title: Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice

status: Public on Apr 14 2016

city: Liverpool

first: Andrew

last: Holmes

address: Institute of Integrative Biology

department: Institute of Integrative Biology

institute: University of Liverpool

summary:
Background: Neuronal and glial differentiation in the murine hypothalamus is not complete at birth, but continues over the first two weeks postnatally. Nutritional status and Leptin deficiency can influence the maturation of neuronal projections and glial patterns, and hypothalamic gliosis occurs in mouse models of obesity. Gnasxl constitutes an alternative transcript of the genomically imprinted Gnas locus and encodes a variant of the signalling protein Gαs, termed XLαs, which is expressed in defined areas of the hypothalamus. Gnasxl-deficient mice show postnatal growth retardation and undernutrition, while surviving adults remain lean and hypermetabolic with increased sympathetic nervous system (SNS) activity. Effects of this knock-out on the hypothalamic neural network have not yet been investigated.

Results: RNAseq analysis for gene expression changes in hypothalami of Gnasxl-deficient mice indicated Glial fibrillary acid protein (Gfap) expression to be significantly down-regulated in adult samples. Histological analysis confirmed a reduction in Gfap-positive glial cell numbers specifically in the hypothalamus. This reduction was observed in adult tissue samples, whereas no difference was found in hypothalami of postnatal stages, indicating an adaptation in adult Gnasxl-deficient mice to their earlier growth phenotype and hypermetabolism. Especially noticeable was a loss of many Gfap-positive α-tanycytes and their processes, which form part of the ependymal layer that lines the medial and dorsal regions of the 3rd ventricle, while β-tanycytes along the median eminence (ME) and infundibular recesses appeared unaffected. This was accompanied by local reductions in Vimentin and Nestin expression. Hypothalamic RNA levels of glial solute transporters were, unchanged, indicating a potential compensatory up-regulation in the remaining astrocytes and tanycytes.

Conclusion: Gnasxl deficiency does not directly affect glial development in the hypothalamus, since it is expressed in neurons, and Gfap-positive astrocytes and tanycytes appear normal during early postnatal stages. The loss of Gfap-expressing cells in adult hypothalami appears to be a consequence of the postnatal undernutrition, hypoglycaemia and continued hypermetabolism and leanness of Gnasxl-deficient mice, which contrasts with gliosis observed in obese mouse models. Since α-tanycytes also function as adult neural progenitor cells, these findings might indicate further developmental abnormalities in hypothalamic formations of Gnasxl-deficient mice, potentially including neuronal composition and projections.

overall_design: 6 wildtype and 6 Gnasxlm+/p- RNA isolates were used, which were pooled in pairs in equal concentrations prior to rRNA removal using the RiboMinus kit (Life Technologies)

middle: P

first: Shi Quan

last: Wong

first: Michela

last: Pulix

first: Kirsty

last: Johnson

first: Niamh

last: Horton

first: Patricia

last: Thomas

first: Joao Pedro

last: de Magalhaes

first: Antonius

last: Plagge


title: Physiology of S. cerevisiae during aerobic cultivation at near-zero specific growth rates

status: Public on Jun 01 2016

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Saccharomyces cerevisiae is an established microbial host for the production of non-native compounds. The synthesis of these compounds typically demands energy and competes with growth for carbon and energy substrate. Uncoupling product formation form growth would benefit product yields and decrease formation of by-product biomass. Studying non-growing metabolically-active yeast cultures provides a first step towards developing S. cerevisiae as a non-growing, robust cell factory. Non-growing metabolically-active cultures can be obtained in retentostat, a glucose-limited, continuous bioreactor system in which biomass accumulates while spent medium is constantly removed. Hitherto retentostat cultures of S. cerevisiae have only been reported under anaerobiosis, condition inappropriate for the production of energy-demanding products. The present study, using retentostat cultures, explores the physiology of non-dividing, fully respiring S. cerevisiae, focusing on industrially-relevant features.  Following model-aided experimental design, retentostat cultivations were optimized for accelerated but smooth transition of S. cerevisiae from exponential growth to near-zero growth rates. During 20 days in retentostat the biomass concentration increased, leading very slow growth rates (specific growth rates below 0.001 h-1) but high culture viability (over 80% of viable cells). The maintenance requirement (mATP) was estimated at 0.64 mmolATP.gX-1.h-1, which is remarkably ca. 35% lower than the mATP measured in anaerobic retentostat cultures. Transcriptional down-regulation of genes involved in biosynthesis and up-regulation of stress-responsive genes towards near-zero growth rates corresponded well with data from anaerobic retentostats. More striking was the extreme heat-shock tolerance of S. cerevisiae, which exceeded by far previously reported heat shock tolerance of notoriously robust yeast cultures such as stationary phase cultures. Furthermore, while the metabolic fluxes in the retentostats were relatively low as a result of extreme caloric restriction, off-line measurements revealed that S. cerevisiae retained a high catabolic capacity.  The high viability and extreme heat-shock tolerance revealed the robustness of S. cerevisiae at near-zero growth in retentostat. In addition, the relatively low maintenance requirements and high metabolic capacity under severe calorie restriction underline the potential of S. cerevisiae as a non-dividing microbial cell factory for the production of energy-intensive compounds. The retentostat is a promising tool to identify the molecular basis of this extreme robustness.

overall_design: The goal of the present study is to investigate the physiology of aerobic fully respiring S. cerevsiae at near-zero growth rates. Fundamental but industrially-relevant questions were addressed thanks to the design, implementation and study of aerobic retentostat cultivations enabling a rapid but smooth transition of S. cerevisiae from exponential growth to near-zero growth rates.

first: Tim

last: Vos

first: Xavier

middle: D

last: Hakkaart

first: Erik

middle: A

last: de Hulster

middle: J

last: van Maris

first: Jack

middle: T

last: Pronk

first: Pascale

last: Daran-Lapujade


title: Long-term Exposure to Sorafenib of Liver Cancer Cells Induces Resistance with Epithelial-to-Mesenchymal Transition, Increased Invasion and Risk of Rebound Growth

status: Public on Mar 14 2016

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Sorafenib leads to a survival benefit in patients with advanced hepatocellular carcinoma but its use is hampered by the occurrence of drug resistance. To investigate the molecular mechanisms involved we developed five resistant human liver cell lines in which we studied morphology, gene expression and invasive potential. The cells changed their appearance, lost E-cadherin and KRT19 and showed high expression of vimentin, indicating epithelial-to-mesenchymal transition. Resistant cells showed reduced adherent growth, became more invasive and lost liver-specific gene expression. Furthermore, following withdrawal of sorafenib, the resistant cells showed rebound growth, a phenomenon also found in patients. This cell model was further used to investigate strategies for restoration of sensitivity to sorafenib.

overall_design: We determined gene expression profiles for 13 samples, grown in 1x106 in 25 cm² tissue flasks.  Three flasks contained control samples: HepG2 cells at 20% O2/ 5% CO2/ 75% N2, not exposed to sorafenib. Four flasks contained samples from condition 1: HepG2S1 cells at 20% O2/ 5% CO2/ 75% N2, exposed to sorafenib.  Three flasks contained samples from condition 2: HepG2S1 cells at 20% O2/ 5% CO2/ 75% N2, withdrawn from sorafenib. Three flasks contained samples from condition 3: HepG2S1 cells at 2% O2/ 5% CO2/ 93% N2, exposed to sorafenib.

first: Hannah

last: van Malenstein

first: Jeroen

last: Dekervel

first: Chris

last: Verslype

first: Eric

last: Van Cutsem

first: Petra

last: Windmolders

first: Frederik

last: Nevens

first: Jos

last: van Pelt


title: METTL3 promotes translation in human cancer cells

status: Public on Jan 01 2016

city: Boston

first: Peng

last: Du

state: MA

address: 1 Blackfan Circle

country: USA

institute: Boston Children’s Hospital, Harvard Medical School

type: Expression profiling by high throughput sequencing

summary: we find METTL3 associates with polyribosomes and promotes translation. METTL3 depletion inhibits translation, and both wild-type and catalytically inactive METTL3 promote translation when tethered to the 3' untranslated region (UTR) of a reporter mRNA. Mechanistically, METTL3 enhances mRNA translation through an interaction with the translation initiation machinery.

overall_design: m6A seq in A549 and H1299 cells, RNA seq in METTL3 knockdown cells

first: R

last: Gregory

first: S

last: Lin


title: shRNA knockdown of the transcription factor NFYA in H322 and HCT116

city: MILANO

first: DILETTA

last: DOLFINI

state: MILANO

address: VIA CELORIA 26

department: DIPARTIMENTO DI BIOSCIENZE

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI MILANO

summary: The trimeric transcription factor -TF- NF-Y binds to the CCAAT box, an element enriched in promoters of genes overexpressed in tumors. The NF-YC subunit was recently identified as an oncogene in choroid plexus carcinomas. Previous studies on the NF-Y regulome identified the general term metabolism as significantly enriched. We dissect here in detail the targeting of metabolic genes by integrating analysis of NF-Y genomic binding and profilings after inactivation of NF-Y subunits in different cell types. NF-Y comprehensively controls de novo biosynthetic pathways of lipids, teaming up with the master SREBPs regulators. It activates glycolytic genes, but, surprisingly, is neutral, or represses mitochondrial respiratory genes. NF-Y targets the SOCG (Serine, One Carbon, Glycine) and Glutamine pathways, as well as genes involved in the biosynthesis of polyamines and purines. Within the different pathways, cancer-driving nodes are under NF-Y positive control. Altogether, these data delineate a coherent strategy to promote expression of metabolic genes fuelling anaerobic energy production, and other anabolic pathways commonly altered in cancer cells. Scrambled control (shSCM) and NF-YA pLKO.1-shRNAs were designed by Sigma-Aldrich. The puromycin resistance cassette was replaced with an EGFP cassette. Viral production and transduction were carried out as previously described (Benatti et al. 2011). H322 and HCT116 were transduced with shSC or shNF-YA viral supernatants, in triplicates and cells collected after 72 hours. RNA was prepared according to Affymetrix standard protocol and hybridized to Hu-Gene 2.0 expression arrays.

overall_design: H322 and HCT116 were transduced with shSC and shNF-YA and harvest after 72 hours

first: D

last: Dolfini

first: P

last: Benatti

first: C

last: Imbriano

last: Mantovani


title: The extracellular interactome of the human Adenovirus family reveals diverse strategies for immunomodulation

status: Public on Mar 04 2016

city: South San Francisco

first: Nadia

last: Martinez

state: California

address: 470 East Grand Avenue

institute: Genentech

summary:
Using a large collection of diverse viral immunomodulatory proteins, and comprehensive human protein microarray libraries, we identify more than 51 virus-host interactions that suggest new immunoregulatory strategies.
Full description of this study will be detailed in Martinez-Martin et al., Nat Communications, under review (this information will be updated when manuscript is accepted).

overall_design: In this study, we systematically analyze a diverse set of human adenovirus immunomodulatory E3 proteins against an unbiased large-scale protein microarray that consists of more than 1,500 secreted or single-transmembrane-containing human proteins. Here we identify and fully validate 51 novel virus-host interactions that suggest previously unidentified strategies of extracellular immunomodulation.

last: Martinez-Martin

first: Lino

middle: C

last: Gonzalez


title: Complementary Expression of Immunoglobulin Superfamily Ligands and Receptors in Synaptic Pairs in the Drosophila Visual System

status: Public on Dec 17 2015

city: Los Angeles

first: Lawrence

middle: S.

last: Zipursky

address: Howard Hughes Medical Institu675 Charles E. Young Drive South 5-784 MacDonald Research Laboratories

institute: University of California, Los Angeles

summary:
Purpose: Information processing in the brain relies on precise patterns of synapses between neurons. The molecular mechanisms by which this specificity is achieved remains elusive.  In the medulla of the Drosophila visual system, different neurons form synaptic connections in different layers.
Methods: we developed methods to purify seven neuronal cell types (R7, R8 and L1-L5 neurons) using Fluorescence Activated Cell Sorting.
Results: we show that neurons with different synaptic specificities express unique combinations of mRNAs encoding hundreds of cell surface and secreted proteins. Using RNA sequencing and MiMIC-based protein tagging, we demonstrate that 21 paralogs of the Dpr family, a subclass of Immunoglobulin (Ig)-domain containing proteins, are expressed in unique combinations in homologous neurons with different layer-specific synaptic connections.  Dpr interacting proteins (DIPs), comprising nine paralogs of another subclass of Ig superfamily proteins, are expressed in a complementary layer-specific fashion in a subset of synaptic partners. We propose that pairs of Dpr/DIP paralogs contribute to layer-specific patterns of synaptic connectivity.
Conclusions: This complexity is mirrored by the complexity of the cell surface and secreted molecules expressed by each of the R cell and lamina neurons profiled in this study. How this complexity contributes to specificity remains elusive, but the convergence of improved histological, genetic and molecular tools promises to provide important insights into the molecular recognition strategies controlling synaptic specificity.

overall_design: We chose 7 time points for RNA-seq analysis of R cells during pupal development corresponding to 24, 35, 40, 45, 53, 65 and 96 hrs after pupal formation (APF).

middle: S

first: Tan

last: Liming

first: Kelvin

last: Zhang


title: The porcine microRNA transcriptome response to porcine cytomegalovirus infection

status: Public on Dec 19 2015

city: Ya’an

first: Xiao

last: Liu

state: Sichuan Province

address: 46# Xinkang Road

department: College of Veterinary Medicine

country: China

institute: Sichuan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Porcine cytomegalovirus (PCMV; genus Cytomegalovirus, subfamily Betaherpesvirinae, family Herpesviridae) is an immunosuppressive virus that mainly inhibits the immune function of T lymphocytes and macrophages, which has caused great distress to the farming industry.
In this study, we obtained the miRNA expression profiles of PCMV-infected and control porcine macrophages, PCMV-infected and control porcine tissues via high-throughput sequencing. The comprehensive analysis of miRNA profiles showed that 306 miRNA database annotated and 295 novel pig-encoded miRNAs were detected.  Gene Ontology (GO) analysis of the target genes of miRNAs in PCMV infected porcine macrophages showed that the differentially expressed miRNAs are mainly involved in immune and metabolic process.   This is the first report of the miRNA transcriptome in PCMV infected porcine macrophages and PCMV infected tissues and the analysis of the miRNA regulatory mechanism during PCMV infection. Further research into the regulatory mechanisms of miRNAs during immunosuppressive viral infections will contribute to the treatment and prevention of immunosuppressive viruses.

overall_design: miRNA expression profiling of PCMV-infected and control porcine macrophages; PCMV-infected and control porcine tissues via high-throughput sequencing.


title: Novel critical insights into the mechanism of cell-based therapy after myocardial infarction

status: Public on Dec 31 2015

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

summary:
Cell transplantation therapy is considered a novel and promising strategy in regenerative medicine. Recent studies point out that paracrine effects and inflammation induced by transplanted cells are key factors for the improvement of myocardial function. The present study aims at differentiating paracrine effects from inflammatory reactions after cell transplantation. Therefore, in vitro induced apoptotic bodies were transplanted after myocardial infarction in a rat model. Eight weeks after transplantation, the functional results showed no improvement in left ventricular function. Histological analysis revealed no significant differences in the amount of infiltrated cells and collagen content did not differ among the four groups, which sustains the functional data. Surprisingly, angiogenesis increased in groups with apoptotic bodies derived from HUVEC and endothelial progenitor cells, but not from fibroblasts. A complex genetic analysis of apoptotic bodies indicated that miRNAs could be responsible for these changes. In conclusion, our study demonstrates both that neoangiogenesis alone is not sufficient to improve function and that inflammation is critical for scar remodeling and improvement of the heart function after cell therapy.
Given what we have learned about microRNAs, we hypthesized that the molecular mechanisms of angiogenesis induction could involve apoptotic bodies exerting paracrine angiogenic effects. Using GeneChip miRNA 3.0 Array, microRNAs were analysed in apoptotic bodies from endothelial progenitor cells (EPCs), human umbilical veno-endothelial cells (HUVECs), and fibroblasts.

overall_design: From human EPCs, human dermal fibroblasts, and HUVECs, apoptotic bodies were isolated after treatment with cycloheximide in hypoxia for 24 hours.

first: B

first: E

last: Liehn


title: Tumor-initiating cell-specific miR-1246 and miR-1290 converge to promote non-small cell lung cancer progression [Illumina]

status: Public on Nov 30 2015

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: The tumor-initiating cell (TIC) model accounts for the phenotypic and functional heterogeneity among cancer cells found within human cancers. MicroRNAs (miRNAs) are key regulatory molecules frequently aberrantly expressed in tumors, and may play important roles in contributing towards tumor heterogeneity and TIC behavior. More recent efforts have focused on miRNAs for diagnosis and as targets for novel therapies. In this study, we identified the miRNAs, miR-1246 and miR-1290, which are crucial for the function of TICs, thereby driving cancer progression in human non-small cell lung cancer (NSCLC). These miRNAs are restricted to patient-derived tumorspheres and CD166+ primary tumor cells, both enriched for TICs. Loss of either miRNA impacted the tumorigenic potential of TICs and their ability to metastasize. Interestingly, longitudinal analyses of serum miR-1246 and miR-1290 levels correlated circulating levels of either miRNA to the clinical response seen in lung cancer patients to epidermal growth factor receptor (EGFR) tyrosine kinase inhibition, chemotherapy and radiotherapy. Functionally, direct inhibition of miR-1246 or miR-1290 with locked nucleic acid (LNA) administered systemically, could arrest the growth of established patient-derived tumors xenografted in immunocompromised mice, thus indicating these miRNAs are clinically useful as biomarkers for tracking disease progression and as therapeutic targets.

overall_design: The Illumina Whole Human Genome Microarray Kit was used to identify genes downregulated in NuLi-1 overexpressing miR-1246 or miR-1290 and genes upregulated in A549 knockdowning mir-1246 or miR-1290.

first: Wen

middle: M

last: Chin

first: He

first: Min

middle: E

last: Nga

first: Declan

last: Lunny

first: Edwin

middle: K

last: Lim

first: Li

middle: L

last: Sun

first: Yin

middle: H

last: Pang

first: Yi

middle: N

last: Leow

first: Shanneen

last: Malusay

first: Priscila

middle: X

first: Jeravan

last: Lee

first: Benedict

last: Tan

first: Ng

last: Shyh-Chang

first: Elaine

first: Bee

last: Tai

first: Ross

last: Soo

first: Wai

last: Tam

first: Bing

last: LIM


title: Tumor-initiating cell-specific miR-1246 and miR-1290 converge to promote non-small cell lung cancer progression

first: Henry

type:
Non-coding RNA profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Expression data from MCF7 breast epithelial cells in normoxic and hypoxic conditions.

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

summary:
G9a is able to silence gene expression in hypoxic condition by increasing histone H3K9me2. We have identified a set of genes that are negatively regulated by G9a in hypoxia-dependent manner.
In this dataset, we include the expression data obtained from MCF7 breast epithelial cells that have been transfected with control (WT) or G9a shRNAs (KD) and exposed to either normoxia or hypoxia. These data are used to obtain 829 genes that are differentially expressed in response to hypoxia, and 205 genes that are sentisive to G9a level.

overall_design: 4 samples were analysed. We generated comparisons between WT and KD in normoxic as well as hypoxic condition. Genes differentially expressed in hypoxic condition were selected followed by selection of genes that lose this differential expression upon G9a knockdown.

first: Jason

first: Jinhyuk

last: Bhin

first: Sung

last: Baek

first: Daehee

last: Hwang


title: Drosophila HNF4 promotes glucose-stimulated insulin secretion and increased mitochondrial function in adults

status: Public on Nov 28 2015

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah, School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing


title: Drosophila HNF4 promotes glucose-stimulated insulin secretion and increased mitochondrial function in adults [ChIP-seq]

summary: Although mutations in the nuclear receptor HNF4A were identified as the cause of Maturity Onset Diabetes of the Young 1 (MODY1) nearly two decades ago, the mechanisms by which HNF4A regulates glucose homeostasis remain unclear. Here we report that loss of Drosophila HNF4 recapitulates hallmark symptoms of MODY1, including adult-onset hyperglycemia, glucose intolerance and impaired glucose-stimulated insulin secretion (GSIS). These defects are linked to an unexpected role for dHNF4 within mitochondria to directly regulate mtDNA transcription, while also promoting the expression of nuclear genes involved in oxidative phosphorylation (OXPHOS) and Hex-C, a homolog of the MODY2 gene Glucokinase. dHNF4 is required in the fat body and insulin-producing cells to maintain glucose homeostasis by supporting a developmental switch toward OXPHOS and GSIS at the transition to adulthood. These findings establish an animal model for MODY1 and define a developmental reprogramming of metabolism to support the energetic needs of the mature animal.

overall_design: Examination of genomic loci bound by endogenous dHNF4 protein in adult Drosophila

first: William

last: Barry


title: miRNA expression in inguinal adipose tissues

status: Public on Nov 07 2015

city: Nanjing

first: Xiaohong

last: jiang

state: Jiangsu

address: Xianlin Road

institute: Nanjing university

summary:
We asked if miRNAs are involved in PRDM16 protein expression. Thus microarray was employed with inguinal adipose tissues from contol, fasted and cold exposure C57BL/6J male mice
In this dataset, we include all the miRNA expression data obtained from dissected mouse inguinal adipose tissues from control, fasted and cold exposure mice.

overall_design: Generally, microRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. Based on previous results, we asked whether miRNAs are involved in the regulation of PRDM16 in ingWAT in response to different physiological stimuli. We therefore performed miRNA microarray analysis using ingWAT from the cold-exposed mice, the fasted mice and the control mice. Given that cold exposure increased the level of PRDM16 protein whereas fasting decreased its expression, miRNAs that have expression patterns opposite to that of PRDM16 were selected。

last: Jiang

first: Hanying

last: Ding


title: Tumor-initiating cell-specific miR-1246 and miR-1290 converge to promote non-small cell lung cancer progression [Agilent]

last: Yang

overall_design: We first identified miRNAs which are enriched in CD166+ TICs relative to CD166- non-TICs (n = 3 patients), and intersected these with miRNAs enriched in patient-derived tumorspheres relative to normal NHBE and SAEC. This method, utilizing two distinct manners of purifying for TICs, enabled us to robustly identify a conserved set of miRNAs which were exclusive to TICs but not non-TICs.

first: Wen

last: Zhang

first: Tan

last: Chin

first: He

first: Min

last: Nga

first: Declan

last: Lunny

first: Edwin

last: Lim

first: Li

last: Sun

first: Yin

last: Pang

first: Yi

last: Leow

first: Shanneen

last: Malusay

first: Priscila

first: Jeravan

first: Benedict


title: Mitochondrial contagion induced by Parkin deficiency in Drosophila hearts and its containment by suppressing mitofusin; germline Parkin knockout mouse hearts.

status: Public on Oct 31 2015

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Dysfunctional Parkin-mediated mitophagic culling of senescent or damaged mitochondria is a major pathological process underlying Parkinson disease and a potential genetic mechanism of cardiomyopathy. Despite epidemiological associations between Parkinson disease and heart failure, the role of Parkin and mitophagic quality control in maintaining normal cardiac homeostasis is poorly understood.We used germline mutants and cardiac-specific RNA interference to interrogate Parkin regulation of cardiomyocyte mitochondria and examine functional crosstalk between mitophagy and mitochondrial dynamics in Drosophila heart tubes.

overall_design:
5 wild-type mouse hearts; 4 germline Parkin knockout mouse hearts

Please note that the mouse cardiac examples were an adjunct to the Drosophila studies that comprised most of the associated publication.  However, mRNA-sequencing was only performed on the mouse samples, not the Drosophila heart tubes.

first: Yun

last: Chen

first: Gerald

middle: W

last: Dorn


status: Public on Jan 27 2016

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

summary: Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs) from three independent tonsil donors.

overall_design: Sequencing libraries were prepared from FACS sorted individual ILCs with the Smart-Seq2 protocol  (Picelli et al. Nature Methods 2013)

first: Simone

last: Picelli

first: Marianne

last: Forkel

first: Jenny

last: Mjosberg

first: Rickard

last: Sandberg


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human early hematopoietic differentiation after LGR4 depletion and R-spondin2 treatment

status: Public on Aug 16 2018

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to identify differential genes and signaling pathways after LGR4 depletion and R-spondin2 treatment through comparing thel transcriptome profilings in hESC samples collected from day2 of co-cutlure hematopoietic differentiation.
Methods: mRNA profiles of hESC samples collected from day 2 of hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Treatment of R-spondin2 promotes up-regulation of mesoderm associated genes and LGR4 depletion severely down-reguletes mesoderm associated genes.

first: Yv

last: Wang


title: A single-cell survey of the small intestinal epithelium

status: Public on Nov 06 2017

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: To understand the diversity of cellular states within mouse intestinal epithelial tissue, we obtained whole intestines from wild type mice, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq.

overall_design:
To understand normal tissue homeostasis, untreated cells were profiled, while to investiage the impact of enteric pathogens on epithelial cells, mice infected with both Salmonella Enterica and the parasitic worm H. polygyrus were profiled using both 3'-droplet-based and full length plate-based single-cell RNAseq. RANKL-mediated differentiation of organoid cultures were used to sequence the rare intestinal M cell, these were then compared to M cells obtained from the in vivo follicle associated epithelium (FAE).

Please note that the FAE_UMIcounts.txt file has been updated on May 7th 2020.

first: Moshe

last: Biton

first: Noga

last: Rogel

first: Rebecca

last: Herbst

first: Karthik

last: Shekhar

first: Christopher

last: Smillie

first: Grace

last: Burgin

first: Toni

last: Delorey

first: Michael

middle: R

last: Howitt

first: Yarden

last: Katz

first: Itay

last: Tirosh

first: Semir

last: Beyaz

first: Danielle

last: Dionne

first: Mei

last: Zhang

first: Raktima

last: Raychowdhury

first: Wendy

last: Garret

first: Hai

last: Shi

first: Orit

last: Rozenblatt-Rosen

first: Omer

last: Yilmaz

first: Ramnik

last: Xavier

first: Aviv

last: Regev


title: Whole blood gene expression from overweight women supplemented with quercetin or placebo

status: Public on Nov 02 2015

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

institute: DUKE-NUS Graduate Medical School

summary: Flavonoids and fish oils have anti-inflammatory and immune-modulating influences. The purpose of the study was to determine if a mixed flavonoid-fish oil supplement (Q-Mix; 1000 mg quercetin, 400 mg isoquercetin, 120 mg EGCG from green tea extract, 220 mg EPA and 180 mg DHA from fish oil, 1000 mg vitamin C, 40 mg niacinamide, and 800 ug folic acid) would reduce inflammatory and oxidative stress markers and alter genomic profiles in overweight women. Women were assigned using a randomized double-blinded placebo-controlled trial to Q-Mix or placebo groups. Overnight fasted blood samples were collected and subjected to RNA expression analysis on Affymetrix Hugene ST1_1 arrays.

overall_design: Randomized, double-blinded, placebo controlled study.Subjects were randomized to either mixed flavonoid-fish oil supplement group (Q-Mix; 1000 mg quercetin, 400 mg isoquercetin, 120 mg EGCG from green tea extract, 400 mg n3-PUFAs (220 mg EPA and 180 mg DHA) from fish oil, 1000 mg vitamin C, 40 mg niacinamide, and 800 µg folic acid) or placebo (n=29 samples, including pre- and post-treatment samples in the Q-Mix and placebo arms).The placebo did not contain quercetin, vitamin C, and niacin. Subjects were instructed to ingest two soft chew supplements twice daily (upon awakening, and between 6:00-7:00 pm) for 70 days. A three-day food record was used to assess typical energy and nutrient intake. No restrictions were placed on diet, supplement usage or medications with the exception that subjects agreed to avoid any non-steroidal anti-inflammatory drugs and dietary supplements that influence inflammation or oxidative stress.

first: Lynn

last: Cialdella-Kam

first: Sujoy

last: Ghosh

first: David

last: Nieman


title: RNA-seq  analysis of Bacteroides xylanisolvens XB1AT grown on pectin or xylan

status: Public on Oct 28 2015

city: Urbana

first: Christopher

middle: John

last: Fields

state: IL

address: 1206 W. Gregory Dr.

department: Carver Biotechnology Center

institute: University of Illinois Urbana-Champaign

summary: Dietary fiber degradation is a key function of the human gut microbiota.  The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide.

overall_design: Simple two-way comparisons between pectin or xylan sources (treatment) and glucose or xylose (control), collected during mid- and late-log phase.  Three replicates per condition.

first: Bryan

last: White

first: Pascale

last: Mosoni

first: Jordane

last: Despres


title: Role of IL-2 inducible T cell kinase (ITK) and Bruton's tyrosine kinase (BTK) in mast cell response to lipopolysaccharide (LPS)

status: Public on Nov 23 2015

city: Ithaca

first: Weishan

last: Huang

state: New York

address: C5 121, Cornell U.

department: Microbiology & Immunology

institute: Cornell University

summary: Mast cells are indispensable for LPS-induced septic hypothermia, in which TNF-α plays an essential role to initiate sepsis. Tec family non-receptor tyrosine kinases ITK and BTK regulate mast cell-derived TNF-α in response to allergic antigen, but their role in LPS-induced TNF-α production by mast cells and related pathology is unclear. We sought to investigate the role(s) of ITK and BTK in mast cell response in septic condition. We found that the absence of ITK and BTK leads to enhanced TNF-α production by bone marrow-derived mast cells (BMMC). Itk-/-Btk-/- mast cells exhibit hyperactive preformed and LPS-induced TNF-α production, along with enhanced expression of other related genes such as NF-κB targeted genes, compared to WT cells.

overall_design: Bone marrow cells from 8-week old WT,  Itk-/-, Btk-/-  and Itk-/-Btk-/- (double knockout: DKO) C57Bl/6 mice were cultured in murine Interleukin-3/Stem cell factor (IL-3/SCF) supplemented medium for 5 weeks to derive mast cells. WT, Itk-/-, Btk-/-  and DKO bone marrow-derived mast cells (BMMC) were factor starved in medium without IL-3/SCF for 12 hours, followed by treatment with PBS (control) or 100 ng/ml LPS for 1 hour. Triplicates of each group were subjected to mouse whole genome genechip microarray analysis. Replicates were randomized on different chips to avoid systematic error.

first: Avery

last: August


title: CGH: Transgenic soybeans and controls

status: Public on Sep 30 2015

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

type: Genome variation profiling by genome tiling array

summary:
Transgenic soybean lines were compared to their parental lines by CGH to catalog structurally variant (e.g. deletion and duplication) regions among these genotypes.
The CGH comparisons reveal reveal putative deletions and duplications among the 5 lines.

overall_design: Transgenic soybean lines were compared to their parent lines ('Bert-MN-01' or 'Wm82-ISU-01', depending on the transgenic plant). Each transgenic line was represented by a single individual T1 generation plant. The reported values show the log2 ratio of the normalized transgenic line hybridization signals (Cy3) over the normalized parent line hybridization signal (Cy5).

first: Adrian

middle: O

last: Stec

first: Justin

last: Anderson


title: Drosophila HNF4 promotes glucose-stimulated insulin secretion and increased mitochondrial function in adults [RNA-seq]

first: Carl

last: Thummel

overall_design:
Examination of poly(A)-selected transcripts in dHNF4 mutant adult males versus genetically matched controls.
Control samples - transheterozygotes from precise excisions of P-elements EP2449 and KG08976 (EP/KG) in the w1118 genetic background
dHNF4 mutants -  dHNF4∆17/∆33  (transheterozygotes derived from imprecise excisions of P-elements EP2449 and KG08976, respectively)

first: William

last: Barry


title: Adult-induced cardiac-specific knockout of Parkin provokes minimal transcriptional effect

first: Scot

middle: J

last: Matkovich

summary: Adult mice bearing homozygous floxed Parkin alleles (PMIDs 15249681, 21376232; T M Dawson), with or without the Myh6-driven MERCreMER transgene, were administered tamoxifen at 6-10 wks of age.  Tissues were obtained from euthanized mice 9-10 weeks after tamoxifen induction.

overall_design: 6 floxed, non-Cre (noninduced) mouse hearts; 6 floxed, MERCreMer, adult-induced, Parkin knockout mouse hearts

first: Moshi

last: Song

first: Gerald

last: Dorn


title: Generation of induced pluripotent stem cells from human mesenchymal stem cells of parotid gland origin

status: Public on Sep 15 2015

city: Beijing

first: Yang

last: Li

address: Xueyuan Road

department: cell biology department

institute: Peking University

summary: Transcriptome analysis between PMSCs and PMSC-iPSCs

overall_design: We compared the global gene expression between  PMSCs and PMSC-iPSCs using the Affymetrix Human U133 gene chip. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Xing

last: Yan


title: microRNAs involved in cardiac differentiation from human pluripotent stem cells

status: Public on Apr 06 2018

city: Belen de Escobar

first: Santiago

last: Miriuka

state: Buenos Aires

address: Ruta 9 Km 52.5

department: LIAN-CONICET

country: Argentina

institute: FLENI

summary: microRNAs are post transcriptional regulators involved in several biological processes. The main objective of this project is to identify all the microRNAs involved in the regulation of the cardiac differentiation from human pluripotent stem cells. The final goal is to understand RNA networks related to cardiac lineage commitment during human embryonic development.

overall_design: Human embryonic stem cells were differentiated towards mesoderm linage and cardiomyocytes. We performed small RNA sequencing using an Illumina platform of three different cells populations: human embryonic stem cells, an early mesoderm progenitor and a cardiac progenitor cells. Each population was studied in triplicate.

first: Ximena

last: Garate

first: Alejandro

last: La Greca


title: The requirement of leukemia inhibitory factor or epidermal growth factor for pre-implantation embryogenesis

status: Public on Sep 01 2015

city: Taichung

first: Jer-Yuh

last: Liu

address: Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

summary: In this study, we further verified the role of LIF by looking at gene expressions in morula stage embryos through DNA microarray. Our results showed that LIF knockdown affected 373 gene expressions, and after LIF supplementation we found that the epidermal growth factor (EGF) is most affected by LIF expression. In order to observe the correlation between LIF and EGF, the LIF knockdown embryos were supplemented with various growth factors including LIF, EGF, GM-CSF, TGF, and IGF II. Only LIF and EGF caused the rate of blastocyst development to recover from 52% of control significantly to 83% and 93%, respectively, and all of the parameters, such as the diameter of blastocysts, the numbers of blastomeres, and cells in ICM and TE, to mostly be restored. Moreover, EGF knockdown also impaired blastocyst development which was reversed by LIF or EGF supplementation. These data suggest that the two growth factors EGF and LIF can be compensatory to each other during early embryonic development, and one of them is necessary for sustaining the normal development of preimplantation embryos.

overall_design: Two-condition experiment, mouse embryos vs. LIF-deficiency mouse embryos at morula stage

first: En-Hui

last: Cheng

first: Maw-Sheng

last: Lee


title: Systems analysis of adaptive responses to MAP Kinase pathway blockade in BRAF mutant melanoma.

status: Public on Sep 16 2015

city: Charlottesville

first: Stefan

last: Bekiranov

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Fifty percent of cutaneous melanomas are driven by activated BRAFV600E, but tumors treated with RAF inhibitors, even when they respond dramatically, rapidly adapt and develop resistance. Thus, there is a pressing need to identify the major mechanisms of intrinsic and adaptive resistance and develop drug combinations that target these resistance mechanisms. In a combinatorial drug screen on a panel of 12 treatment-naïve BRAFV600E mutant melanoma cell lines of varying levels of resistance to MAPK pathway inhibition we identified the combination PLX4720, a targeted inhibitor of mutated BRaf, and lapatinib, an inhibitor of the ERBB family of receptor tyrosine kinases, as synergistically cytotoxic in the subset of cell lines that displayed the most resistance to PLX4720. To identify potential mechanisms of resistance to PLX4720 treatment and synergy with lapatinib treatment we performed a multi-platform functional genomics analysis to profile the genome as well as the transcriptional and proteomic responses of these cell lines to treatment with PLX4720. We found modest levels of resistance correlated with the zygosity of the BRAF V600E allele and RTK mutational status. Layered over base-line resistance was substantial upregulation of many ERBB pathway genes in response to BRaf inhibition, thus generating the vulnerability to combination with lapatinib. The transcriptional responses of ERBB pathway genes are associated with a number of transcription factors, including ETS2 and its associated cofactors that represent a convergent regulatory mechanism conferring synergistic drug susceptibility in the context of diverse mutational landscapes.

overall_design: 12 BRAF mutant melanomas and 4 melanomas with WT BRAF were exposed plx4720 treatment to evaluate their responses after 8 hours of treatment. 5 of the 12 BRAF mutant melanomas responses were also evaluated in response to the treatment of lapatinib alone, masitinib alone, the combination of lapatinib with plx4720, or the combination of masitinib with plx4720. All samples were run in at least triplicate.

first: Brian

last: Capaldo

first: Devin

last: Roller

first: Mark

last: Axelrod

first: Alex

middle: F

last: Koeppel

first: Emanuel

last: petricoin

first: Michael

last: Weber

first: AAaron

last: Mackey

first: Daniel

last: Gioeli


title: A novel function for the melanocortin 1 receptor: positive regulation of cell migration in human artery endothelial cells

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

institute: Centro Cardiologico Monzino IRCCS

summary: We hypothesize that human artery ECs express a functional melanocortin receptor and that its activation might play a role in EC migration. We demonstrated that primary HAOECs express a functional MC1R and that its engagement with melanocortins modulates specific gene expression patterns to accelerate HAOEC migration.

overall_design: Three independent time-course experiments of an in vitro directional cell migration assay of α-MSH-stimulated HAOECs were performed. RNA was collected at 0.5h, 3h, 6h and 12h from α-MSH-stimulated and control cells. Hybridization was performed in duplicate for each sample for a total of 48 samples.

first: Federica

last: Saporiti

first: Luca

last: Piacentini

first: Elisa

last: Bono

first: Mattia

last: Chiesa

middle: I


title: MYB/miR4863p/MAF/ axis in hematopoietic progenitor cell fate decision

status: Public on Aug 07 2015

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Fecal microbiota transplant rescues mice from sepsis

status: Public on Jul 30 2015

city: Chicago

first: John

middle: C

last: Alverdy

address: 5841 South Maryland Avenue

department: Surgery

institute: University of Chicago

summary:
The aim of this study was to test the hypothesis that replenishing the microbiota with a fecal microbiota transplant (FMT) can rescue a host from an advanced stage of sepsis.
We developed a clinically-relevant mouse model of lethal polymicrobial gut-derived sepsis in mice using a 4-member pathogen community (Candida albicans, Klebsiella oxytoca, Serratia marcescens, Enterococcus faecalis) isolated from a critically ill patient.
In order to mimic pre-operative surgical patient condition mice were exposed to food restriction and antibiotics. Approximately 18 hours prior to surgery food was removed from the cages and the mice were allowed only tap water.
Each mouse received an intramuscular Cefoxitin injection 30 minutes prior to the incision at a concentration of 25 mg/kg into the left thigh. Mice were then subjected to a midline laparotomy, 30% hepatectomy of the left lateral lobe of the liver and a direct cecal inoculation of 200 µL of the four pathogen community.
On postoperative day one, the mice were administered rectal enema. Mice were given either 1 ml of fecal microbiota transplant (FMT) or an autoclaved control (AC). This was again repeated on postoperative day two.
Mice were then followed for mortality. Chow was restored to the cages on postoperative day two, approximately 45 hours after the operation.
The injection of fecal microbiota transplant by enema significantly protected mice survival, reversed the composition of gut microflora and down-regulated the host inflammatory response.

overall_design: The cecum, left lobe of the liver, and spleen were isolated from mice for microarray processing with three or more replicates for six expermental conditions:  non-treated control, SAHC POD1, SAHC.AC POD2, SAHC.FMT POD2, SAHC.AC POD7, SAHC.FMT POD7

first: Jennifer

last: Defazio

first: Scott

last: Christley

first: Nikolai

last: Khodarev

first: Sangman

last: Kim

first: Bana

last: Jabri

first: Olga

last: Zaborina


title: Angiopoietin-like 4 Increases Pulmonary Vascular Leakiness and Lung Tissue Damage during Influenza Pneumonia

status: Public on Jun 20 2015

city: Singapore

first: Liang

last: Li

address: 60 Nanyang Drive

institute: Nanyang Technological University

summary:
cANGPTL4 has been shown by our experiments to be associated to influenza-induced pneumonia pathogenesis. cANGPTL4 was produced in abundance during infection and inflammation and showed involvment in regulating blood vessel permeability. By using anti-cANGPTL4 monoclonal antibody, we want to see the overall effect of this antibody treatment, to evaluate the potential of anti-cANGPTL4 antibody as a possible treatment method for pneumonia, and also to gain more insight into the role of cANGPTL4 in infection and inflammation.
We used microarrays to detail the global impact of anti-cANGPTL4 antibody treatment to see the possible mechanism pathways involved, as well as to identify the possible side effects caused by anti-cANGPTL4 antibody treatment to evaluate its potential as a treatment method.

overall_design: Mouse lungs were harvested at different timepoints before and after antibody injection to see the changes caused by antibody injection as well as the overall trend during disease progression. To this end, we infected the mice and injected antibodies starting from day 13 post infection. We did the first harvest of lungs at day 12, before the antibody injection was started, to get a starting status to reflect the effect of antibody treatment. Samples harvested at day 14 post infection was analyzed to see the effect caused by antibody injection after 24 hours, and samples harvested at day 18 post infection was analyzed as the end point because our previous experiments showed significantly improved recovery at day 18 after antibody treatment.

first: Hyung

last: Choi


title: Acinetobacter oleivorans DR1: paraquat-treated and phenazine methosulfate-treated

status: Public on Jun 29 2015

city: Seoul

first: Jisun

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

institute: Korea university

summary: Transcriptional profiling of A. oleivorans DR1 cells in the presence of paraquat and phenazine methosulfate

overall_design: To identify genes involved in oxidative stress response in A. oleivorans DR1, cells were grown to exponential phase (OD600 ~0.4) and treated with paraquat (1 mM) and phenazine methosulfate (200 μM) over a period of 15 min. Total RNA was extracted using an RNeasy Mini kit (Qiagen, USA) following the manufacturer's instructions.

first: Woojun

last: Park


title: Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation [RNA-Seq]

status: Public on Jun 11 2015

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

summary:
Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain
Methods: Total RNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) from cultured neural stem cells derived from male mouse E14.5 brains either wild-type or null for Smchd1. 1 µg total RNA was used to generate sequencing libraries for whole transcriptome analysis with Illumina’s TruSeq RNA Sample Preparation Kit v2 as per standard protocols. Libraries were sequenced on HiSeq 2000 with Illumina TruSeq SBS Kit v3-HS reagents as either 100 bp single-end or paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.10.5) (Liao et al. 2013). Mapped reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014).

overall_design: Total RNA was extracted and purified from each cell line and their transcriptomes analyzed by RNA-Seq.


title: Gene expression analysis of rel knockout and dcpA knockout strains of Mycobacterium smegmatis MC2 155

status: Public on Jun 10 2015

city: Bangalore

first: Dipankar

last: Chatterji

state: Karnataka

address: Malleshwaram

department: Molecular Biphysics Unit

country: India

institute: Indian Institute of Science

summary: The experiment was carried out to study the effect of loss of (p)ppGpp or cyclic di-GMP on the gene expression pattern of Mycobacterium smegmatis MC2 155 strains. The cells were cultured in MB7H9 broth containing 0.2% glycerol and 0.05% Tween 80. The transcriptome analysis was performed using GeneSpring GX12 software. Fold changes were calculated with respect to the median expression of wild type replicates. The number of differentially expressed genes (p <0.1) in rel knockout were 417 whereas those in dcpA knockout were 149. Earlier studies had shown that rel knockout and dcpA knockout had shown lower levels of glycopeptidolipids and polar lipids in the cell wall. The microarray data also corraborates our current findings.

overall_design: Organism : Mycobacterium smegmatis, Agilent Custom Mycobacterium smegmatis  Gene Expression M.smegmatis_gxp_8X15K (AMADID: 029929)  designed  by Genotypic Technology Private Limited.

first: Kuldeepkumar

last: Gupta


title: Cancerous inhibitor of Protein Phosphatase 2A is a novel cell-autonomous regulator governing both T-and B-cell activation in vivo

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary: The generation of optimal immune response requires combined activation of both T- and B-cells. Here, we demonstrate that the cancerous inhibitor of protein phosphatase 2A (CIP2A) is a novel factor that governs activation of both T- and B-cells in vivo. Upon ovalbumin challenge, CIP2A-deficient (CIP2AHOZ) mice show impaired immune response. Furthermore, CIP2AHOZ mice had impaired clearance of Listeria Monocytogenesis (L.m.) infection, combined with decreased numbers of CD8+ T-cells and IFN-γ secretion. In an ovalbumin model of allergic asthma, CIP2AHOZ B-cells were impaired in IgE and IgG secretion, despite of normal Th2 differentiation and unaffected numbers of inflammatory cells or cytokines in bronchoalveolar lavage. Importantly, the cell-autonomous effect of CIP2A deficiency for both T- and B-cell activation was confirmed by in vitro assays. During the T-cell activation CIP2A, was shown to promote expression of ETS-1, whereas in B-cells CIP2A loss resulted in inhibition of MYC-mediated gene expression. Together these results identify CIP2A as a novel cell-autonomous regulator governing both T- and B-cell activation in vivo. They also identify CIP2AHOZ as a novel murine model for investigation of impaired immune response and allergic asthma.

overall_design: Total RNA obtained from 4 male mutant mice was compared to 4 wild type controls.

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Expression data of  CD117+ splenocytes from C57BL/6 WT and RasGRP4 KO mice upon LPS stimulation

status: Public on May 19 2015

city: Boston

first: Richard

middle: Leslie

last: Stevens

state: MA

address: 1 Jimmy Fund Way

department: Medicine

institute: Harvard Medical School

summary:
RasGRP4 is required for CD117+  DCs to optimally induce certain NK cell-dependent immune responses in vivo and in vitro in response to LPSRasGRP4 expressed in DCs played an important role on NK cell IFN-γ secretion .
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated or down-regulated  genes between the two  DCs from WT  and RasGRP4 mice respectively upon LPS stimulation.

overall_design: CD117+splenocytes were extracted from WT and RasGRP4 KO mice spleens aged 9-12 weeks  and plated in 6-well plates with 1ug/mL of LPS for 0h,6h,12h,24h and 48h repectively for  RNA extraction and hybridization on Affymetrix microarrays.  Time course.

first: Steven

last: Krilis

first: Saijun

last: Zhou

first: Miao

last: Qi

first: Jiancheng


title: Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation

type: Methylation profiling by high throughput sequencing


title: The role of aquaporin-3 (AQP3) in functions of alveolar macrophage (AM) during ovalbumin (OVA)-induced asthma

status: Public on Apr 30 2015

city: Kyoto

first: Kohei

last: Ikezoe

address: 54 Shogoin-kawaharacho, Sakyo-ku

department: Department of Respiratory Medicine

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: We compared the gene expression profiles of AMs using microarray analysis between AMs from wild-type (WT) and AQP3-deficient (AQP3-/-) mice before and after OVA challenge

overall_design: RNA was extracted from AMs of WT and AQP3-/- mice before and after OVA challenge. We prepared 4-6 mice for each group and pooled their samples.

first: Toru

last: Oga


title: Genetic Engineering of Hematopoietic Stem Cells to Improve the Chance for Racial Minorities to Match with allogeneic unrelated Donors

status: Public on Mar 21 2015

city: Houston

first: Jianliang

last: Dai

address: 1400 Pressler St

institute: MD Anderson Cancer Center

summary: Mismatch of HLA adversely impacts the outcome of patients after allogeneic hematopoietic stem-cell transplantation (alloHSCT). This translates into the requirement to identify suitable HLA-matched donors which curtails the chances of recipients, especially those from a racial minority, to successfully undergo alloHSCT. We sought to broaden the existing pool of registered unrelated donors based on analysis that eliminating the expression of the HLA-A increases the chance for finding a donor matched at HLA-B, -C, and -DRB1 regardless of patients’ race. This was achieved using artificial zinc finger nucleases to eliminate expression of HLA-A alleles in HSC while demonstrating the ability of these engineered stem cells to reconstitute hematopoiesis. The loss of HLA-A expression decreases the need to recruit large number of donors to match with potential recipients and has particular impact for patients whose HLA repertoire is under-represented in the current donor pool to find an appropriate HLA-matched donor

overall_design: Total RNA obtained from Lineage negative CD34 positive hematopoietic stem cells (with or without ex vivo culture) isolated from umbilical cord blood.

first: Hiroki

last: Torikai

first: Tiejuan

last: Mi

first: Loren

last: Gragert

last: Maiers

first: Amer

last: Najjar

first: Sonny

last: Ang

first: Sourindra

last: Maiti

first: Kirsten

last: Switzer

first: Helen

last: Huls

first: Andreas

last: Reik

first: Edward

last: Reber

first: Michael

last: Holmes

first: Philip

middle: D

last: Gregory

middle: E

last: Champlin

first: Elizabeth

last: Shpall

first: Laurence

last: Cooper


title: Gene predictors of response to bendamustine in CLL cells

status: Public on May 15 2015

city: BARCELONA

first: DOLORS

last: COLOMER

address: VILLARROEL 170

country: Spain

institute: IDIBAPS-HOSPITAL CLINIC

summary:
Bendamustine is a commonly-used drug to treat CLL patients. Because drug-responses among the patients are heterogeneous, we wanted to find candidate genes to predict sensitivity to the compound
We used microarrays to find genes whose expression correlates with the in vitro induced-cytotoxcity by a 24-hour incubation with bendamustine 25 µm

overall_design: RNA was extracted from CD19+ tumoral cells from 38 PBMCs of CLL cases

first: Arnau

last: Montraveta

first: Eriong

last: Lee-Vergés

first: Dolors

last: Colomer


title: DNA methylation profiling of human THP-1 monocytes stimulated with arachidonic acid (AA) or oleic acid (OA) and controls

status: Public on Mar 27 2015

city: Leon

first: Silvio

last: Zaina

state: Gto

address: 20 de Enero no. 929

department: Department of Medical Sciences

country: Mexico

institute: University of Guanajuato

type: Methylation profiling by genome tiling array

summary: High-density array-based DNA methylation profiling of human THP-1 monocytes stimulated for 24 h with 1, 10 or 100uM AA, or the same concentrations of OA, and unstimulated controls. The Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 485,000 CpGs.

overall_design: Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Transcriptome profiling for genes transcriptionally regulated by Smchd1 in lymphoma cell lines.

status: Public on Mar 13 2015

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic modifier Smchd1 in mouse lymphoma cell lines.
Methods: Total RNA was extracted using QIAGEN RNeasy Minikit from sorted lymphoma cell lines derived from mice either wild-type or null for Smchd1. 1µg total RNA was used to generate sequencing libraries for whole transcriptome analysis with Illumina’s TruSeq RNA Sample Preparation Kit v2 as per standard protocols. Libraries were sequenced on HiSeq 2000 with Illumina TruSeq SBS Kit v3-HS reagents as either 100 bp single-end or paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.10.5) (Liao et al. 2013). Mapped reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014).

overall_design: Total RNA was extracted and purified from each cell line and their transcriptomes analysed by RNA-Seq.


title: Genome-wide expression analysis of ramie [Boehmeria nivea (L.) Gaudich] genes in response to ramie moth [Cocytodes coerulea Guenée] infestation

status: Public on Mar 04 2015

city: Changsha

first: Yongting

last: Yu

address: No 348, Xianjiahu West Rd.

institute: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science

summary: Comparative transcriptome analysis was performed to study differentially expressed genes (DEGs) between Cocytodes caerulea Guenée challenged (CH) and unchallenged (CK) leaves of ramie.We obtained 40.2 and 62.8 million reads for CH and CK libraries respectively.De novo assembling of these reads generated 26,759 and 29,988 unigenes respectively. After a integrate assembly for all data of these two libraries, a total of 46,533 unigenes with an average length of 845 bp were obtained.A total of 1179 genes were identified as DEGs, 657 and 1230 of them were up- and down- regulated respectively, in response to C.caerulea infestation.

overall_design: Leaf samples of Cocytodes caerulea infested (T2) and un-infested (T1) ramie were RNA-Seq sequenced to compare differented expressed genes.

first: Liangbin

last: Zeng


title: Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells

city: Montreal

first: Charles

last: St-Pierre

state: Quebec

address: 2950, Chemin de Polytechnique

department: Institute for Research in Immunology and Cancer

country: Canada

institute: Montreal University

summary: Promiscuous gene expression (pGE) of numerous self-antigens in thymic epithelial cells (TEC) enables the elimination of self-reactive T cells. The autoimmune regulator (Aire) is the only known molecular determinant driving pGE in the thymus but the existence of Aire-independent mechanisms has been inferred. Here, we analyzed the poly(A)+ transcriptome of TEC populations by RNA-sequencing (RNA-seq) in order to reveal differential features of Aire-induced vs. –independent pGE. We report an unanticipated effect of Aire deletion on the proliferation and differentiation of cortical TEC. Moreover, the RNA-seq data reveal the breath of Aire-induced and –independent pGE in medullary TEC (mTEC) subsets and the extent of thymic peripheral tissue representation. The results suggest that Aire-induced promiscuously expressed transcripts affect several functions with far reaching biological consequences in mTEC. High-throughput characterization of TEC transcriptomes will enable progress in understanding TEC biology and the establishment of self-tolerance.

overall_design: The mRNA profiles of cTEC, mTEClo and mTEChi from 6-8 week-old wild type (WT) and Aire-/- (KO) mice were generated by RNA-sequencing using Illumina HiSeq2000.

first: Claude

last: Perreault


title: Gene Expression analysis comparison between control and CC214-2 resistant GBM39 xenografts

status: Public on Nov 19 2014

city: La Jolla

first: Paul

last: Mischel

state: California

address: 9500 Gilman Drive, CMME, room 2021

department: Pathology

institute: LICR, UCSD

summary: Here we present gene expression analysis data on two vehicle treated and two CC214-2 (an mTOR kinase inhibitor) resistant GlioBlastoma Multiforme 39 (GBM39) xenografts, showing that the expressioin profiles of 88 genes are significantly different between the two groups.

overall_design:
GBM39 primary neurospheres were cultured in standard cancer stem cell medium conditions and then were injected in the mice flanks to generate xenograft tissues. Mice carrying CC214-2 resistant xenografts were treated with a solution of CC214-2 once every two days, by gavage, for 40 days.
Total RNA was extracted from GBM39 control and CC214-2 resistant xenografts using the Qiagen RNA micro kit protocol and analysed by Affymetrix U133 plus 2.0 array

middle: S

first: James

last: Heath


title: Identification of miR-21 targets in Jurkat cells by AGO2 immunoprecipitation

status: Public on Oct 15 2014

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

institute: Consiglio Nazionale delle Ricerche (CNR)

summary: In order to identify miR-21 targets by a biochemical high-throughput method, we immunopurified RISC Complex and associated mRNAs in both control and miR-21 overexpressing Jurkat cells.

overall_design: Following transduction of miR-21 encoding construct (or a cognate control vector) in Jurkat cells, we used microarray technology to profile Total RNA, AGO2 Immunopurified RNA and control IgG purified RNA.

first: Claudia

last: Carissimi

first: Nicoletta

last: Carucci

first: Silvia

last: Piconese

first: Gianluca

last: Azzalin

first: Emanuela

last: Cipolletta

first: Franca

last: Citarella

first: Vincenzo

last: Barnaba

first: Giuseppe

last: Macino

first: Valerio

last: Fulci


title: Expression profiling identifies deregulated pathways and top diagnostic markers in papillary thyroid carcinoma

status: Public on Nov 01 2014

city: Sao Paulo

first: mateus

middle: camargo

last: barros filho

state: SP

address: Tagua Street 440

country: Brazil

institute: AC Camargo Cancer Center

summary: Expression microarray was used to compare 57 PTC with a reference sample (pool of 9 adjacent normal thyroid tissue) and 4 PTC against 4 matched adjacent normal thyroid tissue. A quality control filter was applied based on Feature Extraction flags (empty spaces replacing values)

overall_design: Experiment condition, 61 PTC and 4 adjacent normal thyroid tissue samples obtained from total thyroidectomies were laleled with Cy3 and a pool of 9 adjacent normal thyroid tissue was labeled with Cy5. Samples Cy3 and Cy5 were mixed and hybridized at slide glasses Agilent 8x60k platform.

first: Mateus

last: Barros Filho

first: Fabio

middle: A

last: Marchi


title: Canine hemangiosarcoma tissues, monolayer- and sphere-cultured cells

status: Public on Dec 11 2014

city: Minneapolis

first: Jong-Hyuk

last: Kim

address: 425 East River Rd.

department: Dept of Veterinary Clinical Science

institute: University of Minnesota

summary: Cell lines and tumor tissues from canine hemangiosarcoma derived cell lines and hemangiosarcoma tissue samples

overall_design: Identification of three molecular and functional subtypes in canine hemangiosarcoma through gene expression profiling

first: Aaron

middle: L

last: Sarver


title: Profiling gene expression changes in the epidermis of embryonic murine Harlequin Ichthyosis skin

status: Public on Sep 16 2014

city: Clayton

first: Ian

last: Smyth

address: Wellington Rd

department: Department of Biochemistry & Molecular Biology, Department of Anatomy & Developmental Biology

institute: Monash University

summary: Gene expression analysis of the epidermis from Lexicon Genetics Abca12 knockout mouse model of Harlequin Ichthyosis compared with wild type embryos to search for pathways specifically altered in the condition. Results indicate a large immune and inflammatory response occurs in the sterile environment of the uterus.

overall_design: Total RNA isolated from E17.5 back skin epidermis from murine Harlequin Ichthyosis model compared with wild type embryos.

middle: M


title: Expression Profiling on Human Cell Lines with Different Acetylation Levels

status: Public on Aug 06 2014

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

institute: Università vita e Salute Ospedale San Raffaele

overall_design: Expression profiling of human cell lines with different acetylation levels.

first: Susanna

last: Chiocca


title: Platelet microRNA expression profiles of acute coronary syndrome patients with high and low platelet reactivity

status: Public on Jul 17 2014

city: Beijing

first: Jing

last: Wang

address: 167 Beilishi Road

department: State Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital, National Center for Cardiovascular Diseases

summary: To explore the diverse platelet microRNA (miRNA) expression between high platelet reactivity (HPR) and low platelet reactivity (LPR) patients with acute coronary syndromes (ACS), we enrolled a cohort of ACS patients and performed miRNA expression profiling of platelets from four HPR and four LPR patients using human miRNA microarray system. VerifyNow P2Y12 assay was applied to indentify HPR and LPR. Venous blood was drawn from the patients and was centrifuged to prepare platelets. Among the candidate differentially expressed miRNAs, miR-15b expression was further confirmed to be lower in platelets of 22 HPR patients than 17 LPR by quantitative reverse-transcription polymerase chain reaction (RT-qPCR).

overall_design: We enrolled a consecutive cohort of 290 ACS patients and assessed the platelet reactivity using VerifyNow P2Y12 assay. In this study, HPR was defined as ≥300 platelet reactivity unit (PRU) while LPR <170 PRU. miRNA microarray analysis was performed in platelets of four HPR and four LPR patients with ACS.


title: Exon Array Data for Colerectal Tumor and Normal Samples

status: Public on Sep 01 2014

city: Riyadh

first: Sathish

last: Periyasamy

state: Select a State or Province

department: Bioinformatics

country: Saudi Arabia

institute: NGHA

summary:
Exon-Level and Gene-Level Expression analysis of Tumor and Normal Samples
The effect of somatic copy number alterations at the functional level can be analyzed by looking into the expression pattern of the affected genes. The task of identifying the ‘affected’ genes is facilitated by robust algorithms that carry out sensitive and confident localization of the targets of somatic copy number alterations in cancer. We had earlier identified 144 genes by GISTIC analysis that were potential targets of SCNAs. In this study we report our findings based on exon level analysis of these genes. Only a subset of these genes was found to have significant changes in expression levels. 8/24 genes were found to have fold change value >1.5 and 3 of them were reported as novel in their association with CRC. The splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumor samples. Causal network analysis was carried out to study the difference in patterns of target genes affected by transcription factors identified by the GISTIC analysis. LIMMA analysis was carried out to find differentially expressed genes and their functional significance was studied using ingenuity pathway analysis.

overall_design: We conducted a group-wise comparison of Tumor vs Normal samples obtained from cancer patients. Array data was processed using Expression Console and AltAnalyze

first: M

last: Aziz

first: S


title: Intrinsic differences between oral and skin keratinocytes

status: Public on Jun 15 2014

city: Chicago

first: Zarema

middle: H

last: Arbieva

address: 835 S. Wolcott A301

department: RRC

country: USA

institute: UIC

summary:
The morphology  and the behavior of skin and oral tissue keratinocytes are different. One significant dissimilarity between the two sites is the response to injury. Oral and skin keratinocytes have intrinsic differences  in the response to injury and such differences are reflected in gene expression profiles.
We used microarrays to investigate differences in global gene expression patterns between baseline skin and oral epithelium sheets without their underlying connective tissue.

overall_design: Paired skin and oral epithelium was separated from the dermis for RNA extraction and hybridization on Affymetrix microarrays.  Skin epidermal tissues were obtained from the tail of mice and oral epidermal tissues were obtained from the hard palate. Enzymatically isolated epithelium was used for analysis.

first: Anna

last: Turabelidze

first: Shujuan

last: Guo

first: Allison

middle: Y

last: Chung

first: Lin

last: Chen

first: Yang

last: Dai

first: Phillip

middle: T

last: Marucha

first: Luisa

last: DiPietro


title: Comparative analysis of D. shibae wild-type vs. ∆luxI1 supplemented with acetylated homoserine-lactones with different length of the side chain and modifications

status: Public on Apr 01 2014

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Comparison of a quorum sensing null mutant supplemented with AHLs with different length of the side chain and modifications with D. shibae wild-type in order to identify traits induced by distinct autoinducers in this organism.

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Loop-design, two to three biological replicates of D. shibae wild-type, ∆luxI1 and ∆luxI1 supplemented with 500 nM C18-HSL, C18en-HSL and C18dien-HSL at cultivation start. Samples were taken in mid-exponential growth phase at OD600 0.4

first: Diana

last: Patzelt

first: Viktoria

last: Michael

first: Irene

last: Wagner-Döbler

first: Jörn

last: Petersen


title: CGH: NAM parent lines vs. Wm82-ISU-01

status: Public on Mar 30 2014

city: Saint Paul

first: Robert

last: Stupar

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

summary:
Soybean nested association mapping (NAM) parent lines were compared by CGH to catalog structurally variant (e.g. deletion and duplication) regions among these genotypes.
The CGH comparisons reveal reveal putative deletions and duplications among the 41 lines.

overall_design: NAM parent lines were compared through a common reference, Wm82-ISU-01 (this is a sub-line isolated from the cultivar Williams 82 stock).  Each NAM parent line was represented by a single individual plant.  The reported values show the log2 ratio of the normalized NAM parent line hybridization signals (Cy3) over the normalized Wm82-ISU-01 hybridization signal (Cy5).

first: Adrian

middle: O

last: Stec

first: Justin

last: Anderson


title: Pro-inflammatory stimulation of human skin-derived precursor cells modulates several of their immunology-related pathways.

status: Public on Mar 03 2014

city: Brussels

first: Joery

last: De Kock

address: Laarbeeklaan 103

department: In Vitro Toxicology and Dermato-Cosmetology

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

summary:
Human skin-derived precursor cells (hSKP) are a stem cell population that represents key candidates for cell based-therapy. Inflammation, however, is often present in situations where cellular replacement therapy is required. These inflammatory conditions, and more specifically the presence of the cytokine interferon (IFN)-γ, might result in an increase of MHC class II antigens in hSKP-derived grafts and facilitate their rejection.
We used microarray analyses to confirm the activated status of the pro-inflammatory condition, induced by exposure to a cocktail of pro-inflammatory cytokines (IL-1β, IFN-γ, TNFα and IFN-α). Consequently, we investigated the modulation by inflammation of canonical pathways related to immunology in hSKP.

overall_design: hSKP obtained from 3 different donors (passage 4) were cultivated in the presence or absence of the pro-inflammatory cocktail. Control and pro-inflammatory stimulated samples were collected 18h after treatment.

first: Philip

last: Meuleman

first: Gordana

last: Raicevic

first: Robim

last: Rodrigues

first: Steven

last: Branson

first: Kesavan

last: Meganathan

first: Veerle

last: De Boe

first: Agapios

last: Sachinidis

first: Geert

last: Leroux-Roels

first: Tamara

last: Vanhaecke

first: Laurence

last: Lagneaux

first: Vera

last: Rogiers

first: Mehdi

last: Najar


title: Gene expression from normal and Msi2 KO mouse LSK cells

status: Public on Jan 05 2014

city: New York

first: Yuheng

last: Lu

state: NY

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

summary: Hematopoietic stem and progenitor cells (Lineagelo ScaI+ c-Kit+) were sorted 4 weeks post pIpC injection. RNA was extracted using TRIZOL and RNEASY RNA extraction kit. RNA was then amplified using NUGEN Pico amplification kit, fragmented and hybridized on Mouse Expression Array 430 2.0. Signal normalization was performed by RMA method. Data were analyzed using GSEA across the complete list of genes ranked by signal-to-noise ratio.

overall_design: Samples came from bone marrow of 4 normal mice and 4 mice with conditional Msi2 knockout.

first: Michael

middle: G

last: Kharas


title: Copy number variation comparison between control and CC214-2 resistant GBM39 xenografts

status: Public on Dec 06 2013

first: Paul

last: Mischel

summary:
Here we present genome-wide copy number variation data on two vehicle treated and two CC214-2 (an mTOR kinase inhibitor) resistant GlioBlastoma Multiforme 39 (GBM39) xenografts,
showing the absence of significant differences between the two groups, demonstrating that resistance to CC214-2 is due to adaptation rather than gene mutations.

overall_design: The genomic DNA extracted from the 4 xenografts samples was analysed with genome-wide Affymetrix SNP6.0 array

first: James

middle: R

last: Heath


title: Microarray analyses of ESAM positive cells in the CD34(+) CD38(-) fraction of collagenase-treated bones

status: Public on Dec 05 2014

city: Suita

first: Tomohiko

last: Ishibashi

state: Osaka

address: C9, 2-2, Yamadaoka

department: Department of Hematology and Oncology

institute: Osaka University Graduate School of Medicine

summary: We previously identified endothelial cell-selective adhesion molecule (ESAM) as a novel functional marker of hematopoietic stem cells (HSCs) in mice. To examine ESAM expression in human, we analyzed diverse HSC sources using flow cytometry. From mononuclear cells of collagenase-treated human hip bones, we obtained two ESAM positive populations in CD34(+) CD38(-) fraction, referred to as ESAM(High) and ESAM(Bright). Then we conducted microarray analyses comparing gene expression signatures between these two populations.

overall_design: Trabecular tissues of the femora were treated with collagenase IV and DNase. Mononuclear cells were collected, and CD34(+) CD38(-) ESAM(High) or ESAM(Bright) cells were sorted.

first: Michiko

last: Ichii

first: Takafumi

last: Yokota


title: Pulmonary toxicity and global gene expression changes in response to sub-chronic inhalation exposure to crystalline silica in rats

status: Public on Jul 01 2014

city: Morgantown

first: Christina

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

summary: Occupational exposure to crystalline silica results in serious health effects, most notably, silicosis and cancer. A proper understanding of the mechanism(s) underlying the initiation and progression of silica-induced pulmonary toxicity is critical for the intervention and/or prevention of the adverse health effects associated with crystalline silica exposure. Rats were exposed to crystalline silica by inhalation at a concentration of 15 mg/m3, 6 hours/day, 5 days/week for 3, 6 or 12 weeks. At the end of each exposure time point, toxicity and global gene expression changes were determined in the lungs. In general, silica exposure resulted in pulmonary toxicity that was dependent on the duration of silica exposure. A significant and silica exposure time-dependent increase in lactate dehydrogenase activity and accumulation of alveolar macrophages and infiltrating neutrophils in the bronchoalveolar lavage fluid suggested crystalline silica-induced pulmonary toxicity in the rats. Histological changes indicative of pulmonary toxicity were detectable only in the lungs of rats that were exposed to silica for 6- or 12-weeks. Minimal, sub-acute pulmonary inflammation consisting mainly of macrophage accumulation and infiltration of neutrophils was seen in 2 out of 8 rats in the 6-week silica exposure group. Chronic active inflammation, type II pneumocyte hyperplasia, and fibrosis were detected following 12-weeks of silica exposure in all rat lungs. In addition, crystalline silica was visible in the lungs of the rats belonging to the 12-week exposure group. A significant increase in the number of neutrophils seen in the blood indicated silica-induced systemic inflammation in the rats. Microarray analysis of the global gene expression profiles of the rat lungs detected significant differential expression (FDR p <0.05 and fold change >1.5) of 38, 77 and 99 genes in the rats exposed to silica for 3-, 6- and 12-weeks, respectively, compared to the time-matched controls. Bioinformatics analysis of the differentially expressed genes identified significant enrichment of functions, networks and pathways related to inflammation, cancer, oxidative stress, fibrosis and tissue remodeling in the lungs of the silica exposed rats. Collectively, the results of our study provided insights into the molecular mechanisms underlying pulmonary toxicity following sub-chronic exposure to silica in rats.

overall_design: 36 samples were analyzed in this experiment. 6 rats were exposed to crystalline silica by inhalation 15 mg/m3, 6 hours/day, 5 days, 3 weeks. 6 rats were exposed to crystalline silica by inhalation 15 mg/m3, 6 hours/day, 5 days, 6 weeks.   6 rats were exposed to crystalline silica by inhalation 15 mg/m3, 6 hours/day, 5 days, 12 weeks.  18 rats served as controls (6 for each 3 week, 6 week, and 12 week exposure) and were exposed to air during treatment times. Lung gene expression profiling was performed using RNA isolated from rat lung samples.

first: Rajendran

last: Sellamuthu

first: Jenny

last: Roberts

first: Shih-Houng

last: Young

first: Diana

last: Richardson

first: Walter

last: McKinney

first: Bean

last: Chen

first: David

last: Frazer

first: Ja

middle: K

last: Gu

last: Kashon

first: Pius

last: Joseph


title: Expression microarray analysis of human pancreatic islets reveals CD59 function

status: Public on Mar 02 2014

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

institute: Lund University

summary: Pancreatic islets are central in type 2-diabetes development, which coincides with increased activity of innate immunity. Intriguingly, human pancreatic islets express many complement genes. The most highly expressed gene was the complement inhibitor CD59 that is GPI anchored to the cell membrane, which unexpectedly was found in high amounts intracellularly in beta cells. Silencing of CD59 strongly suppressed insulin secretion. Importantly, this suppression was unrelated to established CD59 functions, but rather depletion of intracellular CD59. Imaging experiments identified a distal site of inhibition in the exocytotic pathway, but prior to emptying of the insulin granules. Proximity Ligation Assays pin-pointed the mechanism to impaired turnover of exocytosis-regulating SNARE-proteins and CD59 was detected in complex with VAMP2 and syntaxin. CD59 was downregulated by 24-h glucose incubations in human islets, rat cell lines and in islets from three rodent diabetes models.

overall_design: Islets from cadaver donors were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChip® Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.

first: Leif

last: Groop


title: Transcriptional profiling of 53 tissue samples from germ-free and conventionally raised mice

status: Public on Jan 31 2014

city: Gothenburg

first: Erik

last: Larsson

address: Bruna stråket 16

department: Wallenberg Laboratory

institute: University of Gothenburg

summary:
Whole-transcriptome survey of gene expression differences between germ-free (GF) and conventionally raised (CONV-R) mice.
To assess the role of toll-like receptor signalling, both wild-type and Myd88 -/- mice were used.

overall_design: Three different tissues were harvested from 20 mice (5 WT CONV-R, 5 Myd88 -/- CONV-R, 4 WT GF, 6 Myd88 -/- GF) and expression profiles were determines using the Affymetrix Mouse Gene 1.0ST platform.

first: E

first: F

last: Bäckhed

first: C

last: Reigstad


title: Analysis of sex differences in DNA methylation in human pancreatic islets

status: Public on Oct 24 2014

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

summary: Epigenetic factors regulate tissue-specific expression and X-chromosome inactivation. Previous studies have identified epigenetic differences between sexes in some human tissues. However, it is unclear whether epigenetic modifications contribute to sex-specific differences in insulin secretion and metabolism. In this study, we investigated the impact of sex on the genome-wide DNA methylation pattern in human pancreatic islets from 53 males and 34 females, and related the methylome to changes in expression and insulin secretion.

overall_design: 53 male and 34 female human pancreatic islet samples. Normally methylated, non-methylated and fully methylated human DNA samples were included as controls

first: Elin

last: Hall

first: Petr

last: Volkov

first: Tasnim

last: Dayeh

first: Jonathan

last: Esguerra

first: Sofia

last: Salö

first: Lena

last: Eliasson

first: Tina

last: Rönn

first: Karl

last: Bacos


title: High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [MeDIP-seq]

first: Tao

last: Cai

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

country: China

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

summary: Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. Therefore, it becomes indispensable to exploit other reliable molecular markers for evaluating the quality of iPS cells accurately. In the present study, we successfully utilize the sequential reprogramming approach and produce all-iPS mice to six generations using iPS cell lines derived from different cell lineages which contain the same proviral integration in the genome. By comparing the global gene expression and epigenetic modifications of both “tetra-on” and corresponding “tetra-off” iPS cell lines established from either mesenchymal or hematopoietic lineages through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4m2, H3K4me3 and H3K27me3) and DNA methylation, very few differences are detected among all the iPS cell lines investigated. However, we find that two imprinted genes, disruption of which correlate with the reduced pluripotency of iPS cells. Therefore, our data not only provide the first demonstration that producing of all-iPS mice to six generations is feasible, but reveal that two imprinted regions can be served as pluripotency markers of iPS cells

overall_design: Examination of DNA methylation in 13 cell types

first: Gang

last: Chang

first: Shuai

last: Gao

first: Jianhui

last: Tian

first: Shaorong


title: High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells

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

overall_design: Refer to individual Series


title: miRNA expression profile (miEP) of myb-silenced CD34+ HPCs

status: Public on Aug 07 2015

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
The transcription factor cMyb plays a key role in human primary CD34+ hematopoietic progenitor cells (HPCs) lineage choice, by enhancing erythropoiesis at the expense of megakaryopoiesis. We previously demonstrated that cMyb affects erythroid versus megakaryocyte lineage decision in part by transactivating KLF1 and LMO2 expression. To further unravel the molecular mechanisms through which cmyb affects lineage fate decision, we profiled the miRNA and mRNA changes in myb-silenced CD34+ HPCs. mRNA and miRNA expression for each sample were profiled by Affymetrix GeneAtlas U219 strip array and Exiqon Human miRNome PCR Panel, respectively. miRNA/mRNA data were integrated by Ingenuity Pathway Analysis.
The integrative analysis of miRNA/mRNA expression changes upon c-myb silencing in human CD34+ HPCs highlighted a set of 19 miRNA with 150 anticorrelated putative target mRNAs. Among the miRNAs downregulated in myb-silenced progenitors with the highest number of predicted target mRNAs, we selected hsa-miR-486-3p based on the in vitro effects of its overexpression on HPCs commitment. Indeed, morphological and flow cytometric analyses after liquid culture showed that hsa-miR-486-3p overexpression in HPCs enhanced erythroid and granulocyte differentiation while restraining megakaryocyte and macrophage differentiation. Moreover, collagen-based clonogenic assay demonstrated a strong impairement megakaryocyte commitment upon hsa-miR-486-3p overexpression in CD34+ cells. Gene expression profiling of hsa-miR-486-3p overexpressing CD34+ cells enabled us to identify a set of 8 genes downregulated and computationally predicted, putative hsa-miR-486-3p targets. Among them, we selected c-maf transcript as upregulated upon myb silencing. Worth of note, c-maf silencing in CD34+ progenitor cells was able to reverse the affects of myb silencing on erythroid versus megakaryocyte lineage choice.  Integrative miRNA/mRNA analysis highlighted a set of miRNAs and anticorrelated putative target mRNAs modulated upon myb silencing, therefore potential players in myb-driven HPCs lineage choice. Among them, we demonstrated the hsa-miR-486-3p/c-maf pair as partially contributing to the effects of myb on HPCs commitment. Therefore, our data collectively identified myb-driven hsa-miR-486-3p upregulation and subsequent c-maf downregulation as a new molecular mechanism through which cMyb favours erythropoiesis while restraining megakaryopoiesis.

overall_design: RNA from CD34+ HPCs transfected with c-myb-targeting/non targeting control (NegCTR) synthetic siRNAs was collected 24 hours post-Nucleofection for a set of 5 independent experiments.

first: Elisa

last: Bianchi

first: Jenny

last: Bulgarelli

first: Giorgia

last: Sacchi

first: Samantha

last: Ruberti

first: Ruggiero

last: Norfo

first: Sebastiano

last: Rontauroli

first: Valentina

last: Pennucci

first: Roberta

last: Zini

first: Simona

last: Salati

first: Zelia

last: Prudente

first: Sergio

last: Ferrari


title: Ecotype specific nitrogen responses in the Arabidopsis root

status: Public on Sep 01 2013

first: Kenneth

middle: David

last: Birnbaum

address: 12 Waverly Place

department: Biology

institute: New York University

summary:
Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity.  In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies.
We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.

overall_design:
The whole experiment was carried out in triplicate with 42 chips in total (14 experiments).  The nitrogen response in seven Arabidopsis thaliana ecotype (Col0, Kas2, NFA8, SQ8, TAMM27, Ts5, Var2-1) whole roots was assayed using Affymetrix microarrays.  Seedlings were grown hydroponically in low nitrogen for 12 days, then 5mM KNO3 was used as a nitrogen treatment for 2 hours with 5mM KCl used as a control treatment for the same length of time.  At the end of the treatment time roots were harvested and flash-frozen in liquid nitrogen for subsequent RNA extraction.
For *Probe_Elements_Removed* file descriptions, please see the Sample records' "Data processing" annotations.

first: Gloria

last: Coruzzi

first: Miriam

last: Gifford

first: Manpreet

last: Katari


title: High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [ChIP-seq]

first: Tao

last: Cai

overall_design: Examination of 3 different histone modifications in 13 cell types

first: Gang

last: Chang

first: Shuai

last: Gao

first: Jianhui

last: Tian

first: Shaorong


title: Expression data from injected mice overexpressing TFEB specifically in liver

status: Public on Apr 20 2013

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary: In order to identify the effects of transcription factor EB (TFEB) overexpression on the liver transcriptome, we performed Affymetrix GeneChip hybridization experiments on injected mice overexpressing TFEB specifically in the liver.

overall_design: For the analysis of the injected mice overexpressing TFEB, total RNA was extracted from the liver of three mice. RNA extracted from the liver of 3 not-injected mice was used as a control.


title: Transcriptomes of transgenic rice expressing a constitutively active phytochrome OsPHYB-Y283H (OsYHB) allele

status: Public on Jul 01 2013

city: Davis

first: Wei

last: Hu

state: CA

address: One Shields Ave.

department: Department of Molecular and Cellular Biology

institute: Univ of California at Davis

summary: The present study quantifies the transcriptomes of wild-type and transgenic Ubi::OsYHB rice seedlings (in the genetic background of Oryza sativa ssp. japonica CV Nipponbare) grown in the dark or under continous red light (Rc, at 50 µmol m-2 s-1) conditions.

overall_design:
WT (Nipponbare cultivar; Nip) and Ubi::OsYHB/Nip transgenic seedlings were grown at 28°C for 5 days in darkness or under continuous red light at 50 µmol m-2 s-1 (Rc50). Seedlings were harvested in subjective morning, immediately frozen in liquid nitrogen and strored at -80°C until RNA extraction.
The expression of OsYHB is driven by the maize Ubiquitin promoter.
Two biological replicates for each treatment. Two independent, genetically single-insertion, homozygous Ubi::OsYHB/Nip lines (#1 and # 9, with determined 41- and 23-fold overexpression levels of OsYHB in comparison to the wild-type control, respectively) were used.
GeneChip 3' IVT Express Kit (Affymetrix) was used to synthesize and label aRNA.

first: J

middle: C

last: Lagarias


title: Xist exploits three-dimensional chromosome architecture to spread across the X-chromosome

status: Public on May 30 2013

city: Stanford

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

summary: Many large noncoding RNAs (lncRNAs) regulate chromatin, but the mechanisms by which they localize to genomic targets remain unexplored. Here we investigate the localization mechanisms of Xist during X-chromosome inactivation (XCI), a paradigm of lncRNA-mediated chromatin regulation. During the maintenance of XCI, Xist binds broadly across the X-chromosome.  During initiation of XCI, Xist initially transfers to distal regions across the X-chromosome that are not defined by specific sequences. Instead, Xist identifies these regions by exploiting the three-dimensional conformation of the X-chromosome. Xist initially accumulates on the periphery of actively transcribed regions and requires its silencing domain to spread across active regions. This suggests a model where Xist coats the entire X-chromosome by searching in three dimensions, modifying chromosome structure, and spreading to newly accessible locations.

overall_design: We examined the genomic localization of the Xist lncRNA using RNA Antisense Purification (RAP) in multiple cell contexts: 1) differentiated female cells (MLFs);  2) a time-course of Xist localization in male embryonic stem (ES) cells where the endogenous Xist promoter is replaced by a tet-inducible one (pSM33); 3) a time-course of Xist localization in differentiating female ES cells (F1 2-1); and 4) wild-type (delXF6) and A-repeat deletion (delSXC9) Xist transgenes incorporated into the Hprt locus under the control of a tet-inducible promoter.

first: Amy

last: Pandya-Jones

first: Patrick

last: McDonel

first: Alexander

last: Shishkin

first: Klara

last: Sirokman

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