP binding is enhanced at the sites by addition of FGF19. SHP binding is detected preferentially in promoter regions that are enriched in motifs for unexpected non-nuclear receptors. We observe global co-localization of SHP sites with published sites for SREBP-2, a master transcriptional activator of cholesterol biosynthesis. FGF19 increases functional interaction between endogenous SHP and SREBP-2 and inhibits SREBP-2 target genes, and these effects were blunted in SHP-knockout mice. Furthermore, FGF19-induced phosphorylation of SHP at Thr-55 is shown to be important for its functional interaction with SREBP-2 and reduction of liver/serum cholesterol levels.
Conclusion: This study reveals SHP as a global transcriptional partner of SREBP-2 in regulation of sterol biosynthetic gene networks and provides a potential mechanism for cholesterol-lowering action of FGF19.

overall_design: Genome-wide SHP binding profiles in hepatic chromatin in mice under treatment of FGF19 or vehicle were generated using high throughput sequencing followed by chromatin immunoprecipitation.

first: Young-Chae

last: Kim

first: Sangwon

last: Byun

first: Yang

first: Sunmi

last: Seok

first: Byron

first: Jian

last: Ma

middle: K


title: mRNA expression profile in vascular smooth muscle cells (VSMCs) after inducing calcification

status: Public on Nov 07 2015

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

country: South Korea

institute: Chonnam Univ. Med. Sch.

summary: Vascular calcification (VC) is often associated with cardiovascular and metabolic diseases. However, the molecular mechanisms linking VC to these diseases have yet to be elucidated. Here we report that MDM2-induced polyubiquitination of histone deacetylase 1 (HDAC1) mediates VC. Loss of HDAC1 activity via either chemical inhibitor or genetic ablation enhanced VC. HDAC1 protein, but not mRNA, was reduced in cell and animal calcification models and in human calcified coronary artery. In the calcification-provoking condition, proteasomal degradation of HDAC1 preceded VC. The calcification-provoking condition induced MDM2 E3 ligase, which then resulted in HDAC1 K74 polyubiquitination. Overexpression of MDM2 enhanced VC, whereas loss of MDM2 blunted it. Decoy peptides spanning HDAC1 K74 and RG 7112, an MDM2 inhibitor, prevented VC in vivo and in vitro. These results demonstrate a previously unknown ubiquitination pathway and suggest MDM2-mediated HDAC1 polyubiquitination as a new therapeutic target in VC.

overall_design: Calcification was induced in rat aorta vascular smooth muscle cells with inorganic phosphate (Pi). Total RNA were extracted from the cells 3 and 6 days later. mRNA profile of the sample was compared with normal control.

first: Duk-Hwa

last: Kwon

first: Gwang-Hyeon

last: Eom

first: Jeong-Hyeon

last: Ko

first: Sera

last: Shin

first: Hosouk

last: Joung

first: Yoon-Seok

last: Nam

first: Hyun-Ki

last: Min

first: Taewon

last: Kook

first: Somy

last: Yoon

first: Wanseok

last: Kang

first: Yong-Sook

first: Hyung-Seok

first: Hyuck

last: Choi

first: Jeong-Tae

last: Koh

first: Nacksung

first: Youngkeun

last: Ahn

first: Hyun-Jai

last: Cho

first: In-Kyu

last: Lee

first: Dong-Ho

last: Park

first: Kyoungho

last: Suk

first: Sang-Beom

last: Seo

first: Erin

middle: R

last: Wissing

first: Susan

middle: M

last: Mendrysa

first: Kwang-Il

first: Hyun


title: Genome-wide maps of ParBF (SopB) binding along DNA in E. coli

status: Public on Sep 04 2015

city: Toulouse

first: Jean-Yves

last: Bouet

address: 169 avenue Marianne Grunberg-Manago

country: France

institute: CNRS

summary: We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) at very high resolution (about 50 millions reads) of the DNA binding pattern of ParBF (SopB) of plasmid F

overall_design: Differencial examination of ParBF binding by comparing input and IP (anti-SopB antibody) samples

first: Aurore

last: Sanchez


title: Effect of dietary fat and cholesterol on hepatic gene expression of liver-specific Cyp51 knockout male and female mice

status: Public on May 28 2015

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
Cholesterol is one of the key molecules in mammals and the most striking examples of its deficiency are the inborn errors of cholesterol biosynthesis that manifest in severe whole body phenotypes. Liver, the principal site of cholesterol homeostasis, has rarely been investigated in these defects. We thus focused on the hepatocyte-specific deletion of lanosterol 14α-demethylase (CYP51) catalyzing the rate-limiting step in the post-squalene part of cholesterol synthesis.
Liver-specific Cyp51 KO (LKO or K) and littermate control (LWT or W) mice (129/Pas (10%) × C57BL/6J (90%)) of both sexes (F and M) were investigated in the context of different nutritional availability of fat and cholesterol (standard laboratory diet without cholesterol (LFnC or L), high-fat diet without cholesterol (HFnC or H) and high-fat diet with cholesterol (HFC or C) due to the known sexual dimorphism in hepatic gene expression, where lipid metabolic pathways are among the most biased.

overall_design: 3 condition experimental design: 3 diets (LFnC or L, HFnC or H, HFC or C), 2 genotypes (LWT or W, LKO or K), 2 sexes (F, M), 3 biological replicates per condition, 36 mice altogether

first: Gregor

last: Lorbek

first: Damjana

last: Rozman


title: Functional role of miRNAs in the renal stroma during embryonic kidney development

status: Public on Nov 04 2015

city: New York City

first: Dr. Yu Leng

last: Phua

state: New York

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai


title: Recipient myeloid cell subsets in transplanted allografts

status: Public on Sep 01 2015

city: New York

first: Jordi

last: Ochando

address: 1470 Madison Avenue

summary: Balb/c donor hearts were transplanted into C57/BL6 recipients as previously described (Corry et al, 1973). Recipient mice were treated with 250μg anti-CD40L mAb for tolerance induction on days 0, 2, and 4 as previously described (Jiang et al., 2011) or left untreated. On day 5 after transplantation graft infiltrating myeloid subsets were isolated using fluorescence activated cell sorting (FACS). Affymetrix Mouse Gene arrays were run in triplicate with the samples of interest. Raw CEL file data from Affymetrix Expression Console were background corrected, normalized, and summarized using RMA.

overall_design: 18 Samples, 9 treated and 9 untreated, 3 replicates each


title: Epigenome profiling reveals significant DNA demethylation of interferon signature genes in lupus neutrophils

status: Public on Jan 21 2015

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

summary: We identified genome-wide DNA methylation patterns within neutrophils and low-density granulocytes of Lupus patients and demographically matched controls

overall_design: Comparison of 15 Lupus patients vs 15 age-, sex-, and ethnicity-matched controls using the Illumina HumanMethylation 450 beadchip array

first: Amr

middle: H

last: Sawalha


title: Whole genome expression profiling across the life cycle of PfBDP1 overexpressing P. falciparum malaria parasites

status: Public on Jan 07 2015

first: Michaela

last: Petter

summary: Erythrocyte invasion is an essential step in the life cycle of the malaria parasite Plasmodium falciparum that involves specific interactions between host cell receptors and parasite ligands. How the parasite regulates the expression of invasion-related genes is to date largely unknown.  Here we show that a novel, parasite-specific bromodomain protein (PfBDP1) binds to chromatin at the transcriptional start site of invasion-related genes and directly controls their expression. Conditional PfBDP1 knockdown causes a dramatic defect in parasite invasion and growth and results in transcriptional down-regulation of multiple invasion-related genes at a time point critical for invasion. This is the first report of a histone binding protein that activates genes in P. falciparum and our data place PfBDP1 in a central position for controlling the coordinated expression of invasion genes. Bromodomains are emerging therapeutic targets and drugs that specifically inhibit PfBDP1 could be an invaluable tool in the effort to eradicate malaria.

overall_design: P. falciparum 3D7 parasites over-expressing PfBDP1-3xHA (3D7/PfBDP1 OE) [PMID: 23181666] were grown in presence of 5μg/ml BSD-S-HCl. The parasite line 3D7/cam [PMID: 22435676.] grown under the same conditions and expressing hDHFR instead of PfBDP1-3xHA from the same promoter was used as control. RNA extracted from these samples at four consecutive time points each was processed for microarray analysis.

first: Gabrielle

middle: A

last: Josling

first: Sophie

middle: C

last: Oehring

first: Archna

middle: P

last: Gupta

first: Olivier

last: Dietz

first: Danny

middle: W

last: Wilson

first: Thomas

last: Schubert

first: Gernot

last: Längst

first: Paul

last: Gilson

first: Brendan

last: Crabb

first: Suzette

last: Moes

last: Jenoe

first: Melvin

last: Lim

first: Graham

middle: V

last: Brown

first: Zbynek

last: Bozdech

first: Till

last: Voss

first: Michael

last: Duffy


title: Whole genome expression profiling across the asexual life cycle in PfBDP1 knockdown malaria parasites

last: Petter

summary: To study the bromodomain protein PfBDP1 in the malaria parasite P. falciparum, a transgenic parasite line was generated (PfBDP1DD) in which PfBDP1 was tagged with a haemagglutinin tag and a ligand regulatable FKBP destabilization domain that allowed conditional knockdown of PfBDP1 by removal of the stabilizing ligand Shld1 from cultures. Shld1 was removed 30 hours post invasion (hpi) and the cells allowed to reinvade fresh red blood cells. The effects of PfBDP1 knockdown on gene expression were assessed by transcriptional profiling on microarrays over 6 consecutive time points (8 hour intervals) in the intraerythrocytic developmental cycle (IDC).

overall_design: Two condition matched time course experiment, PfBDP1DD ON versus OFF Shld1. Transgenic P. falciparum 3D7 parasites (PfBDP1DD) expressing an endogeneous PfBDP1-HA-DD fusion protein were grown in the presence of 2.5 nM WR99210/500 nM Shld1 (PfBDP1DD_ON) or 2.5 nM WR99210  (PfBDP1DD_OFF). After invasion, RNA was extracted at 6 consectutive time points in 8 hour intervals during the IDC, starting at 4 hpi, and was processed for microarray analysis. Three matched biological replicates were performed for both conditions, independently grown and harvested. Each array represents one RNA sample.


title: Gene signature of CLL cells cultured with activated T cells or CD40L-expressing cells

status: Public on Oct 07 2013

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: Chronic Lymphocytic Leukemia (CLL) cells multiply in secondary lymphoid tissue but the mechanisms leading to their proliferation are still uncertain. In addition to BCR-triggered signals, other microenvironmental factors might well be involved. In proliferation centres, leukemic B cells are in close contact with CD4+CD40L+ T cells. Therefore, we here dissected the signals provided by autologous activated T cells (Tact) to CLL cells. Although the gene expression profile induced by Tact was highly similar to that induced by sole CD40 signaling, an obvious difference was that Tact induced proliferation of CLL cells. We determined that stimulation with only CD40L+IL-21 was sufficient to induce robust proliferation in CLL cells. We then defined an IL-21-induced gene signature in CLL, containing components of JAK-STAT and apoptosis pathways, and this signature could be detected in lymph node (LN) samples from patients. Finally, we could detect IL-21 RNA and protein in LN, and IL-21 production ex vivo by LN CD4+CXCR5+ follicular helper T cells. These results indicate that, in addition to BCR signaling, activated T cells might contribute to CLL cell proliferation via CD40 and IL-21. Targeting these signaling pathways might offer new venues for treatment of CLL.

overall_design: CLL cells were cultured under different conditions for 16 hours and then sorted to purity as CD20+ CD5+ cells.

first: F

last: Pascutti

first: E

last: Eldering


title: Infection exposure is a causal factor in B-precursor acute lymphoblastic leukemia as a result of Pax5 inherited susceptibility

status: Public on Oct 21 2014

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary: We used microarrays to investigate gene expression changes in tumor-bearing Pax5+/- mice

overall_design: Tumor-bearing bone marrows of six Pax5+/- mice compared with B220+ bone marrow B cells from five WT mice and with ProB and PreB cells from three WT mice. ProB and PreB cells from three Pax5+/- mice compared with ProB and PreB cells from three WT mice.

first: Alberto

last: Martín-Lorenzo

first: Julia

last: Hauer

first: Carolina

last: Vicente-Dueñas

first: Franziska

last: Auer

first: Inés

last: González-Herrero

first: Idoia

last: García-Ramírez

first: Sebastian

last: Ginzel

first: Ralf

last: Thiele

first: Stefan

middle: N

last: Constantinescu

first: Christoph

last: Bartenhagen

first: Martin

last: Dugas

last: Gombert

first: Daniel

last: Schäfer

first: Oscar

last: Blanco

first: Andrea

last: Mayado

last: Orfao

first: Diego

last: Alonso-López

first: Javier

last: de las Rivas

first: César

last: Cobaleda

first: Maria

middle: B

last: García-Cenador

first: Francisco

middle: J

last: García-Criado

last: Sánchez-García

first: Arndt

last: Borkhardt


title: Expression of the placental transcriptome in fetal growth restriction in the Baboon is Dependent on Fetal Sex

status: Public on Dec 06 2013

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

summary: Fetal growth restriction (FGR) develops when fetal nutrient availability is compromised and increases the risk for perinatal complications and predisposes for offspring obesity, diabetes and cardiovascular disease later in life. Emerging evidence implicates changes in placental function in altered fetal growth and the subsequent development of adult disease.  The susceptibility for disease in response to an adverse intrauterine environment differs distinctly between boys and girls, with girls typically having better outcomes.  Here, we test the hypothesis that regulation of the placental transcriptome by moderate nutrient reduction is dependent on fetal sex.  We used a non-human primate model of FGR in which maternal global food intake is reduced by 30% starting at gestational day (GD) 30. At GD 165 (term = GD 183) placental genome expression profiling was carried out followed by bioinformatics including pathway and network analysis. Surprisingly, there was no coordinated placental molecular response to decreased nutrient availability when analyzing the data without accounting for fetal sex. In contrast, female placentas exhibited a highly coordinated response that included up-regulation of genes in networks, pathways and functional groups related to programmed cell death and down-regulation of genes in networks, pathways and functional groups associated with cell proliferation. These changes were not apparent in the male placentas. Our data support the concept that female placentas initiate complex adaptive responses to an adverse intrauterine environment, which may contribute to increased survival and better pregnancy outcomes in girls.

overall_design: Total RNA obtained from 165dGA control female (n=3), control male (n=3), nutrient restricted female (n=3), and nutrient restricted male (n=3) pregnancies.

first: Thomas

last: Jansson

first: Peter

last: Nathanielsz

first: Jeremy

last: Glenn

first: Kennet

last: Lange


title: VCCS HEL and U937 cell line study: fresh and fixed cells

status: Public on Nov 30 2013

city: Fitzroy

first: Ruth

last: MacKinnon

state: Vic

address: PO Box 2900

department: Victorian Cancer Cytogenetics Service

institute: St Vincent's Hospital (Melbourne)

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

summary:
This study aims to determine the chromosome content and organisation of two myeloid leukaemia cell lines, HEL and U937. This will be done not only with SNP array data to determine breakpoints and copy number of copy number aberrations, but also with FISH (multicolour FISH, multicolour banding, centromere and single locus FISH) to identify translocation partners, chromosome organistion, centromere content, and provide some information on genome evolution in the cell line.
Although several HEL SNP array karyotypes have been published and are available online the information here shows that there are some differences, and the additional FISH tests provide a greater depth of information on genome organisation and derivation of the abnormal chromosomes. The U937 cell line was also studied using DNA from fresh and fixed specimens for comparison of the quality of the SNP array data. Data from cells fixed using standard cytogenetic fixative (3:1 methanol:acetic acid) were compared to data from cells processed directly from tissue culture.

overall_design:
Three specimens were processed with the Illumina CytoSNP 12 platform. Two of these (U937) represent fresh and fixed specimen for comparison. All samples were processed while in log phase.
The method used in this experiment is described in:

Mackinnon RN, Selan C, Zordan A, Wall M et al. CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens. Mol Cytogenet 2012 Feb 2;5:10. PMID: 22300816

first: Meaghan

last: Wall

first: Adrian

last: Zordan


title: A Novel Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression

first: Michaela

last: Petter

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

sample_organism:
Plasmodium falciparum
Plasmodium falciparum 3D7

overall_design: Refer to individual Series


title: Host transcriptional response to influenza and other acute respiratory viral infections – a prospective cohort study

status: Public on Apr 28 2015

city: Houston

first: John

last: Belmont

state: TX

address: One Baylor Plaza, BCM 320

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The purpose of the study was to assess the patterns of global gene expression in peripheral blood cells and uncover the complex  dynamics of host response to ARIs such as pandemic H1N1. To understand the molecular bases and network orchestration of host responses, we prospectively enrolled 1610 healthy adults in the fall of 2009 and 2010, followed the subjects with influenza-like illness (N=133) for 3 weeks, and examined changes in their peripheral blood gene expression. We discovered distinct phases of the host response spanning 6 days after infection, and identified genes that differentiate influenza from non-influenza virus infection. We examined pre- and post-infection anti-influenza antibody titers defining novel gene expression correlates.

overall_design: Healthy adults were invited to enroll to be followed for acute respiratory illness (ARI) through two consecutive influenza seasons 2009-2010 and 2010-2011. After subjects provided consent, baseline blood specimens were obtained during enrollment. Subjects were given thermometers and instructions to call and report for evaluation within 48 hours of ARI onset. Those persons who had a new ARI were seen within 48 hours of onset (day 0) and 2, 4, and 6 days later for repeat evaluation, blood specimen collections, and medical care (including the antiviral zanamivir if indicated) and 21 days later for collection of convalescent specimens. Nasal wash samples were collected for virus detection by RT-PCR on day 0 and day 2. Surveillance for influenza was terminated after 5.5 months; all subjects were asked to return for specimen collection and to provide a medical and ARI history in spring of next year. Serum specimens obtained at baseline, day 0 and day 21 visits for illnesses, and the terminal visit were tested simultaneously using hemagglutination-inhibition (HAI) antibody assay for Influenza H1N1, H3N2, and Influenza B strains. Peripheral blood RNA (PaxGene) obtained from blood specimens at each visit were analyzed using Illumina Human HT-12 v4. The study was repeated 2010-2011. A total of 880 arrays, corresponding to 133 individuals, passed quality control and are included in this data set.

first: Yijie

last: Zhai

first: Luis

last: Franco

first: Robert

last: Couch


title: Discovered salivary transcriptomic biomarkers for the detection of gastric cancer

status: Public on Jan 15 2015

city: Los Angeles

first: David

last: Wong

address: 10833 Le Conte Ave

department: Dentistry

institute: UCLA

summary:
We have performed gene expression microarray analysis to profile transcriptomic signatures between cancer and noncancerous patients
Gastric cancer is currently the second leading cause of cancer deaths. Due to the difficulty of diagnosing patients in the early stages of gastric cancer, it is critical to develop a method that can diagnose the disease at the early stage to allow for better treatment options. In this study, we discovered salivary transcriptomic and miRNA biomarkers for the detection of gastric cancer and identified there are mRNA-miRNA correlations in saliva.

overall_design: RNA was extracted from saliva supernatant and mRNA candidates were identified that can distinguish gastric cancer from non-gastric cancer patients

first: Janice

last: Yoshizawa

first: Xiaoyan

last: Wang

middle: E

last: Elashoff

first: Hui

last: Zhou

first: Yong

last: Kim

first: Sung

middle: T


title: Comparative analysis of the response to iron-limitation in the absence of oxygen in R. sphaeroides

status: Public on May 30 2013

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen


title: Comparative analysis of the response to iron-limitation in the absence of oxygen in R. sphaeroides [Microarray]

status: Public on May 23 2013

summary: High intracellular levels of unbound iron can contribute to the production of reactive oxygen species (ROS) in the Fenton reaction, while depletion of iron limits the availability of iron containing proteins, some of which have important functions in the oxidative stress defense. Vice versa increased ROS levels lead to damage of proteins with iron sulfur centers. Thus organisms have to coordinate and balance their responses to oxidative stress and iron availability. Our knowledge on the molecular mechanisms underlying the coregulation of these responses is still limited. To discriminate between a direct cellular response to iron limitation and indirect responses, which are the consequence of increased levels of ROS, we compared the response of the alpha proteobacterium Rhodobacter sphaeroides to iron limitation in presence or absence of oxygen. While some genes respond to iron limitation exclusively or much stronger in presence of oxygen, other genes show much stronger response in anaerobic conditions. Remarkably few genes show even opposite response to iron depletion in presence or absence of iron.

overall_design: RNA samples collected from anaerobically grown cultures in presence or absence of iron were analyzed by two-color microarrays

first: Bernhard

last: Remes


title: Gene Expression Analysis of Dermatomyositis Skin

status: Public on Apr 20 2013

city: Gaithersburg

first: Christopher

middle: Allen

last: Morehouse

state: MD

address: One Medimmune Way

institute: Medimmune LLC

summary: The purpose of this study was to use global gene expression analysis to determine major functional pathways and genes dysregulated in the skin of active rashes of dermatomyositis patients.  These data will be used to help assign a diagnosis to skin biopsies from patients with rashes that are not clearly dermatomyositis.  In addition, we will correlate gene expression changes with specific histopathologic changes in skin biopsies that are taken adjacent to those analyzed for gene expression analysis.  Finally, these data will be used to search for genes and pathways that are associated with clinical outcomes and autoantibody status in this cohort of patients.

overall_design: Gene expression profiling of healthy donor and dermatomyositis patient skin biopsy specimens.


title: Expression data from airway epithelial cells stimulated with Poly(I:C) from patients with asthma, rhinitis, and healthy controls

status: Public on Oct 18 2013

first: Ariane

last: Wagener

address: Meibergdreef 9

institute: Academic Medical Center

summary:
Rhinovirus infections are the most common cause of asthma exacerbations. The complex responses by the airway epithelium to rhinovirus can be captured by gene expression profiling. We hypothesized that the upper and lower airway epithelium exhibit differential responses to double-stranded RNA (dsRNA), and that this is modulated by the presence of asthma and allergic rhinitis.
Identification of dsRNA-induced gene expression profiles by microarray of primary nasal and bronchial epithelial cells from the same individuals and examining the impact of allergic rhinitis with and without concomitant allergic asthma on expression profiles.

overall_design: 17 subjects were included in a cross-sectional study (6 allergic asthma and allergic rhinitis; 5 allergic rhinitis; 6 healthy controls). RNA was extracted from isolated and cultured epithelial cells that were stimulated with Poly(I:C) for 24 hours from bronchial brushes and nasal biopsies, and analyzed by microarray (Affymetrix U133+ PM Genechip Array).

first: Silvia

last: Luiten

first: Aeilko

last: Zwinderman

first: Cornelis

last: van Drunen

first: Peter

last: Sterk


title: Whole genome DASL analysis of tumour epithelial and stromal compartments during breast cancer progression

status: Public on May 11 2012

city: Brisbane

first: Amy

last: McCart Reed

state: QLD

address: Building 71/918 Herston

department: UQCCR

institute: The University of Queensland

summary: Analysis of gene expression changes in tumour epithelium (DCIS and invasive breast cancer) and stroma both immediately surrounding the lesions and more distantly.

overall_design:
Total RNA obtained from Formalin Fixed Paraffin Embedded archival material and the individual compartments (stroma and epithelium) compared independently across the samples.

Sample abbreviation key:
BC = breast cancer
DCIS = ductal carcinoma in situ
IDC = invasive ductal carcinoma
RM = reduction mammoplasty
S = stroma
NS = normal stroma.

A= IDC; B= IDC-S; C= DCIS;D=DCIS-S; E=BC-NS

last: Simpson


title: LKB1 and Notch deletion in mouse liver

status: Public on Dec 08 2015

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: We characterize the phenotype of mice in which the deletion of Lkb1 has been targeted in the liver. Lack of Lkb1 in the liver results in bile duct paucity leading to cholestasis. This phenotype is similar to that obtained upon inactivation of Notch signaling in the liver. We test the hypothesis of a functional overlap between the Lkb1 and Notch pathways by gene expression profiling of livers deficent in Lkb1 or in the Notch mediator RbpJκ. We used AlfpCre mice for liver-specific deletion of LKB1 that were crossed with a conditional knockout mouse model (LKB1 floxed mice). We used also AlfpCre mice for liver-specific inactivation of the Notch pathway. AlfpCre mice were crossed with the RbpJκ floxed mice. RNA was extracted from the liver of LKB1 KO mice (Lkb1Floxed, AlfpCre positive mice) and their wild-type counterpart (Lkb1Floxed, AlfpCre negative mice). RNA was also extracted from liver of RbpJK KO mice (RbpJK floxed, AlfpCre positive) and their wild type mice (RbpJK floxed, AlfpCe negative).

overall_design: 6 samples for the liver-specific deletion of LKB1 corresponding to 3 KO LKB1 (Cre positive) and 3 normal liver (Cre negative). 6 samples for the liver-specific inactivation of the Notch pathway corresponding to 3 KO RbpJk (Cre positive) and 3 normal liver (Cre negative).

first: Christine

last: Perret


title: Expression data from healthy volunteers and IBS patients

status: Public on Feb 14 2009

city: Barcelona

first: Cristina

last: Martinez

address: Paseo Valle Hebron 119-129

department: Digestive diseases research unit

institute: Institut de Recerca HUVH

summary:
Micro-inflammation and gut dysfunction are features of diarrhea-irritable bowel syndrome (d-IBS) patients, although the underlying interacting molecular mechanisms remain mostly unknown. Therefore, we aimed to identify critical networks and signaling pathways active in chronic diarrhea-associated inflammation.

Keywords: Comparison of gene expression

overall_design: Healthy volunteers and d-IBS patients were studied. Jejunal biopsies were subjected to chip analysis (Affymetrix Human Genome U133 Plus 2.0 GeneChips).

first: Javier

last: Santos


title: Inflammasome-regulated cytokines are critical mediators of lung injury in humans.

status: Public on Jul 11 2012

city: Boston

first: Judie

middle: Ann

last: Howrylak

state: MA

address: 75 Francis Street

department: Pulmonary and Critical Care Medicine

institute: Brigham and Women's Hospital

summary: A microarray analysis involving whole blood samples isolated from critically ill patients in the medical intensive care unit at Brigham and Women's Hospital.  Four groups of intubated subjects undergoing mechanical ventilation were recruited for the study: those with sepsis alone (Sepsis), those with sepsis + ARDS (se/ARDS), those with SIRS (SIRS), and those whithout sepsis, SIRS, or ARDS (untreated).  Blood was obtained from patients on the day of admission (day 0) and 7 days later.  RNA was isolated from the whole blood samples and microarrays were prepared to determine differential gene expression between the four groups.

overall_design: Total RNA obtained from whole blood samples of critically ill patients

first: Tamas

last: Dolinay

first: Young

middle: S

last: Kin

first: Laura

last: Fredenburgh

first: Anthony

middle: F

last: Massaro

first: Angela

last: Rogers

first: Gary

last: Hunninghake

first: Lee

last: Gazourian

first: Roberto

last: Landazury

first: Sabitha

last: Epannapaly

first: Stefan

last: Fyter


title: Whole genome transcriptome analysis identifies indices of fast and slow disease progression in two ALS mouse models

status: Public on Oct 01 2013

city: Milan

first: giovanni

last: nardo

address: Via La Masa 19

country: Italy

institute: IRCCS-Mario Negri Institute

summary:
Microarray analysis has been applied to the study of ALS in order to investigate gene expression in whole spinal cord homogenates of SOD1 G93A mice and human ALS cases, although the massive presence of glial cells and inflammatory factors has made it difficult to define which gene expression changes were motor neuron specific. Recently, laser capture microdissection (LCM), combined with microarray analysis, has allowed the identification of motor neuron specific changes in gene expression in mouse and human ALS cases.
The aim of the present study is to combine LCM and microarray analysis to compare the gene expression profiles of motor neurons from two SOD1G93A mouse strains (129Sv and C57) with different progression of the disease in order to discover the molecular mechanisms that may contribute to the distinct phenotypes and to uncover factors underlying fast and slow disease progression

overall_design: Motor neurons have been isolated from the spinal cord of 129SvG93A mice, C57G93A mice and non transgenic littermates at different time points and the transcription expression profile of the isolated motor neurons has been analysed

first: Giovanni

last: Nardo

first: Raffaele

last: Iennaco

first: Nicolò

last: Fusi

first: Paul

last: Heath

first: Marianna

last: Marino

last: Ferraiuolo

first: Neil

last: Lawrence

first: Pamela

last: Shaw

first: Caterina

last: Bendotti


title: Expression data in Ischemia and Reperfusion during microsurgical tissue transfer

status: Public on Jul 07 2010

city: Erlangen

last: Schnürer

address: Schuhstr. 37

department: Plastic and Handsurgery

institute: University of Erlangen-Nuremberg

summary:
Gene Expression of muscle tissue during microsurgical free tissue transfer was basicly studied in animal models. There was found activation of inflammatory and apoptotic cascades and of genes regulating intracellular metabolism.
We used microarrays to detail the programme of gene expression in human muscle tissue which is activated during this process.

overall_design: Human muscle which was harvested during microsurgical free tissue transfer was used for RNA extraction and hybridization on Affymetrix microarrays. Muscle samples of the flap were taken during normoxia (I) after ischemia (II) and after reperfusion (III). Ischemia startet after dissecting the sustentative vessel. Reperfusion began after reanastomosing the vessel and restoring the blood supply.

first: Adrian

last: Dragu


title: Analysis of σL dependent traits based on phenotypic and transcriptomic evaluation of  the Listeria monocytogenes EGDe strain

status: Public on Jan 01 2012

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

institute: University of Helsinki

summary: The phenotypic and gene expression traits conferred by the alternative sigma factor protein σL in the food-borne pathogen L. monocytogenes were investigated. σL was shown to be important for the efficient growth of this pathogen exposed to food preservative measures such as low storage temperatures, elevated osmolarity and acidity. Based on high throughput phenotypic analysis, σL function was also found to be protective in L. monocytogenes EGDe cells exposed to several antimicrobial compounds including some of the antibiotics currently applied in listeriosis treatment.  The expression of flagella genes and motility were significantly compromized upon loss of σL function. A comparative transcriptome analysis of exponential growth EGDe wild type and sigL null cells unveiled 394 genes that are positively controlled through σL dependent transcriptional regulation mechanisms in this bacterium during growth at low (3°C) and optimized (37°C) temperature conditions. Genes identified indicate that σL is a pleitropic transcription regulator mediating positive expression control of genes involved in diverse cellular processes including protein synthesis, molecular transport, energy metabolism, respiration, transcription regulation, metabolite biosynthesis, and cell envelope composition modification.  Overall our observations have revealed that the loss of σL function leads to extensive gene expression defects in L. monocytogenes EGDe cells, and these are consistent with compromized nutrient assimilation, energy metabolism, protein synthesis, and metabolite biosynthesis processes as well as altered cell envelope composition and motility.  Numerous gene expression changes imposed by σL loss in EGDe are thus also consistent with pleiotropic phenotypic defects detected in the L. monocytogenes EGDe ∆sigL strain.

overall_design: Gene expression DNA-microarray. Two-color hybridizations on 8*15K Agilent arrays. Wild type and three KO mutants in three temperatures, three biological replicates in each condition.

first: Mirjami

last: Mattila

first: Thomas

last: Rattei

first: Hannu

last: Korkeala

first: Roger

last: Stephan

first: Taurai

last: Tasara