title: Suppression of lung cancer development by aspirin and triptolide

status: Public on Jun 01 2017

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: Chronic inflammation plays important role in lung cancer development. Recently, we found that anti-inflammation drugs aspirin and triptolide when combined showed synergistic effect in suppressing lung cancer development. In this study, we aim to use gene microarray to define the genes and pathways that are affected by aspirin, triptolide individually or in combination.

overall_design: We will isolate lung tissues from mice of untreated control, aspirin, triptolide, or aspirin/triptolide. Total RNA are isolated and subjected to microarray analysis to define the gene expression profiles. Gene expression data are analyzed by IPA analysis to define the pathways and upstream regulators that are significantly inhibited or stimulated by aspirin, triptolide, or a combination of aspirin and triptolide.

first: Li

last: Zheng

first: Huifang

first: Binghui

last: Shen


title: Study of gene targets regulated by oncogenic PIK3CA and/or Her2

city: Detroit

first: Guojun

last: Wu

state: Michigan

address: 4100 John R Street, HWCRC,Room 824, None

department: Oncology

country: USA

institute: Karmanos Cancer Institute

summary:
Mutant PIK3CA and Her2 genes are oncogenic and their co-existence in breast cancer has been well identified. However, the gene targets and cell signalling pathway regulated by mutant PIK3CA, Her2 and both of PIK3CA and Her2 have not been well studied.
We established stable cell models through transfecting mutant PIK3CA, Her2 and both mutant PIK3CA and Her2 into MCF10A cells and performed Affymetrix microarray to identify downstream target genes controlled by either mutant PIK3CA, Her2 or both PIK3CA and Her2.

overall_design: RNA was extracted from 4 cell models (MCF10A/LacZ, MCF10A/Her2, MCF10A/mutant PIK3CA, and MCF10A/Her2+mutant PIK3CA) and purified using the RNeasy plus miniKit. Affymetrix microarray was performed and downstream target genes controlled by either mutant PIK3CA, Her2 or both PIK3CA and Her2 were identified. We also analyzed the cell signaling pathways enrichment.


title: Transcriptional profiling of adult Drosophila antennae by high-throughput sequencing

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

type: Expression profiling by high throughput sequencing

summary:
Background  Antennae of fruit flies are the major organs responsible for detecting environmental volatiles, e.g., egg-laying substrates. An adult antenna contains many sensilla full of olfactory sensory neurons, where olfactory receptor (Or) genes are expressed. Each sensory neuron only expresses up to three receptors, making it difficult to estimate expression levels by conventional methods. In this study, we applied Illumina RNA sequencing (RNA-seq) to study the expression levels of Or and other genes in fly antennae.
Results  RNA from approximately 1,200 pairs of adult antennae from each sex of Drosophila melanogaster was used to obtain the antennal transcriptome of each sex. We detected approximately 12,000 genes expressed in antennae of either sex. The most highly expressed genes included pheromone-binding genes, transmembrane transporter genes, and sensory reception genes. Among the 61 annotated Or genes, we observed 53 and 54 genes (approximately 90%) expressed (fragments per kilobase of exon per million fragments mapped (FPKM) > 0.05) in male and female antennae, respectively; approximately 25 genes were expressed with FPKM > 15. Compared to previous studies, which extracted RNA from the whole body or head and used microarrays, antenna-specific transcriptomes obtained by RNA-seq provided more reliable estimates of gene expression levels and revealed many lowly expressed genes. Ninty-one genes, including one odorant-binding protein (Obp) gene and four Or genes, were differentially expressed between male and female antennae. These sexually biased genes were enriched on the X chromosome and showed enrichment in different gene ontology categories for male and female flies. The present and previous data together suggest that a gene family with putative immune response functions is related to pheromone detection and involved in the courtship behavior of male flies.
Conclusions  Tissue-specific RNA-seq is powerful for detecting lowly expressed genes. Our study provides new insight into the expression of olfactory-related genes in Drosophila antennae.ophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species D. melanogaster and D. simulans.  Although several odorant binding protein (Obp) genes and olfactory receptor (Or) genes were suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking.  We therefore studied the antennal transcriptomes, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species.  Using a very stringent definition of differential gene expression, we found 147 genes (including 11 chemosensory genes) were up-regulated while only 81 genes (including 5 chemosensory genes) were down-regulated in D. sechellia.  Interestingly, Obp50a exhibited the highest up-regulation, a ~100 fold increase, and Or85c – previously reported to be a larva-specific gene– showed ~20 fold up-regulation in D. sechellia.  Furthermore, Ir84a, proposed to be associated with male courtship behavior, is significantly up-regulated in D. sechellia.  We also found expression divergence in most of the receptor gene families between D. sechellia and the two sibling species.  Our observations suggest that the host shift of D. sechellia is associated with expression profile divergence in all chemosensory gene families and is achieved mostly by up-regulation of chemosensory genes.the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species (GSE60428) and HiC analysis in Drosophila melanogaster. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of  PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter

overall_design: RNAseq experiments in wild type drosophila antennaes

first: Meng-Shin

last: Shiao

first: Wen-Lang

last: Fan

first: Shu

last: Fang

first: Mei-Yeh

middle: J

last: Lu

first: Rumi

last: Kondo

first: Wen-Hsiung

last: Li


title: Gene Expression Changes in MDP and CDP from PyMT B6 Tumor Bearing Mice

city: Saint Louis

first: David

last: DeNardo

state: MO

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

summary: To understand how tumor burden influences gene expression in dendritic cell progenitors, we profiled gene expression in macrophage dendritic cell progenitors (MDP) and common dendritic cell progenitors (CDP) by microarray

overall_design: MDPs and CDPs were isolated from the bone marrow of mice bearing end stage orthotopic PyMT B6 mammary tumors, and non-tumor bearing controls. Four independent experiments were performed.

first: Melissa

middle: A

last: Meyer

middle: G


title: Effect of TUNAR silencing and GSK3 inhibition on human b-cell transcriptome

city: Mölndal

first: Alex-Xianghua

last: Zhou

state: - If in U.S, Select a State -

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca R&D Gothenburg

summary: The aim of the study is to identify the target genes of long noncoding RNA TUNAR in human EndoC-βH1 cells with or without treatment of GSK3 inhibitor.

overall_design: Human EndoC-βH1 cells were treated with negative siRNA or TUNAR siRNA, and then subjected to GSK3 inhibitor 1-AKP or not. Differentially expressed genes were identified by quantifying transcriptome by RNA-seq.

first: Magnus

last: Althage


title: MiR-204-3p inhibits the production of TLR4-related cytokines in familial Mediterranean fever by targeting the PI3Kγ signaling pathway

city: Nagasaki

first: Tomohiro

last: Koga

address: 1-7-1 Sakamoto

country: Japan

institute: Nagasaki University

summary: Our data suggest that serum miR-204-3p has a potential as a useful biomarker among patients with FMF and that miR-204-3p plays a critical role as a suppressor to regulate the production of TLR4-related cytokines by targeting PI3K signaling pathway.

overall_design: The RNA was obtained from THP-1 cells after LPS stimulation. Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). We performed the cDNA microarray using the SurePrint G3 Human GE 8x60K Microarray.

first: Tomohito

last: Sato

first: Atsushi

last: Kawakami


title: Natural RNA polymerase aptamers regulate transcription in E. coli [SELEX]

city: Vienna

first: Philipp

last: Rescheneder

address: Dr. Bohr Gasse 9

country: Austria

institute: MFPL

summary: In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP) we deep-sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches we characterized a subset of RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing growth conditions. The mechanism of iRAPs involves active uncoupling of transcription and translation, making the nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription.

overall_design: Examination of RNAP-binding aptamers in E. coli based on a single paired-end SELEX library sequenced on an Illumina GA Iix

first: Nadezda

last: Sedlyarova

first: Andrés

last: Magán García

first: Niko

last: Popitsch

first: Natascha

last: Rziha

first: Ivana

last: Bilusic

first: Vitaly

last: Epshtein

first: Bob

last: Zimmermann

first: Meghan

last: Lybecker

last: Sedlyarov

first: Renée

last: Schroeder

first: Evgeny

last: Nudler


title: Natural RNA polymerase aptamers regulate transcription in E. coli [3' RACE]

overall_design: Examination of E. coli 3' ends with two independent replicates sequenced on Illumina HiSeq 2000


title: Global gene expression in Abp57-overexpressing transgenic rice

city: Bangi

first: Lay Wen

last: Tan

state: Selangor

address: The National University of Malaysia

country: Malaysia

institute: Institute of Systems Biology

summary:
An auxin-binding protein (Abp57) was previously isolated from rice and known to activate plasma membrane proton ATPase. The Abp57 function was characterised by overexpression in the rice and Arabidopsis. The transgene expression was driven by constitutive promoter, CaMV35S. Results from physiological experiments showed that the transgenic lines were tolerant to drought and salinity stress.
The global effects of Abp57 overexpression in rice were studied using microarray platform from Affymetrix.

overall_design: Control and transgenic rice seeds were germinated and grown on MS medium for 10 days under controlled condition. Total RNA was prepared from whole seedling and the experiment was conducted with two groups of samples: control and Abp57-overexpressing lines. Each group of the sample contains three biological replicates and every biological replicates was consisted of at least three seedlings tissue. The total RNA was processed for microarray analysis according to Affymetrix protocol.

first: Zamri

last: Zainal


title: Transcriptome of S. acidocaldarius MW001 strain grown as biofilm or planktonic cells and transcriptomic profile of an RNaseR-treated S. acidocaldarius MW001 small RNA sample

status: Public on May 31 2017

city: Marburg

first: Alvaro

last: Orell

state: Hessen

address: Karl-von-Frisch-Str. 32

department: B

country: Germany

institute: Max Planck Institute for Terrestrial Microbiology

type: Non-coding RNA profiling by high throughput sequencing

summary: Total RNAs were isolated from the thermophilic archaeon Sulfolobus acidocaldarius MW001 and subjected to Illumina sequencing. A differential gene expression analysis was performed to identify ncRNA in biofilm- associated cells and planktonically grown cells. Additionally, the small RNA subpopulation of the transcriptome was subjected to RNaseR digestion prior to Illumina sequencing. An abundant double-stranded RNA was identified.

overall_design: S. acidocaldarius total RNA isolates from biofilm and planktonic cells were subjected to Illumina Hiseq2000 sequencing. In addition, a transcriptome enriched for small RNA sequences was subjected to RNase R digestion and the products were sequenced using Illumina Hiseq2000.

first: Lennart

last: Randau


title: Natural RNA polymerase aptamers regulate transcription in E. coli

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

overall_design: Refer to individual Series


title: Arabidopsis Col0 5 week-old plants: effect of DCMU on high-light treated plants

city: Colchester

first: Ruben

last: Alvarez-Fernandez

address: Wivenhoe Park

department: Biological Sciences

country: United Kingdom

institute: University of Essex

summary: Transcriptional profiling of fully developed leaves of Arabidopsis Col0 plants treated with 50 µM DCMU in high light stress.The aim of the experiment was to determine the specific effect of uncoupling electron transport from Photosystem II (by treatment of leaves with DCMU) under high light conditions compared with the effect of high light treatment alone.

overall_design: two-condition, two-color experiment, HL (Control) vs. DCMU+HL (treatment), 4 biological replicates per treatment. The experiment comprised a single 4x44 Agilent V4 microarray slide with a dye-swap.

first: Phillip

middle: M

last: Mullineaux


title: RNA-seq of sexed adult tissues/body parts from eight Drosophila species

status: Public on Jun 02 2017

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary:
This data set contains polyA+ transcriptional profiling of sexed adult tissues/body parts and whole adults of eight Drosophila species: Drosophila melanogaster (FBsp00000001) from two strains [w1118 (FBst0005905) and Oregon-R (FBst0025211)], Drosophila yakuba (FBsp00000254), Drosophila ananassae (FBsp00000052), Drosophila pseudoobscura (FBsp00000201), Drosophila persimilis (FBsp00000188), Drosophila willistoni (FBsp00000253), Drosophila mojavensis (FBsp00000160), and Drosophila virilis (FBsp00000251).

It is worth noting that the Samples (856) section of this series page only lists the top 500 samples, and the rest of the 356 samples are not shown in the list but are available in GEO by putting the GSM ID in the search box at the top of the page.   All raw data are available by clicking the SRP108530 link (SRA section). It is noteworthy that all of the fourth replicate of our samples are included in the last  356 samples in this series. Please see the supplementary file "All_samples_with_title.txt" for a complete list of GSM IDs and sample titles.

sample_organism:
Drosophila ananassae
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis
Drosophila pseudoobscura
Drosophila virilis
Drosophila yakuba
Drosophila willistoni
synthetic construct

overall_design: Samples were collected in quadruplicate from sexually-mature freely-mated adults (4 to 14 days post-eclosion).  Samples were either sexed whole flies (individual) or tissues/body parts (pooled from 2-5 flies).  For the two strains of D. melanogaster, we profiled whole flies along with seven adult tissues/body parts for each sex.  Dissection examples are shown in Figure 1.  Samples were whole organism (FBbt:00003004), head (FBbt:00003007, Fig. 1A), thorax (FBbt:00003018, Fig. 1B) without digestive system, abdomen (FBbt:00003023, Fig. 1C) without digestive or reproductive system, gonad [female (FBbt:00004865, Fig. 1D) or male (FBbt:00004928, Fig. 1E)], reproductive system [female (FBbt:00004864, Fig. 1F) or male (FBbt:00004927, Fig. 1G)] without gonad or genitalia, genitalia [female (FBbt:00004827, Fig. 1H) or male (FBbt:00004828, Fig. 1I)], and digestive (FBbt:00003123) plus excretory (FBbt:00005724) system (Fig. 1J).  For non-melanogaster species, we dissected as above except genitalia were included in the reproductive system without gonad.  Non-melanogaster strains were: D. yakuba (Drosophila Species Stock Center ID: 14021-0261.01), D. ananassae (14021-0371.13), D. pseudoobscura (14011-0121.94), D. willistoni (14030-0811.24), D. virilis (15010-1051.87), D. persimilis (14011-0111.49), and D. mojavensis (15081-1352.22).  After extracting RNA from each sample, we mixed equal amounts of total RNA (except genitalia samples from D. melanogaster) from each of three genetically distant species (rate of cross-mapping in simulations < 0.6%).  Specifically, we mixed RNA of:  1) D. melanogaster (w1118), D. pseudoobscura, and D. virilis; 2) D. melanogaster (Oregon-R), D. mojavensis, and D. persimilis; 3) D. yakuba, D. ananassae, and D. willistoni.  We isolated polyA+ RNA from these pools and prepared RNA-seq libraries, which were further multiplexed with indexed adaptors and pooled for sequencing.

first: Haiwang

last: Yang

first: Maria

last: Jaime

first: Sharvani

last: Mahadevaraju

first: Maxi

last: Polihronakis


title: RNA-seq analysis of scaffold attachment factor A (SAF-A) knockdown in RPE1 cells

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

department: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary: Analysis of gene expression by RNA-seq upon siRNA mediated knockdown of scaffold attachment factor A (SAF-A) versus control siRNA in RPE1 cells at 24 hour and 48 hour time points post transfection reveals SAF-A loss does not impact on gene transcription

overall_design: Two control RNA-seq libraries where produced (24h and 48h) to compare to the two SAF-A siRNA knockdown RNA-seq libraries, each was a single experimental replicate.

first: Ryu-Suke

last: Nozawa

first: Lora

last: Boteva

first: Dinesh

middle: C

last: Soares

first: Catherine

last: Naughton

first: Alison

middle: R

last: Dun

first: Adam

last: Buckle

first: Bernard

last: Ramsahoye

first: Peter

last: Bruton

first: Rebecca

middle: S

last: Saleeb

last: Arnedo

first: Bill

last: Hill

first: Rory

last: Duncan

first: Sutherland

middle: K

last: Maciver

first: Nick

last: Gilbert


title: Transcriptome analysis of deletion of cre1 in T. reesei upon growth on cellulose in light and darkness

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

institute: University of Vienna

summary: The aim of this study was to evaluate changes in the transcriptome due to the lack of CRE1 in light or darkness.

overall_design: Strains of this study were grown on Mandels Andreotti Minimal Medium with 1 % w/v microcrystalline cellulose as sole carbon source in constant light or constant darkness for 72 hours; 2 biological replicates were included

first: Andre

last: Schuster


title: Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA-mediated miRNA evasion

city: Shenyang City

first: Zhenning

last: Wang

address: 155 North Nanjing Street

department: Department of Surgical Oncology and General Surgery

country: China

institute: The First Affiliated Hospital of China Medical University

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA-mediated miRNA evasion (lncRNA)

summary: Thousands of genes have been well demonstrated to play important roles in cancer progression. As genes do not function in isolation, they can be grouped into “networks” based on their interactions. In this study, we discover a network regulating Claudin-4 (CLDN4) in gastric cancer. We observe that CLDN4 is up-regulated in gastric cancer and is associated with poor prognosis. CLDN4 reinforce proliferation, invasion, and EMT in AGS, HGC-27, and SGC-7901 cells, which could be reversed by miR-596 and miR-3620-3p. Additionally, lncRNA-KRTAP5-AS1 and lncRNA-TUBB2A could act as competing endogenous RNAs to affect the function of CLDN4. Our results suggest that non-coding RNAs (ncRNAs) play important roles in the regulatory network of CLDN4. As such, ncRNAs should be considered as potential biomarkers and therapeutic targets against gastric cancer

overall_design: The gene expression in paired gastric cancer and adjacent non-tumourous tissues were measured. Six independent pairs of gastric cancer tissues and adjacent non-tumorous tissues from different patients were collected for microarray examination


title: Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA-mediated miRNA evasion (miRNA)

overall_design: The miRNA expression in paired gastric cancer and adjacent non-tumourous tissues were measured. Six independent pairs of gastric cancer tissues and adjacent non-tumorous tissues from different patients were collected for microarray examination.


title: Treatment of human AML cell lines MOLM-14 and THP-1 with MUC1 specific shRNA

city: Boston

first: Athalia

middle: Rachel

last: Pyzer

state: MA

address: 3 Blackfan Circle CLS 724

institute: BIDMC

summary: The human acute myeloid leukemia cell lines MOLM-14 and THP-1 were silenced for MUC1 expression by  lentiviral transduction of MUC1 specific shRNA or scrambled control. RNA was extracted and NanoString array for microRNAs was performed.

overall_design: Twelve samples from two cell lines.

first: Dina

last: Stroopinsky


title: Expression profiles of Nrdc-depleted pancreas

city: Kyoto

first: Kozo

last: Ikuta

address: 54 Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Gastroenterology and Hepatology

institute: Kyoto University Graduate School of Medicine

summary: Pancreatic ductal adenocarcinoma (PDA) is the devastating disease in urgent need to identify new strategies for diagnosing and treating. Chronic pancreatitis is a risk factor for PDA in humans. Nardilysin (Nrdc, NRDC), a zinc peptidase of the M16 family has been shown to promote cancer cell growth in vitro. Here, we report that pancreatic deletion of Nrdc dramatically accelerates formation of pancreatic intraepithelial neoplasia (PanIN) and invasive PDA in the presence of oncogenic Kras. Nrdc was expressed in the nucleus of pancreatic acinar cells and pancreatic deletion of Nrdc was dispensable for pancreatic development in mice, but led to spontaneous chronic pancreatitis concomitant with acinar-to-ductal conversion, fibrotic change, infiltrated inflammatory cells, increased apoptosis, and atrophic pancreas in adult mice. Ex vivo acinar cell explants culture experiments showed that acinar-to-ductal conversion was not induced through a cell autonomous mechanism and that expression of several chemokines, including Cxcl10, was markedly up-regulated in Nrdc-null pancreatic acinar cells. Microarray analysis revealed that pathways implicated in pancreatitis and tumorigenesis, including chemotaxis, NF-κB and Erk1/2 signaling, were up-regulated in Nrdc-cKO pancreata compared with WT controls. Finally, immunostaining for NRDC revealed absence of NRDC expression in a subset of human PanINs and PDAs. These data demonstrate a previously unappreciated tumor suppressive function of Nrdc in the pancreas through suppressing chronic pancreatitis with acinar-to-ductal conversion in mice.

overall_design: We sought to clarify the role of Nardilysin in the exocrine pancreas. To determine changes in gene expression in Ptf1a-Cre; Nrdcflox/flox pancreas, we performed global gene expression analyses in WT and Ptf1a-Cre; Nrdcflox/flox pancreas at 5 weeks of age.

first: Akihisa

last: Fukuda


title: miRNA gene expression of human blood cells from healthy donors

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

summary: Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-landscape of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors. For each blood cell population, RNA from 5 healthy donors was hybridized onto three microarray platforms (Arraystar lncRNA V2.0, NCode™-miRNA/-ncRNA), yielding a coverage of more than 40,000 lncRNAs, 25,000 mRNAs and 900 miRNAs on 146 arrays. T-distributed stochastic neighbor embedding (t-SNE) on noncoding genes structured the dataset into groups of samples that matched the input populations, demonstrating their unique lncRNA expression profiles. Self-organizing maps (SOMs) revealed clusters of lncRNAs and mRNAs that were coordinately expressed in HSCs and during lineage commitment. Using a “guilt-by-association” approach we assigned putative functions to lncRNAs regulated during differentiation, which predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. Next, we uncovered a strong and highly coordinated upregulation of miRNAs, small nucleolar RNAs (snoRNAs) and lncRNAs  within the DLK1-DIO3 locus on chromosome 14 (hsa14) during megakaryocytic maturation.  shRNA-mediated knock-down of noncoding members of the locus reduced erythroid colony-formation and megakaryocytic cell proliferation in vitro implicating the functional importance of this ncRNA locus in megakaryopoiesis.

overall_design: Mature blood cells (granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors) and hematopoietic stem and progenitor cells from healthy donors were FACS-purified and total RNA was subjected to Microarray Analysis on the Agilent-021827 Human miRNA Microarray G4470C (miRNA ID version, miRBase v18, GPL22949)

first: Adrian

last: Schwarzer


title: Gene expression analysis in OLETF, a type 2 diabetic rats, and LETO, a non-diabetic control rats

city: Sapporo

first: Masaya

last: Tanno

department: Department of Cardiovascular, Renal and Metabolic Medicine

institute: Sapporo Medical University

platform_organism:
Mus musculus
Rattus norvegicus


title: Mapping PRDM9 binding and its effects in transfected HEK293T cells

city: Berkeley

first: Nicolas

last: Altemose

state: CA

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report ChIP-seq, RNA-seq, and ATAC-seq results from HEK293T cells transfected with various versions of the meiotic recombination protein PRDM9, in order to learn about its DNA-binding properties, its effects on gene expression and chromatin organization, and which epigenetic factors influence binding and recombination outcomes.

overall_design: ChIP-seq data on tagged transfected PRDM9 alleles in HEK293T cells, plus H3K4me3 and H3K36me3 ChIP-seq data and RNA-seq and ATAC-seq data from transfected and untransfected HEK293T cells.

first: Simon

last: Myers


title: Gene expression data of human chord blood hematopoietic progenitor cells subjected to myeloid differentiation and transduced with shRNAs against LINC00173

summary: Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. We predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. In addition, both shRNA and CRISPR-KRAB mediated knock-down of LINC00173 showed reduced cell proliferation in stem cells and NB4 cells (2-3-fold, p≤0.01). Here we assess early effects of LINC00173 knockdown in human HSPC subjected to myeloid differentiation conditions.

overall_design: Human CD34+ HSPC from chord blood were transduced with shRNAs against LINC00173 or a control shRNA. Transduced cells were subjected to myeloid differentiation conditions. We analyzed early gene expression changes of LINC00173 knockdown using Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarrays


title: Coding and noncoding gene expression of 48 pediatric AML samples

summary: Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-transcriptome of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors, which we correlated with the ncRNA expression profile of 48 pediatric AML samples to establish a core lncRNA stem cell signature in AML.Linear (PCA) and nonlinear (t-SNE) dimensionality reduction of 46 pediatric AML samples including Down syndrome AMKL, core-binding factor AMLs (inv[16] or t[8;21]) and MLL-rearranged leukemias mapped most samples to a space between HSCs and differentiated cells together with the myeloid progenitors. A subset of AML-samples mapped closely to healthy HSCs, including most of the DS-AMKLs and MLL-AMLs. Following the incorporation of acute myeloid leukemia (AML) samples into the landscape, we further uncover prognostically relevant ncRNA stem cell signatures shared between AML blasts and healthy hematopoietic stem cells.

overall_design: AML blasts from 48 pediatric AML samples were FACS-purified and total RNA was subjected to Microarray Analysis on the Arraystar Human LncRNA microarray V2.0 (Agilent-033010) platform

first: Jan

last: Henning-Klusmann


title: Coding and noncoding gene expression of human blood cells from healthy donors (Agilent-033010)

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

overall_design: Mature blood cells (granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors) and hematopoietic stem and progenitor cells from healthy donors were FACS-purified and total RNA was subjected to Microarray Analysis on the Arraystar Human LncRNA microarray V2.0 (Agilent-033010) platform.


title: Progressive  motor  neuron  pathology  and  the  role  of  astrocytes  in  a  human  stem  cell model of VCP-related ALS

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

summary: Motor   neurons (MNs)   and   astrocytes   (ACs) are   implicated   in   the   pathogenesis   of amyotrophic  lateral  sclerosis  (ALS),  but  their  interaction  and  the  sequence  of  molecular events leading to MN death remain unresolved. Herewe optimized directed differentiation of induced pluripotent stem cells (iPSCs) into highly enriched (>85%) functional populations of  spinal  cord  MNs  and  ACs.  We  identifysignificantlyincreased  cytoplasmic  TDP-43  and  ER stress as  primary  pathogenic  events in patient-specific  valosin-containing  protein  (VCP)-mutant MNs, with  secondary  mitochondrial  dysfunction  and  oxidative  stress.  Cumulatively these  cellular  stresses  result  in  synaptic  pathology  and  cell death  in  VCP-mutant  MNs. We additionallyidentify  a  cell-autonomous VCP-mutant  AC  survival  phenotype, which   is   not attributable  to  the  same  molecular  pathology  occurring in VCP-mutant MNs. Finally, through iterative  co-culture  experiments,  we  uncover  non-cell-autonomous  effects  of  VCP-mutant ACs  on  both  control  and  mutant  MNs.  This  work  elucidates  molecular  events  and  cellular interplay thatcould guide future therapeutic strategies in ALS.

overall_design: Bulk RNA-seq at different timepoints throughout a 35-day differentiation protocol that converted iPSC cells to highly enriched motor neurons.

first: Claire

last: Hall

first: Zhi

last: Yao

first: Minee

last: Choi

first: Giulia

last: Tyzack

first: Andrea

last: Serio

first: Jasmine

last: Harley

first: Elisavet

last: Preza

first: Charlie

last: Arber

first: Sarah

last: Crisp

first: P

last: Watson

first: Dimitri

last: Kullmann

first: Andrey

last: Abramov

first: Selina

last: Wray

first: Russell

last: Burley

first: Sam

middle: H

last: Loh

first: Miguel

middle: L

last: Martins

first: Molly

last: Stevens

first: Nicholas

last: Luscombe

first: Christopher

last: Sibley

first: Andras

last: Lakatos

first: Jernej

last: Ule

first: Sonia

last: Gandhi

first: Rickie

last: Patani


title: Reduced circulating insulin enhances insulin sensitivity in old mice and extends lifespan

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

summary: The causal relationships between insulin levels, insulin resistance, and longevity are not fully elucidated. Genetic down-regulation of insulin/insulin-like growth factor 1 (Igf1) signaling components can extend invertebrate and mammalian lifespan, but insulin resistance, a natural form of decreased insulin signaling, is associated with greater risk of age-related disease in mammals. We compared Ins2+/- mice to Ins2+/+ littermate controls, on a genetically stable Ins1-null background. Proteomic and transcriptomic analyses of livers from 25 week-old mice suggested potential for healthier aging and altered insulin sensitivity in Ins2+/- mice. Halving Ins2 lowered circulating insulin by 25-34% in aged female mice, without altering Igf1 or circulating Igf1. Remarkably, decreased insulin led to lower fasting glucose and improved insulin sensitivity in aged mice. Moreover, lowered insulin caused significant lifespan extension, observed across two diverse diets. Our study indicates that elevated insulin contributes to age-dependent insulin resistance, and that limiting basal insulin levels can extend lifespan.

overall_design: RNAsequencing expression profiles of livers and triceps surae hindlimb muscle from 25 week-old Ins1-/-;Ins2+/- and Ins1-/-;Ins2+/+ littermate control mice on one of two different diets (Diet A and B)

first: James

middle: D

last: Johnson

first: Nicole

last: Templeman


title: GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary:
Genome-wide transcription studies are revealing increasing examples of ‘dispersed promoters’ that unlike ‘focused promoters’, lack well-conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well-defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters.
Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation and occurs over broad regions without distinct promoter motifs and lacks regulation. Using a combination of site-specific and genome-wide assays, we identified GT-rich promoters that can drive unidirectional transcription and promote the targeted deposition of the histone variant H2A.Z in a genomic context dependent manner. In addition, upon mapping nucleosome occupancy at high resolution, we find nucleosome positioning to correlate with RNA pol II enrichment and gene expression, pointing to a role in RNA maturation. Nucleosome positioning may thus represent a previously unrecognized layer of gene regulation in trypanosomes.
Our findings show that even highly dispersed, unregulated promoters contain specific DNA elements that are able to induce transcription and changes in chromatin structure.

overall_design: 1) The essential RNA pol II subunit RPB9 was tagged with the TY epitope tag and ChIP was performed to generate a genome-wide map of RNA pol II stalling. 2) To map transcription initiation sites small total RNA < 200 nt was purified from T. brucei and enriched for primary transcripts containing a 5´-triphosphate by depletion of 5´-monophsphate-containing RNA using a Terminator 5´-Phosphate-Dependent Exonuclease (TEX). To identify undigested monophosphate-containing RNA contaminants, the sample was split and libraries were prepared from 5´-Polyphosphatase treated and untreated material. 3) Examination of nucleosome positioning in T. brucei bloodstream-form (BF) Wt and GT-rich promoter driven targeted H2A.Z depositioning in genetically modified T. brucei bloodstream-form cells expressing T7 RNA polymerase and Tet repressor (SM). We introduced a 210 bp GT-rich promoter sequence, its reverse complement and a 416 bp GT-rich promoter sequence in the center of a divergent transcription start region in T. brucei. The sequences are located at the genomic location Tb427_01_v4:284987-285196 and Tb427_01_v4:284987-285402, resp.

first: Carolin

last: Wedel

first: T

middle: N

last: Siegel


title: Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models

first: Raphaelle

last: Luisier

overall_design: Refer to individual Series


title: Large-scale assessment of the gliomasphere model system

status: Public on May 27 2017

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary:
Some aspects of the gene expression-based classification method were robust because the gliomasphere cultures retained their classification over many passages, and IDH1 mutant gliomaspheres were all proneural. While gene expression of a subset of gliomasphere cultures was more like the parent tumor than any other tumor, gliomaspheres did not always harbor the same classification as their parent tumor. Classification was not associated with whether a sphere culture was derived from primary or recurrent GBM or associated with the presence of EGFR amplification or rearrangement. Unsupervised clustering of gliomasphere gene expression distinguished 2 general categories (mesenchymal and nonmesenchymal), while multidimensional scaling distinguished 3 main groups and a fourth minor group. Unbiased approaches revealed that PI3Kinase, protein kinase A, mTOR, ERK, Integrin, and beta-catenin pathways were associated with in vitro measures of proliferation and sphere formation. Associating gene expression with gliomasphere phenotypes and patient outcome, we identified genes not previously associated with GBM: PTGR1, which suppresses proliferation, and EFEMP2 and LGALS8, which promote cell proliferation.
This comprehensive assessment reveals advantages and limitations of using gliomaspheres to model GBM biology, and provides a novel strategy for selecting genes for future study.

overall_design: We used 71 gliomasphere cultures from 68 individuals. Using gene expression-based classification, we performed unsupervised clustering and associated gene expression with gliomasphere phenotypes and patient survival.

first: Dan

last: Laks

first: Thomas

last: Crisman

first: Michelle

middle: Y

last: Shih

first: Jack

last: Mottahedeh

first: Fuying

last: Gao

first: Jantzen

last: Sperry

first: Matthew

last: Garrett

first: William

last: Yong

first: Timothy

middle: F

last: Cloughesy

first: Linda

last: Liau

first: Albert

last: Lai

first: Harley

middle: I

last: Kornblum


title: DNA methylation profiling of human prefrontal cortex neurons in heroin users shows significant difference between genomic contexts of hyper- and hypomethylation and a younger epigenetic age

status: Public on May 30 2017

city: Bronx

first: Stella

last: Dracheva

state: New York

address: James J. Peters VA Medical Center,130 W Kingsbridge Rd

department: Dept. of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

type: Methylation profiling by genome tiling array

summary: Illumina 450K Infinium microarray profiling of DNA methylation in FACS-separated neuronal nuclei from the postmortem orbitofrontal (OF) cortex of heroin users, controls and sucide individuals.

overall_design: Genomic DNA was isolated from FACS-sorted human brain neuronal nuclei. DNA was bisulfite-converted and hybridized to the Illumina Infinium 450K Human Methylation Beadchip array. 88 subjects were analyzed.

first: Alexey

last: Kozlenkov


title: Expression data from adolescent mice exposed with ethanol at birth and controls

status: Public on May 26 2017

city: Toronto

first: Eric

middle: J

last: Chater-Diehl

state: ON

address: 686 Bay St.

institute: SickKids Research Institute

summary:
Exposure of mice to ethanol during the first neonatal week models human trimester three fetal ethanol exposure. These mice show characteristic learning and memory impairment that may be explained by gene expression changes in the hippocampus.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Mice were injected with  2.5 g/kg of ethanol in 0.15 M NaCl spaced two hours apart on post natal days 4 and 7. On postnatal day 21, mice were sacrificed via carbon dioxide asphyxiation and cervical spinal dislocation. The hippocampus was dissected and stored at -80 degrees C until RNA and DNA were simultaneously isolated. RNA was hybridized to Affymetrix 2.0 expression arrays.

first: Dustin

last: Sokolowski

first: Shiva

last: Singh


title: Molecular characterization of breast cancer circulating tumor cells (CTCs) associated with brain metastasis

city: Albuquerque

first: Dario

last: Marchetti

state: NM

address: 1 University of New Mexico

department: Internal Medicine

institute: University of New Mexico

summary:
The enumeration of EpCAM-positive circulating tumor cells (CTCs) has allowed clinicians to estimate the overall metastatic burden in breast cancer patients. However, a thorough understanding of CTCs associated with breast cancer brain metastasis (BCBM) is necessary for early identification and evaluation of treatment response to BCBM. In this study, we report that BCBM CTCs are enriched in a distinct sub-population of cells identifiable by their biomarker expression and mutational content.
Here we report the discovery of a unique “CTC gene signature” that is distinct from primary breast cancer tissues. Further dissection of the CTC signature identified signaling pathways associated with BCBM CTCs that may play roles in potentiating BCBM.

overall_design:
Blood samples were collected from 10 advanced-stage breast cancer patients at MD Anderson Cancer Center according to an IRB-approved protocol. While all 10 patients had metastatic breast cancer with multi-organ involvement; only 5 patients had clinically detectable brain metastasis (BCBM), while the other 5 did not have brain metastasis (No BCBM). After red blood cell lysis, the remaining buffy coat layer was subjected to flow cytometry for isolation of circulating tumor cells (CTC) following a workflow made of three sequential steps – (i) doublet discrimination and dead cell elimination (DAPI-), (ii) depletion of cells normally present in the peripheral blood using lineage-specific (CD45-/CD34-/CD105-/CD90-/CD73-) antibodies, and (iii) positive selection of PanCK+ (epithelial) or CD44+/CD24- (stem-like) CTCs. Sorted cells were collected directly into a pre-chilled tube maintained at 4oC containing RNA lysis buffer and total RNA was collected followed by RNA and cDNA amplifications, quality controls and gene expression arrays using the Affymetrix HTA 2.0 array. CTC gene expression was compared to whole gene expression data from 31 breast cancer patient samples representing each of the most common molecular subtypes were obtained from three publicly available GEO datasets (GSE65505 – ER+/PR+/HER2-, GSE67982 – ER+/PR+/HER2+, GSE76250 – triple negative breast cancer. As a control experiment, whole gene expression of CD4+ and CD8+ T-cells were also compared using data from GSE73079 and GSE73081, respectively. Comparison between CTC and primary breast cancer transcriptomes provided the transcriptomic landscape of breast cancer CTCs in general while further dissection into the BCBM and No BCBM subtypes yielded a 126-gene signature of BCBM associated CTCs.
breast cancer without brain metastasis (No BCBM): BrPt1CTC, BrPt2CTC, BrPt3CTC, BrPt4CTC, BrPt5CTC
breast cancer with brain metastasis (BCBM): BrPt6CTC, BrPt7CTC, BrPt8CTC, BrPt9CTC, BrPt10CTC
biological replicate: BrPt1CTC, BrPt2CTC, BrPt3CTC, BrPt4CTC, BrPt5CTC
biological replicate: BrPt6CTC, BrPt7CTC, BrPt8CTC, BrPt9CTC, BrPt10CTC

first: Debasish

last: Boral


title: PRC2 overexpression and PRC2-target gene repression relating to poorer prognosis in small cell lung cancer

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

institute: The University of Tokyo

summary: Small cell lung cancer (SCLC) is a subtype of lung cancer with poor prognosis. Expression array analysis of 23 SCLC cases and 42 normal tissues revealed that EZH2 and other PRC2 members were highly expressed in SCLC. ChIP-seq for H3K27me3 suggested that genes with H3K27me3(+) in SCLC were extended not only to PRC2-target genes in ES cells but also to other target genes such as cellular adhesion-related genes. These H3K27me3(+) genes in SCLC were repressed significantly, and introduction of the most repressed gene JUB into SCLC cell line lead to growth inhibition. Shorter overall survival of clinical SCLC cases correlated to repression of JUB alone, or a set of four genes including H3K27me3(+) genes. Treatment with EZH2 inhibitors, DZNep and GSK126, resulted in growth repression of SCLC cell lines. High PRC2 expression was suggested to contribute to gene repression in SCLC, and may play a role in genesis of SCLC.

overall_design: ChIP using H3K27me3 or Suz12 antibody was performed, and sequencing was performed using Illumina Genome Analyzer Iix.

first: Teruyuki

last: Sato

first: Shingo

last: Tsuji

first: Takayuki

last: Isagawa

first: Shogo

last: Yamamoto

first: Takanori

last: Fujita

first: Ryota

last: Yamanaka

first: Yukiko

last: Tanaka

first: Yuichi

last: Ishikawa

first: Hiroyuki

last: Aburatani


title: Human basal-like breast cancer cell line HCC1143 treated with BET inhibitor JQ1 in combination with MEK inhibitor Trametinib or PI3K/mTOR inhibitor BEZ235

city: Portland

first: Tyler

last: Risom

state: Oregon

address: 2730 SW Moody Ave

department: Molecular Medical Genetics

institute: Oregon Health & Science University

summary: The goal of this experiment was to understand the changes in gene expression in the human basal-like breast cancer cell line HCC1143 following treatment with the MEK inhibitor Trametinib (T), PI3K/mTOR inhibitor BEZ235 (B), the BET inhibition JQ1 (JQ), Trametinib + JQ1 (TJ), or BEZ235 + JQ1(BJ), compared to a DMSO control (D). Samples were treated for 72hr and run in triplicate.

overall_design: The human basal-like breast cancer cell line HCC1143 was treated for 72hr with 1uM Trametinib (T), 1uM BEZ235, 1uM JQ1 (JQ), 1uM Trametinib + 1uM JQ1 (TJ), 1uM BEZ235 + 1uM JQ1 (BJ), or a 0.05% DMSO control. Total RNA was isolated using a QIAGEN total RNA RNeasy kit, libraries were generated with a Truseq kit, and samples were run on the Nextseq500, data processing is described below.

first: Rosalie

last: Sears


title: Gene expression profiles of intestinal tumors originating from different cell compartments

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary:
Introduction of mutations into intestinal stem cells leads to tumorigenesis, therefore intestinal stem cells are believed to function as cell of origin of intestinal tumors. However in the case of additional protumorigenic stimuli differentiated cells can dedifferentiate and can also give rise to intestinal tumors. Expression of stabilized β-catenin (CtnnbloxEx3/+) and mutant KrasG12D/+ in all the intestinal cells by using Cre recombinase driven by the villin promoter (VilCreER) leads to rapid transformation and tumorigenesis. However, when the same mutations are introduced only into the differentited cell by the help of Xbp1sCreER mice also develop tumors.
In this study we wished to investigate if the cell of origin would impact the gene expression profile of intestinal tumors. Therefore we compared the gene expression profiles of early stage tumors derived from VilCreER CtnnbloxEx3/+ KrasG12D/+ mice and early stage tumors derived from Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+ mice by microarray.

overall_design: Mice were treated with 1 mg Tamoxifen on five consecutive days to induce the activity of the Cre recombinase and the expression of CtnnbloxEx3/+ and KrasG12D/+.  Both VilCreER CtnnbloxEx3/+ KrasG12D/+  and  Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+  mice were sacrificed when early intestinal tumors  were already present (day 7 for  VilCreER CtnnbloxEx3/+ KrasG12D/+ and day 21 for  Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+). RNA was extracted from isolated epithelial cell extracts of both genotypes.

first: Florian

last: Greten

first: Julia

last: Varga


title: Expression data from colons of mice fed psyllium fiber

city: Higashi-Hiroshima

first: Takuya

last: Suzuki

state: Hiroshima

address: 1-4-4 Kagamiyama

department: Graduate School of Biosphere Science

institute: Hiroshima University

summary:
Feeding dietary fiber is known to provide us many beneficial effects.
We used microarrays to detail the changes of gene expression in colons of mice fed the psyllium fiber for 5 days.

overall_design: Mice were devided into 2 groups, control and psyllium fiber. The psyllium fiber group fed the diet containing 10% psyllium for 5 days, whereas the control groups fed the diet without psyllium fiber. Total RNA were extracted from mouse colons and applied to the microarrays.


title: Human AsPC1-CFP and AsPC1-AKT PDAC orthotopic tumors: Lean vs Obese

first: Nada

last: Kalaany

address: 3 Blackfan Circle CLS 16067

institute: Boston Children's Hospital

summary: Transcriptional profiling comparing human AsPC1 PDA cells transduced with either CFP control or myristoylated-AKT orthotopically grown in pancreata of lean vs obese Rag1-/- immunodeficient mice for 5 weeks (100,000 cells/pancreas). The Goal was to determine the transcriptional deregulation of Obesity-driven and AKT-driven tumors.

overall_design: Four-condition experiment: AsPC1-CFP lean, AsPC1-CFP obese, AsPC1-AKT lean and AsPC1-AKT obese tumors all normalized to one control: AsPC1-CFP cells.  9 biological replicates per group.  Equal amounts of differentially labeled control AsPC1-CFP cells propagated in culture and sample tumor cRNA were combined such that each sample contained at least 2.5 pmol dye on dual-labeling arrays.

first: Tamara

last: Zaytouni


title: Coding and noncoding gene expression of human blood cells from healthy donors (Agilent-021441)

first: Jan-Henning

last: Klusmann

overall_design: Mature blood cells (granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors) and hematopoietic stem and progenitor cells from healthy donors were FACS-purified and total RNA was subjected to Microarray Analysis on the Agilent-021441 NCode Human Long Non-coding RNA microarrays (GPL18348)

first: Adrian

last: Schwarzer


title: Gene repression and ChIP-seq in Human Small Cell Lung Cancer

status: Public on May 25 2017

first: Atsushi

last: Kaneda

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


title: Expression data of chondrocytes subpopulations from WT, 13del and 13del:Chop-/- mice at P10 stage

city: Hong Kong S.A.R.

first: Kathryn

last: Cheah

state: Hong Kong

address: 3/F, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

department: School of Biomedical Sciences

institute: University of Hong Kong

summary:
The human metaphyseal chondrodysplasia type Schmid is an autosomal dominant disorder associated with mutations in COL10A1 gene that result in ER retention of misfolded alpha(X) collagen in hypertrophic chondrocytes (HCs). In a MCDS transgenic mouse model (13del), we have previously implicated HC response and adaptation to ER stress as the underlying molecular pathogenesis of the disease.
We generate microarray data from chondrocytes in WT, 13del and 13del:Chop-/- mice to elucidate the etiological role of ER stress signaling in MCDS.

overall_design: Proximal tibia growth plates from WT, 13del and 13del:Chop-/- mice at P10 stage were fractionated and global gene expression data were generated from different chondrocyte populations for systematic comparison to identify the key factors of chondrocyte adaptation to ER stress.

first: Zhijia

last: TAN

first: Cheng

last: Wang

first: Ben

last: Niu


title: Menin controls the memory Th2 cell function by maintaining the epigenetic integrity of Th2 cells. [RNA-Seq]

city: Chiba

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

institute: Chiba University

summary: Post-translational modifications of histones are well-established epigenetic modifications that play an important role in gene expression and regulation.  These modifications are partly mediated by the Trithorax group (TrxG) complex, which regulates the induction or maintence of gene transcription.  We investigated the role of Menin, a component of the TrxG complex, in the acquisition and maintenance of T helper type 2 (Th2) cell identity using T cell-specific Menin-deficient mice.  Our gene expression analysis revealed that Menin was involved in the maintenance of the high level expression of the previously identified Th2-specific genes rather than the induction of these genes.  This result suggests a role of Menin in the maintenance of Th2 cell identity.  Menin directly bound to the Gata3 gene locus, and this Menin-Gata3 axis appeared to form a core unit of the Th2-specific gene regulatory network.  Consistent with the phenotype of Menin-deficient Th2 cells observed in vitro, Menin deficiency resulted in the attenuation of effector Th2 cell-induced airway inflammation.  In addition, in memory Th2 cells, Menin was found to play an important role in the maintenance of the expression of Th2-specific genes, including Gata3, Il4, and Il13.  Consequently, Menin-deficient memory Th2 cells showed an impaired abiliy to recruit eosinophils to the lung, resulting in the attenuation of memory Th2 cell-induced airway inflammation.  This study confirmed the critical role of Menin in Th2 cell-mediated immune responses.

overall_design: Functions of Menin, a component of Trithorax group (TrxG) complex, are assessed by ChIP-seq and RNA-seq.

first: Masahiro

last: Kiuchi

first: Kota

last: Kokubo

first: Miki

last: Kato

first: Tomohiro

last: Ogino

first: Shu

last: Horiuchi

first: Urara

last: Kanai

first: Kiyoshi

last: Hirahara

first: Toshinori

last: Nakayama


title: Gene expression differences between fast and slow growing individuals of carpet-shell clam (Ruditapes decussatus) assessed with a microarray in gills

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: Gene expression profiles of fast and slow growing adult individuals of  Ruditapes decussatus

overall_design: In this work we studied individual growth rate for a three month period in a sample of clams taken from the Ria Formosa (Portugal). Gene expression was studied in tindividuals that showed the fastest (F) and the slowest (S) growth rates. The study was carried out separately in the gills and the digestive gland. In detail, fifty adult clams of ca. 30 mm were captured in February in Ria Formosa, near Faro (Portugal). Animals were labeled and transferred to the nearby Ramalhete Marine Station, where they were placed in a 400 L PVC tank located outdoors and supplied with running sea water pumped directly from the nearby sea. The animals therefore had access to the same food that they ingested in the natural habitat. The tank was covered with a nylon mesh that let the air flow normally but kept the animals out of the view of potential predators such as seagulls. Clams were inspected daily to check for mortality or stress symptoms. Temperature and salinity in the sea water was recorded daily.   Growth was recorded by measuring the increase in two dimensions of the animal shells. Measures of length and height were taken with a caliper at the onset and at the end of the experiment (12 weeks). The two measures were added up to give a single value of shell size. The growth rate for the study period was estimated as (Sf-Si)/Si, where Sf and Si stand for final and initial shell sizes, respectively.  Clams were opened by cutting the adductor muscles with a scalpel blade. Then the gills and the digestive gland were excised with the help of sterile forceps and scissors, and placed in separate 2 ml plastic tubes containing 1.5 ml of RNA Later® solution. The tissues were let soak at 4⁰C for 12 h and then stored at -80⁰C until further processed. Here gills data are reported

first: Milan

last: Massimo

first: Saavedra

last: Carlos

first: Bargelloni

last: Luca


title: Gene expression differences between fast and slow growing individuals of carpet-shell clam (Ruditapes decussatus) assessed with a microarray


title: Gene expression differences between fast and slow growing individuals of carpet-shell clam (Ruditapes decussatus) assessed with a microarray in digestive gland

overall_design: In this work we studied individual growth rate for a three month period in a sample of clams taken from the Ria Formosa (Portugal). Gene expression was studied in the 5 individuals that showed the fastest (F) and the slowest (S) growth rates. The study was carried out separately in the gills and the digestive gland. In detail, fifty adult clams of ca. 30 mm were captured in February in Ria Formosa, near Faro (Portugal). Animals were labeled and transferred to the nearby Ramalhete Marine Station, where they were placed in a 400 L PVC tank located outdoors and supplied with running sea water pumped directly from the nearby sea. The animals therefore had access to the same food that they ingested in the natural habitat. The tank was covered with a nylon mesh that let the air flow normally but kept the animals out of the view of potential predators such as seagulls. Clams were inspected daily to check for mortality or stress symptoms. Temperature and salinity in the sea water was recorded daily.   Growth was recorded by measuring the increase in two dimensions of the animal shells. Measures of length and height were taken with a caliper at the onset and at the end of the experiment (12 weeks). The two measures were added up to give a single value of shell size. The growth rate for the study period was estimated as (Sf-Si)/Si, where Sf and Si stand for final and initial shell sizes, respectively.  Clams were opened by cutting the adductor muscles with a scalpel blade. Then the gills and the digestive gland were excised with the help of sterile forceps and scissors, and placed in separate 2 ml plastic tubes containing 1.5 ml of RNA Later® solution. Digestive gland was minced before soaking. The tissues were let soak at 4⁰C for 12 h and then stored at -80⁰C until further processed. Here digestive gland data are reported


title: Loss of sterol demethylase activity reduces both azole and echinocandin antifungal susceptibility in a clinical isolate of C. parapsilosis

city: Memphis

first: Katherine

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary: The present study describes a novel mechanism of antifungal resistance affecting the susceptibility of both the azole and echinocandin antifungals in an azole-resistant isolate from a matched pair of C. parapsilosis isolates obtained from a patient with prosthetic valve endocarditis.  Transcriptome analysis indicated differential expression of several genes in the resistant isolate including upregulation of ERG1, ERG2, ERG5, ERG6, ERG11, ERG24, ERG25, ERG27, DAP1 and UPC2, of the ergosterol biosynthesis pathway.  Whole genome sequencing revealed a mutation in the ERG3 gene leading to a G111R amino acid substitution in the resistant isolate. Subsequent introduction of this allele in the native ERG3 locus in the susceptible isolate resulted in a fluconazole MIC of >64 mg/ml and a caspofungin MIC of 8 mg/ml.  Corresponding allelic replacement of the wildtype allele for the mutant allele in the resistant isolate resulted in a drop in MIC to 1 mg/ml for both fluconazole and caspofungin.  Sterol profiles indicated a loss of sterol demethylase activity as a result of this mutation. This work demonstrate that this G111R mutation is wholly responsible for the resistant phenotype in the C. parapsilosis resistant isolate and is the first report of this multidrug resistance mechanism.

overall_design: RNA-sequencing of an antifungal drug-susceptible isolate and a multi-drug resistant isolate of C. parapsilosis.

first: Jeffrey

last: Rybak

first: Michael

last: Dickens

first: Josie

middle: E

last: Parker

first: Kelly

last: Caudle

first: Kayihura

last: Manigaba

first: Sujoy

last: Roy

first: Qing

last: Zhang

first: Thomas

last: Sutter

first: Ramin

last: Homayouni

first: Stephen

last: Kelly

first: Nathan

last: Wiederhold

first: Sarah

last: Whaley

first: Glen

last: Palmer

first: Arturo

last: Luna Tapia

first: P

last: Rogers


title: Menin controls the memory Th2 cell function by maintaining the epigenetic integrity of Th2 cells. [ChIP-Seq]

first: Atsushi

last: Onodera

first: Masahiro

last: Kiuchi

first: Kota

last: Kokubo

first: Miki

last: Kato

first: Tomohiro

last: Ogino

first: Shu

last: Horiuchi

first: Urara

last: Kanai

first: Kiyoshi

last: Hirahara

first: Toshinori

last: Nakayama


title: Genome-wide maps of R-loops in Arabidopsis

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

summary: Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops, and demonstrate its high efficiency, low bias, and strand-specificity when profiling the R-loops in Arabidopsis. Using this single-strand DNA ligation based library construction technique, we find that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews. R-loops are prevalent in regions with multiple chromatin modifications, and are negatively correlated with CG DNA hypermethylation. R-loops are strongly enriched in gene promoters and gene bodies, highly associated with noncoding RNA and repetitive genomic regions, and correlated with activated and repressed gene loci. In summary, our analysis reveals that R-loop is a common feature of the Arabidopsis genome, and suggests diverse roles for R-loops in genome organization and gene regulation, thereby providing novel insights into plant nuclear genome formation and function.

overall_design: DRIP in 12-day-old Arabidopsis seedlings

first: Wei

last: Xu

first: Qianwen

last: Sun


title: Transcriptomic analysis of haustorium formation in Phelipanche ramosa

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

summary: The parasitic lifestyle of parasitic plants relies on the development of a haustorium, a specific infectious organ required for attachment to host roots. While haustorium development is initiated upon chemodetection of host-derived molecules in hemiparasitic plants, the induction of haustorium formation remains largely misunderstood in holoparasitic species such as Phelipanche ramosa. This work demonstrates that the root exudates of the host plant Brassica napus contain allelochemicals displaying a haustorium-inducing activity on P. ramosa germinating seeds which increases the parasite aggressiveness. A de novo assembled P. ramosa transcriptome and a microarray approach during early haustorium formation upon treatment with B. napus root exudates allowed the identification of differentially expressed genes involved in hormone signaling. Bioassays using exogenous cytokinins and the specific cytokinin receptor inhibitor PI55 showed that cytokinins induced haustorium formation and increased parasite aggressiveness. Root exudates triggered the expression of cytokinin responsive genes during early haustorium development in germinated seeds and bio-guided UPLC-MS analysis showed that these exudates contain a cytokinin with dihydrozeatin characteristics. These results suggest that cytokinins constitutively exudated from host roots play a major role in haustorium formation and aggressiveness in P. ramosa.

overall_design: Two-condition experiment: germinated seeds treated with incubation medium (12NI) for 12h versus germinated seeds treated with crudeB napus root exudates (12I) for 12h. Biological replicates: 4 control (incubation medium), 4 treatment (root exudate), independently grown and harvested. Two replicates per array.

first: Vincent

last: Goyet

first: Gregory

last: Montiel

first: Philippe

last: Simier

last: Delavault

first: Muriel

last: Bahut


title: Global transcriptional responses to oxidative stress conditions in lactobacillus plantarum

first: Yang

last: Yang

address: No. 17 Tsing Hua East Road，HaiDian District

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

summary: Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of lactobacillus plantarum CAUH2 to oxidative stress conditions was investigated via RNA-seq. The work provides detailed insights into the mechanisms through which L. plantarum responds to oxidative stress conditions and increases understanding of bacterial adaptation in natural and industrial settings.

overall_design: 6 samples were analyzed. Cells challenged by oxidative stress (H2O2) for 30 min were tested compared to the control. The control group and the H2O2-treated group both has 3 biological replicas.

first: Yanling

last: Hao


title: Transcriptional profiling defines histone acetylation as a regulator of gene expression during human-to-mosquito transmission of the malaria parasite Plasmodium falciparum

status: Public on May 24 2017

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: Transmission of the malaria parasite Plasmodium falciparum from the human to the mosquito is mediated by the intraerythrocytic gametocytes, which, once taken up during a blood meal, become activated to initiate sexual reproduction. Because gametocytes are the only parasite stages able to establish an infection in the mosquito, they are crucial for spreading the tropical disease. During gametocyte maturation, different repertoires of genes are switched on and off in a well-coordinated sequence, pointing to regulatory mechanisms of gene expression. While epigenetic gene control has been studied during erythrocytic schizogony of P. falciparum, little is known about this process during parasite human-to-mosquito transmission of the parasite. To unveil the potential role of histone acetylation during gene expression in gametocytes, we carried out a microarray-based transcriptome analysis on gametocytes treated with the histone deacetylase inhibitor trichostatin A (TSA).

overall_design: Plasmodium falciparum Percoll enriched immature (stages II-IV) gametocytes (imGC), mature (stage V) gametocytes (mGC) and gametocytes at 1 h post-activation with 100 µM Xanthurenic acid at RT (aGC) were obtained. Each enriched gametocyte sample was treated with TSA at IC90 concentrations (0.26 µM) or with 0.5% vol. ethanol (untreated control) for 1 h and 6 h, respectively and total RNA was isolated using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol. The extracted RNA was then processed for microarray analysis.

first: Che

last: Ngwa

first: Meike

last: Kiesow

first: Olga

last: Papst

first: Lindsey

last: Altenhofen

first: Michael

last: Filarsky

first: Alina

last: Rosinski

first: Till

last: Voss

last: Llinás

first: Gabriele

last: Pradel


title: Predicting species-resolved macronutrient acquisition during succession in a model phototrophic biofilm using an integrated 'omics approach

city: West Lafayette

first: Stephen

last: Lindemann

state: IN

address: 745 Agriculture Mall Drive

department: Food Sciences

institute: Purdue University

summary: The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.

overall_design: Cultures of Oscar UCC were split on day 0 into 12 flasks and grown in nitrate alone. Triplicate samples were taken at 7, 14, 21 and 28 days. RNA was extracted and libraries were constructed using standard SOP. There was no rRNA depletion. After sequencing, reads were mapped against Hot Lake community GTF file version 0715. Reads were converted to RPKM for each bin (organism) after filtering out tRNA and other non-CDS reads. Final data files contain summary of sample results and results separated into individual species.

first: Jennifer

last: Mobberley

first: Jessica

last: Cole

first: Lye

last: Markillie

first: Ronald

last: Taylor

first: Eric

last: Huang

first: H

last: Wiley

first: Mary

last: Lipton

first: William

last: Nelson

first: James

last: Fredrickson

first: Margaret

last: Romine


title: Mouse lens gene expression profile based on cDNA microarray analysis

city: Durham

first: Rupalatha

last: Maddala

state: NC

address: 2351 Erwin Road, AERI 4th floor

department: Ophthalmology

institute: Duke University Medical center

summary:
To determine the relative gene expression profile in the lens tissue, total RNA extracted from the neonatal (P7) and adult (P60) mouse lenses were subjected to cDNA microarray analysis using the Affymetrix Mouse Genome 430 2.0 array.
The expressed genes were annotated and organized them from their relative high to low expression. The genetic background of mouse strain used was C57/BL6.

overall_design: Total RNA was extracted from the pooled mouse lenses and their respective quality and quantity was evaluated with standards techniques. About 500 ng of total RNA at a concentration of approximately 50 ng/ml was used for the hybridization

first: Vasantha

last: Ponugoti


title: Dynamic changes in murine forebrain miR-211 expression associate with cholinergic imbalances and epileptiform activity

city: Jerusalem

first: uriya

last: Bekenstein

address: Safra

department: Dept. of Biological Chemistry

country: Israel

institute: HUJI

summary: Epilepsy is a common neurological disease, manifested in unprovoked recurrent seizures. Epileptogenesis may develop due to genetic or pharmacological origins or following injury, but it remains unclear how the unaffected brain escapes this susceptibility to seizures. Here, we report that dynamic changes in forebrain microRNA (miR)-211 in the mouse brain shift the threshold for spontaneous and pharmacologically-induced seizures alongside changes in the cholinergic pathway genes, implicating this miR in the avoidance of seizures. We identified miR-211 as a putative attenuator of cholinergic-mediated seizures by intersecting forebrain miR profiles that were Ago-precipitated, synaptic vesicle target-enriched or differentially expressed under pilocarpine-induced seizures, and validated TGFBR2 and the nicotinic anti-inflammatory acetylcholine receptor nAChRa7 as murine and human miR-211 targets, respectively. To explore the link between miR-211 and epilepsy, we engineered dTg-211 mice with doxycycline-suppressible forebrain overexpression of miR-211. These mice reacted to doxycycline exposure by spontaneous electrocorticography-documented non-convulsive seizures, accompanied by forebrain accumulation of the convulsive seizures-mediating miR-134. RNA-sequencing demonstrated in doxycycline-treated dTg-211 cortices over-representation of synaptic activity, Ca2+ transmembrane transport, TGFβR-II signaling and cholinergic synapse pathways. Additionally, a cholinergic dis-regulated mouse model over-expressing a miR-refractory acetylcholinesterase-R splice variant showed a parallel propensity for convulsions, miR-211 decreases and miR-134 elevation. Our findings demonstrate that in mice, dynamic miR-211 decreases induce hyper-synchronization, non-convulsive and convulsive seizures, accompanied by expression changes in cholinergic and TGFBR2 pathways as well as in miR-134. Realizing the importance of miR-211 dynamics opens new venues for translational diagnosis of and interference with epilepsy.

overall_design: polyA selected RNA from mouse cortex samples from CamK-control or double transgenic miR-211 expressing mice with or without Dox addministration

first: Hermona

last: Soreq

first: Alon

last: Friedman


title: Gene Expression Profile of Resistant vs Sensitive Breast Cancer Tissues to Taxane Treatment

city: Guadalajara

first: Mariel

last: Garcia-Chagollan

state: Jalisco

address: Sierra Mojada 950

department: Departamento Fisiologia

country: Mexico

institute: Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud

summary:
The present project aims to evaluate the gene expression profile of breast cancer tissue resistant to treatment with taxanes.
Biopsies from tumor tissues were obtained from breast cancer patients without prior treatment. Histopathological analysis and ex vivo exposure to antineoplastic chemotherapeutics were carried out.
Alamar Blue and lactate dehydrogenase release assays were performed for quantitative analysis of tumor viability after treatment and to asses the sensibility or resistant behaviour.
Sensitive and resistant tumor tissues samples without prior exposure to therapeutic drugs were analyzed by gene expression microarrays.

overall_design: Two resistant and two sensitive samples were analyzed by duplicated (for a total of 8 microarrays). Total RNA was isolated using the Rneasy Plus mini kit (Qiagen) and converted to doble stranded cDNA by the cDNA synthesis kit system (Roche). Doble stranded DNAs were label with Cy3 and hybridized to Gene expression arrays 12x35k (Roche) which consist of aproximately 132k probes for 42k genes.

first: Irma

last: Carranza-Torres

first: Pilar

last: Carranza-Rosales

first: Nancy

last: Guzmán-Delgado

first: Adriana

last: Aguilar-Lemarroy

first: Luis

last: Jave-Suarez


title: Microarray screening of differentially expressed lncRNAs between resting and IL-4 stimulated microglia

city: Shanghai City

first: li

last: cao

address: 800 Xiangyin Road

department: Department of neurobiology

institute: second military medical university

summary: To find potential lncRNAs participating in the regulation of microglial polarization, we employed microarray screening to find differentially expressed lncRNAs between resting and IL-4 stimulated primary cultured microglia

overall_design: The microarray assay was performed using the Mouse LncRNA Array V2.0 (Arraystar) between microglia treated with IL-4 for 24 hr and the untreated control, in triplicate.

first: Li

last: Cao


title: DNA array analysis in OLETF, a type 2 diabetic rats, and LETO, a non-diabetic control rats

city: Sapporo

first: Masaya

last: Tanno

department: Department of Cardiovascular, Renal and Metabolic Medicine

institute: Sapporo Medical University

summary: AMP deaminase (AMPD) plays a crucial role in adenine nucleotide metabolism, and its upregulated activity contributes to diastolic dysfunction of the heart caused by type 2 diabetes mellitus (T2DM) via reduction of the adenine nucleotide pool. Here we examined the mechanism of AMPD upregulation by T2DM. The protein level of 90-kDa full-length AMPD3 was increased in whole myocardial lysates and in the sarcoplasmic reticulum (SR) fraction by 55% and 123%, respectively, in OLETF, a rat model of T2DM, compared to those in LETO, a non-diabetic control, though AMPD mRNA level was unchanged in OLETF. MicroRNA array analysis revealed downregulation (>50%) of 57 microRNAs in OLETF compared to those in LETO, among which miR-301b was predicted to interact with the 3’UTR of AMPD3 mRNA. The 90-kDa AMPD3 level was significantly increased by miR-301b inhibitor, but decreased by a miR-301b mimetic in H9c2 cells. A luciferase reporter assay indicated binding of miR-301b to the 3’UTR of AMPD3 mRNA.  The results indicate that translational regulation by miR-301b mediates AMPD3 upregulation in the diabetic heart.  Since ATP generated by SR-associated glycolytic enzymes contributes to Ca2+ uptake by SERCA2a, upregulated AMPD3 in the vicinity of the SR may be a therapeutic target for diabetic cardiomyopathy.

overall_design: Total RNA was isolated from left ventricular tissues of OLETF, a type2-diabetic rats, or LETO, a non-diabetic control rats. One-color microarray analysis for global gene expression was performed using Rat GE 4x44K v3 (Agilent Technologies).  Three independent experiments were performed for both OLETF and LETO.

first: Yuki

last: Tatekoshi

first: Takayuki

last: Miki

first: Atsushi

last: Kuno

first: Toshiyuki

last: Yano

first: Satoko

last: Ishikawa

first: Tetsuji

last: Miura


title: miRNAs profile of goose normal liver and fatty liver

city: Wuhan

first: fang

last: chen

state: Hubei

address: No1, Nanhu Road

institute: Hubei Academy of Agricultural Sciences

summary: We identified the differentially expressed miRNAs in Landes goose liver after overfeeding for 21 days using high-throughput sequencing. We obtained 21453493 and 21525819 clean reads in normal liver and fatty liver by high-throughput sequencing, respectively. Of these clean reads, we respectively gained 9244896 and 9847086 miRNAs sequences in two groups by filtering the known non-miRNA reads, such as rRNA, tRNA, snRNA, and snoRNA by screening against ncRNA deposited in the GenBank and Rfam databases. These findings provided insights into the expression profiles of miRNAs in goose liver, and deepened our understanding of miRNAs in hepatic steatosis of geese.

overall_design: Examination of miRNAs expression profile in normal and fatty liver samples

first: Fang

last: Chen

first: Lizhi

last: Lu


title: Comparison analysis of microRNAs in response to infection of Dengue virus type 2 adapted strain of Vero cells and its source strain in vero cells

city: Kunming

first: Qiangming

last: Sun

state: Yunnan

address: 935 Jiaoling Road

institute: Chinese Academy of Medicine Science and Peking Union Medical College

summary: To compare MicroRNA expression in Vero cells infected with DENV-2 adapted strain of Vero cells and its source srain derived from C6/36 cells

overall_design: we defined the following experimental groups: DENV-2-none-6h, DENV-2 adapted srtrain-6h, DENV-2 source strain-6h

first: Jiajia

last: Yang


title: RNA editing in the Rat brain

city: Haifa

first: Hiba

last: Zaidan

state: Israel

address: 199 Aba Khoushy Ave

department: Psychology

institute: University of Haifa

summary: Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain. Using microfluidics-based multiplex PCR sequencing (mmPCR-seq) to assess A-to-I editing at 146 pre-selected, conserved sites, we found that editing was generally higher in adult compared to neonatal rat brain, and that at birth, global editing was lower in prefrontal cortex than in amygdala. Prereproductive stress (PRS) affected editing at the serotonin receptor 2c, and editing at this site was significantly altered in offspring of PRS rats across two generations. Changes in ADAR expression did not correlate with editing changes induced by development or stress. Our findings indicate that mmPCR-seq can accurately detect RNA editing in rat brain samples, and confirm previous accounts of a developmental increase in RNA editing rates. Altered RNA editing rates in offspring of stress-exposed rats complements growing literature on the transgenerational effects of stress.

overall_design: We report the application of mmPCR-seq to the Rat brain and oocytes. We quantified RNA editing at 146 different loci in 85 samples from different groups (Age, tissue, stress) using a microfluidic multiplex PCR method coupled with deep sequencing.

first: Gokul

last: Ramaswami


title: LUC7 is an U1snRNP component that plays a role in alternative splicing and terminal introns removal in plants

city: Cologne

first: Eva-Maria

last: Willing

address: Carl-von-Linne Weg 10

institute: MPIPZ

summary: Introns are removed by the spliceosome, a large complex composed of five ribonucleoprotein subcomplexes (U snRNP). In metazoans, the U1 snRNP, which binds to 5’ splice sites, also fulfills regulatory roles in splice site selection and possesses non-splicing related functions. Here, we show that an Arabidopsis U1 snRNP subunit, LUC7, affects constitutive and alternative splicing. Interestingly, LUC7 specifically promotes splicing of a subset of terminal introns. Splicing of LUC7-dependent terminal introns is a prerequisite for nuclear export and can be modulated by stress. Globally, intron retention under stress conditions occurs preferentially among first and terminal introns, uncovering an unknown bias for splicing regulation in Arabidopsis. Taken together, our study reveals that the Arabidopsis U1 snRNP is important for alternative splicing and removal of terminal introns and it suggests that Arabidopsis terminal introns fine-tune gene expression under stress conditions.

overall_design: Poly A libraries from wild type plants (WT Col-0) and a triple mutant (luc7 a-2, b-1, rl-1) were performed in triplicates

first: Marcella

last: Amorim

first: Emese

middle: X

last: Szabo

first: Korbinian

last: Schneeberger

first: Sascha

last: Laubinger


title: Menin controls the memory Th2 cell function by maintaining the epigenetic integrity of Th2 cells.

last: Onodera

institute: Chiba University

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

overall_design: Refer to individual Series


title: Wild-type and daf-16(mgDf50) L1 larvae 3 hours after hatching in the presence or absence of food

first: Brad

middle: T

last: Moore

address: Box 90338, Duke University

department: Biology

institute: Duke University

summary: This experiment was designed to identify early targets of daf-16/FoxO during L1 starvation in C. elegans. Previous work (Baugh et al 2009) examined temporal dynamics of gene expression in fed and starved L1 larvae using the same platform and methods. Here, a single time point was analyzed (~3 hr after hatching) in fed and starved larvae also comparing wild-type and a daf-16 null mutant. Statistical analysis includes pairwise comparisons between the four conditions as well as a two-factor analysis to explicitly identify genes affected by nutrient availability in daf-16-dependent fashion.

overall_design: Synchronized collections of eggs of two separate strains, N2 (wild-type) and GR1307 (daf-16), were hatched in the presence or absence of food (E. coli HB101 at 25 mg/ml) and samples were taken at 2-4 hours.  Each strain and condition combination was peformed in triplicate for a total of 12 samples (2 x 2 x 3).

first: L

last: Baugh

first: B

first: J

last: Hibshman


title: Differential requirements for Tcf1 long isoforms in CD8+ and CD4+ T cell responses to acute viral infection

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

summary: Comparison of the transcriptome between control Tfh and Tcf1 long isoform-deficient Tfh cells

overall_design: SMARTA CD4+ T cells (control or Tcf1 long isoform deficient) were adoptively transferred into B6.SJL recipient mice and then infected with LCMV-Arm. On day 8 after infection, the splenocytes were isolated, and CD45.2+CD4+CXCR5+PD-1 negative cells were sorted as Tfh cells and used in RNAseq analysis.

first: Hai-Hui

last: Xue


title: Deep sequencing and high-throughput analysis of PIWI-associated small RNAs

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

institute: Keio University School of Medicine

summary: Small RNAs are now known to be major regulatory factors of gene expression. Emerging methods based on deep-sequencing have enabled the analysis of small RNA expression in a high-throughput manner, leading to the identification of large numbers of small RNAs in various species. Moreover, profiling small RNA data together with transcriptome data enables transcriptional and post-transcriptional regulation mediated by small RNAs to be hypothesized. Here, we isolated PIWIL1 (MIWI)-associated small RNAs from mouse testes, and performed small RNA-seq analysis. In addition, directional RNA-seq was performed using Piwil1 mutant mouse testes. Using these data, we describe protocols for analyzing small RNA-seq reads to obtain profiles of small RNAs associated with PIWI proteins. We also present bioinformatic protocols for analyzing RNA-seq reads that aim to annotate expression of piRNA clusters and identify genes regulated by piRNAs.

overall_design: PIWIL1-associated small RNA-seq from mouse testes (two replicates), and directional RNA-seq from Piwil1 mutant mouse (Piwil1+/- and Piwil1-/-).

middle: W

first: Kyoko

last: Ishino

first: Haruhiko

last: Siomi


title: RNA pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD phosphorylation and transcriptional direction

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

summary: Using pol II mutants in human cells we found that slow transcription repositioned specific co-transcriptionally deposited chromatin modifications; H3K36me3 shifted within genes toward 5’ ends and H3K4me2 extended further upstream of start sites. Slow transcription also evoked a hyperphosphorylation of CTD Ser2 residues at 5’ ends of genes that is conserved in yeast. We propose a “dwell-time in the target zone” model to explain the effects of transcriptional dynamics on establishment of co-transcriptionally deposited protein modifications. Promoter-proximal Ser2 phosphorylation is associated with longer pol II dwell time at start sites and reduced transcriptional polarity due to strongly enhanced divergent antisense transcription at promoters.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: The effect of transcription elongation rate on histone H3K36me3, H3K4me2 and pol II CTD phosphorylation was analyzed by ChIP-seq in isogenic human HEK293 cell lines that inducibly express a-amanitin resistant mutants of the RNA polymerase II large subunit with slow elongation rates. Anti-pol II total nascent RNA sequencing (tNET-seq) was developed to assay transcription by WT and slow pol II. Slow pol II mutants in S. cerevisiae were also assayed for pol II CTD Ser2 phosphorylation.

first: Ben

last: Erickson


title: MicroRNA-202 maintains spermatogonial stem cells by inhibiting cell cycle regulators and RNA binding proteins

status: Public on May 23 2017

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: As miRNAs regulate gene expression either by inhibiting translation or by initiating mRNA degradation, we performed RNA sequencing to identify genes regulated by miR-202, using a Cas9/double gRNAs mediated and doxycycline induced knockout approach.

overall_design: We carried out RNA-Seq analysis of miR-202 induced knockout single clonies of spermatogonial stem cells (SSCs) with or without treatment of doxycycline. Two single clonies (iKO-SC-1 and iKO-SC-2) were included for each condition.

first: Jian

last: Chen

first: Xiwen

last: Lin


title: Expression data from Rb family deficient Cd150+ HSC

city: Philadelphia

first: Patrick

last: Viatour

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Loss of Rb family in HSC results in their sustained proliferation, impaired homeostasis and extramedullar mobility.

overall_design: We have isolated KLS CD48- CD150+ HSC from wild-type (WT) and Rb family deficient HSC two weeks after the acute inactivation of Rb family genes. Each sample is composed by a pool of 3 mice.

first: Eunsun

last: Kim


title: Expression data from SW1990, HCT-116 and Hep3B cancer cell lines

city: GUANGZHOU

first: LIANG

middle: JIAN

last: KAI

state: GUANGDONG

address: NO.74 ZHONGSHAN NO.2 ROAD YUEXIU DISTRICT

department: PHARMACOLOGY

institute: SUN YAT-SEN UNIVERSITY


title: Plasma MicroRNA alterations between EGFR-activating mutational NSCLC patients with and without primary resistance to TKI

city: XIAMEN

first: Hanxiang

last: An

state: Fujian

address: siming district Zhenhai road 55#, 1st affiliated hospital of xiamen university

institute: xiamen cancer hospital

summary: The aim of the present study was to examine differentially expressed miRNAs in plasma between EGFR-TKIs sensitive and EGFR-TKIs primary resistance patients.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: MiRNA microarray of plasma from patients’ blood identified 16 differentially expressed miRNAs of which 15 (hsv2-miR-H19, hsa-miR-744-5p, hsa-miR-3196, hsa-miR-3153, hsa-miR-4791, hsa-miR-4803, hsa-miR-4796-3p, hsa-miR-372-5p, hsa-miR-138-2-3p, hsa-miR-16-1-3p, hsa-miR-1469, hsa-miR-585-3p, ebv-miR-BART14-5p, hsa-miR-769-3p, hsa-miR-548aq-5p) were down regulated while only hsa-miR-503-3p was up regulated in primary resistant patients’ plasma. Volcano plot and hierarchical clustering were performed to examine the accuracy of the miRNAs. Then validation with quantitative real-time PCR was performed and the result was in accordance with the array data. Functional analysis of these differentially expressed miRNAs with Ingenuity Pathway Analysis (IPA) revealed a common signaling network including MYC, CCND1, IGF1 and RELA.

first: Xiaoyan

last: Pan


title: Niche microenvironments are essential for maintaining the phenotypic heterogeneity of primary cancer

city: Osaka

first: Norikatsu

last: Miyoshi

state: Osaka

address: 3-1-69, Otemae, Chuo-ku

department: Surgery

institute: Osaka International Cancer Institute

summary: Cancer is among the major causes of death worldwide, and treatment can be individualized according to a patient’s genotype. Primary cultures of cancer and normal cells provide more accurate information about tumour pathology compared with tumour-derived cell lines, and several methods are available for establishing primary cultures. However, these methods are inefficient, complicated and expensive. Here we describe a method to establish primary cultures of tumour cells, which we designate “isolated tumour-derived Cancer Cells” (iCCs) that retains the phenotypic heterogeneity of primary cancer cells in their in situ niche microenvironments. We used a custom filter, a Matrigel-coated plate, and modified embryonic stem cell (ESC) culture medium to isolate iCCs from tumour tissues of patients with colorectal cancer. All iCCs were viable, and approximately 90% of the cultures were passaged. The morphologies, genotypes and transcription profiles of iCCs were similar to those of their respective tumours of origin. Further, iCCs comprised a specific cell population that expressed Platelet-derived growth factor receptor (PDGFR), which contributes to forming the structure of the original ductal carcinoma. Our results demonstrate that ESC culture medium maintained the heterogeneity of ICCs by supporting the viability of PDGFR-expressing cells. The responses of iCCs to standard anti-cancer drugs differed compared with those of colon cancer cell lines. Moreover, the drug sensitivities of iCCs closely correlated with patients’ clinical outcomes. For example, a clinically significant finding was the reduction of the IC50 of crenolanib, an inhibitor of PDGFR signalling, for iCCs. Therefore, crenolanib may serve as an effective chemotherapeutic agent for managing colorectal cancer.

overall_design: We analysed gene expression microarrays prepared from three pairs of iCCs and parental tumours, four other iCCs, one CRC tissue sample, three samples of normal colon mucosal tissue and from the colorectal cancer cell lines HCT116, RKO and DLD1.

first: Shiki

last: Fujino


title: LncRNA Sequencing Analysis of Mouse spermatogonial stem cells during  retinoic acid treatment

city: Nanjing

first: Lufan

last: Li

address: No.101 Longmian Blvd

institute: Nanjing Medical University

summary: Retinoic acid triggers differentiation of spermatogonial stem cells by activating the expression of differentiating genes. Long noncoding RNAs (lncRNA) are transcripts longer than 200 nucleotides that do not code for proteins, providing a new perspective of RNA species in gene regulation. However, the function of lncRNAs in determining SSC differentiation has not been investigated. Here, we used high-throughput sequencing to profile all lncRNAs in SSCs, and report the dataset of lncRNAs during SSC differentiation.

overall_design: Spermatogonial stem cells were incubated with trans-retinoic acid(0.3mM in 0.1% EtOH,RA_T) or vehicle solution(0.1% EtOH,RA_C) for 24 hr. After treatment, SSC clumps were collected and followed the standard extraction protocol for RNA before sequencing by Illumina HiSeqTM 2000.

first: Xin

last: Wu


title: Expression data from the human neuroblastoma line SH-SY5Y treated with okadaic acid

city: Ningbo

first: Jin

last: Xu

address: 818 Fenghua Road

institute: Ningbo University

summary:
Okadaic acid (OA) is a widely distributed marine toxin produced by several phytoplank-tonic species and responsible for diarrheic shellﬁsh poisoning in humans. At the molecular level OA is a speciﬁc inhibitor of several types of serine/threonine protein phosphatases.However, the underlying regulatory mechanisms involved in OA-induced cytotoxicity are not well understood.
In the present study, we applied a toxicogenomic approach to investigate the effects of OA on gene expression in  the human neuroblastoma line SH-SY5Y.

overall_design: The SH-SY5Y cells were treated with 0 nM (C0), 20 nM(C1) and 60 nM (C2) OA for 12 h, and three biological replicates for each concentration.

first: Mei

last: Feng

first: Lingling

last: Fu

first: Mi

last: Zhou