title: Nck2 Regulates Adiposity and Adiposity-Related Metabolic Disorders in Mice and Human

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

summary: Obesity is linked to the development of metabolic disorders. Expansion of white adipose tissue (WAT) from hypertrophy of pre-existing adipocytes and/or differentiation of precursors into new mature adipocytes contributes to obesity. We found that Nck2 expression is largely restricted to WAT, raising the hypothesis that it may play a unique function in that tissue. Using mice lacking Nck2, we found that Nck2 regulates adipocyte hypertrophy thus contributing to increased adiposity and progressive glucose intolerance, insulin resistance and hepatic steatosis. These findings were recapitulated in humans such that Nck2 expression in omental WAT was inversely correlated with the degree of obesity. Mechanistically, Nck2 deficiency promoted the induction of an adipocyte differentiation program and signaling by the PERK-eIF2α-ATF4 pathway in agreement with a role for the unfolded protein response in adipogenesis. These findings uncover Nck2 as a novel regulator of adipogenesis and that perturbation in its functionality contributes to adiposity-related metabolic disorders.

overall_design: Differential gene expression profile between epididymal white adipose tissue of Nck2-/- and Nck2+/+ mice by RNA sequencing (Illumina HiSEq 2000)

first: Louise

last: Larose

first: Jean-François

last: Côté


title: A transcriptome map of Actinobacillus pleuropneumoniae at single-nucleotide resolution using RNA-seq

status: Public on Jul 01 2016

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

country: China

institute: Huazhong Agricultural University

type: Expression profiling by high throughput sequencing

summary: We used the RNA-seq technology to do a genome-wide transcriptional analysis of A. pleuropneumoniae strain JL03 and investigated the transcriptome structure at a single-nucleotide resolution.The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures).

sample_organism: Actinobacillus pleuropneumoniae serovar 3 str. JL03

overall_design: Transcript profiling of a single sample by RNA-Seq

first: Zhipeng

last: Su

first: Zhuofei

last: Xu

first: Rui

last: Zhou


title: Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by Marek's disease oncoprotein, Meq

city: East Lansing

first: sugalesini

last: Subramaniam

state: MI

address: 3606 E Mount Hope Rd

department: CMIB

country: USA

institute: Michigan State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Marek’s disease (MD) is an economically significant disease in chickens caused by the highly oncogenic Marek’s disease virus (MDV). A major unanswered question is the mechanism of MDV-induced tumor formation. Meq, a bZIP transcription factor discovered in the 1990s, is critically involved in viral oncogenicity but only a few of its host target genes have been described impeding our understanding of MDV-induced tumorigenesis. Using ChIP-seq and microarray analysis, a high confidence list of Meq-binding sites in the chicken genome and a global transcriptome of Meq-responsive genes was generated. Meq binding sites were found to be enriched in the promoter regions of up-regulated genes, but not in those of down-regulated genes. ChIP-seq was also performed for c-Jun, a known heterodimeric partner of Meq. Close location of binding sites of Meq and c-Jun was noted, suggesting cooperativity between these two factors in modulating transcription. Pathway analysis indicated that Meq transcriptionally regulates many genes that are part of several signaling pathways include the ERK/MAPK, Jak-STAT, and ErbB pathways that are critical for oncogenesis and/or include signaling mediators involved in apoptosis. Meq activates oncogenic signaling cascades by transcriptionally activating major kinases in the ERK/MAPK pathway and simultaneously repressing phosphatases, as verified using inhibitors of MEK and ERK1/2 in a cell proliferation assay. This study provides significant insights into the mechanistic basis of Meq-dependent cell transformation.

overall_design: ChiP-Seq of Meq-DF-1 clone 5G (DF-1 stably expressing Meq driven by the CMV promoter) with Meq and Jun antibodies

first: Sugalesini

first: John

last: Johnston

first: Likit

last: Preeyanon

first: C

middle: T

last: Brown

first: Hsing-Jien

last: Kung

first: Hans

middle: H

last: Cheng


title: Dissecting the Precise Role of Histone H3 K9 Methylation in Crosstalk with DNA Maintenance Methylation in Mammalian Cells

status: Public on Jun 30 2016

city: Shanghai

first: Hao

address: 320,Yueyang Road

institute: PICB,SIBS,CAS

type: Methylation profiling by high throughput sequencing

summary: Our study supports a role for H3K9 methylation in promoting DNA methylation, it  demonstrates  for the first time that DNA maintenance  methylation  in  mammalian  cells  is  to  large  extent independent on H3K9 methylation.

overall_design: Examination of DNA methylation levels in UHRF1 knock in and wide type mice.

first: Jiemin

last: Wong


title: Genes and pathways involved in cellular transformation by Marek's disease oncoprotein Meq

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

overall_design: Refer to individual Series


title: LncRNA Chaer contributes to the transcriptome reprogramming during phenylephrine-induced hypertrophy in neonatal rat ventricular myocytes

city: Los Angeles

first: Yibin

last: Wang

state: Ca

institute: University of California Los Angeles

summary: We compared the transcriptome modified by siRNA-mediated cardiac hypertrophy associated epigenentic regulator (Chaer) with negative control siRNA treated neonatal rat ventricular myocytes with or without phenylephrine treatment. The results suggest that Chaer knockdown broadly blocks the phenylephrine-induced hypertrophic programming of the transcriptome.

overall_design: Transcripts profiles from neonatal rat ventricular myocytes with or without phenylephrine and with or without Chaer-specific siRNA compared to negative control siRNA

first: Zhihua

first: Ashley

last: Cass

first: Xinshu

middle: G

last: Xiao


title: Detection of plant microRNAs in EVOO and plasma samples of healthy volunteers 2 hours postingestion of 40 mL of EVOO.

city: Madrid

first: Lidia

middle: Ángeles

last: Daimiel-Ruiz

state: Madrid

address: Ctra. Cantoblanco, Km 8

department: Nutritional Genomics of Cardiovascular Disease and Obesity

country: Spain

institute: Institute IMDEA Food

type: Non-coding RNA profiling by high throughput sequencing

summary:
NGS has been applied to microRNA-enriched RNA obtained from Extra Virgin Olive Oil (EVOO), beer and plasma samples of healthy volunteers that usually consume EVOO hours after the ingestion of 40 mL of EVOO.
Results: We did not detect significant amount of microRNA in the EVOO samples. Plasma samples did not contain EVOO microRNAs nor other microRNAs from plant origin.

sample_organism:
Olea europaea
Homo sapiens

platform_organism:
Olea europaea
Homo sapiens

overall_design: Starting plant material was 30 mL of EVOO or a pool of plasma samples of 5 volunteers

first: Victor

last: Micó-Moreno


title: Transcriptome sequencing of Gluconobacter oxydans with different PQQ production

city: Wuxi

first: Hui

last: Wan

state: Jiangsu

address: No 1800 Lihu Avenue

institute: Jiangnan University

summary: We reported that analysis of PQQ metabolism in Gluconobacter oxydasns strain at gene expression level. Acoording to present study that pqqB gene can strengthen the transport of PQQ. Wild type strain and pqqB-overexpression strain were compared to find other candidate key genes which can encoded proteins are involved in PQQ transport. Results provide important information of the response of pqqB-overexpression, such as genes encoded membrane proteins and other indirectly functional genes.

overall_design: The mRNA of wild type (WT) and pqqB-overexpression mutant (TB) strains, collected at exponential growth phase, were generated by deep sequencingusing Illumina Miseq.

first: Jingwen


title: Single-nucleus RNA-seq on undifferentiated human KD3 myoblasts and differentiated myotubes and mononucleated cells.

city: Irvine

first: Weihua

last: Zeng

state: CA

address: 2300E Bio Sci III

department: Dev & Cell Biology

institute: UCIrvine

summary: We report the application of single-nucleus-based sequencing technology for high-throughput profiling of transcriptome in immortazalized human myoblast KD3. By obtaining over sixty billion bases of sequence from mRNA, we generated comprehensive transcriptome profiles from KD3 undifferentiated myoblast and differentiated  multi-nucleated myotube and mono-nucleated cells. We find that the data from single-nucleus RNA-seq is consistent with the transcriptome from single-cell RNA-seq.  The pri-mRNA expression characterized by single-nucleus RNA-seq can reflect the actual miRNA level in the whole cell.

overall_design: Examination of transcriptome in 1 cell type in 3 differential stages.

first: Shan

last: Jiang

first: Kyoko

last: Yokomori

first: Ali

last: Mortazavi


title: Allele-specific ATAC-seq

city: Stanford

first: Howard

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Dermatology

institute: Stanford University

summary: One of the two X chromosomes in female somatic cells is transcriptionally silenced across cell generations, a classic paradigm of epigenetic regulation.  Although most genes are stably silenced, certain X-linked genes escape X-chromosome inactivation (XCI), providing a fundamental dosage difference between females and males.  A role for chromosome conformation has been proposed in XCI as the process is  accompanied by a massive structural reorganisation. However a detailed molecular understanding of the three-dimensional architecture of the Xi has been lacking.  Here we reveal an unusual three-dimensional configuration of the Xi, that provides novel insights into the relationship between gene expression and TAD organisation.  Using allele-specific Hi-C, RNA-Seq and ATAC-seq, as well as DNA FISH, we show that the Xi is spatially segregated into two ‘mega-domains’ separated by a 200kb boundary including the DXZ4 macrosatellite, and is globally devoid of typical autosomal structural features such as active/inactive compartments and topologically associating domains (TADs). However, we find that a few regions along the Xi display TAD signatures corresponding to regions containing escape genes, and display DNA accessibility at promoter-proximal TF binding sites.  Strikingly, when the DXZ4-containing boundary region is deleted prior to XCI, most facultative escapees are no longer expressed from the Xi, and the escape associated  chromatin domains are no longer observed. Deletion of the DXZ4-containing boundary region from the Xi also results in fusion of the two mega-domains.   We show that Xist A-repeat containing (gene silencing competent) RNA is sufficient to induce this spatial segregation of the X chromosome. Combined, our results point to a critical role for the DXZ4-boundary region, together with Xist RNA, in shaping the higher order structure of the Xi and in allowing facultative escape from XCI during differentiation. They also point to direct and uncover a close relationships between transcription and TAD formation organisation in the context of the Xi.

overall_design: ATAC-seq was performed in mESCs and mNPCs as well as deltaFT NPCs.  Libraries(2 replicates per line) were sequenced on an Illumina NextSeq (2x75bp) and data was analyzed allele-specifically.  ATAC-seq was also performed inmale  mESCs containing a doxycycline-inducible Xist construct at the endogenous locus with or without the functional RepA region.  Samples with Xist induction (+dox) and without (-dox) are included.

first: Ava

middle: C

last: Carter

first: Jin

last: Xu

middle: Y


title: RNA-sequencing analysis of liver from mice overexpressing miR-30c

city: Chapel Hill

first: Bailey

last: Peck

state: NC

address: 120 Mason Farm Rd, 5100H Genetic Medicine Bldg

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: This study aims to investigate the role of microRNA-30c on hepatic and metabolic gene expression and physiology

overall_design: For this experiment, we used male C57BL/6 mice. At an age of 8 weeks, we started them on Western diet for one month and then injected them with either PBS or increasing dose of Scr or miR-30c mimic (2.5, 5.0, and 7.5 mg/kg) for 6 weeks. Liver from these mice were harvested and flash frozen. RNA from the livers of these mice were extracted and RNA-seq was performed.

first: Praveen

last: Sethupathy

first: Mahmood

last: Hussain

first: Sara

last: Irani

first: Xiaoyue

last: Pan

first: Jahangi

last: Iqbal


title: Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection

city: London

last: Chen

state: Ontario

address: 1391 Sandford St.

country: Canada

institute: Agriculture and Agri-Food Canada

summary: We profiled the global gene and miRNA expression in soybean following infections by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain) by small RNA (sRNA)-seq, degradome-seq and as well as a genome-wide transcriptome analysis.

overall_design: mRNA, miRNAs and degradome profiles of williams82 (susceptible) after 14 days post-inoculation (dpi) by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain) and as well as Mock (control) were generated by deep sequencing, pooled from three biological replicates (5 plants in each replicate) for each treatment, using Illumina Miseq.

first: Andrej

middle: A

last: Arsovski

first: Kangfu

last: Yu

first: Aiming

last: Wang


title: Transcriptome analysis of virus-specific H2-Db-GP33-41+CD8+ T cells from WT or PSGL-1 KO mouse spleens at day 9 post LCMV Cl 13 infection

city: La Jolla

first: Linda

middle: M

last: Bradley

address: 10901 N. Torrey Pines Rd.

department: Inflammatory Diseases

institute: Sanford Burnham Prebys Discovery Institute

summary: Chronic viruses and cancers thwart immune responses in humans by inducing T cell dysfunction. Using a murine chronic virus that models human infections, we investigated the function of the adhesion molecule, P-selectin glycoprotein ligand-1 (PSGL-1) that is upregulated on responding T cells. PSGL-1-deficient mice unexpectedly cleared the virus due to dramatic increases in the intrinsic survival of multifunctional effector T cells that had downregulated PD-1 and other inhibitory receptors. Notably, this response resulted in CD4+ T cell-dependent immunopathology. Mechanistically, PSGL-1 ligation on exhausted CD8+ T cells inhibited TCR and IL-2 signaling, and upregulated PD-1, leading to diminished survival with TCR stimulation. In models of malignant melanoma where T cell dysfunction occurs, PSGL-1-deficiency led to PD-1 downregulation, improved T cell responses, and tumor control. Thus, PSGL-1 plays a fundamental role in balancing viral control and immunopathology, and also functions as a checkpoint that regulates T cell responses in the tumor microenvironment.

overall_design: WT or PSGL-1 KO mice were infected with 2 x 10^6 PFU LCMV Clone 13. Spleens from 10 WT or 10 PSGL-1 KO animals were pooled and processed. CD8+ T cells were negatively enriched from WT or PSGL-1 KO spleens (EasySep Stemcell). Purified T cells were stained with propidium iodide (PI) for 10 minutes on ice, cells were washed. CD8+ T cells were stained with H2-Db-GP33-41 tetramers (NIH) and FACS sorted (BD FACS Aria). Sorted tetramer+ cells were PI negative and purity was >98%. Experiment was repeated twice to generate 2 WT (WT 1; WT 2) and 2 PSGL-1 KO (KO 1; KO 2) samples that represented 10 pooled spleens per sample.

first: Roberto

last: Tinoco


title: Histone variant 3 regulates RNA polymerase II transcription termination and dual strand transcription of siRNA loci in Trypanosoma brucei

city: Athens

first: David

last: Reynolds

state: Georgia

address: 120 E Green St

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: Histone variant 3 (H3V) is a kinetoplastid specific histone variant that is enriched at RNA polymerase II termination sites and telomeres. We previously found that the DNA modification base J, which co-localizes with H3V, functions to prevent readthrough transcription within gene clusters in T. brucei. We now demonstrate a similar role for H3V, where the loss of this histone variant results in increased expression of downstream genes. The effect is larger when both H3V and J are lost. Additionally, removal of H3V results in increased siRNAs from dual strand transcribed loci as well as increased expression of silent VSGs, indicating a role of H3V in the regulation of antigenic variation

overall_design: The role of H3V in regulating transcription termination was investigated using WT and H3V KO T. brucei cell lines. The role of J was also studied by treating each of these cell lines with DMOG, an inhibitor of J synthesis. We used small RNA seq libraries to identify transcriptional changes following the loss of H3V and J.

first: Robert

last: Sabatini

first: Laura

last: Cliffe

first: Nicolai

last: Siegel

first: Magdy

last: Alabady

first: Brigitte

last: Hofmeister

middle: J

last: Schmitz


title: RNA-sequencing of abdominal fat body-enriched tissue of Drosophila fat body-specific Sdc RNAi knockdown and control

city: Birmingham

first: Maria

last: De Luca

state: Alabama

address: Webb 451 - 1720 Second Ave. South

institute: UAB

summary: We report the transcriptome profile of one sequenced sample of mRNA isolated  from pooled (20 from each genotype) abdomen fly extracts enriched in fat body content of fat body-specific Sdc RNAi knockdown and control flies

overall_design: Abdominal fat body mRNA profiles of 4-6-day old control and fat body-specific Sdc RNAi knockdown were generated by deep sequencing using Illumina HiSeq 2500

first: Susan

last: Harbison

first: Chia-Hua

last: Lue

first: Matthew

last: Eveland

first: Jeff

last: Leips

first: Gabrielle

last: Brokamp


title: Histone methylation by the Kleefstra Syndrome protein EHMT1 mediates homeostatic synaptic scaling.

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

summary: Homeostatic plasticity, a form of synaptic plasticity, maintains the fine balance between overall excitation and inhibition in developing and mature neuronal networks. Although the synaptic mechanisms of homeostatic plasticity are well characterized, the associated transcriptional program remains poorly understood. We show that the Kleefstra syndrome-associated protein, EHMT1, plays a critical and cell-autonomous role in synaptic scaling by responding to attenuated neuronal firing or sensory drive. Chronic activity deprivation increased the amount of neuronal dimethylated H3 at lysine 9 (H3K9me2), the catalytic product of EHMT1 and an epigenetic marker for gene repression. Genetic knockdown and pharmacological blockade of EHMT1 or EHMT2 prevented the increase of H3K9me2 and synaptic scaling up. Furthermore, BDNF repression was preceded by EHMT1/2-mediated H3K9me2 deposition at the Bdnf promoter during synaptic scaling up, both in vivo or in vivo. These findings suggest that changes in chromatin state through H3K9me2 governs a repressive program to achieve synaptic scaling.

overall_design: 12 samples (4 conditions in biological triplicate), 3 wt, 3 wt tetradotoxin treated, 3 k.d., 3 k.d. tetradotoxin treated

first: Marco

last: Benevento

first: Giovanni

last: Iacono

first: Martijn

last: Selten

first: Huiqing

last: Zhou

first: Henk

last: Stunnenberg

first: Hans

last: van Bokhoven

first: Nael

middle: N

last: Kasri


title: Transcriptome profile form oviduct samples of endocrine manipulated cows (isthmus)

city: Pirassununga

first: Angela

middle: Maria

last: Gonella

state: SP

address: Rua Duque de Caxias Norte, 255

department: Departamento de Reprodução Animal

country: Brazil

institute: Universidade de São Paulo

summary:
Purpose: evaluate if different proestrus-estrus concentrations of estradiol (E2) and metestrus progesterone (P4) concentrations specifically regulate oviductal gene expression.
Methods: ampulla and isthmus samples of animals whit a large pre-ovulatory follicle and a large CL (LF/LCL) and animals whit a small pre-ovulatory follicle and a small CL (SF/SCL) were collected after slaughter at day four of the estrous cycle. Total RNA was extracted and RNA sequencing was performed using the Illumina HiScanSeq (ampulla samples) and the Illumina HiSeq 2500 (isthmus samples) platforms.
Results: After using HTSeq-count, approximately ~60% of the total reads uniquely mapped to the UMD 3.1 reference genome. In the ampulla samples, a total of 692 genes showed differential expression, of which 325 and 367 were up-regulated in the LF-LCL and SF-SCL samples, respectively. In the isthmus samples, a total of 590 genes showed differential expression, of which 274 and 316 were up-regulated in the isthmus of LF/LCL and SF/SCL samples, respectively.
Conclusions: Our study represents the first detailed analysis of oviduct transcriptomes, generated by RNA-seq technology. Differential global gene expression profiles identified indicate that the biology of the bovine oviductal tissue is modulated by the periovulatory endocrine milieu. The LF-LCL group transcriptome may potentially reveal molecules associated with higher fertility.

overall_design: Oviductal mRNA profiles of cows whit different endocrine milleus were generated by next generation sequencing.

last: Gonella-Diaza.

first: Sonia

last: Andrade

first: Gustavo

last: Gasparin

first: Luiz

middle: L

last: Coutinho

first: Mario

last: Binelli


title: Transcriptome profile form oviduct samples of endocrine manipulated cows


title: Human and mouse DRIP-seq and DRIPc-seq

city: Davis

first: Yoong Wearn

last: Lim

address: One Shields Avenue

department: Molecular and Cellular Biology

institute: University of California, Davis

summary: This study profiles RNA:DNA hybrid formation in human and mouse cell lines.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: DRIPc-seq (strand-specific R-loop mapping) was performed on human NT2 cells and mouse 3T3 cells. DRIP-seq (R-loop mapping) was performed on human NT2 and K562 and mouse E14 and 3T3 cell lines. MethylC-seq and RNA-seq were performed on NT2.

first: Lionel

last: Sanz

first: Yoongwearn

first: Stella

middle: R

last: Hartono

first: Aparna

last: Rajpurkar

first: Frederic

last: Chedin


title: Transcription analysis on difference of copper body concentrations in Crassostrea angulate

city: Xiamen

first: Huang

last: zekun

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

summary: The aim of this study was to gain insight into the molecular mechanisms of intraspecies difference of copper accumulation in Crassostrea angulata. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster (gill and mantle). Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden.

first: B

last: Shi

first: Z

middle: K

last: Huang

first: X

last: Xiang

first: C

last: Ke


title: Identification of candidate thermotolerance genes during early seedling stage in upland cotton (Gossypium hirsutum L.) revealed by comparative transcriptome analysis

city: Anyang

first: Du

last: Xiongming

state: Henan

address: 38# Huanghe Avenue

institute: Institute of cotton research of CAAS

summary: High temperature (HT) stress is a major environmental stress that limits cotton growth, metabolism, and yield worldwide. The identification and characterization of thermotolerance is restricted by the plant growth environment and growth stage. In this study, four genotypes of upland cotton (Gossypium hirsutum L.) with known field thermotolerance were evaluated under normal and HTs at the seedlings stage in a growth cabinet with 11 physiological, biochemical, and phenotypic assays. Consistent with previous field observations, the thermotolerance could be identified by genotype differences at the seedling stage under HT in a growth cabinet. Comparative transcriptome analysis was performed on seedlings of two contrasting cotton genotypes after 4 and 8 hours of HT exposure. Gene ontology analysis combined with BLAST annotations revealed a large number of HT-induced differentially expressed genes (4,698) that either exhibited higher expression levels in the heat-tolerant genotype (Nan Dan Ba Di Da Hua) compared with the heat-sensitive genotype (Earlistaple 7), or were differentially expressed only in Nan Dan Ba Di Da Hua. These genes encoded mainly protein kinases, transcription factors, and heat shock proteins, which were considered to play key roles in thermotolerance in upland cotton. Two heat shock transcription factor genes (homologs of AtHsfA3, AtHsfC1) and AP2/EREBP family genes (homologs of AtERF20, AtERF026, AtERF053, and AtERF113) were identified as possible key regulators of thermotolerance in cotton. Some of the differentially expressed genes were validated by quantitative real-time PCR analysis. Our findings provide candidate genes that could be used to improve thermotolerance in cotton cultivars.

overall_design: Leaf mRNA profiles of  20-day-old seedlings of two cotton genotypes, one heat tolerant and the other heat sensitive during a 8-h high-temperature exposure were generated by deep sequencing, using Illumina HiSeq 2000 system.

first: Xiongming

last: Du

first: Zhen

last: Peng


title: RNASeq identified human transcriptome alterations in Chinese Nasopharyngeal Carcinoma

first: Hua

last: Dong

address: 199 Liangjing Rd.

institute: astrazeneca

summary: Our study is the first transcriptome profiling of Chinese NPC patients. These results provide both molecular basis and therapeutic opportunities for Chinese NPC patients.

overall_design: mRNA profiles of 42 Chinese Nasopharyngeal Carcinoma patients and 4 non-NPC tissues by Illumina Hiseq 2000.

first: Lily

last: Tang

first: Ming

last: Xie

first: Liang

last: Zhou

first: Qunsheng

last: Ji


title: Genes identified by poly(A)+ transcriptome sequencing as overexpressed in trf5-Δ98-117

status: Public on Jun 29 2016

city: Houston

first: Ambro

last: van Hoof

state: TX

address: 6431 Fannin Street

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center-Houston

summary:
Purpose: To study the effects of disrupting the Trf5-Mtr4 interaction
Methods: Analyzed TRF5 and trf5-Δ98-117 strains by transcriptome sequencing of poly(A)+ RNA
Results: The set of most significantly affected genes included 71 that were overexpressed in trf5-Δ98-117 and only 5 that were down-regulated.The set of 71 overexpressed genes was predominated by known TRAMP substrates
Conclusions: Disruption of the Trf5-Mtr4 interaction results in a snoRNA processing defect

overall_design: Duplicate RNA samples of trf4Δ, trf5Δ yeast strains expressing either TRF5 or trf5-Δ98-117 were enriched for poly(A)+ transcripts and converted to a sequencing library. Transcriptome sequencing was performed on a HiSeq 2500. Each sequenced library yielded between 10 and 14 million 50nt reads that were mapped to the annotated yeast genes using Bowtie. Significantly up- or down-regulated genes in the trf5-Δ98-117 mutant were identified via edgeR.


title: RNA sequencing expression analysis of murine MLL-AF9;NRAS acute myeloid leukemia cells silenced for E2-2.

city: Melbourne

first: Margherita

last: Ghisi

state: Victoria

address: St Andrews Place

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: We investigated the role of the transcriptional regulators Id2 and E2-2 (encoded by Tcf4) in the context of MLL-rearranged acute myeloid leukemia (AML). Using an AML mouse model driven by a Tet-off inducible MLL-AF9 allele co-expressed with oncogenic NRASG12D, we demonstrated that MLL-AF9 regulates the E protein pathway by suppressing Id2, while activating the expression of its target E2-2. Moreover, we found that Id2 over-expression in MLL-AF9 AML cells results inhibition of leukemia growth, loss of leukemia stem cell-associated gene expression pattern and induction of differentiation. E2-2 silencing phenocopies Id2 overexpression in MLL-AF9-AML cells. To study the gene expression changes associated with E2-2 depletion in the context of MLL-rearranged AML, RNA sequencing analysis was performed on MLL-AF9;NRAS AML cells transduced with vectors expressing hairpins against E2-2 (shTcf4#654 and shTcf4#3646) or a control hairpin against Renilla luciferase (shRen).

overall_design: Primary AMLs driven by MLL/AF9 expression linked to cherry reporter, in association with oncogenic NRASG12D (MLL/AF9;NRAS) were generated by reconstituting lethally irradiated congenic mice with fetal liver cells co-transduced with the MSCV-MLL/AF9-IRES-cherry retroviral vector and a second vector co-expressing NRASG12D together with luciferase (MSCV-luciferase-IRES-NRASG12D). RNA sequencing analysis sequencing analysis was performed on MLL-AF9;NRAS AML cells transduced in vitro with vectors expressing hairpins against E2-2 (shTcf4#654 and shTcf4#3646) or a control hairpin against Renilla luciferase (shRen) linked to the reporter GFP. Viable GFP-positive cells were FACS-sorted 2 days after transduction and used for RNA sequencing analysis. Two independent biological replicates of the experiment were used for the RNA sequencing (9-5-14 and 14-4-14).

first: Lev

last: Kats

last: Masson

first: Jason

last: Li

first: Tobias

last: Kratina

first: Eva

last: Vidacs

first: Omer

last: Gilan

first: Maria

last: Doyle

first: Andrea

last: Newbold

first: Jessica

middle: E

last: Bolden

first: Kirsten

last: Fairfax

first: Carolyn

last: de Graaf

first: Matthew

last: Firth

first: Johannes

last: Zuber

first: Ross

last: Dickins

first: Mark

last: Dawson

first: Lynn

last: Corcoran

first: Gabrielle

last: Belz

first: Ricky

middle: W

last: Johnstone


title: Gene expression profiling in dentate granule cells from patients with mesial temporal lobe epilepsy with or without hippocampal sclerosis

city: New York

first: Erin

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University

summary: Hippocampal sclerosis (HS) is the most common neuropathological finding of medically intractable cases of mesial temporal lobe epilepsy (MTLE), the most common form of partial epilepsy. Within the dentate gyrus, HS may be associated with granule cell dispersion and aberrant mossy fiber sprouting, and these pathological changes are accompanied by a range of molecular changes. In this study, we analyzed the gene expression profiles of dentate granule cells of MTLE patients with and without HS to show that next-generation sequencing methods can produce interpretable genomic data from RNA collected from small homogenous cell populations and to shed light on the transcriptional changes associated with HS.

overall_design: 12 samples of dentate granule cells from patients with mesial tempora lobe epilepsy, 5 with hippocampal sclerosis and 7 without hippocampal sclerosis. 10 samples had replicates.

first: Nicole

last: Griffin


title: HNF6 and Rev-erba Integrate Hepatic Lipid Metabolism By Overlapping and Distinct Transcriptional Mechanisms

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Adipose Rab10 Knockout Causes Insulin Resistance through Impaired Glucose Uptake

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Insulin action in adipocytes affects whole-body insulin sensitivity. Studies of adipose-specific Glut4 knockout mice have established that adipose Glut4 contributes to the control of systemic glucose homeostasis. Presumably, this reflects a role for Glut4-mediated glucose transport in the regulation of secreted adipokines. In cultured 3T3-L1 adipocytes, Rab10 GTPase is required for insulin-stimulated translocation of Glut4 (Sano et al., 2007). The physiological importance of adipose Rab10 and the significance of its role in the control of Glut4 vesicle trafficking in vivo are unknown. Here we report that adipocytes from adipose-specific Rab10 knockout mice have a ~50% reduction in glucose uptake and Glut4 translocation to the cell surface in response to insulin, demonstrating a role for Rab10 in Glut4 trafficking.  Moreover, hyperinsulinemic-euglycemic clamp shows decreased whole-body glucose uptake as well as impaired suppression of hepatic glucose production in adipose Rab10 knockout mice. Thus, fully functional Glut4 vesicle trafficking in adipocytes is critical for maintaining insulin sensitivity. Comparative transcriptome analysis of perigonadal adipose tissue demonstrates significant transcriptional similarities between adipose Rab10 knockout mice and adipose Glut4 knockout mice, consistent with the notion that the phenotypic similarities between the two models are mediated by reduced insulin-stimulated glucose transport into adipocytes.

overall_design: Transcriptome sequencing of perigonadal white adipose tissue

first: Reema

last: Vazirani

first: Timothy

last: McGraw

first: Olivier

last: Elemento


title: Single-Cell RNAseq Reveals That Pancreatic β-Cells From Very Old Male Mice Have a Young Gene Signature

city: Tarrytown

first: Yurong

last: Xin

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

summary: Aging improves pancreatic β-cell function in mice. This is a surprising finding since aging is typically associated with functional decline. We performed single-cell RNA sequencing of β-cells from 3 and 26 month old mice to explore how changes in gene expression contribute to improved function with age. The old mice were healthy, had reduced blood glucose levels and increased β-cell mass, which correlated to their body weight. β-cells from young and old mice had similar transcriptome profiles. In fact, only 193 genes (0.89% of all detected genes) were significantly regulated (≥ 2-fold; false discovery rate < 0.01; normalized counts > 5). Of these, 183 were downregulated and mainly associated with pathways regulating gene expression, cell cycle, cell death and survival as well as cellular movement, function and maintenance. Collectively, our data show that β-cells from very old mice have transcriptome profiles similar to those of young mice. These data support previous findings that aging is not associated with reduced β-cell mass or functional β-cell decline in mice.

overall_design: Single-cell RNA sequencing of mouse pancreatic islet beta cells

first: Jesper

last: Gromada


title: HNF6 and Rev-erba Integrate Hepatic Lipid Metabolism By Overlapping and Distinct Transcriptional Mechanisms [ChIP-Seq]

summary: We address the function of HNF6 in the mouse liver metabolism and Rev-erba cistrome

overall_design: We performed Rev-erba ChIP-seq in mouse livers at 5pm of the day and compared between WT and HNF6-depleted livers.

first: Yuxiang

last: Zhang

first: Manashree

last: Damle


title: RNA-seq analysis of vorinostat-resistant HCT116 cells following gene knockdown of GLI1 or PSMD13 with or without vorinostat treatment

city: East Melbourne

first: Katrina

middle: Joy

last: Falkenberg

department: Research Division

summary: Transcriptome analysis was conducted on vorinostat resistant HCT116 cells (HCT116-VR) upon knockdown of potential vorinostat resistance candidate genes in the presence and absence of vorinostat.  Potential vorinostat resistance candidate genes chosen for this study were GLI1 and PSMD13, which were identified through a genome-wide synthetic lethal RNA interference screen.  To understand the transcriptional events underpinning the effect of GLI1 and PSMD13 knockdown (sensitisation to vorinostat-induced apoptosis), cells were first subjected to gene knockdown, then to treatment with vorinsotat or the solvent control.  Two timepoints for drug treatment were assessed: a timepoint before induction of apoptosis (4hrs for siGLI1 and 8hrs for siPSMD13) and a timepoint when apoptosis could be detected (8hrs for siGLI1 and 12hrs for siPSMD13).

overall_design: There are 42 samples in total, from triplicate independent biological experiments of 14 samples each.

first: Cathryn

last: Gould

first: Kaylene

last: Simpson


title: Genome-wide analysis of gene expression in control and Lats1/2 deficient neonatal mice

city: DaeJon

first: Da-Hye

last: Lee

address: 335 Gwahangno

department: Biological science

country: South Korea

institute: KAIST


title: Transcriptome profile form oviduct samples of endocrine manipulated cows (ampulla)

first: Angela

last: Gonella

summary:
Purpose: evaluate if different proestrus-estrus concentrations of estradiol (E2) and metestrus progesterone (P4) concentrations specifically regulate oviductal gene expression.
Methods: ampulla and isthmus samples of animals with a large pre-ovulatory follicle and a large CL (LF/LCL) and animals with a small pre-ovulatory follicle and a small CL (SF/SCL) were collected after slaughter at day four of the estrous cycle. Total RNA was extracted and RNA sequencing was performed using the Illumina HiScanSeq (ampulla samples) and the Illumina HiSeq 2500 (isthmus samples) platforms.
Results: After using HTSeq-count, approximately ~60% of the total reads uniquely mapped to the UMD 3.1 reference genome. In the ampulla samples, a total of 692 genes showed differential expression, of which 325 and 367 were up-regulated in the LF-LCL and SF-SCL samples, respectively. In the isthmus samples, a total of 590 genes showed differential expression, of which 274 and 316 were up-regulated in the isthmus of LF/LCL and SF/SCL samples, respectively.
Conclusions: Our study represents the first detailed analysis of oviduct transcriptomes, generated by RNA-seq technology. Differential global gene expression profiles identified indicate that the biology of the bovine oviductal tissue is modulated by the periovulatory endocrine milieu. The LF-LCL group transcriptome may potentially reveal molecules associated with higher fertility.

overall_design: Oviductal mRNA profiles of cows with different endocrine milleus were generated by next generation sequencing.

last: Gonella-Diaza.

first: Sonia

last: Andrade

first: Gustavo

last: Gasparin

first: Luiz

last: Coutinho

first: Mario

last: Binelli


title: MicroRNA expression analysis of integrin-linked kinase gene silencing in A2780 cell line

status: Public on Jun 28 2016

city: Harbin

first: Wenliang

last: Zhu

address: 246 Xuefu Road

institute: the Second Affiliated Hospital of Harbin Medical University

summary: Available evidence has suggested that integrin-linked kinase (ILK) underwent over-expression in ovarian cancer while specific gene silencing of ILK resulted in apoptosis of ovarian cancer cells. Here, potential mechanisms in which ILK induces cell apoptosis was explored from the perspective of microRNA (miRNA) expression.

overall_design: Alteration in global miRNA expression profile was detected by miRNA microarray technique after ILK shRNA expression lentivirus was transfected into A2780 cells (n = 3). Additionally, the A2780 cells infected by scrambled shRNA lentivirus were treated as negtive control (n = 3).


title: Identification of microRNAs and microRNA targets in Xenopus ectoderm

first: Vrutant

middle: V

last: Shah

address: 1515 Holcombe Blvd #1000

department: EMC

institute: UT MD Anderson Cancer Center

summary:
Purpose: The establishment of cell lineages occurs via a dynamic progression of gene regulatory networks that underlie developmental commitment and differentiation. To investigate how microRNAs (miRs) function in this process, we compared miRs and miR targets at the initiation of the two major ectodermal lineages in Xenopus.

Methods: We injected Xenopus laevis embryos with noggin or constitutively active BMP4 receptor (CABR) at two-cell stage and cut animal caps at stg. 8. Isolated animal caps were grown separately till mid gastrula and processed for either RNA isolation or immunoprecipitation.

Results: We have identified over 400 miRNAs in early neural and epidermal ectoderm. The Ago-RNP RNAs from these tissues represent overlapping, yet distinct, subsets of genes. Moreover, the profile of Ago-RNP associated genes differs substantially from the profile of total RNAs in these tissues.

overall_design: Identification of microRNAs and microRNA targets in establishment of early ectodermal tissues in Xenopus.

first: Amy

last: Sater


title: Genome-wide analysis of gene expression using in vitro cultured control and Lats1/2 deficient hepatoblasts [RNA-Seq]

summary: RNA-sequencing results with in vitro cultured control and Lats1/2 deficient hepatoblasts, in vitro differentiated control and Lats1/2 deficient hepatocytes and biliary epithelial cells

overall_design: To investigate changes in gene expression by loss of Lats1 and Lats2 during hepatocyte or biliary epithelial cell differentiation, we performed multiplex RNA-sequecing with in vitro cultured hepatoblasts, in vitro differentiated hepatocytes and biliary epithelial cells

first: Dae-Sik

last: Lim


title: Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids

city: East Lansing

first: Dae Kwan

last: Ko

state: MI

address: 612 Wilson Rd.  Plant Biology RM 122

department: Plant Research Laboratories

institute: Michigan State University

summary: we determine genome-wide binding profiles of a maize CCA1 homolog, ZmCCA1b, in maize inbreds and F1 hybrids at different times of the day. ZmCCA1b is characterized as a central clock regulator gene with evolutionarily conserved molecular and circadian functions and nonadditively expressed in F1 hybrid seedlings. ZmCCA1b binds to over 4,300 target genes in the maize genomes, of which annotation confirms energy metabolic pathways as the main output. We report that an altered temporal binding activity of ZmCCA1b in the hybrid seedlings, which increases expression of carbon fixation genes, increases carbon fixation rates and biomass, demonstrating a novel example of how circadian-regulatory networks directly contribute to growth vigor in maize hybrids. These results collectively offer new insights into clock-mediated regulation of growth vigor in hybrid plants and crops.

overall_design:
Profiling genome-wide binding events of ZmCCA1b in the maize inbreds and F1 hybrids at ZT3, ZT9 and ZT15 using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). 2 biological replicates for each sample were used. Input DNA sample corresponding to each ChIP sample was also sequenced in parallel.
We have developed a native antibody for the protein (GRMZM2G014902; epitope: residues 11-77) for the ChIP-seq study.

first: Dae

first: Qinxing

last: Song

first: Z

last: Chen


title: Id2 and E proteins orchestrate the initiation and maintenance of MLL-rearranged acute myeloid leukemia

first: Margherita

last: Ghisi


title: TRIM28 is an epigenetic barrier to induced pluripotent stem cell reprogramming

city: PARKVILLE

first: Denise

last: Miles

state: VIC

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: Since the discovery of induced pluripotent stem cells there has been intense interest in understanding the mechanisms that allow a somatic cell to be reprogrammed back to a pluripotent state. Several groups have studied the alterations in gene expression that occur as somatic cells modify their genome to that of an embryonic stem cell. Underpinning many of the gene expression changes are modifications to the epigenetic profile of the associated chromatin. We have used a large-scale shRNA screen to identify epigenetic modifiers that act as barriers to reprogramming. We have uncovered an important role for TRIM28 in cells resisting transition between somatic and pluripotent states. TRIM28 achieves this by maintaining the H3K9me3 repressed state and keeping endogenous retroviruses silenced. We propose that knockdown of TRIM28 during reprogramming results in more plastic H3K9me3 domains, dysregulation of genes nearby H3K9me3 marks, and up regulation of endogenous retroviruses, thus facilitating the transition through reprogramming.

overall_design: Gene expression profiling using high through put sequencing at day 7 of Oct4, Sox2, Klf4 and cMyc (OSKM) expression in mouse embryonic fibroblasts with or without Trim28 / Setdb1 knockdown

first: Nienke

last: de Vries

first: Santiago

last: Gisler

first: Cor

last: Lieftink

first: Waseem

last: Akhtar

first: Ewa

last: Gogola

first: Inka

last: Pawlitzky

first: Danielle

last: Hulsman

first: Ellen

last: Tanger

first: Martijn

last: Koppens

first: Roderick

last: Beijersbergen

first: Maarten

last: van Lohuizen


title: Zfp281 Coordinates Opposite Functions of Tet1 and Tet2 for Alternative Pluripotent States [RNA-Seq]

first: Jianlong

last: Wang

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Pluripotent cell identity comprises a spectrum of cell states including naive and primed states, which are typified by mouse embryonic stem cells (ESCs) and epiblast-derived stem cells (EpiSCs), respectively. Here we define a pluripotent cell fate (PCF) gene signature based on RNA-seq analysis associated with naive and primed pluripotency acquisition, and identify Zfp281 as a key transcriptional regulator for primed pluripotency and also as a barrier to achieve the naive pluripotency of both mouse and human ESCs.

overall_design: RNA sequencing analysis was performed in WT and Zfp281 null mouse embryonic stem cells under different pluripotent culture conditions. RNA-seq Experiments were carry out in two biological replciates. Genome binding/occupancy profiling of Zfp281 was performed in mouse embryonic stem cells by ChIP sequencing.

first: Miguel

last: Fidalgo

first: Xin

last: Huang


title: Zfp281 Coordinates Opposite Functions of Tet1 and Tet2 for Alternative Pluripotent States


title: Zfp281 Coordinates Opposite Functions of Tet1 and Tet2 for Alternative Pluripotent States [ChIP-Seq]


title: Systematic characterization of seminal plasma piRNAs as molecular biomarkers for male infertility

city: Nanjing

first: Zhen

last: Zhou

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

summary: Although piwi-interacting RNAs (piRNAs) play pivotal roles in spermatogenesis, little is known about piRNAs in the seminal plasma of infertile males. In this study, we systematically investigated the profiles of seminal plasma piRNAs in infertile males to identify piRNAs that are altered during infertility and evaluate their diagnostic value. Seminal plasma samples were obtained from 211 infertile patients (asthenozoospermia and azoospermia) and 91 fertile controls. High-throughput sequencing technology was employed to screen piRNA profiles in seminal plasma samples pooled from healthy controls and infertile patients. The results identified 61 markedly altered piRNAs in the infertile patient groups compared with the control group. Next, a quantitative RT-PCR assay was conducted in the training and validation sets to measure and confirm the concentrations of altered piRNAs. The results identified a panel of 5 piRNAs that were significantly decreased in the seminal plasma of infertile patients compared with healthy controls. The areas under the ROC curves for these piRNAs ranged from 0.796 to 0.996, suggesting that the diagnostic potential of these 5 piRNAs to distinguish asthenozoospermic and azoospermic individuals from healthy controls was high. In summary, this study identifies a panel of piRNAs that can accurately distinguish fertile from infertile males. This finding may provide pathophysiological clues that are involved in the development of infertility.

overall_design: Fresh samples were collected and stored at -80℃.Total RNA of seminal plasma were extracted and solexa sequencing was performed.

first: Yeting

last: Hong

first: Cheng

first: Xi

last: Chen


title: Gene expression analysis of developing Sea Lamprey  (Petromyzon marinus)

city: Lexington

first: Mark

last: Evers

state: Kentucky

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

summary: This project is designed to measure changes in gene expression during sea lamprey development

overall_design: RNA was extracted from sea lamprey embryos at 1, 2, 2.5, 3, 4, and 5 days post-fertilization and used to generate RNAseq data

first: Jeramiah

last: Smith

first: Stephanie

last: Bryant

first: Joseph

last: Herdy


title: RNA sequencing expression analysis of murine Tet-off MLL-AF9;NRAS acute myeloid leukemia cells over-expressing Id2 and upon MLL-AF9 withdrawal

first: Margherita

last: Ghisi

summary: We investigated the role of the transcriptional regulator Id2 in the context of MLL-rearranged acute myeloid leukemia (AML). Using an AML mouse model driven by tet-regulated MLL-AF9 co-expressed with oncogenic NRASG12D (Tet-off MLL-AF9), we demonstrated that MLL-AF9 regulates the E protein pathway by suppressing Id2, while activating the expression of its target E2-2. Moreover, we found that Id2 over-expression in Tet-Off MLL-AF9 AML cells in vitro partially phenocopies MLL-AF9 depletion and results inhibition of leukemia growth, loss of leukemia stem cell-associated gene expression pattern and induction of differentiation. To compare gene expression changes associated with enforced Id2 expression and MLL-AF9 withdrawal, RNA sequencing analysis was performed on Tet-off MLL-AF9 cells transduced with an Id2 over-expressing or a control vector, or upon MLL-AF9 dox-inducible knock-down.

overall_design: Primary AMLs driven by Tet-off inducible MLL/AF9 expression linked to dsRED reporter, in association with oncogenic NRASG12D (Tet-off MLL-AF9) were generated by reconstituting lethally irradiated congenic mice with foetal liver cells co-transduced with a Tet-Off-MLL-AF9-dRED retroviral vector and a second vector co-expressing NRASG12D together with the Tet-Off responsive transcriptional activator. RNA sequencing analysis sequencing analysis was performed on Tet-Off MLL-AF9/dsRED+ AML cells treated in vitro with doxycycline (DOX) for 4 days to inactivate MLL-AF9 expression or left untreated (UT). For the Id2 over-expression experiment, Tet-Off MLL-AF9/dsRED+ AML cells were transduced in vitro with an Id2-GFP  or a control-GFP retroviral vector. Viable GFP-positive cells were FACS-sorted 2 days after transduction and used for RNA sequencing analysis.

first: Frederic

last: Masson

first: Jason

last: Li

first: Tobias

last: Kratina

first: Eva

last: Vidacs

first: Maria

last: Doyle

first: Johannes

last: Zuber

first: Ross

last: Dickins

last: Dawson

first: Lynn

last: Corcoran

first: Gabrielle

middle: T

last: Belz

first: Ricky

last: Johnstone


title: RNA sequencing analysis of murine MLL-AF9 acute myeloid leukemia cells expressing different levels of Id2 and Kit

summary: We investigated the role of the transcriptional regulator Id2 in the context of MLL-rearranged acute myeloid leukemia (AML). Using an Id2/GFP-reporter mouse model of MLL-AF9-driven AML, we showed that Id2 is expressed heterogeneously across the leukemic population. Moreover, differential expression of Id2 and the stemness marker Kit defines subsets of AML cells with different leukemogenic properties with lower levels of Id2 associated with enrichment in leukemia stem cell potential. To define gene expression patterns associated with distinct endogenous levels of Id2 and higher LSC potential, RNA sequencing analysis was performed on FACS-sorted KitHI–Id2HI (BM_Kplus-Iplus), KitHI–Id2LOW(BM_Kplus-Iminus), KitLOW–Id2HI (BM_Kminus-Iplus) and KitLOW–Id2LOW (BM_Kminus-Iminus) MLL-AF9-cherry+ AML cells obtained from bone marrow of terminally sick mice.

overall_design: Primary MLL-AF9+ AMLs were generated by reconstituting lethally irradiated congenic mice with foetal liver cells obtained from Id2-GFP reporter mice and transduced with a retroviral vector co-expressing MLL-AF9 and the cherry reporter protein. KitHigh–Id2High, KitHigh–Id2Low, KitLow–Id2High and KitLow–Id2Low MLL-AF9/cherry+ AML cells obtained from bone marrow of terminally sick primary recipients were FACS-sorted and used for RNA sequencing analysis (3 samples/subset).


title: The methyltransferase Setdb1 is essential for meiosis and mitosis in mouse oocytes and early embryo

status: Public on Jun 27 2016

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: Oocytes develop the competence for meiosis and early embryogenesis during their growth. Setdb1 is a histone H3 lysine 9 (H3K9) methyltransferase required for post-implantation development and has been implicated in the transcriptional silencing of genes and endogenous retroviral elements (ERVs). To address its role in oogenesis and pre-implantation development, we conditionally deleted Setdb1 in growing oocytes. Loss of Setdb1 expression greatly impaired meiosis. It delayed meiotic resumption, altered the dynamics of chromatin condensation, and impaired kinetochore-spindle interactions, bipolar spindle organization, and chromosome segregation in more mature oocytes. The observed phenotypes related to changes in abundance of specific transcripts in mutant oocytes. Setdb1 maternally deficient embryos arrested during pre-implantation development and showed comparable defects during cell cycle progression and in chromosome segregation. Finally, transcriptional profiling data indicate that Setdb1 down-regulates rather than silences expression of ERVK and ERVL-MaLR retrotransposons and associated chimearic transcripts during oogenesis. Our results identify Setdb1 as a novel meiotic and embryonic competence factor in meiosis and mitosis, safeguarding genome integrity at the onset of life.

overall_design: We performed expression profiling on pools of 16 denuded GV-oocytes isolated per mouse. We used oocytes from 4 Setdb1 f/+; Zp3-cre mice and 2 Setdb1 f/- mice as controls and oocytes from 4 Setdb1 f/-; Zp3-cre mice as mutant.

first: Angeline

last: Eymery

first: Evgeniy

last: Ozonov

first: Michael

middle: B

last: Stadler

middle: H


title: CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells [ChIP-Seq]

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: CTCF and cohesinSA-1 are regulatory proteins involved in a number of critical cellular processes including transcription, maintenance of chromatin domain architecture, and insulator function. To assess changes in the CTCF and cohesinSA-1 interactomes during erythropoiesis, chromatin immunoprecipitation coupled with high throughput sequencing and mRNA transcriptome analyses via RNA-seq were performed in primary human HSPC hematopoietic stem and progenitor cells (HSPC) and primary human erythroid cells from single donors. Sites of CTCF and cohesinSA-1 co-occupancy were enriched in gene promoters in HSPC and erythroid cells compared to single CTCF or cohesin sites. Cell type-specific CTCF sites in erythroid cells were linked to highly expressed genes, with the opposite pattern observed in HSPCs. Chromatin domains were identified by ChIP-seq with antibodies against trimethylated lysine 27 histone 3, a modification associated with repressive chromatin. Repressive chromatin domains increased in both number and size during hematopoiesis, with many more repressive domains in erythroid cells than HSPCs. CTCF and cohesinSA-1 marked the boundaries of these repressive chromatin domains in a cell-type specific manner. These genomic data support the hypothesis that CTCF and cohesinSA-1 have multiple roles in the regulation of gene expression during erythropoiesis including transcriptional regulation at gene promoters and maintenance of chromatin architecture.

overall_design: CD34+-selected stem and progenitor cells were expanded for three days in the absence of EPO. The cells were further cultured in the presence of EPO, and formaldehyde crosslinked chromatin was isolated after cells differentiated into R3/R4 nucleated erythroid cells. Chromatin Immunoprecipitation followed by sequencing (chIP-seq) was performed using antibodies against CTCF, Cohesin SA1 and H3K27me3, along with a total input control. Two replicates for CTCF and Cohesin SA1 were obtained.

first: Laurie

last: Steiner

first: Vincent

middle: P

first: Yelena

last: Maksimova

first: Kimberly

last: Lezon-Geyda

first: Patrick

middle: G

last: Gallagher


title: Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes: molecular insight into sex-specific processes and translational repression

city: Nijmegen

first: Richard

middle: Csaba

last: Bartfai

address: Geert Groteplein 26-26

department: Department of Molecular Biology

country: Netherlands

institute: Radboud University

summary: Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilisation in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organisation and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilisation; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.

overall_design: Examining the transcriptome of p47-mCherry positive female and pDynGFP positive (or double positive) male gametocytes by RNA-seq.

first: Edwin

last: Lasonder

first: Sanna

last: Rijpma

first: Ben

middle: C

last: van Schaijk

first: Wieteke

middle: A

last: Hoeijmakers

first: Philip

last: Kensche

first: Mark

middle: S

last: Gresnigt

first: Annet

last: Italiaander

first: Martijn

last: Vos

first: Rob

last: Woestenenk

first: Teun

last: Bousema

first: Gunnar

last: Mair

first: Shahid

last: Khan

first: Chris

last: Janse

first: Richárd

last: Bártfai

first: Robert

last: Sauerwein


title: CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells [RNA-Seq]

first: Vince

last: Schulz

overall_design: CD34+-selected stem and progenitor cells were expanded for three days in the absence of EPO. The cells were further cultured in the presence of EPO, and cells differentiated into R3/R4 nucleated erythroid cells. RNA was isolated from three biological replicates of each cell type and sequencing libraries were prepared from poly A selected RNA.

first: Laurie

last: Steiner

first: Vincent

first: Yelena

last: Maksimova

first: Kimberly

last: Lezon-Geyda

first: Patrick

last: Gallagher


title: DNAse-Seq of Cultured Mouse Podocytes

first: Shawn

middle: Samson

last: Badal

address: 2121 W. Holcombe Blvd

department: Nephrology

institute: MD Anderson Cancer Center

summary: Investigation of DNAse Hypersensitivity changes in podocytes cultured under normal or high glucose conditions transfected with a miR-93 mimic or a nontargeting mimic.

overall_design: Examination of the changes in hypersensitivity induced by high glucose culture conditions compared to normal glucose conditions to mimic the diabetic millieu. Further, to see if miR-93 overexpression can reverse these changes.

first: Farhad

last: Danesh


title: CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells

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

overall_design: Refer to individual Series


title: Cultured Mouse Podocytes


title: Microbial-Derived Metabolites Regulate the Colonic Crypt Niche

city: St Louis

first: Gerard

last: Kaiko

state: Missouri

address: 660 S Euclid avenue

institute: Washington University in St Louis

summary: In the mammalian intestine, crypts of Leiberkühn house intestinal epithelial stem /progenitor cells at their base. We found that the presence of this structure was supported by the physiologic role of a prominent bacterial metabolite, butyrate. This bacterially-produced short chain fatty acid inhibited intestinal epithelial proliferation at physiologic concentrations. During homeostasis, butyrate did not suppress epithelial stem proliferation because it was metabolized by differentiated colonocytes. Provision of butyrate access to stem/progenitor cells either through mucosal injury or application to a crypt-less host led to inhibition of proliferation. The mechanism was dependent on HDAC inhibition in stem cells and the transcription factor Foxo3. Thus, the mammalian crypt unit structure provides energy for differentiated cells at a distance from the crypt base and this action prevents suppression of stem/progenitor proliferation.

overall_design: In total 4 samples were analyzed from 2 independent experiments. Two samples of colonic stem cells treated with 1mM Butyrate and two samples of colonic stem cells treated with 1mM NaCl (mock) as a control

first: Olivia

middle: I

last: Koues

first: Eugene

middle: M

last: Oltz

first: Thaddeus

last: Stappenbeck


title: RNA-Seq of Cultured Mouse Podocytes

summary: Investigation of mRNA changes in podocytes transfected with a miR-93 mimic or a nontargeting mimic.

overall_design: The design was meant to identify biologically significant, novel targets of the miR-93 microRNA in podocytes

middle: R


title: Transcriptome-wide profiling of Spadetail-regulated genes in early somite progenitors

city: Stanford

first: James

last: Chen

state: CA

address: 269 W. Campus Drive, CCSR 3150

department: Chemical and Systems Biology

institute: Stanford University

summary: We integrate zebrafish embryology with photoactivatable caged morpholinos (cMO), the photoactivatable lineage tracer caged fluorescein-dextran (cFD), fluorescence-activated cell-sorting (FACS) and RNA sequencing (RNA-seq) to identify Spadetail-regulated genes in mesodermal cells enriched for early somite progenitors.

overall_design: 1 to 4-cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hours post-fertilization (hpf).  Early ventral somite progenitors were then optically targeted with ultraviolet (360 nm) light using a 100-μm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf, dechorionated, and dissociated into single-cells. Fluorescein-positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL-Seq protocol (Hashimshony, T et al.  Cell Reports. 2012). In short, total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL-seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.

first: Alexander

middle: Y

last: Payumo

middle: K


title: Comprehensive transcriptomes of mouse pancreatic islet delta, beta, and alpha cells

status: Public on Jun 26 2016

city: Davis

first: Mark

middle: O.

last: Huising

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

summary: Rodent models are widely used to study diabetes. Yet, significant gaps remain in our understanding of mouse islet physiology. We generated comprehensive transcriptomes of mouse delta, beta and alpha cells using two separate triple transgenic mouse models generated for this purpose. This enables systematic comparison across thousands of genes between the three major endocrine cell types of the islets of Langerhans whose principal hormones control nutrient homeostasis.

overall_design:
FACS purified delta or alpha cells and beta cells from the same islets. Islets were isolated from triple transgenic offspring of a cross between mIns1-H2b-mCherry (Jax # 028589) and either Sst-Cre (delta) or Gcg-cre (alpha) cells and a floxed YFP allele to label delta or alpha cells, respectively.
Islets from replicate groups of 10 to 12 triple transgenic animals for each group were pooled by sex to obtain sufficient material. Pooled islets were dissociated, sorted and collect in Trizol for RNA isolation and library construction.

first: Talitha

last: van der Meulen

first: Alex

last: Mawla

middle: O


title: Regulation of Lin28b and let-7 in developmental myelopoiesis

city: Boston

first: Areum

last: Han

state: MA

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

summary: We isolated RNA from sorted common myeloid progenitor cells from wild-type fetal liver, wild-type adult bone marrow, transgenic Lin28b bone marrow, let-7b/c knock-out bone marrow, and Lin28b-deficient fetal liver and compared mRNA expression profiles.

overall_design:
Examination of mRNA expression in common myeloid progenitors from multiple developmental time points and genotypes.
Please note that iLin28* samples represent Lin28-induced samples, while the iLin28_*_vavcre samples represent hematopoietic-specific induction of Lin28.

first: George

middle: Q

last: Daley

first: Robert

last: Rowe

first: Silvia

last: Coma


title: global gene expression profiling experiments of HSC cultured in cysteine or valine deficient medium by RNA-sequencing analysis

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: We investigated the role of amino acid to maintain HSC function. To identify essential amino acids for HSCs, CD34-KSL cells were cultured in single amino acids deficient medium. And cultured cells were transplanted into lethally irradiated mice. Then, the donor chimerism and lineage contribution was estimated. Surprisingly, HSC proliferation was prevented in valine and cysteine deficient medium in vitro. Donor cells cultured in these medium were also not engrafted. To elucidate the effects and influences of cysteine and valine in HSCs, we performed global gene expression profiling experiments by RNA-sequencing analysis. Gene sets categorized with cell cycle, mitosis, cell division or DNA replication were strongly down-regulated in both valine- or cysteine-depleted conditions These results imply distinctive amino-acid metabolism involved in HSC division.

overall_design: Gene expression profiles of ten thousand HSCs cultured in cysteine or valine deficient medium for 24 hours were compared with that of HSCs cultured in complete medium by using RNA-sequencing analysis

first: Yuki

last: Taya

first: Satoshi

last: Yamazaki

first: Hiroshi

last: Watarai

first: Ayano

last: Kanazawa


title: Role of PARP1 in cocaine-related memory retrieval

status: Public on Jun 25 2016

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

summary: Reward-related memory is an important factor in cocaine seeking. One necessary signaling mechanism for long-term memory formation is the activation of poly(ADP-ribose) polymerase-1 (PARP-1), via poly(ADP-ribosyl)ation. We demonstrate herein that auto-poly(ADP-ribosyl)ation of activated PARP-1 was significantly pronounced during retrieval of cocaine-associated contextual memory, in the central amygdala (CeA) of rats expressing cocaine-conditioned place preference (CPP). Intra-CeA pharmacological and shRNA depletion of PARP-1 activity during cocaine-associated memory retrieval abolished CPP. In contrast, PARP-1 inhibition after memory retrieval did not affect CPP reconsolidation process and subsequent retrievals. Chromatin Immuoprecipitation (ChIP) sequencing revealed that PARP-1 binding in the CeA is highly enriched in genes involved in neuronal signaling. We identified amongst PARP targets in CeA a single gene, yet uncharacterized and encoding a putative transposase inhibitor, at which PARP-1 enrichment dramatically increases during cocaine-associated memory retrieval and positively correlates with CPP. Our findings have important implications for understanding drug-related behaviors, and suggest possible future therapeutic targets for drug abuse.

overall_design: 4 samples, each is pooled central amygdalae tissues collected from 2 rats. Rats were trained for cocaine-conditioned place-preference (CPP), tissues were harvested immediately following cocaine-CPP retrieval. Three groups of rats were used: high cocaine CPP, low cocaine CPP and control saline only trained rats.

first: Elad

last: Lax

last: Friedman

first: Renaud

last: Massart

first: Royi

last: Barnea

first: Litel

last: Abraham

first: David

last: Cheishvili

first: Mor

last: Zada

first: Hadas

last: Ahdoot

first: Tzofnat

last: Bareli

first: Gal

last: Warhaftig

first: Leonid

last: Visochek

first: Matthew

last: Suderman

first: Malka

last: Cohen-Armon

last: Yadid


title: ChIP-Seq of RNA polymerase and co-factors in Jurkat T-ALL cells

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Transcription of oncogenes is regulated by co-factors, some of which are now targetable with small molecules.  This series contains ChIP-Seq targeting transcriptional co-factors and RNA polymerase from cells treated with small molecules targeting co-factors.

first: Jessica

last: Reddy


title: mature piRNAs expression profile in human bronchial epithelial (HBE) and non-small cell lung cancer (NSCLC) cells

city: Baltimore

first: Priti

last: Kumari

state: MD

address: 801 W Baltimore St

department: Institute For Genome Sciences

institute: University Of Maryland Baltimore School Of Medicine

summary: To elucidate potential roles of piRNA in lung cancer, we analyzed global piRNA expression profiles in 8 NSCLC and 3 HBE cell lines. RNA-seq results showed that >99% of the approximately 4.5 million reads were between 26 and 32 bases. Most of the piRNA loci are represented by two or more identical reads. We observed a total 555 expressed mature piRNAs, distributed among chromosomes and mitochondria with bias in chromosomes 1 and 6. 99% of the piRNAs are mapped to intergenic regions (64%) or introns (35%) and 1% to exons. Of the 555 mature piRNAs, 260 (47%) have been recorded in NCBI whereas 295 (53%) are novel. These results provide a comprehensive view of piRNA expressed in human bronchial epithelial cells and NSCLC cells.

overall_design: To get the purified mature piRNAs, small RNA (<200nt) was separated from total RNAs firstly, and then piRNA were purified in one nucleotide resolution gel. A unique 6 nt barcode for every cell line to distinguish each reads from each specific cell line, and the right size of small RNAs were used library for Illumina sequencing.

first: Yuping

last: Mei

first: Naomi

last: Sengamalay


title: Meis1 induces and Prep1 suppresses tumors by exploiting low affinity AP1 binding sites.

city: Milan

first: Francesco

last: Blasi

address: Via Adamello 16

country: Italy

institute: IFOM

summary: We have defined the tumor and tumor suppressor signature for Meis1 and Prep1 (pKnox1), respectively, using ChIP-seq and RNA-seq in a cell system in which tumor suppressor Prep1 and oncogene Meis1 compete for tumorigenesis [GSE54221; GSE58802]. In this paper we report that the number of Meis1 or Prep1 DNA binding sites increases linearly with the level of expression of the two transcription factors. Overexpression of Meis1 induces tumors. At the molecular level it modifies the DNA target specificity by increasing the number of low-affinity binding sites, which results in a different choice of consensus sequences with predominance of sites normally bound by the AP1 transcription factor family. Upon concomitant overexpression of Prep1 and Meis1 tumorigenesis is inhibited. Prep1 dominates over Meis1 not only because it partially decreases Meis1 protein level but also because it prevents the binding to a substantial fraction of the low affinity binding sites. Overall, overexpression of Prep1 reverses the nature of the bound and regulated genes from stimulatory to inhibitory of signal transduction and transcription, which suppresses tumorigenesis. By identifying the Meis1 tumor signature, specific relevant signaling pathways are identified. In line with these results, tumorigenic Meis1-overexpressing cells are uniquely hypersensitive to inhibitors of the MAPK/Akt pathways.

overall_design: Examination of Prep1 and Meis1 in five cell type

first: Leila

last: Dardaei


title: Genome-wide recruitment profiling of transcription factor Crz1 in response to high pH stress

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

summary:
Exposure of the budding Saccharomyces cerevisiae to an alkaline environment produces a robust transcriptional response involving hundreds of genes. Part of this response is triggered by an almost immediate burst of calcium that activates the Ser/Thr protein phosphatase calcineurin. Activated calcineurin dephosphorylates the transcription factor Crz1, which moves to the nucleus and binds to calcineurin/Crz1 responsive gene promoters. In this work we present a genome-wide study of the binding of Crz1 to gene promoters in response to high pH stress.
Environmental alkalinization promoted a time-dependent recruitment of Crz1 to 152 intergenic regions, the vast majority between 1 to 5 min upon stress onset. Positional evaluation of the genomic coordinates combined with existing transcriptional studies allowed identifying 139 genes likely responsive to Crz1 regulation. Gene Ontology analysis confirmed the relevant impact  of calcineurin/Crz1 on a set of genes involved in glucose utilization, and uncovered novel targets, such as genes responsible for trehalose metabolism. We also identified over a dozen of genes encoding transcription factors that are likely under the control of Crz1, suggesting a possible mechanism for amplification of the signal at the transcription level. Further analysis of the binding sites allowed refining the consensus sequence for Crz1 binding to gene promoters and the effect of chromatin accessibility in the timing of Crz1 recruitment to promoters.
The present work defines at the genomic-wide level the kinetics of binding of Crz1 to gene promoters in response to alkaline stress, confirms diverse previously known Crz1 targets and identifies many putative novel ones. Because the relevance of calcineurin/Crz1 in signaling diverse stress conditions, our data will contribute to understand the transcriptional response in other circumstances that also involves calcium signaling, such as exposition to sexual pheromones or saline stress.

overall_design: ChIP-Seq from five time points after alkalinization (t=0, 1, 2, 5 and 20 min) was collected from two independent experiments (A and B) and the ratio Tx/T0 was calculated.

first: Joaquin

last: Ariño

first: Silvia

last: Petrezselyova


title: Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation

first: Christian

last: Munch

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

summary: The mitochondrial matrix is unique in that it must integrate folding and assembly of proteins derived from nuclear and mitochondrial genomes. In C. elegans, the mitochondrial unfolded protein response (UPRmt) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis. While misfolded mitochondrial matrix-localized ornithine trans-carbamylase (OTC) induces chaperonin expression, our understanding of mammalian UPRmt is rudimentary, reflecting a lack of acute triggers for UPRmt activation. This limitation has prevented analysis of the cellular responses to matrix protein misfolding and the effects of UPRmt on mitochondrial translation to control protein folding loads. Here, we combine pharmacological inhibitors of matrix-localized HSP90/TRAP1 or LON protease, which promote chaperonin expression, with global transcriptional and proteomic analysis to reveal an extensive and acute response of human cells to UPRmt. This response involved widespread induction of nuclear genes, including matrix-localized proteins involved in folding, pre-RNA processing and translation. Functional studies revealed rapid but reversible translation inhibition in mitochondria occurring concurrently with defects in pre-RNA processing due to transcriptional repression and LON-dependent turnover of the mitochondrial pre-RNA processing nuclease MRPP3. This study reveals that acute mitochondrial protein folding stress activates both increased chaperone availability within the matrix and reduced matrix-localized protein synthesis through translational inhibition, and provides a framework for further dissection of mammalian UPRmt.

overall_design: triplicate experiment of 3 conditions (untreated, GTPP treatment, CDDO treatment)

last: Münch

first: J

middle: W

last: Harper


title: Barley transcriptional responses to specialist and generalist spider mite herbivores

status: Public on Jun 24 2016

city: Salt Lake City

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

summary: Spider mites, including the two-spotted spider mite (Tetranychus urticae, TSSM) and the Banks grass mite (Oligonychus pratensis, BGM), are becoming increasingly important agricultural pests. The TSSM is an extreme generalist documented to feed on more than 1100 plant hosts. In contrast, the BGM is a grass specialist, with hosts including important cereal crops like maize, wheat, sorghum and barley. Historically, studies of plant-herbivore interactions have focused largely on insects. However, far less is known about plant responses to spider mite herbivores, especially in grasses, and whether responses differ between generalists and specialists. To identify plant defense pathways responding to spider mites, we collected time course RNA-seq data from barley (Hordeum vulgare L.) infested with TSSMs and BGMs. Additionally, and as a comparison to the physical damage caused by spider mite feeding, a wounding treatment was also included.

overall_design: The experiment was performed with four biological replicates across each of the following (28 samples in total): no infestation (C, control), 2hr after wounding (W2), 24hr after wounding (W24), 2hr after TSSM infestation (T2), 24hr after TSSM infestation (T24), 2hr after BGM infestation (B2), and 24hr after BGM infestation (B24).

first: Huyen

last: Bui

first: Robert

last: Greenhalgh

first: Alice

last: Ruckert

first: Ricardo

last: Ramirez


title: MLL-AF9 Expression in Hematopoietic Stem Cells Drives a Highly Invasive AML Expressing EMT-Related Genes Linked to Poor Outcome [RNA-Seq]

first: Antoine

last: Peters

summary: To address the impact of cellular origin on AML, we generated an inducible transgenic mouse model for MLL-AF9 driven leukemia. MLL-AF9 expression in long-term hematopoietic stem cells (LT-HSCs) in vitro resulted in unprecedented clonogenic growth and expression of genes involved in migration and invasion. In vivo, some LT-HSC-derived AMLs were particularly aggressive with extensive tissue infiltration, chemo-resistance and expression of genes related to epithelial-mesenchymal transition (EMT) in solid cancers. Knockdown of the EMT regulators Zeb1 and Tcf4 significantly reduced leukemic blast invasion. By classifying mouse and human leukemia according to Evi1/EVI1and Erg/ERG expression, reflecting aggressiveness and cell-of-origin and performing comparative transcriptomics we identified numerous EMT-related genes that were significantly associated with poor overall survival of AML patients.

overall_design: RNA from FACS sorted bone marrow subpopulations was isolated, RNA-sequencing libraries were prepared and sequenced on an Illumina HiSeq 2000. Reads mapping to RefSeq transcripts were counted.

first: Vaya

last: Stavropoulou

first: Susanne

last: Kaspar

first: Stephane

last: Thiry

middle: H

first: Jürg

last: Schwaller


title: MLL-AF9 Expression in Hematopoietic Stem Cells Drives a Highly Invasive AML Expressing EMT-Related Genes Linked to Poor Outcome


title: Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation (Human_RWPE1_RNA-Seq)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary: Analysis of transcriptome of human RWPE1 cells over-expressing wild type NKX3.1 and mutant NKX3.1 (T164A).

overall_design: Total RNA obtained from RWPE1 cells engineered with empty vector (altered pTRIPZ), NKX3.1 wild type over-expression, and NKX3.1 (T164A) mutant over-expression. Engineered RWPE1 cells were harvested and processed for RNA isolation and transcriptome analysis using the MagMAX RNA isolation kit (Ambion).

first: Aditya

last: Dutta

first: Clementine

last: Le Magnen

first: Cory

last: Abate-Shen


title: DNA Methylation Predictors of Gene Expression in the 1st Trimester Chorionic Villus: Implications for Prenatal Diagnosis

city: Pittsburgh

first: Varsha

last: Shridhar

state: PA

address: 204 Craft Ave

institute: Magee-Womens Research Institute

summary: Placental gene expression is a finely controlled process, yet little is known about the factors that regulate it, including epigenetic factors such as DNA methylation.  In this study, we quantified the effects of DNA methylation on placental gene expression.  Using targeted high throughput sequencing, we generated methylation profiles of 3.7 million CpG dinucleotides from 6 karyotypically normal CVS samples and compared these to gene expression data obtained from a publically available database.  We found a broad association between methylation and gene expression at both the chromosome and individual gene levels.  At the chromosome level, we found alternating domains of high and low methylation.  Within each gene, we found distinct methylation patterns at different regulatory genetic elements.  For example, the promoters of highly expressed genes were neither highly methylated, nor completely unmethylated. Rather, they had < 50% of the CG dinucleotides in their sequences in the methylated state. In contrast, promoters of unexpressed genes tended to be either highly methylated or fully unmethylated. Similarly, patterns of methylation in exons and introns differed between highly expressed and unexpressed genes. Our data show that the relationship between DNA methylation and gene expression is nuanced: highly expressed and unexpressed genes differ, not only by their extent of methylation, but also by minute changes in the locations of their methylation sites.  DNA methylation analysis of placental genes may help predict abnormal placental gene expression and pregnancy complications, making it a possible tool for prenatal diagnosis.

overall_design: DNA from 6 chorionic villus samples from the 1st trimester (from 3 male and 3 female fetuses) as well as 3 maternal blood cell samples was extracted, hybridized to probes in the Agilent SureSelectXT Methyl-Seq Target Enrichment kit, targeting 84Mb of the genome and then bisulfite converted before sequencing.

first: Patricia

last: Shaw


title: Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation (Mouse_Recomb_RNA-Seq)

summary: Analysis of transcriptome of tissue recombinants (mouse seminal vesicle epithelial [SVE] cells or prostate epithelial [PE] cells, and rat urogenital sinus [UGS] mesenchymal cells) grown under the kidney capsule in athymic nude mice for 3 months.

overall_design: Total RNA obtained from tissue recombinants generated from combining engineered mouse epithelial cells (SVE or PE from 2-month-old C57Bl/6J mice) and rat UGS mesenchymal cells. Tissue recombinants were harvested and processed for RNA isolation and transcriptome analysis using the RNeasy kit (Qiagen).


title: A single-cell transcriptome atlas of the human pancreas

city: Utrecht

first: Mauro

last: Muraro

state: Utrecht

address: Uppsalalaan, 8

institute: Single Cell Discoveries

summary: To understand organ (dys)function it is important to have a complete inventory of its cell types and the corresponding markers that unambiguously identify these cell types. This is a challenging task, in particular in human tissues, because unique cell-type markers are typically unavailable, necessitating the analysis of complex cell type mixtures. Transcriptome-wide studies on pancreatic tissue are typically done on pooled islet material. To overcome this challenge we sequenced the transcriptome of thousands of single pancreatic cells from deceased organ donors with and without type 2 diabetes (T2D) allowing in silico purification of the different cell types. We identified the major pancreatic cell types resulting in the identification of many new cell-type specific and T2D-specific markers. Additionally we observed several subpopulations within the canonical pancreatic cell types, which we validated in situ. This resource will be useful for developing a deeper understanding of pancreatic biology and diabetes mellitus.

overall_design: Human cadaveric pancreata were used to extract islets of Langerhans, which were kept in culture until single-cell dispersion and FACS sorting. Single-cell transcriptomics was performed on live cells from this mixture using CEL-seq or on cells stained for CD63, CD13, TGFBR3 or CD24 and CD44. The RaceID algorithm was used to identify clusters of cells corresponding to the major pancreatic cell types and to mine for novel cell type-specific genes as well as subpopulations within the known pancreatic cell types.

middle: J

first: Gitanjali

last: Dharmadhikari

first: Dominic

last: Grün

first: Eelco

last: de Koning

first: Alexander

last: van Oudenaarden


title: The transcriptome of central nervous system myelin

city: MAinz

first: Vijay

last: Tiwari

address: Ackermannweg 4

country: Germany

institute: IMB Mainz

summary: Rapid nerve conduction in the CNS is facilitated by the insulation of axons with myelin, a specialized oligodendroglial compartment distant from the cell body. Myelin is turned over and adapted throughout life; however, the molecular and cellular basis of myelin dynamics is not well understood. Hypothesizing that only a fraction of all myelin-related mRNAs has been identified so far, we subjected myelin biochemically purified from mouse brains at various ages to RNA sequencing. We find a surprisingly large pool of transcripts abundant and/or enriched in myelin. Furthermore, a comprehensive analysis showed that the myelin transcriptome is closely related to the myelin proteome but clearly distinct from the transcriptomes of oligodendrocytes and brain tissues, suggesting that the incorporation of mRNAs into the myelin compartment is highly selective. The mRNA-pool in myelin displays maturation-dependent dynamic changes of composition, abundance, and functional associations; however ageing-dependent changes after 6 months of age were minor. We suggest that this transcript pool provides a basis for the local modulation of myelin turnover and adaptation, i.e. in the individual internode.

overall_design: A light-weight membrane fraction enriched for myelin was purified from mouse brains as described previously (Jahn et al., Neuromethods, 2013). For RNA-Seq, RNA was isolated from myelin of mice from indicated ages.

first: Sudhir

last: Thakurela

first: Angela

last: Garding

first: Ramona

middle: B

last: Jung

first: Christina

last: Müller

first: Sandra

last: Goebbels

first: Robin

last: White

first: Hauke

last: Werner


first: Christian

last: Munch

overall_design: triplicate experiment of 2 conditions (untreated, GTPP treatment)

last: Münch

first: J

last: Harper


title: Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment

city: Seattle

first: Hao Yuan

last: Kueh

state: WA

address: 3720 15th Ave NE

department: Division of Biology

institute: University of Washington

summary: During T cell development, multipotent progenitors relinquish competence for other fates and commit to the T cell lineage by turning on Bcl11b, which encodes a transcription factor. To clarify lineage commitment mechanisms, we followed developing T cells at the single-cell level using Bcl11b knock-in fluorescent reporter mice. Notch signaling and Notch activated transcription factors collaborate to activate Bcl11b expression irrespectively of Notch-dependent proliferation. These inputs work via three distinct, asynchronous mechanisms: an early locus ‘poising’ function dependent on TCF-1 and GATA-3, a stochastic-permissivity function dependent on Notch signaling, and a separate amplitude-control function dependent on Runx1, a factor already present in multipotent progenitors. Despite their necessity for Bcl11b activation, these inputs act in a stage specific manner, providing a multitiered mechanism for developmental gene regulation.

overall_design: Two sets of samples were generated from DN T-cell sub-populations derived from culture of bone marrow progenitors from mice containing a knock-in Bcl11b-YFP reporter

first: H

last: Zhang

first: E

middle: V

last: Rothenberg


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

overall_design: Refer to individual Series


title: m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome

city: Los Angeles

first: Jinkai

last: Wang

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

summary: N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (“m6A levels”), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3’ untranslated regions (3’-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications.

overall_design: m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates

first: Benoit

last: Molinie

first: Yi

last: Xing

first: Cosmas

middle: C

last: Giallourakis


title: Highly sensitive sequencing reveals dynamic  modifications and activities of small RNAs in  mouse oocytes and early embryos

status: Public on Jun 23 2016

city: Shanghai

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

summary: Small RNAs play important roles in early embryonic development. However, their expression dynamics and  modifications are poorly understood because of the scarcity of RNA that is obtainable for sequencing analysis.  Using an improved deep sequencing method that requires as little as 10 ng of total RNA or 50 oocytes, we  profile small RNAs in mouse oocytes and early embryos. We find that microRNA (miRNA) expression starts soon  after fertilization, and the mature miRNAs carried into the zygote by sperm during fertilization are relatively  rare compared to the oocyte miRNAs. Intriguingly, the zygotic miRNAs display a marked increase in 3′ mono-  and oligoadenylation in one- to two-cell embryos, which may protect the miRNAs from the massive degradation  taking place during that time. Moreover, bioinformatics analyses show that the function of miRNA is suppressed  from the oocyte to the two-cell stage and appears to be reactivated after the two-cell stage to regulate genes  important in embryonic development. Our study thus provides a highly sensitive profiling method and valuable  data sets for further examination of small RNAs in early embryos.

overall_design: Investigate small RNAs in the mouse oocyte and early embryo development, evaluate the reproducibility and sensitivity of the improved method in HEK293 cell lines. The SRA Study accession is SRP045287 , and The BioProject accession  is PRJNA257532.

first: Qiyuan

last: Yang

first: Jimin

last: Lin

first: Miao

last: Liu

first: Ronghong

last: Li

first: Bin

last: Tian

first: Xue

first: Beiying

last: Xu

first: Mofang

first: Xuan

first: Yiping

first: Huijuan

last: Shi


title: Identification of cranial-specific neural crest genes by comparative transcriptomics

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

summary: We employ RNA-seq of FACS sorted cell populations to identify genes that are enriched in cranial neural crest in relationship to the trunk.

overall_design: Transcriptional profiling of delaminating cranial and trunk neural crest subpopulations.

first: Marianne

middle: E

last: Bronner


title: Single-cell RNA-seq of sorted and micro-dissected mouse bone marrow cells

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: We here systematically studied the interaction network of bone marrow cells. To this end, we micro-dissected many small interacting structures (cell doublets, triplets etc.) into single cells, and sequenced their mRNAs, to infer cell identity. After grouping the cells into cell types (based on the single-cell transcriptomes), we identified actual physical interactions that occurred more, or less, than what would be expected by chance. We compared the micro-dissected data to sorted hematopoietic stem cells.

overall_design:
After mild dissociation of the bone marrow, we micro-dissected many small interacting structures (cell doublets, triplets etc.) into single cells, and sequenced their mRNAs. In addition, single hematopoietic stem cells were sorted (Lineage- Kit+ Sca1+ CD150+ CD48-) to sequence their transcriptome.
In detail, the bone marrow was mildly flushed. Structures composed of about 10 to 20 cells were set apart. With needles and a micro-dissection microscope, we trimmed of smaller structures from these big structure. These smaller structures are mainly two to four cells attached together. These small structures were then further micro-dissected to single cells. The goal of doing these sequential dissections was to keep track of which cells were interacting with which.

Each micro-dissected cell sample contains RNA-seq data for 96 single cells. Each single cells received a different barcode that allow us to entangle them, and to produce the processed .coutt.csv file. Each sorted hematopoietic stem cell sample represents a single cell. The processed data file expdata_BMJhscC.csv contains transcript counts for all analyzed cells.

first: Dominic

last: Grün

first: Alexander

last: van Oudenaarden