title: Comparison of the functional microRNA expression in immune cell subsets of neonates and adults

status: Public on Nov 16 2016

city: Kaohsiung

first: Yu

middle: Hong

last: Ren

address: No.123, Ta-Pei Road, Niao-Sung district

institute: Kaohsiung Chang Gung Memorial Hospital

summary: Diversity of biological molecules in newborn and adult immune cells contributes to differences in cell function and atopic properties. Micro RNAs (miRNAs) are reported involve in the regulation of immune system. Therefore, determining the miRNA expression profile of leukocyte sub-populations is important for understanding immune system regulation. In order to explore the unique microRNA profiling that contribute to altered immune in neonates, we comprehensively analyzed the functional miRNA signatures of eight leukocyte subsets (polymorphonuclear cells, monocytes, CD4+ T cells, CD8+ T cells, natural killer cells, B cells, plasmacytoid dendritic cells (pDCs), and myeloid dendritic cells (mDCs)) from both neonatal and adult umbilical cord and peripheral blood samples, respectively. We observed distinct miRNA profiles between adult and neonatal blood leukocyte subsets, including unique miRNA signatures for each cell lineage. Leukocyte miRNA signatures were altered after stimulation. Adult peripheral leukocytes had higher let-7b-5p expression levels compared to neonatal cord leukocytes across multiple subsets, irrespective of stimulation. Transfecting neonatal monocytes with a let-7b-5p mimic resulted in a reduction of LPS-induced IL-6 and TNF-a production, while transfection of a let-7b-5p inhibitor into adult monocytes enhanced IL-6 and TNF-a production. With this functional approach, we provide intact differential microRNA expression profiling of specific immune cell subsets between neonates and adults. These studies serve as a basis to further understand the altered immune response observed in neonates and advance the development of therapeutic strategies

overall_design: we set out to comprehensively analyze the miRNA expression signatures of eight leukocyte subsets (polymorphonuclear cells (PMNs), monocytes, CD4+ T cells, CD8+ T cells natural killer (NK) cells, B cells, pDCs, and myeloid dendritic cells (mDCs)) between neonatal and adult samples.

first: Hong-Ren

last: Yu

first: Te-Yao

last: Hsu

first: Hsin-Chun

last: Huang

first: Ho-Chang

last: Kuo

first: Sung-Chou

last: Li

first: Kuender

last: Yang

first: Kai-Sheng

last: Hsieh


title: Infection with Enterovirus 71 induces modulation of the microRNA profile of the mouse brain

status: Public on Oct 23 2016

city: Beijing

first: Xiaoxia

address: 20 Dongda Street, Fengtai District

country: China

institute: Institute of Disease Control and Prevention, Academy of Military Medical Sciences

summary: To further understand the molecular pathogenesis of Enterovirus 71 infection, we profiled cellular microRNAs of brain tissue from suckling Kunming mice infected with EV71 and uninfected mice as comparison.

overall_design: Suckling mice infected with EV71 and mice brains were harvested on three and five days post infection. Three of each were chosen for microRNAs detection and three uninfected mice on the same time.

first: Shaofu

last: Qiu

first: Hongbin

last: Song


title: Nono, a novel bivalent domain factor, regulates Erk signaling and mouse embryonic stem cell pluripotency

status: Public on Oct 18 2016

city: Shanghai

first: Li

last: Wenjing

address: DongAn Road 130, Mingdao Building Room 509, Shanghai 200032, P.R.China

department: Institutes of Biomedical Sciences

institute: Fudan University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Nono, a novel bivalent domain factor, regulates Erk signaling and mouse embryonic stem cell pluripotency [RNA-Seq]

summary: Here we report that Nono instead functions as a chromatin regulator cooperating with Erk to regulate mESC pluripotency. We demonstrate that Nono loss leads to robust self-renewing mESCs with enhanced expression of Nanog and Klf4, epigenome and transcriptome re-patterning to a “ground-like state” with global reduction of H3K27me3 and DNA methylation resembling the Erk inhibitor PD03 treated mESCs and 2i (both GSK and Erk kinase inhibitors)-induced “ground state”. Mechanistically, Nono and Erk co-bind at a subset of development-related, bivalent genes. Ablation of Nono compromises Erk activation and RNA polymerase II C-terminal Domain serine 5 phosphorylation, and while inactivation of Erk evicts Nono from chromatin, revealing reciprocal regulation. Furthermore, Nono loss results in a compromised activation of its target bivalent genes upon differentiation and the differentiation itself. These findings reveal an unanticipated role of Nono in collaborating with Erk signaling to regulate the integrity of bivalent domain and mESC pluripotency.

overall_design: mRNA-seq of parental and Nono-KO mES cells

first: Chun

last: Ma

first: Fei

last: Lan

first: Yang

last: Shi


title: Nono, a novel bivalent domain factor, regulates Erk signaling and mouse embryonic stem cell pluripotency [ChIP-Seq]

summary: Here we report that NONO, a nuclear para-speckle component, instead functions as a chromatin regulator in mESCs acting in the ERK signaling pathway to regulate the balance between ground state versus mESCs primed for differentiation. NONO loss increases a \u201cground-like\u201d population of mESCs favoring self-renewal and more resist to differentiation, partially mimicking the effects of 2i. Mechanistically, NONO and ERK mainly co-binds a subset of development related, bivalent genes. Importantly, NONO and ERK reciprocally regulate one another, i.e. NONO regulates ERK activation while ERK controls NONO chromatin association, forming a self-reinforcing feedback loop. Our findings thus reveal a cell intrinsic mechanism involving NONO and ERK, which impact the balance between self-renewal and differentiation, respectively.

overall_design: We examined Nono, H3K4me3, H3K27me3, PolIIS5P in mES cells, using Illumina HiSeq 2500.


title: Cry2 and Fbxl3 promote circadian destruction of c-Myc

status: Public on Oct 22 2016

city: La Jolla

first: Katja

last: Lamia

state: California

address: 10550 North Torrey Pines Road

country: USA

institute: The Scripps Research Institute

summary: Examination of gene expression changes caused by genetic deletion of Cry2 in MEFs with samples collected over a 24 hour time course after circadian synchronization

overall_design: Primary wildtype and Cry2-/- MEFs derived from littermate embryos were treated with dexamethasone to synchronize circadian rhythms. Samples were collected in quadruplicate every four hours for 24 hours.

first: Anne-Laure

last: Huber

first: Stephanie

middle: J

last: Papp

first: Emma

last: Henriksson

first: Sabine

middle: D

last: Jordan

first: Anna

last: Kriebs

first: Madelena

last: Nguyen

first: Martina

last: Wallace

first: Zhizhong

first: Christian

middle: M

last: Metallo

middle: A


title: Proteomics and transcriptomics of peripheral nerve tissue and cells unravel new aspects of the human Schwann cell repair phenotype

status: Public on Dec 01 2016

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

country: Austria

institute: Children's Cancer Research Institute

summary: The remarkable feature of Schwann cells (SCs) to transform into a repair phenotype turned the spotlight on this powerful cell type. SCs provide the regenerative environment for axonal re-growth after peripheral nerve injury (PNI) and play a vital role in differentiation of neuroblastic tumors into a benign subtype of neuroblastoma, a tumor originating from neural crest-derived neuroblasts. Hence, understanding their mode-of-action is of utmost interest for new approaches in regenerative medicine, but also for neuroblastoma therapy. However, literature on human SCs is scarce and it is unknown to which extent human SC cultures reflect the SC repair phenotype developing after PNI in patients. We performed high-resolution proteome profiling and RNA-sequencing on highly enriched human SC and fibroblast cultures, control and ex vivo degenerated nerve explants to identify novel molecules and functional processes active in repair SCs. In fact, we found cultured SCs and degenerated nerves to share a similar repair SC-associated expression signature, including the upregulation of JUN, as well as two prominent functions, i.e., myelin debris clearance and antigen presentation via MHCII. In addition to myelin degradation, cultured SCs were capable of actively taking up cell-extrinsic components in functional phagocytosis and co-cultivation assays. Moreover, in cultured SCs and degenerated nerve tissue MHCII was upregulated at the cellular level along with high expression of chemoattractants and co-inhibitory rather than -stimulatory molecules. These results demonstrate human SC cultures to execute an inherent program of nerve repair and support two novel repair SC functions, debris clearance via phagocytosis-related mechanisms and type II immune-regulation.

overall_design: mRNA of 27 samples were sequenced (50bp, single end) and analyzed. Biological replicates were performed.

first: Tamara

last: Weiss

last: Taschner-Mandl

first: Andrea

last: Bileck

first: Astrid

last: Slany

first: Florian

last: Kromp

last: Frech

first: Reinhard

last: Windhager

first: Hugo

last: Kitzinger

first: Chieh-Han

last: Tzou

first: Peter

middle: F

last: Ambros

first: Christopher

last: Gerner

first: Inge


title: Dynamic gene expression response to altered gravity in human T cells (sounding rocket flight)

status: Public on Aug 11 2017

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: We investigated differentially regulated genes in human Jurkat T lymphocytic cells in 20s and 5min microgravity and in hypergravity and compared expression profiles to identify potential gravity-regulated genes and adaptation processes.

overall_design: Human Jurkat T cells were exposed to altered gravity during a sounding rocket flight

middle: S

first: Swantje

last: Hauschild

first: Andreas

last: Huge

first: Svantje

last: Tauber

first: Beatrice

last: Lauber

first: Jennifer

last: Polzer

first: Katrin

last: Paulsen

first: Hartwin

last: Lier

first: Frank

last: Engelmann

first: Burkhard

last: Schmitz

last: Schütte

first: Liliana

middle: E

last: Layer

first: Oliver

last: Ullrich


title: Effects Of An Encapsulated Fruit And Vegetable Juice Concentrate On Obesity-Induced Systemic Inflammation

status: Public on Sep 29 2016

city: New Lambton

first: Evan

middle: James

last: Williams

state: NSW

address: 1 Kookaburra Crt

department: Respiratory

country: Australia

institute: The University of Newcastle, Australia

summary: Analysis of the effect of using a fruit and vegetable juice concentrate to reduce systemic inflammation in obesity. The hypothesis tested whether the presence of polyphenols in the fruit and vegetable juice concentrate could reduce the expression of systemic inflammatory genes in the blood of Obese patients with high levels of plasma CRP (≥3.0).  Results provide evidence that systemic inflammatory genes/ and or pathways may be modulated by the fruit and vegetable juice concentrate.

overall_design: Total RNA obtained from blood of 16 Obese individuals, with High plasma CRP (≥3.0), before and after 8 week intervention with fruit and vegetable juice concentrate.

first: Katherine

last: Baines

first: Bronwyn

last: Berthon

first: Lisa

middle: G

last: Wood


title: REGION-SPECIFIC NEURAL STEM CELL LINEAGES REVEALED BY SINGLE-CELL RNA-SEQ FROM HUMAN EMBRYONIC STEM CELLS [Smart-seq]

status: Public on Sep 30 2016

city: Seattle

first: Zizhen

last: yao

state: WA

department: MAT

institute: Allen Institute for Brain Science

summary: During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.      During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.     During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.

overall_design: The transcriptomes of 1846 single cells were profiled by SmartSeq2 at different timepoints throughout a 54-day differentiation protocol that converted H1 human embryonic stem cells to a variety of brain cell types.  Some cells were positively labeled by a expression of a barcoded viral transgene to help establish clonality (marked by an "SK").

last: Yao

first: John

middle: K

last: Mich

first: Sherman

last: Ku

first: Vilas

last: Menon

first: Anne-Rachel

last: Krostag

first: Refugio

last: Martinez

first: Joshua

last: Grimley

first: Yanling

last: Wang

first: Sharad

last: Ramanathan

first: Boaz

middle: P

last: Levi


title: Expression data from human adipose tissue-derived mesenchymal stem cells

status: Public on Sep 22 2016

first: 思

last: 陈

address: 22 Zhongguancun South Avenue, Haidian District

department: Prosthodontics

institute: Peking University School and Hospital of Stomatology

summary:
miR-375 play an important role in regulating the osteogenesis in human adipose tissue-derived mesenchymal stem cells, following specific genes are up-regulated or down-regulated.
We used microarrays to detail the global programme of gene expression underlying osteogenesis and identified distinct classes of up-regulated genes or down-regulated genes during this process.

overall_design:
Samples from human adipose tissue-derived mesenchymal stem cells transfected with pre-miR-375 or control vector on the 7 days of osteogenic induction were for RNA extraction and hybridization on Affymetrix microarrays.
The human adipose tissue-derived mesenchymal stem cells were obtained from ScienCell Company, and the catalog number is 7510


title: Gene expression profiling study by RNA-seq in PDX model based diffuse type gastric cancers.

status: Public on Nov 01 2018

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: We established PDX lines from diffuse type gastric cancers (DGCs). Using these cells, we carried out RNA-seq based transcriptome profiling using 15 stomach samples including three PDX lines (HGC-3, HGC-8, and HGC-20) and normal-looking surrounding tissues. Via comparative analysis between cells and tissues, we identified significant gene set associated with each cell and observed that genes involved in AKT signalling pathway were commonly associated with all PDX lines.

overall_design: RNA-seq data of 15 gastric samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using Hiseq-2500 (Illumina).

first: Jeong-Hwan

first: Dong-Hyuck

last: Bae

first: Yong-Sung

first: Hiroshi

last: Fukamachi


title: Gene expression analysis of hematological malignancies and healthy (non-)hematopoietic cell types

status: Public on Sep 01 2016

city: Leiden

first: Marieke

last: Griffioen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

summary:
Cellular immunotherapy has proven to be effective in the treatment of hematological cancers by donor lymphocyte infusion after allogeneic hematopoietic stem cell transplantation and more recently by targeted therapy with chimeric antigen or T-cell receptor-engineered T-cells. However, dependent on the tissue distribution of the antigens that are targeted, anti-tumor responses can be accompanied by undesired side effects. Therefore, detailed tissue distribution analysis is essential to estimate efficacy and toxicity of candidate targets for immunotherapy of hematological malignancies. In this study, we performed microarray gene expression analysis of hematological malignancies of different origins, healthy hematopoietic cells and various non-hematopoietic cell types from organs that are often targeted in detrimental immune responses after allogeneic stem cell transplantation leading to graft-versus-host disease. Non-hematopoietic cells were also cultured in the presence of IFN-γ to analyze gene expression under inflammatory circumstances. Gene expression was investigated by Illumina HT12.0 microarrays and quality control analysis was performed to confirm the cell-type origin and exclude contamination of non-hematopoietic cell samples with peripheral blood cells. Microarray data were validated by quantitative RT-PCR showing strong correlation between both platforms. Detailed gene expression profiles were generated for various minor histocompatibility antigens and B-cell surface antigens to illustrate the value of the microarray dataset to estimate efficacy and toxicity of candidate targets for immunotherapy. In conclusion, our microarray database provides a relevant platform to analyze and select candidate antigens with hematopoietic (lineage)-restricted expression as potential targets for immunotherapy of hematological cancers.
Microarray gene expression analysis was performed on hematological malignancies of different origins and their healthy hematopoietic counterparts as well as on healthy non-hematopoietic cell types from organs that are often targeted in Graft-versus-Host Disease (166 samples in total). Various non-hematopoietic cell types were cultured in the presence of IFN-γ or T-cell culture supernatant to allow gene expression analysis under inflammatory conditions. Malignant and healthy hematopoietic cells were isolated by flow cytometry based on expression of specific surface markers and healthy non-hematopoietic cell types were isolated or cultured from tissue biopsies or surgically removed specimen. Various non-hematopoietic cell types were in vitro cultured for 4 days in the presence of IFN-γ or T-cell culture supernatant to mimic inflammation. The dataset allows comparison of gene expression between hematological malignancies and healthy non-hematopoietic cell types to estimate efficacy and toxicity of immunotherapeutic targets for hematological malignancies.

overall_design: Total RNA was isolated from (malignant) hematopoietic cells isolated by flow cytometry based on expression of specific surface markers and from healthy non-hematopoietic cell types isolated or cultured from tissue biopsies or surgically removed specimen. From various non-hematopoietic cell types, total RNA was also isolated after 4 days of in vitro culture in the presence of IFN-γ or T-cell culture supernatant.

first: Margot

last: Pont


title: Characterization of melanoma cells exposed to melanoma-specific CD8+ T cells

status: Public on Aug 30 2016

city: Epalinges

first: Natalie

middle: J.

last: Neubert

address: Chemin des Boveresses 155

department: Ludwig Center for Cancer Research

institute: University of Lausanne

summary: Human low passage melanoma cell lines were compared after 24h culture alone or in presence of melanoma-specific CD8+ T cell clones

overall_design: Three melanoma cell lines where either left untreated or co-cultured with melanoma-specific CD8+ T cells for 24h

first: Daniel

last: Speiser

first: Silvia

last: Fuertes-Marraco

first: Charlotte

last: Soneson

first: David

last: Barras


title: Genome-wide mRNA sequencing of Panc-1 cells with or without fused IL-35 gene up-regulated

status: Public on Aug 02 2016

city: Tianjin

first: Chongbiao

last: Huang

address: Huanhu Xi Road

department: Senior Ward

institute: Tianjin Medical University Cancer Institute and Hospital

summary: To screen out the downstream genes of IL-35

overall_design: The two subunits of IL-35, EBI3 and P35, were fused together and transfected into Panc-1 cell via lentivirus. The sequence of the fused gene is identical to that of a commercial IL-35-overexpessed plasmid (InvivoGEN, pORF9-hIL35elasti). An empty vector was used as the control. The two cell lines were subjected to a genome-wide RNA sequencing.

first: Jihui

last: Hao

first: He

last: Ren


title: Human cervical cells HELP-tagging cytosine methylation data

status: Public on Aug 22 2016

city: Bronx

first: Neil

middle: Ari

last: Wijetunga

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: We pursued the hypothesis that epigenetic regulators of transcription are involved in both the development and the progression of HPV-associated CIN.  Using HELP-tagging, we performed the most comprehensive study to date of DNA methylation in HPV-associated cervical neoplasia, testing ~2 million loci throughout the human genome in biopsies from 78 HPV+ women, identifying changes starting in early CIN and maintained through carcinogenesis.  We identified loci at which DNA methylation is consistently altered, beginning early in the course of neoplastic disease and progressing with disease advancement.

overall_design: DNA methylation profiles for cervical biopsies of 19 normals, 20 CIN1, 16 CIN2/3, and 23 cervical cancers.

first: N.

first: John

last: Greally


title: Differentiation of Human Embryonic Stem Cells to Endothelial Progenitor Cells on Laminins in Defined and Xeno-free Systems

city: Singapore

first: Xiaoran

last: Chai

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: A major hurdle for in vitro culturing of primary endothelial cells (ECs) is that they readily de-differentiate, hampering their use for therapeutic applications. Human embryonic stem cells (hESCs) may provide an unlimited cell source; however, most current protocols deriving endothelial progenitor cells (EPCs) from hESCs use direct differentiation approaches albeit on undefined matrices, yet final yields are insufficient. We developed a method to culture monolayer hESCs on stem-cell niche laminin (LN) LN511 or LN521 matrix. Here, we report a chemically defined, xeno-free protocol for differentiation of hESCs to EPCs using LN521 as the main culture substrate. We could generate ~95% functional EPCs defined as VEGFR2+CD34+CD31+VE-Cadherin+. RNA sequencing analyses of hESCs, EPCs and primary HUVECs showed differentiation-related ECs expression signatures, regarding basement membrane composition, cell-matrix interactions, and changes in endothelial lineage markers. Our results may facilitate production of stable ECs for treatment of vascular diseases and in vitro cell modeling.

overall_design: 2 reference samples: hESC line H1 and human umbilical vein endothelial cells; 2 hESCs-derived endothelial progenitor cells from 2 different protocols

first: Mien

middle: T

last: Nguyen

first: Elena

last: Okina

first: Kok-Hian

last: Tan

first: Outi

last: Hovatta

first: Sujoy

last: Ghosh

first: Karl

last: Tryggvason


title: Human gastric cancer_Tumor samples_Paired normal samples_10 replicates

status: Public on Jul 26 2016

first: Jianjun

last: Zhang

state: Shanghai

address: No.639, Zhizaoju road

institute: Shanghai Jiaotong University

summary:
To identify the lncRNA profiles of gastric cancer samples, we performed microarray analysis using tumor samples and paired normal samples.
66 lncRNAs were statistically dysregulated more than 2-fold.

overall_design: The samples were divided into two groups, paired normal samples (negative control group_Rep10) and tumor samplea (Experiment group_Rep10).

first: Bin

last: Wang

first: Jun

last: Liu


title: hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells

status: Public on Jul 14 2016

city: Vancouver

first: Matthew

last: Lorincz

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: RNA-seq of hnRNP K-depleted mouse embryonic stem cells

overall_design: RNA-seq was performed on two biological replicates of control- or Hnrnpk siRNA-transfected TT2 ES cells, 72 h post transfection.

first: Peter

last: Thompson

first: Vered

last: Dulberg

first: Kyung-Mee

last: Moon

first: Leonard

last: Foster

first: Carol

last: Chen

first: Mohammad

last: Karimi


title: An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene

status: Public on Jul 07 2016

city: Majadahonda

first: Antonio

last: Martin-Galiano

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

country: Spain

institute: Instituto de Salud Carlos III

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

overall_design: Refer to individual Series


title: An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene [RNA-Seq]

summary: We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. Likewise, recovery of viability and DNA-supercoiling were observed when cells were treated with those SCN concentrations and the drug was removed. The main DNA topoisomerase gene affected was topA, whose transcription depended on the supercoiling level. A two stage global transcriptomic response with 8 µM seconeolitsine was detected. The early stage (5 and 15 min, 10% of the genome) represented a response induced by increased supercoiling. The second stage represented supercoiling recovery (30 min, 2.0% of the genome). Almost 25% of the early responsive genes formed clusters with coordinated transcriptional regulation. Twelve clusters were evident, with sizes of 6.7 to 31.4 Kb (9 to 22 responsive genes). Strikingly, clusters did not contradict those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using overlapping responses. This is the first study describing a global transcriptomic response triggered by an increase in DNA supercoiling in bacteria.

overall_design: Total RNA was extracted from S. pneumoniae R6 cultures during exponential growth and used for RNA-Seq. Two independent replicates per condition were performed.

first: María

last: Ferrándiz

first: Adela

last: de la Campa


title: REGION-SPECIFIC NEURAL STEM CELL LINEAGES REVEALED BY SINGLE-CELL RNA-SEQ FROM HUMAN EMBRYONIC STEM CELLS

first: Zizhen

last: yao

last: Yao

first: John

last: Mich

first: Sherman

last: Ku

first: Vilas

last: Menon

first: Anne-Rachel

last: Krostag

first: Refugio

last: Martinez

first: Joshua

last: Grimley

first: Yanling

first: Sharad

last: Ramanathan

first: Boaz

last: Levi


title: Transcriptome profiling of influenza virus-infected human bronchial epithelial cells

status: Public on Aug 24 2016

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: We report the whole genome sequencing of human bronchial cells infected with influenza A (PR/8/34) for 8 or 24 h.

overall_design: Examination influenza virus-specific human gene profiling at early or late stage of viral infection.

first: Eun-Young

last: Lee

first: Myung

middle: H


title: Integrative analysis of pathology, mRNA and microRNA in a polygenic diabetes model, NONcNZO10/LtJ mice

status: Public on Jun 30 2016

city: Edogawa-ku

first: Tsuyoshi

last: Hirata

state: Tokyo

address: 1-16-13, Kitakasai

department: Discovery Science and Technology Department

country: Japan

institute: DAIICHI SANKYO RD NOVARE CO., LTD

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

summary: The NONcNZO10/LtJ mouse is a polygenic model of type-2 diabetes (T2D)  that shows moderate obesity and diabetes, and is regarded as a good model reflective of the conditions of human T2D. In this study, we analyzed pathological changes of pancreases with the progress of time by using histopathology and gene expression analysis, including microRNA. A number of gene expression changes associated with decreased insulin secretion (possibly regulated by miR-29a/b) were observed, and zinc homeostasis (Slc30a8, Mt1 and Mt2) or glucose metabolism (Slc2a2) was suggested as being the candidate mechanism of pancreas failure in NONcNZO10/LtJ mice. These results demonstrate NONcNZO10/LtJ mice have a complex pathogenic mechanism of diabetes, and moreover, this fundamental information of NONcNZO10/LtJ mice would offer the opportunity for research and development of a novel antidiabetic drug.

platform_organism:
Mus musculus
synthetic construct

overall_design: To identify the diabetes related genes that changed expression during the development of T2D in NONcNZO10/LtJ mice, we analyzed gene expression profiles of 7-, 13-, and 22-week old NONcNZO10/LtJ mice using GeneChip Mouse Gene 2.0 ST Arrays. On the other hand, we compared gene expression profiles of 7-week old NONcNZO10/LtJ mice with 7-week old NON/ShiLtJ mice to investigate the differences of gene expression before developing T2D. Furthermore, to validate the hypothesis generated by the results of mRNA analysis, we identified differentially expressed microRNAs in 13- and 22-week compared with 7-week old NONcNZO10/LtJ mice using Affymetrix miRNA GeneChip 3.0 Arrays.

first: Tomomi

last: Yoshitomi

first: Minoru

last: Inoue

first: Yutaka

last: Iigo

first: Koij

last: Matsumoto

first: Kazuishi

last: Kubota

first: Akira

last: Shinagawa


title: Chromosomal abnormalities in hepatic cysts point to novel polycystic liver disease genes

city: The Hague

first: Edgar

last: Wills

address: Andrej Sacharowstraat 37

department: Gastroenterology & Hepatology

institute: RadboudUMC

type: Genome variation profiling by genome tiling array

summary:
Autosomal dominant polycystic liver disease (ADPLD) is caused by mutations in PRKCSH, SEC63, and LRP5, while autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1, and PKD2. Liver cyst development in these disorders is explained by somatic loss-of-heterozygosity (LOH) of the wild type allele in the developing cyst. We hypothesize that we can use this mechanism to identify novel disease genes that reside in LOH regions. In this study, we aim to map abnormal genomic regions using high-density SNP microarrays to find novel polycystic liver disease genes.
We collected 46 cysts from 23 patients with polycystic or sporadic hepatic cysts, and analyzed DNA from those cysts using high-resolution microarray (n=24) or Sanger sequencing (n=22).  We here focused on regions of homozygosity on the autosomes (>3.0Mb), and large CNVs (>1.0Mb).
We found frequent LOH in PRKCSH (22/29), and PKD1/PKD2 (2/3) cysts of patients with known heterozygous germline variants in the respective genes. In the total cohort, 12/23 patients harbored abnormalities outside of familiar areas. In individual ADPLD cases, we identified germline events: a 2q13 complex rearrangement resulting in BUB1 haploinsufficiency, a 47XXX karyotype, chromosome 9q copy number loss, and LOH on chromosome 3p. The latter region was overlapping with an LOH region identified in two other cysts.
Unique germline and somatic abnormalities occur frequently in and outside of known genes underlying cysts. Each liver cyst has a unique genetic makeup. LOH driver gene BUB1 may imply germline causes of genetic instability in PLD.

overall_design: 24 liver cysts from 23 patients

first: E

first: W

middle: R

last: Cnossen

first: J

last: Veltman

first: R

last: Woestenenk

first: M

last: Steehouwer

last: Salomon

last: te Morsche

last: Huch

middle: Y

last: Hehir-Kwa

last: Banning

last: Pfundt

last: Roepman

first: A

last: Hoischen

first: P

last: Drenth


title: Genome-wide analysis of long noncoding RNA and messager RNA expression in ApoE-deficient mice

status: Public on Jun 09 2016

city: Changsha

first: Mei-hua

last: Bao

state: Hunan

address: No. 1501, Leifeng Road

department: Anatomy, Histology and Embryology

institute: Changsha Medical University

summary: Atherosclerosis is a multifactorial chronic inflammatory disease with high prevalence and has become the first reason for death worldwide. Long non-coding RNAs (lncRNAs) are non-coding RNAs with a length of >200 bp. LncRNAs participate in many biological and pathological processes such as carcinogenesis, cardiovascular diseases. The present study was designed to investigate the lncRNA and mRNA expression in the aorta of diet-induced ApoE(-/-) mice using microarray analysis. The homozygous male apoE(-/-) mice were randomly divided into two groups, with 3 animals for each group. The normal diet group was fed with normal chow, while the treated group was fed with a high-fat, high-cholesterol diet containing 20% fat and 2.5% cholesterol. The treatment duration is 8-week. After treatment, the aorta of each mouse was taken, and the lncRNA and mRNAs profiles were detected using Agilent mouse lncRNA Microarray (4*180K, Design ID: 049801) which contains 51302 lncRNAs and 39430 mRNAs. As a result, a total of 354 differentially expressed lncRNAs, including 168 up-regulated and 186 down-regulated, were identified (≥2.0 folds). Simultaneously, we also identified 357 differentially expressed protein coding mRNAs from the same chip, including 211 up-regulated 146 down-regulated mRNAs. The present study identified a panel of dysregulated lncRNAs and mRNAs that may be potential biomarkers or drug targets and correlated with the pathogenesis of atherosclerosis.

overall_design: The homozygous male apoE(-/-) mice were randomly divided into two groups, with 3 animals for each group. The normal diet group was fed with normal chow, while the treated group were fed with a high-fat, high-cholesterol diet containing 20% fat and 2.5% cholesterol. The treatment duration is 8-week. After treatment, the aorta of each mouse was taken, and the lncRNA and mRNAs profiles were detected using Agilent mouse lncRNA Microarray (4*180K, Design ID: 049801) which contains 51302 lncRNAs and 39430 mRNAs.

first: Huai-qing

last: Luo

first: Li-hua

last: Chen

first: Liang

last: Tang

first: Ju

last: Xiang

first: Li-ping

last: Dong

first: Jie

last: Zeng

first: Guang-yi

last: Li

first: Jian-ming


title: Gene expression data from MDSC subsets, cell lines and tumor cells

status: Public on May 21 2016

city: Lyon

first: Anne-Pierre

last: Morel

state: Rhone-Alpes

address: 28, rue Laennec, Cheney D 2nd floor

country: France

institute: Cancer Research Center of Lyon

summary: We demonstrate that monocytic and granulocytic subsets of myeloid derived suppressor cells (mMDS, gMDSC) infiltrated in the primary tumor and distant organs with different time kinetics regulate spatiotemporal tumor plasticity. Using co-culture experiments and syngeneic mouse models, we provide evidence that tumor infiltrated mMDSCs facilitate tumor cell dissemination from the primary site by inducing EMT/CSC phenotype. In contrast, pulmonary gMDSC infiltrates support the metastatic growth by reverting EMT/CSC phenotype and in turn promote tumor cell proliferation. Furthermore, lung-derived gMDSCs isolated from tumor bearing animals significantly enhance metastatic growth of already disseminated tumor cells. A “metastatic gene signature” identified in aggressive murine tumors following co-culture with MDSC subsets predicts poor patient survival in majority of human solid tumors suggesting clinical implications of our studies.

overall_design: We utilized monocytic and granulocytic subsets of myeloid derived suppressor cells (mMDS, gMDSC) from the bone marrow , and infiltrated in the primary tumor and lungs to determine their gene expression profile. Using co-culture experiments we analyzed the mMDSC and gMDSC induced gene expression signature of the tumor cells

first: Hasan

last: Korkaya

first: Maria

last: Ouzounova

first: Eun

last: Lee


title: Effect of demeclocycline on brain tumor initiating cells

status: Public on May 18 2016

city: Calgary

first: Voon

middle: Wee

last: Yong

state: Alberta

address: 3330 Hospital drive NW

department: Clinical Neurosciences

institute: University of Calgary

summary: We have determined that demeclocycline reduces the growth of brain tumor initiating cells (BTICs).  Specifically, we sought to obtain insights into the mechanisms by which demeclocycline directly regulates BTIC growth.  Analysis of the array data identified several genes that were altered with demeclocycline treatment that could regulate BTIC growth.  The study provides the mechanistic basis for the regulation of BTIC growth with demeclocycline treatment.

overall_design: We subjected 3 BTIC lines to microarray analyses to identify genes involved in the regulation of BTIC growth by demeclocycline.  Three BTIC lines (BT012, BT025 and BT048) were treated with 10 µM demeclocycline for 6h.  One (1) control and 1 treatment (demeclocycline treated) sample was generated from each BTIC line.  Thus, a total of 6 RNA samples from 3 BTIC lines were obtained for microarray analysis.

first: V

middle: W

first: Y

first: S

last: Sarkar


title: Effects of MBTD1 on gene expression

status: Public on Apr 30 2016

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

summary:
The NuA4/TIP60 acetyltransferase complex is a key regulator of genome expression and stability. Here, we identified MBTD1 as a new stable subunit of the complex and gleaned intriguing insights into TIP60’s function. Harboring a histone reader domain for H4K20me1/2, MBTD1 allows TIP60 to associate with specific gene promoters and to promote the repair of DNA double strand breaks by homologous recombination.
Total RNA was analyzed on Illumina Human HT-12 V4.0 expression beadchip by McGill University and Genome Québec innovation Centre

overall_design: CRISPR/Cas9 technology was used to produce MBTD1 knockout cells in U2OS and to perform genome-wide expression analysis on three different clones compared to wild type cells.

first: Karine

last: Jacquet

first: Jacques

last: Côté


title: Investigation of the Fusarium virguliforme transcriptomes induced during infection of soybean roots suggests that enzymes with hydrolytic activities could play a major role in root necrosis

city: Ames

first: Madan

last: Bhattacharyya

state: IA

address: G 303 Agronomy Hall

department: Agronomy

institute: Iowa State University

summary: Sudden death syndrome (SDS) caused by the fungal pathogen, Fusarium virguliforme, is a major threat to soybean production in North America. There are two major components of this disease: (i) root necrosis and (ii) foliar SDS. Root symptoms consist of root necrosis with vascular discoloration that extends upto several nodes and internodes into the stem. Foliar SDS symptom is characterized by interveinal chlorosis and necrosis in leaves which finally curl and fall off, and in severe cases by flower, pod abscission and immature seed formation. A major toxin involved in initiating foliar SDS has been identified. Nothing is known about how root necrosis develops. In order to unravel the mechanisms used by the pathogen to cause root necrosis, the transcriptome of the pathogen in infected soybean root tissues of a susceptible cultivar (Williams 82) was investigated. The transcriptomes of the germinating conidia and mycelia were also examined. Of the 14,845 predicted F. virguliforme genes, we observed that 12,017 (81%) were expressed in germinating conidial spores and 12,208 (82%) in mycelia and 10,626 (72%) in infected soybean roots. Of the 10,626 genes induced in infected roots, 224 were transcribed only following infection. Expression of several infection-induced genes encoding enzymes with oxidation-reduction properties suggests that degradation of antimicrobial compounds such as the phytoalexin, glyceollin could be important in establishing the biotrophic phase. Enzymes with hydrolytic and catalytic activities could play an important role in the transitioning of the pathogen from biotrophic to necrotrophic phase. Expression of a large number of genes encoding enzymes with catalytic and hydrolytic activities during late infection stage suggests cell wall degradation by some of these enzymes could be involved in root necrosis and establishing the necrotrophic phase in this pathogen.

sample_organism:
Glycine max
Fusarium virguliforme Mont-1

overall_design:
RNA-seq data for Fusarium virguliforme Mont-1 germinating conidial spores, mycelia and soybean root tissue 3 and 5 days or 10 and 24 days post water incubation or infection with Fusarium virguliforme Mont-1 conidial spores.

Raw data for Fusarium virguliforme Mont-1 germinating conidial spores and mycelia are not available due to server failure.

first: B

middle: B

last: Sahu

first: M

last: Srivastava


title: Role of light in cyanophage infection of Prochlorococcus

status: Public on Mar 18 2016

city: La Jolla

first: Luke

last: Thompson

state: CA

address: 9500 Gilman Dr

institute: UC San Diego

summary: We report the full transcriptome of T4-like cyanophage P-HM2 infecting Prochlorococcus in light and dark

sample_organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

overall_design: Inoculate Prochlorococcus culture growing in constant light with cyanophage or spent medium, then transfer back to light or to dark (separate experiments done on separate days), then measure total RNA at 0.5, 1.5, 2.5, 4.5, and 8.5 h post-inoculation.

first: Qinglu


title: Coupled electrophysiological recording and single-cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation

status: Public on May 26 2016

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

summary: The mammalian brain is heterogeneous, containing billions of neurons and trillions of synapses forming various neural circuitries, through which sense, movement, thought, and emotion are generated. The cellular heterogeneity of the brain has made it difficult to study the molecular logic of neural circuitry wiring, pruning, activation, and plasticity, until recently, transcriptome analyses with single-cell resolution makes decoding of gene regulatory networks underlying aforementioned circuitry properties possible. Here, we report success in performing both electrophysiological and whole-genome transcriptome analyses on single human neurons in culture. Using Weighted Gene Coexpression Network Analyses (WGCNA), we identified gene clusters highly correlated with neuronal maturation judged by electrophysiological characteristics. A tight link between neuronal maturation and genes involved in ubiquitination and mitochondrial function was revealed. Moreover, we identified a list of candidate genes, which could potentially serve as biomarkers for neuronal maturation. Coupled electrophysiological recording and single-cell transcriptome analysis will serve as powerful tools in the future to unveil molecular logics for neural circuitry functions.

overall_design: Patch-Seq of 20 hESC/hiPSC-derived neurons.

first: Xiaoying

last: Chen

first: Liqiang

last: Zhou

first: Xinpei

last: Gao

first: Junbang

last: Wang

first: Yinan

last: Yao

first: Fei

last: He

first: Yuping

last: Luo

first: Yongchun

last: Yu

first: Siguang

first: Liming

last: Cheng

first: Yi

last: Sun


title: TIP60 complex

first: Eric

last: Paquet


title: Regulation of microRNA expression by rifampin in human hepatocytes

status: Public on Apr 06 2016

city: Indianapolis

first: Hai

last: Lin

address: 410 W 10th St

institute: IUPUI

summary: Rifampin causes drug interactions by altering hepatic drug metabolism. Because microRNAs (miRNAs) have been shown to regulate genes involved in drug metabolism, we determined the effect of rifampin on the expression of  hepatic miRNAs. Primary human hepatocytes from seven subjects were treated with rifampin, and the expression of miRNA and cytochrome P450 (P450) mRNAs was measured by TaqMan assays and RNA-seq, respectively. Rifampin induced the expression of 10 clinically important and 13 additional P450 genes and repressed the expression of 9 other P450 genes (P < 0.05). Rifampin induced the expression of 33 miRNAs and repressed the expression of 35 miRNAs (P < 0.05). Several of these changes were highly negatively correlated with the rifampin-induced changes in the expression of their predicted target P450 mRNAs, supporting the possibility of miRNA-induced regulation of P450 mRNA expression. In addition, several other miRNA changes were positively correlated with the changes in P450 mRNA expression, suggesting similar regulatory mechanisms. Despite the interindividual variability in the rifampin effects on miRNA expression, principal components analysis clearly separated the rifampin-treated samples from the controls. In conclusion, rifampin treatment alters miRNA expression patterns in human hepatocytes, and some of the changes were correlated with the rifampin-induced changes in expression of the P450 mRNAs they are predicted to target.

overall_design: Primary human hepatocytes were treated rifampin or vehicle for 24 hours.  Rifampin-treated samples are not available for the 30Jul10 patient or the Hep2 patient due to raw data file corruption.

first: Todd

middle: C

last: Skaar

first: Yunlong

last: Liu


title: Analysis of global gene expression of a human T-ALL cell lines, comparing GATA3low ETP-ALL (i.e. PER-117) and "typical" T-ALL

status: Public on Feb 26 2016

city: Berlin

first: Lars

last: Fransecky

address: Hindenburgdamm 30

department: Hematology and Oncology

country: Germany

institute: Charité University Hospital Berlin

summary: Cell lines representing human T-ALL were analyzed to compare GATA3low ETP-ALL (i.e. PER-117) with "typical" T-ALL. Moreover, changes in global gene expression were assessed comparing GATA3low ETP-ALL (i.e. PER-117) and GATA3high ETP-ALL (i.e. Loucy) upon treatment with Decitabine, a hypomethylating agent.

overall_design: Analysis of 6 human cell lines representing "typical" T-ALL (BE13, Jurkat, Molt4, RPM18402) and ETP-ALL (Loucy, PER-117).  Additionally, global gene expression was assessed before and after treatment of ETP-ALL cell lines with Decitabine

first: Martin

last: Neumann

first: Sandra

last: Heesch

first: Lorenz

last: Bastian

first: Karsten

last: Spiekermann

first: Tobias

last: Herold

first: Claudia

middle: D

last: Baldus


title: Differentially expressed long noncoding RNA expression between periodontal ligament stem cells from healthy periodontal tissue and periodontal ligament stem cells from inflammatory periodontal tissue.

status: Public on Feb 19 2016

city: Xi’an

first: Liying

last: Wang

state: shaanxi

address: 145 West Changle Road

institute: School of Stomatology, The Fourth Military Medical University,

summary: Periodontitis can impair the osteogenic differentiation of human periodontal mesenchymal stem cells, but the underlying molecular mechanisms are still poorly understood. Long noncoding RNAs (lncRNAs) have been demonstrated to play significant roles under both physiologic and pathological conditions. We performed comprehensive lncRNAs profiling by lncRNA microarray to identify differentially expressed long noncoding RNA expression between Periodontal ligament stem cells from healthy Periodontal tissue and periodontal ligament stem cells from inflammatory periodontal tissue. Our analysis identified 233 lncRNAs and 423 mRNAs that were differently expressed (fold change >2.0, p-value < 0.05) between the two groups of cells. The GO analysis revealed that the significantly down-regulated biological processes included multicellular organismal process, developmental process and multicellular organismal development and the significantly up-regulated biological processes included cellular process, biological regulation and response to stimulus in periodontal ligament stem cells from inflammatory periodontal tissue. The Pathway analysis revealed that the differentially expressed mRNAs may involved in Focal adhesion, ECM-receptor interaction, Bacterial invasion of epithelial cells, Long-term depression, Circadian entrainment and HIF-1 signaling pathway.

overall_design: Two-condition experiment, periodontal ligament stem cells from healthy periodontal tissue (hPDLSCs) vs. periodontal ligament stem cells from inflammatory periodontal tissue (pPDLSCs), Biological replicates: 3 control replicates (hPDLSCs), 3 testing replicates (pPDLSCs).

first: Zuolin

last: Jin


title: Expression data of medulloblastoma cell lines with OCT4A overexpression

status: Public on Feb 17 2016

city: São Paulo

first: Oswaldo

middle: Keith

last: Okamoto

state: São Paulo

address: Rua do Matão, 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

summary: Medulloblastoma is a highly aggressive pediatric brain tumor, in which expression of the pluripotency factor OCT4 has been recently correlated with poor patient survival. However, the contribution of OCT4 transcript variants to tumor aggressiveness is still poorly understood. In this study, we found that transcripts encoding OCT4A, but not OCT4B or OCT4B1, were significantly correlated with LIN28A expression, which encodes another well-known pluripotency factor. LIN28A was found to specifically bind OCT4A transcripts and interact with poly(A) binding protein and RNA helicase A in polysomal fractions of medulloblastoma cells, favoring increased OCT4A protein levels in these cells. Medulloblastoma cells stably overexpressing OCT4A displayed significantly enhanced clonogenic activity, tumorsphere generation and invasion capability, as well as increased tumorigenicity. In an orthotopic metastatic model of medulloblastoma, OCT4A overexpressing cells generated more developed, aggressive and infiltrative tumors, with tumor-bearing mice attaining advanced metastatic disease and shorter survival rates. Pro-oncogenic effects of OCT4A were found to be expression-level dependent and accompanied by distinct subchromosomal aberrations and differential expression of newly discovered, still poorly characterized, non-coding RNAs. Altogether, our findings support the relevance of pluripotency-related factors in the aggravation of medulloblastoma traits classically associated with poor clinical outcome, and underscore the prognostic and therapeutic value of OCT4A in this challenging type of pediatric brain cancer.

overall_design: Total RNA of 2-3 clones of each cell line (Control and OCT4A overexpression) was extracted with the RNeasy Mini kit (Qiagen), following the manufacturer’s protocol. Gene expression profiling was carried out independently for each sample using Affymetrix GeneChip® Human Gene 2.0 ST whole-transcript arrays (Affymetrix, Santa Clara, CA, USA). The quality control and normalization of data were processed by Affymetrix® Expression Console Software (Affymetrix). Differentially expressed genes were identified with the One-Way ANOVA, with a p-value cutoff of 0.05, using Transcriptome Analysis Console v3.0 (Affymetrix).

first: Patrícia

last: Silva


title: Identification of Zfp423-dependent genes in adult inguinal white adipocytes

status: Public on Feb 10 2016

city: Durham

first: Rana

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

summary: We derived a model that allows for doxycycline-inducible deletion of Zfp423 in mature adipocytes of adult mice (Adiponectin-rtTA; TRE-CRE; Zfp423 loxP/loxP).  In these animals deletion of Zfp423 results in a spontaneous conversion of white adipocytes into beige-like adipocytes at room temperature. The goal of this expression analysis was to 1) determine the gene programs dependent on adipocyte Zfp423 in inguinal WAT, and 2) determine the similarity between the converted beige-like cells to normal beige adipose tissue that accumulates upon cold exppsure.

overall_design: Inguinal white adipose tissues were isolated from adult control (Adiponectin-rtTA; TRE-Cre; Zfp423+/+ mice) and doxycycline inducible adipocyte Zfp423 knockout mice (Adiponectin-rtTA; Tre-CRE; Zfp423loxP/loxP mice) maintained at room temperature on a doxcycyline-containing diet for 28 days.  In parallel, inguinal white adipose tissues were isolated from control mice fed the doxycycline-containing diet for 28 days, but exposed to cold (6 °C) for the last 14 days to induce beige adipocyte accumulation. We sought to compare the similarity of Zfp423-deficient adipocytes with cold-induced beige adipocytes at the level of gene expression.

first: Mengle

last: Shao


title: Transcriptome study on Aspergillus niger during citrate fermentation.

city: Wuxi

first: Xian

last: Yin

address: Lihu road 1800

department: school of biotechnology

institute: Jiangnan University

summary: We report the genes regulated during citrate fermentation.

overall_design: Examination of 5 different time points during fermentation in Aspergillus niger H915-1.

first: Jianghua

last: Li

first: Guocheng

last: Du

first: Jian

last: Chen

first: Long


title: Whole Blood long non-coding RNA and mRNA Expression Profiles in Humans Exposed to Multi-walled Carbon Nanotubes

status: Public on Mar 09 2016

city: morgantown

first: Anna

middle: A

last: Shvedova

state: WV

address: 1095 willowdale Rd

department: HELD

institute: CDC/NIOSH

summary: As the application of carbon nanotubes (CNT) in consumer products continues to rise, studies have expanded to determine the associated risks of exposure on human and environmental health. In particular, several lines of evidence indicate that exposure to multi-walled carbon nanotubes (MWCNT) could pose a carcinogenic risk similar to asbestos fibers. However, to date the potential markers of MWCNT exposure are not yet explored in humans.

overall_design: Global mRNA and lncRNA expression profiles in the whole blood of exposed workers, having direct contact with MWCNT aerosols for atleast 6 months (n=8), were compared with expression profiles of non-exposed (n=7) workers (e.g., proffessional and/or technical staff) from the same manufacturing facility.

first: Naveena

last: Yanamala

first: Liliya

last: Fatkhutdinova


title: Dynamics of DNA methylation patterning during in vitro propagation of human spermatogonial stem cells

status: Public on Feb 27 2016

city: Amsterdam

first: Robin

last: Struijk

address: Meibergdreef 9-15

department: Center for Reproductive Medicine

institute: AMC Amsterdam

type: Methylation profiling by genome tiling array

summary: Autotransplantation of in vitro proliferated spermatogonial stem cells (SSCs) has been advocated as a way to restore fertility in childhood cancer survivors. In this study we determined the effects of cell culture on DNA methylation patterning in human SSCs, to evaluate the safety of future clinical application of SSC autotransplantation.

overall_design: Bisulfite converted DNA of 34 human spermatogonial stem cell samples, 4 sperm samples and 3 seminoma samples were hybridized to Illumina Infinium 450k Human Methylation Beadchips

first: Robert

first: Ans

middle: M

last: van Pelt


title: Bone marrow micro-environment mediated drug resistance in Acute promyelocytic leukemia

status: Public on Sep 01 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: About 5-10% newly diagnosed and about 20-30% of relapsed acute promyelocytic leukemia (APL) patients will have disease recurrence after receiving currently accepted standards of care. While there are reports of micro-environment mediated drug resistance (EM-DR) in AML, there is no data on the effect of malignant promyelocyte and stromal interaction on Arsenic trioxide (ATO) induced apoptosis. We undertook a preliminary study to evaluate the role of EM-DR to ATO in APL. In direct co-culture (contact dependent system) of malignant promyelocyte with stromal cells, the stromal cells gave a significant protective effect against ATO at different concentrations used (1 to 8 μmol; NB4 (APL cell line) In a gene expression profiling comparing NB4 cells in co-culture with NB4 cells alone, 1846 genes were differentially regulated. On a preliminary analysis, we observed an up-regulation of various pathways such as adhesion (ITGB1, ITGB2, ITGB7, etc.), Cytokines (IL-6, IL-8, IL-18, CCL2, CCL10, etc.) Wnt signalling (Wnt5a, Wnt11, NFATC4, etc,) NF-kB pathway (ICAM1, BIRC2, BIRC3, XIAP1, etc.) in the leukemic cells. The NF-kB pathway has been validated using real time PCR which correlated with the genes being differentially regulated in NB4 cells co-cultured in stroma.

overall_design: Agilent one-color experiment,Organism: Homo sapiens  ,Custom Agilent 8x60k Human Whole Genome Microarray Gene expression  (AMADID: 039494)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Vikram

last: Mathews

first: Saravanan

last: Ganesan

first: Ansu

last: Alex


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to Bedaquiline

status: Public on May 05 2016

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

type: Expression profiling by genome tiling array

summary: Bacteria commonly adapt to stresses by altering gene expression.  To understand the response of M. tuberculosis (MTB) to bedaquiline, we performed transcriptomics over a time-course on MTB bacilli exposed to the drug.

overall_design:
Bacteria were harvested at 1, 6, 24, 48, 96 hrs after being exposed to concentrations of bedaquiline (no drug, 1.5μM, 15μM) during a 7-day drug exposure time course experiment (as indicated in each sample title). RNA was isolated and applied to custom Agilent tiled arrays.
Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the  results as though they are single channel (Cy3 and Cy5 signals are calculated). Therefore, there are two sample records per each raw data file and the raw data file associated with each sample is indicated in the corresponding sample description field.

first: Eliza

middle: J

last: Peterson

first: David

last: Sherman

first: Nitin

middle: S

last: Baliga


title: H5N1 and X179A influenza infection of mice

status: Public on Dec 20 2016

city: Oxford

first: Suzanne

last: Cole

address: John Radcliffe Hospital, Headley Way

department: University of Oxford

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

summary: Analysis of lung samples from mice infected with a severe H5N1 influenza virus (VN/1203/04/H5N1) or a mild H1N1 influenza virus (NYMC-X-179A) on day 3 and day 5 post-infection. Uninfected controls were used for comparison.

overall_design: Lung samples collected from uninfected mice, or mice on day 3 and 5 post infection with H5N1 or X-179A. One H5N1 sample per time point (2-3 biological replicates per time point pooled and hybridised onto one chip [2 uninfected, 2 day 3, 3 day 5]); three X179A samples per time point (each biological replicate hybridised separately)

middle: L

first: Wai-Ling

last: Kok

first: Ling-Pei

last: Ho


title: Gene expression signatures of iNKT-subpopulations sorted from thymus of BALB/c and C57BL/6 mice

status: Public on Oct 05 2016

city: Hanover

first: Günter

last: Bernhardt

address: Carl Neuberg Strasse 1

department: Institue of Immunology

institute: Hannover Medical School

summary: iNKT cells can be classified based on functional criteria into iNKT1, iNKT2 and iNKT17 cells, respectively. Here, a protocol was applied allowing sorting of living cells from thumus of BALB/c and C57BL/6 mice. The obtained gene expression profiles confirmed already existing information regarding the iNKT subtypes and will therefore provide useful hints for further investigations.

overall_design: Samples of iNKT1, iNKT2 and iNKT17 cells were obtained in two completely independent flow cytometric sorts for both, (BALB/c) and (C57BL/6). As a source, cells from thymi from 5 to 6 female mice were prepared for each sort. Moreover, iNKT1 cells from BALB/c thymus were sorted into CD4(lo-int) and CD4 (int-hi) fractions.

first: Hristo

last: Georgiev


title: Overexpression of a panel of miRNA mimics in DU145 prostate cancer cells.

status: Public on Jun 01 2017

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: The role of a number of miRNAs found to be differentially expressed in prostate cancer was functionally investigated by overexpressing them in DU145 prostate cancer cells and by analyzing gene expression profiles.

overall_design: gene expression profiles of DU145 cells transfected with synthetic miRNA mimics (triplicate) were compared to those of DU145 cells transfected with a mock molecule (triplicate).

first: Paolo

last: Gandellini

first: Stefano

last: Percio


title: Comparative transcriptomics of endometrial stromal fibroblasts

status: Public on Aug 01 2016

city: West Haven

first: Koryu

last: Kin

state: CT

address: 840 West Campus Drive

department: EEB

institute: Yale University

summary: We sequenced mRNA of endometrial stromal fibroblasts from six mammalian species.

sample_organism:
Homo sapiens
Bos taurus
Oryctolagus cuniculus
Rattus norvegicus
Monodelphis domestica
Neogale vison

overall_design: Examination of mRNA levels in endometrial stromal fibroblasts from six mammalian species grown in culture with two biological replicates for each species


title: Effects of selection on residual feed intake and diet on gene expression in pig perirenal adipose tissue

status: Public on Jul 01 2016

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

institute: INRA

summary: Transcriptional profiling in peritoneal adipose tissue of 48 pigs (132 days of age) originated from two lines divergently selected for residual feed intake (RFI) : low-RFI pigs (RFIneg), high-RFI pigs (RFIpl). Both lines were offered isocaloric and isoproteic diets with contrasted energy source and nutrients:  low fat, low fiber (LF) diet or a high fat, high fiber (HF)diet during 10 weeks. Effects of RFI selection, diet and interaction between diet and line were investigated.

overall_design: Four experimental groups: low-RFI pigs fed high fat, high fiber diet (HF_RFIneg), high-RFI pigs fed high fat, high fiber diet(HF_RFIpl),  low-RFI pigs fed low fat, low fiber diet (LF_RFIneg) and high-RFI pigs fed low fat, low fiber diet(LF_RFIpl). 12 pigs per condition. One replicate per array.

first: Isabelle

last: Louveau

first: Florence

last: Gondret


title: Effects of selection on residual feed intake and diet on gene expression in pig subcutaneous adipose tissue

summary: Transcriptional profiling in subcutaneous adipose tissue of 48 pigs aged (132 days of age) originated from two lines divergently selected for residual feed intake (RFI) : low-RFI pigs (RFIneg), high-RFI pigs (RFIpl). Both lines were offered isocaloric and isoproteic diets with contrasted energy source and nutrients:  low fat, low fiber (LF) diet or a high fat, high fiber (HF)diet during 10 weeks. Effects of RFI selection, diet and interaction between diet and line were investigated.


title: Activation of P-TEFb by androgen receptor-regulated enhancer RNAs in androgen deprivation conditions [ChIP-Seq]

status: Public on Feb 12 2016

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: Androgen receptor (AR) is required for castration resistant prostate cancer (CRPC) progression, but the function and disease relevance of AR-bound enhancers remain poorly understood.  Here, we identify a group of AR-regulated enhancer RNAs (e.g. PSA eRNA) that are upregulated in CRPC cells, patient-derived xenografts (PDX) and patient tissues.  PSA eRNA binds to CYCLIN T1, activates P-TEFb and promotes in cis and trans gene transcription by increasing serine-2 phosphorylation of RNA polymerase II (Pol II-Ser2p).  To avoid the total Pol II changing by PSA eRNA. We measured the total Pol II using N20 and 8WG16 antibodies with or without PSA eRNA knocking down. To avoid the AR binding changes by PSA eRNA, we also  measured the AR binding using AR N20 antibodies with or without PSA eRNA knocking down.

overall_design: Androgen receptor (AR) binding sites in human prostate cancer cell lines, C4-2, were studied using ChIP-seq. Total Pol II Ser-2p and AR binding sites in human prostate cancer cell lines C4-2 with or without PSA eRNA knockdown, were studied using ChIP-seq. ChIP enriched DNA were sequenced using Illumina HiSeq 2500and input DNA were sequenced using Illumina HiSeq 2000.

first: Haojie

last: Huang

first: Yu

last: Zhao

first: Liguo

last: Wang


title: Global gene expression analysis of human embryonic stem cells, fibroblast iPSC, and low passage stromal primed myeloid iPSC before and after conversion to the naïve state

status: Public on Sep 13 2016

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

overall_design: Total RNA was harvested from indicated donor cells, hESC, or iPSC. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series. A single sample of each cell line was used for this analysis.

first: Ludovic

last: Zimmerlin

first: Tea

last: Park

first: Jeffrey

last: Huo

first: Wayne

last: Yu


title: Transcriptomes of aneuploid mouse liver tumors and T-ALL

status: Public on Mar 20 2017

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

institute: University Medical Center Groningen

summary:
Transcriptome analysis to map transcriptomes of Mad2 p53null-driven aneuploid liver cancers and T-ALLs, to determine correlation between copy number changes and expression changes and to map the transcriptional response to CIN
Chromosome instability (CIN) leads to aneuploidy and copy number variations (CNVs). Even though both are hallmarks of cancer cells, aneuploidy inhibits proliferation of untransformed cells, suggesting that cancer cells have adapted to cope with CIN. The spindle assembly checkpoint (SAC) prevents CIN by monitoring chromosome attachment and sister chromatid tension in mitosis. By conditionally inactivating Mad2, an essential SAC gene, we find that SAC inactivation in T-cells or hepatocytes is remarkably well tolerated and becomes tumorigenic when placed in a p53null or p53+/- predisposed background. The resulting T-ALLs and HCCs are highly aneuploid, exhibit clonal copy number changes that are tumor specific despite ongoing CIN, indicating that CIN is a powerful driver of tumor evolution.

overall_design: Transcriptomes of liver tumors or T-ALL samples described in the accompanying manuscript were compared to the transcriptomes of healthy liver or thymus samples isolated from healthy mice

first: Lee

last: Albacker

first: Peter

middle: K

last: Sorger


title: ChIP-seq of TIP60 complex

status: Public on Apr 30 2016

city: Lausanne

first: Eric

last: Paquet

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

summary: Genome-wide mapping of TIP60 complex subunits in K562 cells. The objectives of this study are to describe TIP60 genome wide localization, confirm MBTD1 co-localization with  already known unique subunits and observe the impact of MBTD1 on TIP60 complex targeting to chromatin. The TIP60 acetyltransferase complex is a key regulator of genome expression and stability. Here, we identified MBTD1 as a new stable subunit of the complex and revealed interesting insights about TIP60 function during the repair of DNA double strand breaks. MBTD1 binds H4K20me1/2, helping TIP60 association to specific promoters but also the DNA repair process by homologous recombination. While pro-end joining factor 53BP1 engages chromatin through simultaneous binding of H4K20me2 and H2AK15ub, TIP60 regulates the resolution of 53BP1 foci after DNA damage through a related bivalent mechanism. MBTD1 competes with 53BP1 for the H4K20me2 mark, affecting its retention at the break cooperatively with H4 acetylation by TIP60. In addition, we show that H2AK15ub deposition by RNF168 inhibits chromatin acetylation by TIP60, whereas H2AK15 can also be acetylated by TIP60 in vivo, therefore blocking its ubiquitylation. Altogether, these results uncover an intricate mechanism orchestrated by the TIP60 complex to regulate 53BP1-dependent repair pathway selection, through incompatible bivalent binding/action on chromatin.

overall_design: Chromatin immunoprecipitation was performed on K562 stable cell lines expressing 3xFLAG tagged TIP60 complex subunits integrated at AAVS1 locus. TIP60 complex genome wide localization is defined by the overlap of different subunits.

first: Karine

last: Jacquet

first: Jacques

last: Côté


title: Mapping karyotypic heterogeneity in chromosomal instable murine T-cell acute lymphoblastic lymphomas using single-cell sequencing

summary: Chromosome instability (CIN) leads to aneuploidy and copy number variations (CNVs). Even though both are hallmarks of cancer cells, aneuploidy inhibits proliferation of untransformed cells, suggesting that cancer cells have adapted to cope with CIN. The spindle assembly checkpoint (SAC) prevents CIN by monitoring chromosome attachment and sister chromatid tension in mitosis. By conditionally inactivating Mad2, an essential SAC gene, we find that SAC inactivation in T-cells or hepatocytes is remarkably well tolerated and becomes tumorigenic when placed in a p53null or p53+/- predisposed background. The resulting T-ALLs and HCCs are highly aneuploid, exhibit clonal copy number changes that are tumor specific despite ongoing CIN, indicating that CIN is a powerful driver of tumor evolution.

overall_design: Whole genome single cell sequencing was performed on individual T-cells from untransformed thymus or Mad2f/f p53f/f Lck-Cre+T-ALLs. Two individual tumours were sequenced, as well as an untransformed thymus control.

first: Diana

last: Spierings

last: Lansdorp


title: Activation of P-TEFb by enhancer RNAs associated with lethal prostate cancer [ChIP-seq]

last: WANG

summary: Castration resistant prostate cancer (CRPC) is a lethal disease.  Sustained aberrant activation of androgen receptor (AR) becomes a central mechanism that contributes to endocrine therapy resistance.  Here, we demonstrate that AR-bound enhancer RNAs (AR-eRNAs), including eRNA of the KLK3 (or PSA) gene, are upregulated in human CRPC cells and patient tissues.  By enhancing C-termine domain (CTD) serine-2 phosphorylation of RNA polymerase II (Pol II-Ser2p), PSA eRNA acts in cis to promote PSA mRNA transcription and in trans to induce mRNA expression of a large set of genes involved in androgen action, cell cycle progression and tumorgenesis.  Accordingly, we demonstrate that PSA eRNA binds in vitro and in vivo to CYCLIN T1, a regulatory subunit of the positive transcription elongation factor b (P-TEFb) complex that mediates Pol II-Ser2p.  To identify the PSA eRNA’s functions on the Pol II-Ser2p and CYCLINT1 in the CRPC C4-2 cells, we detected the Pol II-Ser2p and CYCLINT1 ChIP-seq with or without PSA eRNA knockdown in the C4-2 cells. Moreover, to rule out the AR binding changes and identify the AR binding sites around the new genes, we detected the AR ChIP-seq in LNCaP and C4-2 cells with or without the androgen.

overall_design: Androgen receptor (AR) binding sites in human prostate cancer cell lines, LNCaP and C4-2, were studied using ChIP-seq. Pol II Ser-2p and CYCLINT1 binding sites in human prostate cancer cell lines C4-2 with or without PSA eRNA knockdown, were studied using ChIP-seq. ChIP enriched and input DNA were sequenced using Illumina HiSeq 2000.


title: Chromosome copy number changes in Mad2-null-driven p53 null HCC and T-ALL samples

summary:
Mad2 and p53 loss were combined in liver or T-cells specificely leading to early onset and highly aggressive aneuploid HCC and T-ALL. Tumours were characterized for (recurrrent) copy number changes with a focus on whole chromosome abnormalities. DNA content was compared to the DNA content of sex-matched uninfiltrated control liver samples from litter mates
Chromosome instability (CIN) leads to aneuploidy and copy number variations (CNVs). Even though both are hallmarks of cancer cells, aneuploidy inhibits proliferation of untransformed cells, suggesting that cancer cells have adapted to cope with CIN. The spindle assembly checkpoint (SAC) prevents CIN by monitoring chromosome attachment and sister chromatid tension in mitosis. By conditionally inactivating Mad2, an essential SAC gene, we find that SAC inactivation in T-cells or hepatocytes is remarkably well tolerated and becomes tumorigenic when placed in a p53null or p53+/- predisposed background. The resulting T-ALLs and HCCs are highly aneuploid, exhibit clonal copy number changes that are tumor specific despite ongoing CIN, indicating that CIN is a powerful driver of tumor evolution.

overall_design: DNA content of 29 Mad2f/f p53f/f or Mad2f/f p53f/+ Alb-Cre+ liver tumors and 9 Mad2f/f p53 f/f Lck-Cre+ T-ALLs compared to control tissue DNA


title: Expression data from human kidney cells (HK2) knocked down for OCRL

city: Napoli

first: Giovanna

last: De Leo

address: via Castellino 111

institute: Tigem

summary:
In order to identify the effects of OCRL depletion on the proximal tubular renal cells transcriptome, we performed Affymetrix Gene-Chip hybridization experiments
Transcriptome analysis of the proximal tubular cells depleted of OCRL

overall_design: For the analysis on proximal tubular cells depleted of OCRL, total RNA was extracted from the HK2 cells of three independent experiments; RNA extracted also from HK2 treated siRNA-non targeting used as control.

first: Maria

middle: G


title: Six1 homeoprotein drives myofiber type IIA specialization in soleus muscle

status: Public on Aug 23 2016

city: Paris

first: iori

last: sakakibara

address: 22 rue Méchain

institute: Cochin institut

summary: Six homeoproteins regulate fast MYH expression and calcium homeostasis

overall_design: soleus muscles were collected from cSix1 KO and control mice. Total RNAs were extracted by Trizol Reagent (Invitrogen) according to manufacturer's instruction. After validation of RNA quality with the Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 50 ng of total RNA were reverse transcribed following the Ovation PicoSL WTA System (Nugen). Briefly, the resulting double-strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5 μg of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5 μg of Sens Target DNA were fragmented and labelled with biotin using Encore Biotin Module kit (Nugen). After control of fragmentation using Bioanalyzer 2100, the cDNA was then hybridized to GeneChip® Mouse Gene 1.0 ST (Affymetrix) at 45°C for 17 hours. After overnight hybridization, the ChIPs were washed using the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The analysis of some of these metrics and the study of the distribution of raw data show no outlier experiment.

first: Iori

last: Sakakibara

first: Marc

last: Santolini

first: Pascal

last: Maire


title: Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs [RNA-Seq]

first: LIGUO

summary: Castration resistant prostate cancer (CRPC) is a lethal disease1-4.  Aberrant activation of the androgen receptor (AR) becomes a central mechanism contributing to the resistance of endocrine therapies2,3.  Here we demonstrate that non-coding RNAs transcribed from the AR bound-enhancers RNAs (AR-eRNAs) are upregulated in human CRPC cells in vitro, xenografts in vivo and patient tissues.  Expression of a subset of genes with elevated AR-eRNAs, including TLE1 and HTR3A, is inversely correlated with biochemical recurrence-free survival of CRPC patients.  We identify aan HIV-1 TAR-like (TAR-L) motif in AR-eRNAs of AR target genes including KLK3 (or PSA) and TMPRSS2.  The TAR-L motif is important for these eRNAs to bind to CYCLIN T1 of the positive transcription elongation factor b (P-TEFb) complex.  Knockdown of PSA eRNA diminishes RNA polymerase II (Pol II) serine-2 (Ser-2) phosphorylation at the PSA promoter.  The TAR-L motif in KLK3 eRNA is crucial for effective transcription of PSA mRNA.  Together, wWe demonstrate a P-TEFb activation function of eRNA and reveal aberrant eRNA expression as a functional indicator of AR abnormality in CRPC.  Our results also suggest that eRNAs as amay be a potential target for CRPC therapy.

overall_design: Total RNA sequencing of two prostate cancer cells. Data were generated by deep sequencing, in diplicate, using Illumina HiSeq 2000.

first: Haojie

last: Huang

first: Yu

last: Zhao

first: Liguo

last: Wang


title: Transcriptomic analysis of LSD1

status: Public on Jun 13 2017

city: LYON

first: Jean-Marc

last: Vanacker

address: 28 rue A Fleming

institute: IGFL

summary: Determination of the genes regulated by LSD1 in MDA-MB231 cells

overall_design: MDA-MB231 cells were inactivated for LSD1 using siRNA. Two different siRNAs were used (siL1, siL2). Cells treated with a control siRNA (siC samples) were used for comparison. Duplicate samples were analyzed. Transcriptomic analysis was performed by RNA-Seq

first: Violaine

last: Tribollet


title: Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs [ChIP-Seq]

overall_design: Androgen receptor (AR) binding sites in human prostate cancer cell lines, LNCaP and C4-2, were studied using ChIP-seq. ChIP enriched and input DNA were sequenced using Illumina HiSeq 2000.


title: Copy number changes (average and single cell) and matching transcriptomes of HCCs and T-ALLs isolated from Mad2 p53 conditional double knockout mice

first: Floris

last: Foijer

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

overall_design: Refer to individual Series


title: Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs


title: The prognostic and predictive value of a five-microRNA-based classifier in breast cancer

status: Public on Jan 01 2018

city: Guangzhou

first: jingye

last: hu

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

summary: microRNA profiling of  breast cancer specimens vs noncancerous breast tissues

overall_design: 422 breast cancer specimens and 31 noncancerous breast tissues

first: Jingye

last: Hu

first: Huiyun


title: Comprehensive microarray analysis of reprogramming fidelity in a library of non-integrated induced pluripotent stem cell lines prepared with various derivation methods

first: Elias

last: Zambidis

country: USA

type:
Expression profiling by array
Methylation profiling by array


title: Construction of prostate cancer cell line (PC-3)-specific interactome

status: Public on Dec 21 2016

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

institute: Seoul National University College of Medicine

type:
Expression profiling by array
Third-party reanalysis

summary:
The purpose of our study was to construct prostate cancer cell-specific interactome by aggregating microarray samples available in public, and identify novel transcriptional regulators that control prostate cancer cell cycle progression.

We collected 121 samples of PC-3 cell microarray data from 11 prior studies and our own study data, GSE45567, and performed pre-processing steps, such as quality control test, normalization, and batch effect adjusting. In quality control test, 10 low-quality samples were removed. The matrix data we deposited in GEO has normalized log2 signal intensity of 11,877 genes common in 110 samples, as the 110 samples came from different Affymetrix. The Gene IDs were identified by Entrez Gene IDs that overlapped across different Affymetrix platforms (File: GSE67157_Matrix_PC-3cell_Interactome.txt).

In GSE45567 dataset, which is one of the 12 data sets, we selected microarray samples of vehicle-, cineol-, linalool-, and geraniol-treated PC-3 cells, and performed unsupervised clustering analysis to establish dependable clusters of a clear phenotypic transition. Then, the gene set specifically enriched or depleted in the geraniol cluster against vehicle cluster was used for gene set enrichment analysis (GSEA). We found cell cycle-related gene signatures were specifically down-regulated in the geraniol cluster.

PC-3 cell-specific interactome was assembled from 110 microarray samples by Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe, PMID: 16723010). We used Master Regulator Analysis-Fisher’s Extact Test (MRA-FET, PMID: 20531406) to infer transcription factors which are geraniol target molecules and control cell cycle gene signatures. We discovered E2F8 is as a master regulator to modulate geraniol-specific genes toward G2/M cell cycle arrest.

Our findings will provide biological insights into the role of E2F8 in prostate cancer for transcriptional regulation leading to the development of cell cycle-targeting chemotherapeutic reagent. In addition, our approach serves as an example to decide the most potent anti-cancer regime in other cancer types and identify the target molecules of cancer-preventive reagents through computational analyses.

relation:
Affiliated with: GSE3737
Affiliated with: GSE33455
Affiliated with: GSE14405
Affiliated with: GSE33182
Affiliated with: GSE14464
Affiliated with: GSE10832
Affiliated with: GSE34112
Affiliated with: GSE38972
Affiliated with: GSE43489
Affiliated with: GSE42913
Affiliated with: GSE45567

overall_design:
A total number of 12 datasets containing 121 microarray samples were downloaded from NCBI GEO (http://ncbi.nlm.nih.gov/geo) or ArrayExpress (http://www.ebi.ac.uk/arrayexpress). The individual data sets had been used to address various types of research questions, such as the effects of various chemotherapeutic reagents. We focused on microarray data that had been obtained using the Human Genome U133A, U133 Plus 2.0, and 1.0 ST Affymetrix platforms because they constitute the majority of available microarray samples for the PC-3cell type and data can be combined across these platforms with ease.

Pre-processing
We applied quality-control test to each sample to remove low-quality samples, normalized only high-quality samples by Single-Channel Array Normalization (SCAN) algorithm (PMID:  22959562), and adjusted for intra- and inter-study batch effects across data sets.

Unsupervised clustering analysis and validation
We used 12 of monoterpene-treated microarray samples in GSE45567 and filtered out 5,000 genes of the high variance across samples. Then, we performed unsupervised clustering analysis to confirm transcriptional transition based on gene expression profile. Principal Component Analysis (PCA) and supervised classification were carried out to internally validate the clustering result and to evaluate cluster compactness.

Significant gene set
SAM analysis (PMID: 11309499) was used to identify differentially expressed genes out of the 5,000 genes between the vehicle and the geraniol clusters. We found out the get set specifically enriched in the geraniol cluster and applied this gene set for MRA-FET to infer geraniol-targeted transcription factors.

PC-3 cell-specific interactome and Master Regulator Analysis (MRA)
From the 110 microarray samples that have passed quality control test, normalization, and batch adjusting, we selected the same 5,000 genes of high variance which were used in the clustering analysis. Then, ARACNe built up regulatory interactions between the 5,000 genes and 472 human transcription factors (TFs) as hub markers through mutual information (MI) calculation. From the PC-3 cell-specific interactome, MRA-FET inferred master regulator (MR) candidates which control the geraniol-specific cell cycle signatures.
The information of 121 microarray data samples are summarized in the meta-data spreadsheet. The meta-data have 121 samples with GSE accession number, array platform, original experiment type, quality control test and clustering analysis result. The matrix data txt file (Matrix_PC-3cell_interactome.txt) has normalized log2 expression values of 110 samples after excluding 11 low-quality samples. The 11 low-quality samples are indicated in the meta-data spreadsheet.

first: Sanghoon

last: Lee

first: Jung

last: Chun

first: Su-Hwa

last: Kim

first: Hyun

last: Park

first: Insuk

last: So


title: Global DNA CpG methylation profiling of human embryonic stem cells, fibroblast iPSC, and low passage stromal primed myeloid iPSC before and after conversion to the naïve state

overall_design: Total DNA was harvested from indicated donor cells, hESC, or iPSC. A single sample of each cell line was used for this analysis.

first: Ludovic

last: Zimmerlin

first: Tea

first: Jeffrey

last: Huo

first: Wayne

last: Yu

middle: T


title: Gene expression profiling of human and murine in vitro muscle differentiation

status: Public on Jan 19 2016

city: Rome

first: Irene

last: Bozzoni

address: p.le A. Moro 5

department: Biology and Biotechnology

institute: Sapienza University of Rome

type: Non-coding RNA profiling by high throughput sequencing

summary: Total RNA sequencing of human and murine myoblasts and myotubes was extracted, depleted of ribosomal RNA and subjected to Illumina stranded paired end library prep and sequencing. Samples from Duchenne Muscular Dystrophy patients-derived myoblasts were included  in this study

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 12 samples were analysed: murine C2C12 myoblasts and myotubes differentiated for 4 days, each in two biological replicates; human 9208 myoblasts and myotubes differentiated for 6 days, each in two biological replicates; human Duchenne Muscular Dystrophy patients derived myoblasts and myotubes differentiated for 10 days.

first: Ivano

last: Legnini

first: Francesca

last: Briganti

first: Olga

last: Sthandier


title: Genome-wide analysis of DNA methylation between nasopharyngeal carcinoma tissues and normal nasopharyngeal epithelial tissues

status: Public on Jan 08 2016

first: Jun

last: Ma

address: 651 Dongfeng Road East

summary: Nasopharyngeal carcinoma (NPC) is rare malignancy in most parts around the world but common in Southern China and Southeast Asia, Annually, approximately 80,000 new NPC cases and 50,000 deaths are reported worldwide. In NPC, recent advances have shown that many genes that are predominantly or even exclusively silenced by DNA methylation in epithelial cells during pathogenesis of NPC. However, the causal relationship between DNA methylation status and outcome in NPC remains not well understood. To investigate this problem, we used Illumina 450K BeadChips to examined methylation patterns and survival in NPC. and ultimately provided insight into prognostic value of DNA methylation in NPC clinical management.

overall_design: We employed Illumina Human Methylation450K Beadchip  to analyze a genome-wide of DNA methylation in a cohort of 48 samples (between 24 nasopharyngeal carcinoma tissues and 24 normal nasopharyngeal epithelial tissues) to identify aberrant methylation genes.

first: Wei

last: Jiang

last: Liu

first: Xiao-Zhong

last: Chen

first: Ying

last: Sun


title: One-day old broilers exposed to amoxicillin

status: Public on Jan 29 2016

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

institute: Wageningen UR

summary:
The objective of this study was to investigate the impact of short-term antibiotic treatment in early life on both early microbial colonization of the gut and functional development of intestinal tissue.
From both control and antibiotic treated birds intestinal content samples were taken for microbiota analyzes and intestinal tissue samples were extracted for gene expression analyzes, both at three subsequent time-points (days 1, 5, and 14).

overall_design: 1-day-old chicks (Cobb500) were housed in a floor pen system in which the chicks had ad libitum access to feed and water. At day 1, 2 groups were created; control and antibiotic treated (amoxicillin, 24h in drinking water). At days 1, 80 birds of the control group were sacrificed for tissue sampling. At days 5 and 14, per time-point 80 birds of the control group and 80 birds of the antibiotic treated group were sacrificed for tissue sampling. Subsequently, samples from these 80 birds were pooled in 8 pools of ten birds.

first: D

first: S

last: Vastenhouw

first: M

last: Smits

first: J

last: Rebel


title: Genome-wide RNA sequencing of B6 mouse islets

status: Public on Jan 05 2016

city: Madison

first: Gloria

last: Sheynkman

state: WI

address: 1101 University Ave.

department: Chemistry

institute: UW-Madison

summary: Isoform quantification results for B6 mouse using Bowtie and RSEM.

overall_design: ~400 islets were isolated and pooled from two B6 mice.  Whole islet RNA was isolated using Rneasy purification columns (Qiagen), quantified (Nanodrop) and integrity verified (Agilent) prior to sequencing.  ~94M total paired-end RNA-Seq reads were sequenced.

first: Mark

middle: P

last: Keller


status: Public on Dec 23 2015

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Gene expression profiling of Bone Marrow FoxP3+ Treg cells. Glatman Zaretsky et al. revealed an unexpected role for Tregs in plasma cell biology. Here we determined the gene-expression profile of this new subset of FoxP3+ Treg cell, which express high levels of Treg effector molecules, similar to other non-lymphoid tissue Tregs.

overall_design: Gene-profiling of BM Tregs. Bone marrow Treg cells (30k) (gfp+CD25hiCD4+TCRβ+) (dump negative: CD19-CD8α-TCRγδ-CD11b-CD11c-NK1.1-Gr-1-Ter-119-) were triple-sorted from pools of two to three reporter mice (C57BL/6 Foxp3-IRES-gfp, 9 week-old males) into trizol per ImmGen SOP. RNA was amplified, labeled and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays (Expression Analysis)

first: Fabien

last: Depis

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Gene expression profiling of L-540, SUP-HD1, KM-H2 and L-428 Hodgkin lymphoma cell lines after in vitro and in vivo treatment with the dual PI3K/ERK inhibitor AEZS-136 [2 hours]

status: Public on Jan 01 2016

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

institute: Cerevance ltd

summary: Disease relapse and resistance to chemotherapy represent challenging issues in a subset of Hodgkin Lymphoma (HL) patients. Activity and mechanism(s) of action of a novel PI3K/ERK dual inhibitor AEZS-136 (Æterna Zentaris GmbH, Germany, EU) were examined in L-540, SUP-HD1, KM-H2 and L-428 cell lines. Despite exposure to AEZS-136 induced a significant cell growth inhibition (range, 30-80%), levels of caspase-independent cell death and mitochondrial dysfunction, were only observed in L-540 (62 ±9 vs 14 ±3%, P ≤.0001) and SUP-HD1 (46 ±2% vs 15 ±2%, P ≤.0001) cells. Gene expression profiling indicated that the effects of AEZS-136 treatment are associated with the modulation of cell cycle and cell death pathways. Exposure to AEZS-136 resulted in sustained production of reactive oxygen species (ROS) and activation of necroptotic cell death. The necroptosis inhibitor Necrostatin-1 prevented AEZS-136-induced ROS production, mitochondrial injury, activation of JNK and cell death. Knockdown experiments identified the immediate early response 3 (IER3) as a key signaling molecule that mediates AEZS-136-resistance to oxidative death of HL cells. Furthermore, in vivo xenograft studies demonstrated a 40-70% reduction in tumor burden (P < 0.0001) and a 10-fold increase in tumor necrosis in AEZS-136-treated animals compared to control mice. These data support further clinical evaluation of AEZS-136 in refractory/relapsed HL.

overall_design: The Hodgkin lymphoma cell lines  were obtained from the DSMZ (Braunschweig, Germany, EU). Cells were routinely maintained in RPMI medium 1640 (Lonza, Basel, Switzerland) supplemented with 20% FBS (Lonza) and 2 mM glutamine (Lonza). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 4x106 HL cells were seeded in 75 cm2 flask and, after 24 hrs, cells were treated with 10 µM AEZS-136 (Aeterna Zentaris, Frankfurt, Germany, EU)  in culture medium for 2 hours. At the end of treatment, cells were collected and RNA extracted.

first: G