title: STAT4 and T-bet control follicular helper T cells development in viral infections [RNA-seq]

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: Follicular helper T (Tfh) cells promote germinal center (GC) B cell survival and proliferation, and guide their differentiation and Ig isotype switching by delivering contact-dependent and soluble factors, including IL-21, IL-4, IL-9, and IFN-g. IL-21 and IFN-g are co-expressed by Tfh cells during acute and chronic infections, but transcriptional regulation of these cytokines in the GC is incompletely understood. We show that the Th1 transcriptional regulators T-bet and STAT4 are co-expressed with Bcl6 in Tfh cells following acute murine lymphocytic choriomeningitis virus infection, albeit with temporal decline in T-bet expression as the GC response evolved. T-bet was important for Tfh cell production of IFN-g, but not IL-21, and for the generation of a robust germinal center reaction. STAT4, phosphorylated in Tfh cells upon infection, was required for their expression of T-bet and Bcl6, and that of IFN-g and IL-21. These data indicate that T-bet is concomitantly expressed with Bcl6 in Tfh cells and is required alongside STAT4 phosphorylation to coordinate Tfh cell IL-21 and IFN-g production, and for promotion of the GC response following acute viral challenge.

overall_design: Each group consisted of 5 mice pooled together.  Two replicates of each group were used for RNA-seq.  Three groups were studied: Wild-type, heterozygous and homozygous Tbet knockout mice.

first: Jason

last: Weinstein

first: Brian

middle: J

last: Laidlaw

first: Yisi

last: Lu

first: Jessica

middle: K

first: Vincent

middle: P

first: Edward

middle: I

last: Herman

first: Ningcheng

last: Li

first: Patrick

middle: G

last: Gallagher

first: Joe

middle: E

last: Craft


title: mRNA and miRNA expression profiling of CUL4B knockdown in MKN45 cells

status: Public on Nov 25 2017

city: Jinan

first: Han

last: Bo

address: #44, Wenhua Xi Rd

department: Department of Pathology

country: China

institute: Shandong University Medical School

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptome analysis of murine T-cell lymphoblastic lymphomas induced by HrasG12V, p53 KO and CIC loss-of-function

status: Public on Nov 24 2017

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: RNA sequencing of T-ALL tumors derived from genetically modified mouse models: CIC loss-of-function, HRASG12V driven from the Kras promoter and Trp53 KO. Results provide insight into the role of the RAS/CIC axis in T-ALL development.

overall_design: RNA-Sequencing of 5 CIC LOF, 3 K:HrasG12V and 4 Trp53 KO T-ALL murine tumor samples.

first: Lucía

last: Simón-Carrasco

first: Matthias

last: Drosten


title: Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis [168 human cardiac fibroblasts]

status: Public on Nov 22 2017

city: Singapore

first: Sonia

last: Chothani

address: 8 College Road

country: Singapore

institute: Duke-NUS school of medicine

summary: Cardiac fibrosis is the final common pathology in heart disease. Here we establish an integrated imaging-genomic discovery platform using primary human heart fibroblasts to identify new drug targets for cardiac fibrosis. Genome wide analyses identify IL11, a secreted cytokine amenable to therapeutic inhibition, as the leading pro-fibrotic candidate. We demonstrate an autocrine loop of IL11 activity that is critical for fibrosis and acts as a nexus of signalling convergence for multiple pro-fibrotic stimuli. IL11 signals in cis and trans via the ERK cascade to activate a programme of fibrosis primarily at the level of protein translation. Injection of IL11 to mice causes fibrosis of the heart, kidney, lung, skin and liver whereas genetic ablation of the IL11 receptor prevented fibrosis across tissues. These data define a new non-canonical fibrogenic pathway and prioritise IL11 as a novel therapeutic target for fibrosis of the heart and other organs

overall_design: 168 human cardiac fibroblasts. 84 control, 84 TGFB1 induced. Cardiac fibroblasts were cultured in serum-free media for at least 16 hours prior to treatment with TGFB1.

first: Stuart

middle: A

last: Cook

first: Sebastian

last: Schafer

first: Kingsley

last: Chow

first: Aida

last: Moreno-Moral

first: Anissa

last: Widjaja

first: Chee

last: Pua


title: Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis [human]

overall_design: 24 human cardiac fibroblasts. 10 basal, 10 IL11 induced, 4 TGFB1 induced. Cardiac fibroblasts were cultured in serum-free media for at least 16 hours prior to treatment with either TGFB1 or IL11.


title: Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [ChIP-seq]

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

country: USA

institute: Baylor college of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We present the high resolution HiC study of genome folding in primary cells, specifically hematopoietic stem and progenitor cells. We investigated the relationship of chromosomal contacts with other epigenetic marks, particularly DNA methylation and histone modifications which is known to be important for appropriate stem cell differentiation.

overall_design: We use histone ChIP-seq to probe relationship of chromosomal contacts and epigenetic modification.

first: Jaime

middle: M

last: Reyes

first: Mira

last: Jeong

first: Margaret

last: Goodell

first: Erez

middle: L

last: Aiden


title: Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis [GRO-Seq]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression.  To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer.  In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif p-values, and enrichment of H3K4me1 and H3KK27.  When applied across the 13 different breast cancer cell lines, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype specific transcription factors that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes.

first: Hector

last: Franco

first: Anusha

last: Nagari

first: Venkat

last: Malladi

first: Wenqian

last: Li

first: Yuanxin

last: Xi

first: Dana

last: Richardson

first: Kendra

last: Allton

first: Kaori

last: Tanaka

first: Jing

first: Khandan

last: Keyomarsi

first: Mark

middle: T

last: Bedford

first: Xiaobing

last: Shi

first: Wei

first: Michelle

middle: C

last: Barton

first: Sharon

middle: Y

last: Dent

first: W


title: Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis [RNA-Seq]

first: W. Lee

overall_design: To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer.


title: Single cell mRNAseq of Olfactory Epithelium and Neurog1-eGFP+ progenitors

city: Boston

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

summary: Single cell mRNAseq maps a global landscape of transcriptomes in uninjured tissue, showing clear transitions from neuronally fated progenitors to mature neurons and other mature cell types. Comparison with injured Neurog1-eGFP+ cells shows a dedifferentiation of cells towards a multipotent stem cell transcriptome.

overall_design: Single cell transcriptomic analysis using Fluidigm C1 Autoprep of uninjured, unsorted mouse olfactory epithelium as a reference, compared to Neurog1-eGFP+ progenitors sorted from uninjured, 5 and 14 days post olfactory bulbectomy, and OMP-eGFP+ mature sensory neurons post olfactory bulbectomy

first: James

last: Schwob


title: Global microRNA profiling in human bone marrow skeletal (stromal or mesenchymal) stem cells revealed candidates for bone tissue engineering

status: Public on Nov 23 2017

city: Aarhus N

first: Morten

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary: We performed small RNA sequencing on telomerized human bone marrow skeletal (stromal or mesenchymal) stem cells (hMSC-TERT) at various timepoints during differentiated into osteoblasts

overall_design: Small RNA sequencing of undifferentiated (day 0) mesenchymal stromal/stem cells and various time points (6 hour, 12 hour, 24 hour, 3 days, 7 days, 10 days, 13 days) after start of differentiation protocol. Sequencing libraries are prepared with Illumina TruSeq small RNA sample preparation kit

last: Venø

first: Chi-Chih

last: Chang

first: Jørgen

last: Kjems


title: The dynamic recruitment of TRBP to neuronal membranes mediates dendritogenesis during development

status: Public on Nov 27 2017

city: Marburg

first: Anna

last: Antoniou

address: Karl-von-Frisch str.1

country: Germany

institute: Philipps University Marburg

summary: MicroRNAs are important regulators of local protein synthesis during neuronal development. We investigated the dynamic regulation of microRNA production and found that the majority of the microRNA-generating complex, consisting of Dicer, TRBP and PACT, specifically associates with intra-cellular membranes in developing neurons. Stimulation with brain-derived neurotrophic factor (BDNF), which promotes dendritogenesis, caused the re-distribution of TRBP from the endoplasmic reticulum into the cytoplasm, and its dissociation from Dicer, in a Ca2+-dependent manner. As a result, the processing of a subset of neuronal precursor microRNAs, among them the dendrite-enriched pre-miR16, was impaired. Decreased production of miR-16-5p, which targeted the BDNF mRNA itself, was rescued by expression of a membrane-targeted TRBP. Moreover, miR-16-5p or membrane-targeted TRBP expression blocked BDNF-induced dendritogenesis, demonstrating the importance of neuronal TRBP dynamics for activity-dependent neuronal development. We propose that neurons employ specialized mechanisms to modulate local gene expression in dendrites, via the dynamic regulation of microRNA biogenesis factors at intracellular membranes of the endoplasmic reticulum, which in turn is crucial for neuronal dendrite complexity and therefore neuronal circuit formation and function.

overall_design: miRNA expression profiles of control- and BDNF-treated DIV rat cortical neurons were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Sharof

last: Khudayberdiev

first: Agata

last: Idziak

first: Silvia

last: Bicker

first: Ralf

last: Jacob

first: Gerhard

last: Schratt


title: Chromatin state changes during neural development revealed by in vivo cell-type specific profiling

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

summary: A key question in developmental biology is how cellular differentiation is controlled during development. Particular interest has focused upon changes in chromatin state, with transitions between Trithorax-group (TrxG) and Polycomb-group (PcG) chromatin states shown to be vital for  the differentiation of ES cells to multipotent stem cells in culture. However, little is known as to the role of chromatin states during the development of complex organs such as the brain. Recent research has also suggested a number of other chromatin states exist in cell culture, including an active state lacking TrxG proteins and a repressive “Black”, “Basal” or “Null” chromatin state devoid of common chromatin marks. The role that these new chromatin states play during development is unknown. Here we show that large scale chromatin remodeling occurs during in vivo Drosophila melanogaster neural development. We demonstrate that the majority of  genes that are activated during neuronal differentiation are repressed by the Null chromatin state and a novel TrxG-repressive state in neural stem cells (NSCs).  Furthermore, almost all key NSC genes are switched off via a direct transition to HP1-mediated repression. In contrast to previous studies of  ES cell to neural progenitor cell development, PcG-mediated repression does not play a significant role in regulating either of these transitions; instead,  PcG chromatin specifically regulates lineage-specific transcription factors that control the spatial and temporal patterning of the brain. Combined, our data suggest that forms of chromatin other than canonical PcG/TrxG transitions take over key roles during  neural development.

overall_design: Targeted DamID.  Six samples per condition: Brm-Dam, Pc-Dam, HP1a-Dam, H1-Dam, RPII215-Dam (polII-Dam) and Dam alone.  Two biological replicates for wor-GAL4, two or three biological replicates for GMR71C09-GAL4, three or four biological replicates for elav-GAL4.

first: Andrea

middle: H

last: Brand


title: Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis

last: Kraus


title: Myc and YAP roles in the control of the cell cycle [3T9 ChIP-seq]

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

summary: ChIPseq analysis of YAP and Myc induced in quiescent and confluent 3T9 fibroblasts

first: Stefano

last: Campaner

first: Serena

last: De Fazio

first: Ottavio

last: Croci


title: Knockout of the Arp2/3 complex in epidermis causes a psoriasis-like disease hallmarked by hyperactivation of transcription factor Nrf2

city: Amsterdam

first: Metello

last: Innocenti

address: Plesmanlaan 121

country: Netherlands

institute: NKI


title: Comprehensive analysis of Long non-coding RNA expression in dorsal root ganglion reveals cell type specificity and dysregulation following nerve injury

status: Public on Nov 21 2017

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

country: United Kingdom

institute: Oxford University

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Comprehensive analysis of Long non-coding RNA expression in dorsal root ganglion reveals cell type specificity and dysregulation following nerve injury [human iPS]

summary: Dorsal root ganglion (DRG) neurons provide connectivity between peripheral tissues and spinal cord. Transcriptional plasticity within DRG sensory neurons after peripheral nerve injury contributes to nerve repair but also leads to maladaptive plasticity, including the development of neuropathic pain. This study presents tissue and neuron specific expression profiling of both known and novel Long Non-Coding RNAs (LncRNAs) in rodent DRG following nerve injury. We have identified a large number of novel LncRNAs expressed within rodent DRG, a minority of which were syntenically conserved between mouse and rat and which including both- intergenic and antisense LncRNAs. We have also identified neuron type-specific LncRNAs in mouse DRG, and LncRNAs that are expressed in human IPS cell-derived sensory neurons. We show significant plasticity in LncRNA expression following nerve injury, which in mouse is strain dependant. This resource is publicly available and will aid future studies of DRG neuron identity and the transcriptional landscape in both naïve and injured DRG.

overall_design: RNA-seq Illumina HiSeq4000 of IPSC and IPS derived sensory neurons

first: Lucy

last: McDermott

first: Alex

last: Clark

first: David

last: Bennet


title: STAT4 and T-bet control follicular helper T cells development in viral infections

first: Vince

last: Schulz


title: Myc and YAP roles in the control of the cell cycle [3T9 RNA-seq pharmacological treatment]

summary: RNAseq analysis of YAP and Myc induced in quiescent and confluent 3T9 fibroblasts treated with Y27632 and Verteporfin

first: Elisa

last: Donato


title: Egr1 deficiency induces browning of inguinal subcutaneous white adipose tissue in mice

city: Paris

first: Mickael

last: Orgeur

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: We sequenced strand-specific rRNA-depleted librairies performed from total RNAs isolated from subcutaneous inguinal fat pads of three 2-week-old wild-type female mice and three 2-week-old Egr1-deficient female mice.

overall_design: Gene expression profiling of mouse Egr1-deficient subcutaneous white adipose tissue

first: Emmanuelle

last: Havis

first: Fanny

last: Coulpier

first: Christophe

last: Antoniewsky

first: Delphine

last: Duprez


title: New insights into diagnosis and therapeutic options for proliferative hepatoblastoma

city: Bordeaux

first: Katarzyna

middle: B

last: Hooks

address: 146, rue Léo Saignat

department: CBIB

institute: Univ. Bordeaux

summary: Surgery and cisplatin-based treatment of hepatoblastoma (HB) currently guarantee the survival of 70-80% of patients. However, some important challenges remain in diagnosing high risk tumors and identifying relevant targetable pathways offering new therapeutic avenues. Previously, two molecular subclasses of hepatoblastoma tumors have been described, namely C1 and C2; C2 being the subgroup with the poorest prognosis, a more advanced tumor stage and the worst overall survival rate. An associated 16-gene signature to discriminate the two tumoral subgroups was proposed but it has not been transferred into clinical routine. To address these issues we performed RNA sequencing of 25 tumors and matched normal liver samples from patients. The transcript profiling separated HB into three distinct subgroups named C1, C2A and C2B, identifiable by a concise four-gene signature: HSD17B6, ITGA6, TOP2A and VIM, with TOP2A being characteristic for the proliferative C2A tumors. Differential expression of these genes was confirmed by RT-qPCR on an expanded cohort and by immunohistochemistry. We also revealed significant overexpression of genes involved in Fanconi Anemia (FA) pathway in the  C2A subgroup. We then investigated the ability of several described FA inhibitors to block growth of HB cells in vitro and in vivo. We demonstrated that bortezomib, an FDA-approved proteasome inhibitor, strongly impairs the proliferation and survival of HB cell lines in vitro, blocks FA pathway associated double-strand DNA repair and significantly impedes HB growth in vivo.  In conclusion, the highly proliferating C2A subtype is characterized by TOP2A gene up-regulation and FA pathway activation and HB therapeutic arsenal could include Bortezomib for the treatment of patients with the most aggressive tumors.

overall_design: mRNA profiles from hepatoblastoma cell lines and hepatoblastoma tissues together with corresponding normal livers were generated by deep sequencing using Illumina HiSeq 2500

first: Jérôme

last: Audoux

first: Helena

last: Fazli

first: Sarah

last: Lesjean

first: Tony

last: Ernault

first: Nathalie-Dugot

last: Senant

first: Thierry

last: Leste-Lasserre

first: Martin

last: Hagedorn

first: Benoit

last: Rousseau

first: Coralie

last: Danet

first: Sophie

last: Branchereau

first: Laurence

last: Brugières

last: Taque

first: Catherine

last: Guettier

first: Monique

last: Fabre

first: Anne

last: Rullier

first: Marie-Annick

last: Buendia

first: Thérèse

last: Commes

middle: F

last: Grosset

first: Anne-Aurélie

last: Raymond


title: Transcriptomic analysis of hair cells from the pigeon Columba livia

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: To gain further insight into the molecular architecture of cuticulosome containing hair cells, we performed a transcriptomics experiment comparing RNA expression profiles of hair cells with and without cuticulosomes. To do so we adapted existing methods that enable ultra low input RNA sequencing, applying it to avian hair cells. RNA from 30 hair cells per sample was extracted, cDNA prepared using a full length RNA Seq from single cells protocol (Picelli et al. 2014), before next generation sequencing on an Illumina HiSeqV4 system. We generated approximately 42 million reads per sample that were aligned with TopHat against the Columba livia genome and subjected to differential expression analysis with DESeq2 . We report that 387 genes were upregulated (more than 3 fold increase) in cuticulosome positive cells, with 18 reaching significance (P<0.05) following correction for multiple testing.

overall_design: Transcriptomic analysis of two auditory hair cell types from the pigeon basilar papilla

middle: R

first: David

last: Keays

first: Simon

last: Nimpf


title: STAT4 and T-bet control follicular helper T cells development in viral infections [ATAC-seq]

first: Vince

last: Schulz

overall_design: Each group consisted of 5 mice pooled together.  Two replicates of each group were used for ATAC-seq.  Two groups were studied: Wild-type and homozygous STAT4 knockout mice.

first: Jason

middle: S

last: Weinstein

first: Brian

middle: J

last: Laidlaw

first: Yisi

last: Lu

first: Jessica

last: Wang

first: Vincent

first: Edward

last: Herman

first: Ningcheng

last: Li

first: Patrick

last: Gallagher

first: Joe

last: Craft


title: High-resolution transcriptome analysis of mouse subventricular zone reveals features of stem cell lineage, anatomy, and aging

city: New York

first: Dan

middle: Richard

last: Laks

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Single cell RNA sequencing of mouse subventricular zone (SVZ) harboring a CGD1 transgene expressing GFP.

overall_design: Whole SVZ dissected, FACS sorted for GFPhi, Low, negative, and Unsorted Viable (6600 cells) or Aged SVZ samples, 2 weeks, 2 months, 6 months, 12 months, FACS sorted for viable cells, undergone Drop-seq single cell RNA sequencing.

first: Asaf

last: Poran

first: Ashley

last: Laughney

first: Xuanhua

middle: P

last: Xie


title: The soluble guanylate cyclase CYG12 is required for the acclimation to hypoxia and trophic regimes in Chlamydomonas reinhardtii

city: Bochum

first: Anja

middle: Christine

last: Hemschemeier

address: Universitätsstr. 150

department: Plant Biochemistry

institute: Ruhr-University of Bochum

summary: We studied the role of the soluble guanylate cyclase CYG12 in the response of Chlamydomonas reinhardtii to anoxia and darkness. To gain insights into potentially disturbed signaling pathways resulting in different responses of the transcriptome, we performed an RNA-sequencing study to obtain transcriptome profiles of the C. reinhardtii wild-type and a CYG12 knockdown strain in aerobiosis and anaerobiosis in darkness compared to normoxia in the light

overall_design: The C. reinhardtii wild-type (strain CC-124) as well as a transformant in which the CYG12 gene was post-transcriptionally down-regulated by an artificial microRNA were grown under standard growth conditions (in TAP medium in the light, aerated = 0h RNA-samples) and then incubated for 6h in darkness either in sealed flasks, where the cell suspensions become anoxic (RNA-samples 6h-O2), or in open beakers (aerated; RNA-samples 6h+O2). Each strain was analyzed in biological duplicate, i.e., the project generated 12 RNA-samples that were sequenced.

first: Melis

last: Düner


title: LRPPRC-mediated folding of the mitochondrial transcriptome [RNase footprinting]

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

summary: The roles of RNA-binding proteins as chaperones in the lifecycles of mRNAs are not well understood. The mammalian mitochondrial genome has been compressed over evolution to a size of just 16 kb, nevertheless the expression of its genes requires transcription, RNA processing, translation and RNA decay, much like the more complex chromosomal systems, providing an opportunity to use it as a model system to understand the fundamental aspects of gene expression. Here we combine RNase footprinting with PAR-CLIP at unprecedented depth to reveal the importance of RNA-protein interactions guided by the LRPPRC/SLIRP complex in dictating RNA folding within the mitochondrial transcriptome. We show that LRPPRC, in complex with its protein partner SLIRP, binds throughout the mitochondrial transcriptome, with a preference for mRNAs, and its loss affects the entire secondary structure and stability of the transcriptome. We demonstrate that the LRPPRC/SLIRP complex is a global RNA chaperone that stabilizes RNA structures to expose the required sites for translation, stabilization and polyadenylation. Our findings reveal a general mechanism where extensive RNA-protein interactions ensure that RNA is accessible for its biological functions.

overall_design: RNase footprinting of LRPPRC and SLIRP knockout and control mice, in technical duplicate.

first: Aleksandra

last: Filipovska

first: Oliver

last: Rackham


title: Argonaute HITS-CLIP in wild-type and APOBEC1-deficient BMDMs

first: F.

middle: Nina

last: Papavasiliou

state: New York

address: 1230 York Ave.

institute: Rockefeller University

summary: To investigate the possible consequences of APOBEC1 editing for miRNA targeting, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) of the Argonaute (Ago) proteins (Chi et al., 2009) was performed in BMDMs derived from wild-type and Apobec1-/- littermates.

overall_design: High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation using antibodies specific to the Argonaute proteins was peformed on BMDMs isolated from wild-type and APOBEC1-deficient littermate mice. The RNA in the Ago complexes was radiolabeled, purified by gel electrophoresis and then visualized by radiography, where two complex sizes were apparent at ~110kDa and ~130kDa, corresponding to miRNA and mRNA complexes respectively. After proteinase digestion to remove Ago, previously Ago-bound mRNA and miRNA pools were reverse transcribed, PCR amplified and subjected to ultra high-throughput sequencing. Resultant high-throughput sequencing reads were separated by read length into mRNA (≥25nt) and miRNA (≤24nt) pools and aligned to the genome (mm9).  A list of bound miRNAs was generated from the miRNA alignment. Ago clusters, or loci with abundant Ago binding, were defined as regions with ≥ 5 nucleotide overlap and a total of ≥ 8 mRNA reads. The Ago footprint (-30,+32; or more narrowly -24,+22) was extracted from the peak of the cluster, and these footprints were normalized to RNA-Seq transcript expression, defining the relative “Ago occupancy” of the Ago-bound region. High-confidence footprints were defined as occurring in at least 2 replicates of one genotype (biological complexity of 2 for either wild-type or Apobec1-/-).High-confidence Ago footprints were then intersected with APOBEC1 editing events to identify regions of Ago-APOBEC1 overlap across the transcriptome.

first: Claire

middle: E

last: Hamilton

first: F

middle: N


title: Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis [mouse]

first: Sonia

last: Chothani

address: 8 College Road

institute: Duke-NUS school of medicine

summary: Cardiac fibrosis is the final common pathology in heart disease. Here we establish an integrated imaging-genomic discovery platform using primary human heart fibroblasts to identify new drug targets for cardiac fibrosis. Genome wide analyses identify IL11, a secreted cytokine amenable to therapeutic inhibition, as the leading pro-fibrotic candidate. We demonstrate an autocrine loop of IL11 activity that is critical for fibrosis and acts as a nexus of signalling convergence for multiple pro-fibrotic stimuli. IL11 signals in cis and trans via the ERK cascade to activate a programme of fibrosis primarily at the level of protein translation. Injection of IL11 to mice causes fibrosis of the heart, kidney, lung, skin and liver whereas genetic ablation of the IL11 receptor prevented fibrosis across tissues. These data define a new non-canonical fibrogenic pathway and prioritise IL11 as a novel therapeutic target for fibrosis of the heart and other organs

overall_design: 18 mouse cardiac fibroblasts. 3 wildtype, 3 knockout IL11RA-/- , 3 conditions (Basal, TGFB1, IL11). Cardiac fibroblasts were cultured in serum-free media for at least 16 hours prior to treatment with either TGFB1 or IL11.

first: Stuart

middle: A

last: Cook

first: Sebastian

last: Schafer

first: Kingsley

last: Chow

first: Aida

last: Moreno-Moral

first: Anissa

last: Widjaja

first: Chee

last: Pua


title: Neuron-specific transcriptome response to loss of shep

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: We report RNA-seq data obtained from FACS-isolated live neurons at third instar larval or P14 pupal stage, and from BG3 cells. RNA from neurons with RNAi-based loss of shep or GFP control is used to construct stranded RNA-seq library. RNA from BG3 cells treated with dsRNA targeting shep or GFP is used to construct RNA-seq library.

overall_design: RNA-seq data of loss-of-shep neurons and control neurons in larval and pupal stages, and from shep-depleted or control BG3 cells.

first: Dahong

last: Chen

first: Elissa

last: Lei


title: Robust detection of chromosomal contacts from small cell numbers using low-input Capture-C

status: Public on Nov 20 2017

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin structure in rare cell populations. We present two new low-input Capture-C protocols that generate high-quality, reproducible interaction profiles from fewer than 20,000 cells, and show that these are not biased by PCR amplification or the degree of formaldehyde fixation.

overall_design: The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. In this case, the promoters of alpha-globin, beta-globin and Slc25a37 were used as viewpoints. To optimise Capture-C technology for small cell numbers, we developed Low-Input (LI) Capture-C and Tag-Capture-C, and performed experiments with both protocols using 200 ng, 100 ng and 50 ng mouse erythroid 3C libraries, all in triplicates. In the reduced cross-linking experiments, we compared NG Capture-C interactions profiles generated from primary mouse erythroid cells fixed with 5%, 4%, 3%, 2%, 1%, 0.5% or 0% formaldehyde. Experiments were performed in technical duplicates.

first: A

middle: M

first: James

middle: O

last: Davies

first: Damien

last: Downes

first: Douglas

last: Higgs

first: Jim

last: Hughes


title: Comparing the transcriptomes of ovaries from prolific Jintang black goat and non-prolific Tibetan goat (Capra hircus) during follicular phase

city: Chengdu

first: Xiang-dong

last: Zi

address: Yi Huan Lu

institute: Southwest University for Nationalities

summary: The present study, for the first time, compared the transcriptomes of ovaries from the prolific Jintang black goat and the non-prolific Tibetan goat during follicular phase using the Illumina RNA-Seq method. The study provides insight into the transcriptional regulation in the ovaries of two distinct breeds of goats that might serve as a key resource for understanding goat fecundity.

overall_design: Total RNA obtained from ovaries of the prolific Jintang black goat and the non-prolific Tibetan goat during follicular phase, then tanscriptomes of the two breeds were campared.

first: X

first: J

last: Lu

first: L

last: Ma

first: W

last: Xia


title: Myc and YAP roles in the control of the cell cycle [3T9 RNA-seq]

first: stefano

last: campaner

summary: RNAseq analysis of YAP and Myc induced in quiescent and confluent 3T9 fibroblasts

first: Stefano

last: Campaner

first: Serena

last: De Fazio

first: Ottavio

last: Croci


title: Small non-coding RNA contents in preeclamptic and normotensive trophobalst debris

city: AUCKLAND

first: Larry

last: Chamley

address: 85 Park Road

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

summary: Small RNA sequencing on trophoblast debris samples was employed to profile the small RNA contents in either normotensive or preeclamptic trophoblast debris. We have identified 1278 miRNAs and 2646 non-miRNA small RNA fragments across all trophoblast debris samples. Differential expression analysis was executed by iSRAP small RNA sequencing analysis pipeline and we identified 16 miRNAs, 5 tRNA fragments from 3 different tRNAs, 13 snRNA fragments and 85 rRNA fragments differentially contained between preeclamptic and normotensive trophoblast debris

overall_design: Trophblast debris isolated from four individual preeclamptic placentae and four gestational matched normotensive placentae

first: Lawrence

middle: W

first: Jia

last: Wei

first: Cherie

last: Blenkiron


title: Effects of oxidative stress on mitotic recombination and genomic stability in yeast after 20 passages

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

summary: Oxidative stress is a common factor threatening genomic stability in almost all aerobic organisms. Using a yeast screening system, we measured the frequency of mitotic recombination was greatly elevated after H2O2 treatment. H2O2 was able to break chromatid directly in G1 synchronized cells and homologous recombination was induced to repair DNA double stand breaks at S/G2 phase. By whole genome SNP microarray and sequencing, the patterns of H2O2 induced loss of heterozygosity (LOH; gene conversion and crossover), chromosomal rearrangement, and aneuploidy changes were revealed. LOH events were the most common genomic alterations induced by H2O2 and were randomly distributed throughout the genome.

overall_design: To allow accumulation of recombination events, 30 JSC25-1-derived isolated colonies were independently treated with H2O2 (100 mM) for 20 passages. In each passage, cells were treated with 100 mM H2O2 for 1 h, washed, and then plated on YPD medium to form colonies. After 20 sequential treatments of H2O2, 30 JSC25-1-derived mutants (named as HOS1-30) from the last treatment were examined by whole genome SNP microarrays.

first: Dao-Qiong

first: Thomas

middle: D

last: Petes


title: PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Aberrant activation of embryonic signaling pathways is frequent in pancreatic ductal adenocarcinoma (PDA) making developmental regulators therapeutically attractive. Here, we demonstrate diverse functions for PDX1, a transcription factor indispensable for pancreas development, in the progression from normal exocrine cells to metastatic PDA. We identify a critical role for PDX1 in maintaining acinar cell identity, thus resisting the formation of PanIN-derived PDA. Upon neoplastic transformation, the role of PDX1 changes from tumor suppressive to oncogenic. Interestingly, subsets of malignant cells lose PDX1 expression while undergoing EMT and PDX1 loss is associated with poor outcome. This stage-specific functionality arises from profound shifts in PDX1 chromatin occupancy from acinar cells to PDA. In summary, we report distinct roles of PDX1 at different stages of PDA, suggesting that therapeutic approaches against this potential target need to account for its changing functions at different stages of carcinogenesis. These findings provide insight into the complexity of PDA pathogenesis and advocate a rigorous investigation of therapeutically tractable targets at distinct phases of PDA development and progression.

overall_design: This study consists of 3 Bru-seq samples.  Mouse pancreatic cancer cells (NB490) expressing inducible PDX1 shRNA were (1) untreated/uninduced, (2) doxycycline treated for 48 h, or (3) grown-out after 3 weeks of doxycycline treatment.

first: Nilotpal

last: Roy

first: Kenneth

middle: K

last: Takeuchi

first: Jeanine

last: Ruggeri

first: Peter

last: Bailey

first: David

last: Chang

first: Joey

last: Li

first: Laura

last: Leonhardt

first: Sapna

last: Puri

first: Megan

middle: T

last: Hoffman

first: Shan

last: Gao

first: Christopher

last: Halbrook

first: Yan

last: Song

first: Shivani

last: Malik

last: Wright

last: Dawson

first: Andrew

middle: V

last: Biankin

first: Matthias

last: Hebrok

first: Howard

middle: C

last: Crawford


title: Myc and YAP roles in the control of the cell cycle [Liver RNA-seq]

first: stefano

last: campaner

address: via adamello 16

institute: fondazione Istituto italiano di tecnologia

summary: RNAseq analysis was performed on liver of  tet-YAP and tet-Myc  transgenic mice induced for 2 days (R26-mice) or 4 weeks (laptTA-mice) or in liver tumor noduli.

first: Stefano

last: Campaner

first: Serena

last: De Fazio

first: Ottavio

last: Croci


title: Single cell RNA-seq of 444 epithelial cells from the mammary glands of pubescent and adult mice

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Mammary glands were collected from 8 pubescent (4.7-4.9 week-old) female mice and 8 adult (10 week old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads.

overall_design: RNA-seq profiling was completed for 221 cells from pubescent mice and 223 cells from adult mice.

first: Yunshun

last: Chen

first: Bhupinder

last: Pal

first: Jane

last: Visvader


title: Differential expression of microRNAs in monocytes and derived macrophages in culture.

city: Montreal

first: Eric

last: Cohen

state: Quebec

address: 110 Ave des Pins Ouest

country: Canada

institute: IRCM

summary: HIV-1 infection of monocytes/macrophages is modulated by several host factors. For instance, although HIV-1 successfully enters monocytes, antiviral restriction factors inhibit HIV-1 productive infection in these cells. We recently identified two microRNAs, miR-221 and miR-222, which limit HIV-1 entry during infection of monocyte-derived macrophages (MDM) by down-regulating CD4 expression. Interestingly, CD4 is also down regulated during the differentiation of monocytes into macrophages. In this study, we compared microRNA expression in monocytes and macrophages by RNAseq and found that miR-221/miR-222 are enhanced in macrophages.Taken together, these results show that both miR-221 and miR-222 act as modulators of CD4 mRNA expression throughout the monocyte/macrophage lineage, having roles in their differentiation, activation processes and modulating macrophage resistance to HIV-1.

overall_design: Macrophages derived from the blood of 2 different adults (n=2 adults) were used. MicroRNAseq was performed on monocytes and their corresponding derived macrophages.

first: Robert

last: Lodge

first: Éric


title: Aryl Hydrocarbon Receptor Preferentially Marks and Promotes Gut Regulatory T Cells

city: Gainesville

first: Liang

last: Zhou

state: FL

department: Department of Infectious Diseases and Immunology

institute: University of Florida

summary: Here, we generated mouse genetic models to ablate or activate Ahr expression specifically in Tregs. We showed that Ahr was expressed more abundantly by peripherally induced Treg (pTregs) in the gut than by Tregs in other lymphoid organs, and its expression was independent of microbiota. Ahr was important for Treg gut homing and function. Ahr inhibited pro-inflammatory cytokines produced by Tregs but was dispensable for Treg stability. Furthermore, Ahr-expressing Tregs had enhanced in vivo suppressive activity compared to Tregs lacking Ahr expression in a T cell transfer model of colitis. Our data suggest that Ahr signaling in Tregs may be important for gut immune homeostasis.

overall_design: RNA-seq (2 replicates) and ATAC-seq (2 replicates) analysis of large intestine regulatory T cells from Ahr wildtype and knockout mice.

first: Jian

last: Ye

first: Ju

last: Qiu

first: John

last: Bostick


title: Microbiome influences prenatal and adult microglia in a sex-specific

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

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

overall_design: Refer to individual Series


title: Dynamic transcriptional control of macrophage miRNA signature via inflammation responsive enhancers revealed using a combination of next generation sequencing-based approaches

status: Public on Nov 18 2017

city: Orlando

first: Laszlo

last: Nagy

state: Hungary

address: Sanger Road

institute: Sandford Burnham Prebys Institute

summary: MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets. We investigated the LPS-induced expression changes at mature miRNA and pri-miRNA levels in mouse macrophages utilizing a small RNA-seq method and publicly available GRO-seq dataset, respectively. Next, we identified an enhancer set associated with LPS-responsive pri-miRNAs based on publicly available H3K4 mono-methylation-specific ChIP-seq  and GRO-seq datasets. This enhancer set was further characterized by the combination of publicly available ChIP and ATAC-seq datasets. Finally, direct interactions between the miR-155-coding genomic region and its distal regulatory elements were identified using a 3C-seq approach. Our analysis revealed 15 robustly LPS-regulated miRNAs at the transcriptional level. In addition, we found that these miRNA genes are associated with an inflammation-responsive enhancer network. Based on NFκB-p65 and JunB transcription factor binding, we showed two distinct enhancer subsets associated with LPS-activated miRNAs that possess distinct epigenetic characteristics and LPS-responsiveness. Finally, our 3C-seq analysis revealed the LPS-induced extensive reorganization of the pri-miR-155-associated functional chromatin domain as well as chromatin loop formation between LPS-responsive enhancers and the promoter region. Our genomic approach successfully combines various genome-wide datasets and allows the identification of the putative regulatory elements controlling miRNA expression in classically activated macrophages.

overall_design:
Small RNA-seq samples were derived from LPS-treated (3 hours) and unstimulated bone marrow-derived macrophages in triplicates.
3C-seq samples were derived from LPS-treated (3 hours) and unstimulated bone marrow-derived macrophages.

first: Attila

last: Horvath


title: Comparison of Liver Tumor Models to Regenerating Liver Tissues

status: Public on Nov 19 2017

first: Russell

middle: Erick

last: Ericksen

address: 11 Biopolis Way, #02-02

department: Singapore Bioimaging Consortium (SBIC)

institute: Agency for Science, Technology, and Research (A*Star Singapore)

summary: To identify genes and pathways sepcific to tumorigenesis, we harvested tissues from two different liver tumor models as well as regenerating tissues. Genes significantly different in the two tumor models, but not in regenerating tissues, were used for further investigation

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Analysis consists of three primary groups. 1) DEN tumors: C57BL6 mice were injected with a 50mg/kg dose of  diethylnitrosamine (DEN) at 14 days of age and a 2mg/kg dose of TCPOBOP 30 days later. Liver tissues with tumors (at 8 months) were harvested compared with liver tissues prior to tumor development (5 months). 2) Morris hepatoma tumors: 10 week-old ACI rats were anesthetized and 1 million MH3924a cells were injected directly into the liver. Tumors were harvested two weeks later and compared to age-match control ACI rat liver tissue. 3) Regenerating: 10-12 week-old rats were anesthetized, two-thirds of the liver was removed, and tissues were harvested 24 hours later. All animals were male.

first: Weiping

last: Han


title: Single-cell transcriptome analysis of mouse fetal livers from different developmental stages

city: Shanghai

first: Xianbin

last: Su

address: Dongchuan Road 800

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells from seven stages between embryonic day 11.5 and postnatal day 2.5 during mouse liver development. Our data demonstrated the existence of two types of stem/progenitor cells with distinct molecular patterns during liver development. Both types of cells exhibit heterogeneity of transcriptional program within each cell population, suggesting they be in distinct status of self-renewal, cell proliferation and different sub-stages of differentiation and maturation. In general, our data depicting the dynamic trajectories with transcriptional profiles at single-cell resolution during mouse liver development provides insights into the fate decision and transcriptional control of self-renewal, differentiation and maturation of liver stem/progenitor cells.

overall_design: The transcriptomes of 507 single cells from E11.5, E12.5, E13.5, E14.5, E16.5, E18.5 and P2.5 mouse livers were analyzed in this study. ERCC Spike-ins were included in each sample as control. For E11.5 stage, we analyzed 70 single cells from one embryonic mouse (pooled sibling livers); for E12.5 stage, we analyzed 2 biological replicates (2 embryonic mouse), with 83 single cells from replicate 1 and 17 single cells from replicate 2; for E13.5 stage, we analyzed 71 single cells from one embryonic mouse; for E14.5 stage, we analyzed 2 biological replicates, with 75 single cells from replicate 1 and 24 single cells from replicate 2; for E16.5 stage, we analyzed 2 biological replicates, with 56 single cells from replicate 1 and 22 single cells from replicate 2; for E18.5 stage, we analyzed 2 biological replicates, with 39 single cells from replicate 1 and 19 single cells from replicate 2; for P2.5 stage, we analyzed 2 biological replicates, with 21 single cells from replicate 1 and 10 single cells from replicate 2. All single cell samples were processed on the microfluidic system.

first: Yi

last: Shi

first: Ze-Guang


title: Correlating anatomy and function with gene expression in individual neurons by combining in vivo labeling, patch clamp and single cell RNA-seq

city: La Jolla

first: Carsten

last: Pfeffer

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: The classification of neurons into distinct types is an ongoing effort aimed at revealing and understanding the diversity of the components of the nervous system. Recently available methods allow us to determine the gene expression pattern of individual neurons in the mammalian cerebral cortex to generate powerful categorization schemes. For a thorough understanding of neuronal diversity such genetic categorization schemes need to be combined with traditional classification parameters like position, axonal projection or response properties to sensory stimulation. Here we describe a method to link the gene expression of individual neurons with their position, axonal projection or sensory response properties. Neurons are labeled in vivo based on their anatomical or functional properties and, using patch clamp pipettes, their RNA individually harvested in vitro for RNAseq. With this method we can determine the genetic expression pattern of functionally and anatomically identified individual neurons.

overall_design: single cortical neurons were patch clamped and the RNA harvested; single neuron mRNA profiles were generated by deep sequencing

first: Massimo

last: Scanziani


title: Interactions between mitochondrial and nuclear DNA in mammalian cells are non-random

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

institute: University of Auckland

summary: There is evidence for the on-going recurrent transfer of mitochondrial DNA (mtDNA) into the nucleus in both germ line and somatic cells. However, the outcomes associated with the transfer of mtDNA into somatic cell nuclei are poorly understood. High-resolution Chromosome Conformation Capture (HiC) techniques, which are used to identify global patterns of chromatin interactions, regularly capture physical interactions between mitochondrial and nuclear DNA (i.e. mito-nDNA interactions) in mammalian cells. These mito-nDNA interactions are routinely considered a consequence of nonspecific ligation events during chromatin library preparation. Here, we have evaluated mito-nDNA interactions captured by HiC in six human cell lines, and by Circular Chromosome Conformation Capture (4C) in mouse cortical astrocytes. We show that mito-nDNA interactions are statistically significant and shared between biological and technical replicates in the HiC and 4C experiments. The most frequent interactions between mtDNA and nuclear loci in the HiC and 4C data occur with repetitive DNA sequences including the centromeric regions in the six human cell lines and 18S rDNA in mouse cortical astrocytes. Such findings confirm previous observations of mtDNA forming interactions with rDNA genes in budding yeast and centomeres in rat bone marrow cells. Finally the mitochondrial D-loop tends to be enriched in the captured mito-nDNA interactions. Collectively our results imply a degree of selective regulation in the identity of the interacting mitochondrial partners confirming that mito-nDNA interactions in mammalian cells are not random.

overall_design:
We used 4C to capture interactions between mouse mitochondrial genes (ND1, ND2, CO1, CO2, ATPase8, ATPase 6) and nuclear chromosomes in primary mouse cortical astrocytes derived from animals in their first two days of postnatal life. To reduce the chances of identifying false positive mito-nDNA interactions we prepared a digested, but not ligated library. This enabled the identification of non-specific products that were likely caused by mis-priming during the PCR amplification step of the procedure. We also reduced the signal due to the PCR amplification of the sequences adjacent to the bait fragment, which are expected to interact, by including blocker primers in the PCR reactions that were on the 4C libraries. The blocker primers are modified with three carbons on their 5’ and 3’ ends and are designed to anneal to the sequences adjacent to the baits. The capping of the blocker primers with carbons blocks polymerase activity and prevents amplification through the sequences to which they are annealed.
This series includes the Circular Chromosome Conformation Capture (4C) in mouse cortical astrocytes data.

first: J

last: O’Sullivan

first: M

last: Doynova

middle: B

last: Jones

middle: H

last: Vickers

first: C

middle: L

last: Jasoni

first: A

last: Berretta


title: The circadian transcriptional landscape in primary human mammary epithelial cells

city: New Orleans

first: Aaron

last: Hoffman

state: LA

address: 1700 Tulane University

department: Epidemiology

institute: Tulane University

summary: Cells in peripheral tissue maintain a cell-autonomous molecular clock which is regulated through transcription-translation feedback mechanisms initiated by a core set of circadian proteins. Among these clock proteins are transcription factors and histone modifying enzymes which act in trans to influence the expression of a broad array of clock-controlled genes (CCGs). The CCG set, defined as transcripts with cyclic expression approximating a 24h period, is tissue-specific, such that the circadian transcriptome can only be assembled through experiments conducted in the cell type of interest. Here, we describe for the first time the circadian transcriptome in primary human mammary epithelial cells using time-series massively parallel sequencing. We also show that clinical instruments relying on gene expression, such as molecular subtyping and RNA-based predictive or prognostic biomarkers, provide measurements that are variable across circadian time. This data represents a valuable resource for advancing our understanding of the molecular underpinnings of circadian rhythm.

overall_design: mRNA profiles of temperature synchronized (non-immortalized) human breast epithelial cells isolated from a 28 year-old woman undergoing breast reduction mammoplasty.  The experiment was carried out over a 24-hour time period in duplicate and the samples were analyzed using the Illumina HiSeq 2000.

first: Tracy

last: Peters


title: microRNA profiling in the parasite Neospora caninum using a high-throughput approach

city: Changchun

first: Jigang

last: Yin

address: 5333# Xi An Da Lu

institute: Jilin university

summary: Small RNA libraries from N. caninum tachyzoites were analyzed using a high-throughput RNA sequencing technology combined with systematic bioinformatics analysis.

overall_design: Two small RNA libraries from N. caninum tachyzoites were analyzed using a high-throughput RNA sequencing technology combined with systematic bioinformatics analysis


title: RNA-seq of mouse myeloid progenitors reveals two independent pathways for monocyte production via GMPs and MDPs

city: Los Angeles

first: Helen

middle: S

last: Goodridge

address: 8700 Beverly Boulevard

institute: Cedars-Sinai Medical Center

summary: Granulocyte-monocyte progenitors (GMPs) and monocyte-dendritic cell progenitors (MDPs) produce monocytes during homeostasis and in response to increased demand during infection. Both progenitor populations are thought to derive from common myeloid progenitors (CMPs), and a hierarchical relationship (CMP-GMP-MDP-monocyte) is presumed to underlie monocyte differentiation. Here, however, we demonstrate that mouse MDPs arose from CMPs independently of GMPs, and that GMPs and MDPs produced monocytes via similar, but distinct, monocyte-committed progenitors. GMPs and MDPs yielded classical (Ly6Chi) monocytes with gene expression signatures that were defined by their origins and impacted their function. GMPs produced a subset of “neutrophil-like” monocytes, whereas MDPs gave rise to a subset of monocytes that yielded monocyte-derived dendritic cells. GMPs and MDPs were also independently mobilized to produce specific combinations of myeloid cell types following the injection of microbial components. Thus, the balance of GMP and MDP differentiation shapes the myeloid cell repertoire during homeostasis and following infection.

overall_design: RNA-seq of myeloid progenitors and Ly6Chi monocytes from mouse bone marrow.  4 progenitor fractions (GMPs, MDPs, GPs and a mixed fraction of MPs + cMoPs) were isolated from the pooled bone marrow of 20 mice. GMPs and MDPs were also cultured in vitro and the monocyte-committed progenitors and Ly6Chi monocytes they produced were also harvested. RNA was extracted from the 4 ex vivo progenitor fractions, and the 4 populations derived in vitro (GMP-derived monocyte progenitors = MP; MDP-derived monocyte progenitors = cMoP; GMP-derived Ly6Chi monocytes = G-mono; MDP-derived Ly6Chi monocytes = M-mono). The whole process was repeated using 20 additional mice to obtain a replicate set of samples.

first: Alberto

last: Yáñez

first: Simon

middle: G

last: Coetzee

first: Andre

last: Olsson

first: David

last: Muench

first: Benjamin

middle: P

last: Berman

first: Dennis

middle: J

last: Hazelett

first: Nathan

last: Salomonis

first: H

last: Grimes


title: Histone exchange assay in loss of DOT1

city: Daejeon

first: Daeyoup

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Strain background is Saccharomyces cerevisiae wzy42 histone mutant strain with pWZ403 Myc-HHT2-HHF2 plasmid and pGAL1/10 FLAG-HHT1-HHF1 integrated gene. Cells were grown in YP+2% raffinose until mid-log (OD600=0.5) and arrested with alpha factor. When most of Cells were in G1 phase, added galactose (final conc. 2%) and harvested cells after 1 hour. Fixed cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. ChIP cells were disrupted by glass bead vortexing in ChIP lysis buffer and sonicated by Sonic Dismembrator Model 500, Fisher Scientific. Sonicated soluble lysate were immunoprecipiated by FLAG antibody (F1804; Sigma).

overall_design: ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccaromyces cerevisiae.

first: Soyun

first: Seunghee

last: Oh

first: Kwiwan

last: Jeong

first: Hyelim

last: Jo

first: Yoonjung

last: Choi

first: Hogyu

last: Seo

first: Minhoo

last: Kim

first: Joonho

last: Choe

first: Chang

last: Kwon


title: Non-synchronized cell cycle transcriptomics in U2OS and HeLa cancer cells

city: Stockholm

first: Michael

last: Andäng

address: Nanna Svartz Väg 2

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: Sorting U2OS and HeLa cells genetically modified with the Fucci System allowed us to separate cells according to cell cycle progression followed by RNA Sequencing to characterize the oscillating transcriptome in cells without the need for chemical synchronization.

overall_design: HeLa cells were sorted at three timepoints, while U2OS cells were sorted at two timepoints. Each time into three groups, categorized as "G1", "S", and "G2".

first: Johan

last: Boström

first: Zuzana

last: Sramkova

first: Alena

last: Salasova

first: Peter

last: Lönnberg

first: Sten

last: Linnarsson

first: Petra

last: Sekyrova

first: Mikael

last: Altun


title: The histone demethylase Kdm6 regulates a mature gene expression program in differentiating cerebellar granule neurons

city: Durham

first: Anne

last: West

state: NC

address: 311 research drive

department: Neurobiology

institute: Duke University

summary: The histone H3 lysine 27 (H3K27) demethylase Kdm6b (Jmjd3) can promote cellular differentiation, however its physiological functions in neurons remain to be fully determined. We studied the expression and function of Kdm6b in differentiating granule neurons of the developing postnatal mouse cerebellum. At postnatal day 7, Kdm6b is expressed throughout the layers of the developing cerebellar cortex, but its expression is upregulated in newborn cerebellar granule neurons (CGNs). Atoh1-Cre mediated conditional knockout of Kdm6b in CGN precursors either alone or in combination with Kdm6a did not disturb the gross morphological development of the cerebellum. Furthermore, RNAi-mediated knockdown of Kdm6b in cultured CGN precursors did not alter the induced expression of early neuronal marker genes upon cell cycle exit. By contrast, knockdown of Kdm6b significantly impaired the induction of a mature neuronal gene expression program, which includes gene products required for functional synapse maturation. Loss of Kdm6b also impaired the ability of Brain-Derived Neurotrophic Factor (BDNF) to induce expression of Grin2c and Tiam1 in maturing CGNs. Taken together, these data reveal a previously unknown role for Kdm6b in the postmitotic stages of CGN maturation and suggest that Kdm6b may work, at least in part, by a transcriptional mechanism that promotes gene sensitivity to regulation by BDNF.

overall_design: Biological triplicate RNA-seq samples from cultured CGNs with Kdm6b being knocked down by lentiviral shRNA (3 biological replicates per KD and 3 controls).

first: Fang

last: Liu

first: Ranjula

last: Wijayatunge

first: Karl

last: Shpargel

first: Nicole

last: Wayne

first: Urann

last: Chan

first: Jane-Valeriane

last: Boua

first: Terry

last: Magnuson

middle: E


title: small RNA libraries from petals of Antirrhinum majus (sulf mutant and wild-type revertants)

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

institute: University of Oxford

summary: Our aim was to study quantitative and qualitative small RNA differences between sulf and SULF+ plants. We used sulf-660 and its revertant, derived by transposon excision from the sulf-660 allele, to minimise background variation and highlight key differences associated with the SULF locus.

overall_design: Four HD sRNA libraries were prepared; 2 from A. majus line JI660 (sulf) and 2 from JI661 (SULF+ Revertant). Each library comprised 5-6 corollas harvested from 2-3 plants (buds of 10-30 mm).

first: Desmond

last: Bradley

first: Rosemary

last: Carpenter

first: Enrico

last: Coen

first: Lucy

last: Copsey

first: Matthew

last: Couchman

first: Tamas

last: Dalmay

first: Hugo

last: Tavares

first: Annabel

last: Whibley

first: Ping

last: Xu


title: Hi-C of early Drosophila melanogaster embryos

city: San Francisco

first: Michael

last: Stadler

state: California

address: 1519B York St.

summary: We use deep-sequencing of Hi-C libraries to identify topological boundaries at high resolution and show that boundaries, insulators, and polytene interbands converge on the same short genomic elements.

overall_design: Hi-C on whole nc12 and nc14 embryos, anterior and posterior halves of nc14 embryos

middle: R

last: Eisen


title: Gene expression analysis using RNA Sequencing of the Saccharomyces cerevisiae BY4741 Spt4-T42A/S43A mutant strain upon osmotic stress.

city: Barcelona

first: Francesc

last: Posas

address: Baldiri Reixac 10

institute: IRB Barcelona

summary: To study the relevance of the phosphorylation of Spt4 in residues T42 and S43, we assessed the genome-wide transcriptional response of the non-phosphorylatable Spt4-T42A/S43A mutant (Spt4-AA) upon osmotic stress. Results point out that the unphosphorylatable Spt4-T42A/S43A protein showed an impaired stress responsive gene expression indicating that these specific residues play a relevant role in osmotic  stress responsive transcriptional regulation.

overall_design: Total RNA obtained from the Saccharomyces cerevisiae BY4741 Spt4-TAP (WT) or BY4741 Spt4-T42A/S43A-TAP mutant (Spt4-AA) untreated or subjected to osmotic stress (15 min at 0.4M NaCl). Experiment was done by triplicate.

first: Eulàlia

last: deNadal


title: Spatial control of gene expression by miR319-regulated TCP transcription factors in leaf development

city: Rosario

first: Edgardo

middle: Gabriel

last: Bresso

state: Santa Fe

address: Ocampo y Esmeralda, Predio CONICET-Rosario

country: Argentina

institute: IBR-CONICET

summary: The characteristic leaf shapes we see in all plants are in good part outcome of the combined action of several transcription factor networks that translate into cell division activity during the early development of the organ. We show here that wild-type leaves have distinct transcriptomic profiles in center and marginal regions. Certain transcripts are enriched in margins, including those of CINCINNATA-like TCPs, and members of the NGATHA (NGA) and STYLISH (STY) gene families. We study in detail the contribution of miR319 regulated TCP (Teosinte branched, Cycloidea, PCF1/2) transcription factors to the development of the center and marginal regions of Arabidopsis leaves. We compare in molecular analyses wildtype, a tcp2 tcp4 mutant that has enlarged flat leaves and a tcp2 tcp3 tcp4 tcp10 mutant with strongly crinkled leaves. The different leaf domains of the tcp mutants show changed expression patterns for many photosynthesis related genes, indicating delayed differentiation, especially in the marginal parts of the organ. At the same time, we found an upregulation of cyclin genes and other genes that are known to participate in cell division, specifically in the marginal regions of tcp2 tcp3 tcp4 tcp10. Using GUS reporter constructs we confirmed extended mitotic activity in the tcp2 tcp3 tcp4 tcp10 leaf which persisted in small defined foci in the margins when the mitotic activity had already ceased in wild-type leaves. Our results describe the role of miR319-regulated TCP transcription factors in the coordination of activities in different leaf domains during the organs development.

overall_design: Examination of gene expression of two portions of leaves of different TCP transcription factors mutant lines

first: E

first: U

last: Chorostecki

first: R

last: Rodriguez

first: J

middle: F

last: Palatnik

first: C

last: Schommer


title: Serum miR-122-5p and miR-206 expression: Non-invasive prognostic biomarkers for renal cell carcinoma

city: Bonnn

first: Jörg

last: Ellinger

state: NRW

address: Sigmund-Freud-Straße 25

department: Urologie

institute: Universitätsklinikum Bonn

summary: Analysis of the small non-coding RNA expression profile in cell-free serum RNA of patients with clear cell renal cell carcinoma (RCC) and patients with benign renal tumors (BRT) in order to identify novel non-invasive biomarkers for patients with RCC. Aims: (1) to compare the expression profile of patients with RCC and BRT. (2) to compare the expression profile of patients with localized (M=0) and metastatic (M=1) RCC.

overall_design: small RNA expression profiling and sequencing in serum of patients with clear cell renal cell carcinoma (RCC) and benign renal tumors (BRT)

first: Frauke

last: Heinemann

first: Yuri

last: Tolkach

first: Mario

last: Deng

first: Doris

last: Schmidt

first: Sven

last: Perner

first: Glen

last: Kristiansen

first: Stefan

last: Müller


title: Single cell RNA-seq of 186 basal and luminal epithelial cells from the mammary gland of adult mice

city: Parkville

first: Gordon

middle: K

last: Smyth

address: 1G Royal Pde

institute: Walter and Eliza Hall Institute of Medical Research

summary: Mammary glands of 8 adult (10 week-old) female mice were collected. Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100bp paired-end reads.

overall_design: 96 basal and 90 luminal cells were profiled from 8 mice.

first: Yunshun

last: Chen

first: Bhupinder

last: Pal

first: Jane

last: Visvader


title: Single cell RNA-seq of 346 epithelial cells from the mammary glands of pre-pubescent, pubescent and adult mice

summary: Mammary glands were collected from pre-pubescent (2 weeks old), pubescent (4.7- 4.9 weeks old) and adult (10 week-old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100 bp paired-end reads.

overall_design: RNA-seq profiling was completed for 144 cells from 8 pre-puberty (2 week old) mice, 136 cells from 8 pubescent (4.7-4.9 week old) mice and 66 cells from 8 adult (10 week old) mice.


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines IV

status: Public on Nov 17 2017

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines (pancreatic cancer, esophageal cancer and lung squamous cell carcinoma) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (T24, A498, A549 and TE8) were treated with miRNAs (miR-223-5p, 223-3p, 145-5p and 145-3p), siRNAs (si-PMM2).

first: Yasutaka

last: Yamada


title: Single cell RNA-seq of 312 basal epithelial cells from the mammary glands of pregnant and adult mice

summary: Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 adult (10 week old) female mice. Basal epithelial cells were FACS sorted. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads.

overall_design: RNA-seq profiling was completed for 75 cells from pregnant mice and 237 cells from adult mice.


title: Single-cell transcriptome analysis of EpCAM+ cells from P3.25 mouse fetal livers

first: Xianbin

last: Su

country: China

summary: We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 52 EpCAM+ cells from postnatal day 3.25 mouse fetal livers. These cells show characters of cholangiocytes. Combined with our previous single cell data of E11.5~P2.5 mouse fetal livers, our data depict the dynamic trajectories with transcriptional profiles at single-cell resolution during mouse liver development, and provide insights into the fate decision and transcriptional control of self-renewal, differentiation and maturation of liver stem/progenitor cells.

overall_design: The transcriptomes of EpCAM+ single cells from P3.25 mouse livers were analyzed in this study. ERCC Spike-ins were included in each sample as control. We analyzed 52 single cells from pooled sibling livers. All single cell samples were processed on the C1 microfluidic system.

first: Yi

last: Shi

first: Ze-Guang

last: Han


title: SOX10 Single Transcription Factor Based Fast and Efficient Generation of Oligodendrocytes from Human Pluripotent Stem Cells

city: Leuven

first: Juan

middle: Antonio Garcia

last: Leon

address: Oude Markt 13

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

summary: We report the use of a single transcription factor, SOX10, for the generation of oligodendrocytes from human pluripotent stem cells. We further used RNA sequencing to compare the oligodendrocytes derived from pluripotent stem cells to different primary cells. It was revealed that oligodendrocytes derived from pluripotent stem cells are representative of intermediate oligodendrocytes during embryonic development.

overall_design: Examination of different primary cells and oligodendrocytes derived from different human pluripotent stem cell lines

middle: A

last: Garcia Leon

first: David

last: Chau


title: 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

city: Beijing

first: Cheng

last: Li

state: Beijing

address: 5 Yiheyuan Road, Haidian District

department: Center for Life Science, Academy for Advanced Interdisciplinary Studies

institute: Peking University

type: Genome variation profiling by high throughput sequencing

summary: Hi-C technique has been widely applied to study the three-dimensional architecture of the whole genome. Genome structures such as compartment A/B, TAD (topologically associated domain) and chromatin loops can be identified from Hi-C data in both normal cells of human and other species, and are found to be associated with features such as epigenetic markers, DNA-binding proteins and gene expression. But such technique had been rarely used in cancer studies. Here we used Hi-C to study the aneuploid cancer genomic architecture in multiple myeloma cells. Our results indicate that Hi-C interaction matrix of cancer cells is affected by CNVs and should be adjusted for copy number. After correcting this CNV bias, we found a significant overlapping between the boundaries of CNV blocks and boundaries of TADs, which suggests that TAD boundaries are fragile sites for CNV breakpoints. In addition, the compartment A/B switching is associated with differential gene expression, from which we found important genes that are related with multiple myeloma. We build a 3D structure model of the aneuploidy genome and found that there are great changes both in the whole genome spatial interactome and local chromosome territories. In summary, our research builds the first 3D genome interaction maps of multiple myeloma and the first time notice this CNV-driven bias in Hi-C studies, which may deepen our understanding of changes in cancer 3D genome.

overall_design: Integrated analysis of 3D genome architecture, gene expression, and genome structure variations in multiple myelomas.

first: Tingting

first: Lumeng

last: Jia

first: Ruifeng

first: Pengze

last: Wu


title: Gene expression data from whole blood of a Phase II randomized clinical trial of the treatment of methamphetamine dependence with topiramate

first: Tianhua

last: Niu

state: Louisiana

address: 1430 Tulane Avenue #8643

department: Biochemistry and Molecular Biology

country: USA

institute: Tulane University School of Medicine

summary:
A genome-wide RNA expression study based on a Phase II randomized placebo-controlled clinical trial of topiramate (TPM) treatment of methamphetamine (METH) dependence.
Gene expression data were analyzed based on TPM responses at Weeks 8 and 12, to identify differentially expressed genes and related pathways.

overall_design: From a previously conducted randomized, Phase II double-blind, multi-center, placebo-controlled clinical trial of treatment of METH dependence with TPM (Elkashef et al., Addiction. 2012, PMID: 22221594), 99 gave consent to participate in a genome-wide expression study were included in this report. The total RNA was collected from whole blood for each of the 50 TPM- and 49 placebo-treated participants at three time points: baseline, week 8, and week 12, respectively. Gene expression data of a total of 209 Affymetrix Human Genome U-133 Plus 2.0 chips passed quality control from 50 TPM- and 48 placebo-treated participants at baseline (88 chips), Week 8 (65 chips), and Week 12 (56 chips). Gene expression data were analyzed based on METH-dependent participants’ TPM responses at Weeks 8 and 12, to identify differentially expressed genes and related pathways that could be related to differential TPM responses among METH-dependent study participants.

first: Ming

middle: D

first: Ju

last: Wang

first: Jennie

middle: Z

last: Ma

first: Chamindi

last: Seneviratne

first: Nassima

last: Ait-Daoud

first: Jim

last: Saadvandi

first: Rana

last: Morris

last: Weiss

first: Jan

last: Campbell

first: William

last: Haning

last: Mawhinney

first: Denis

last: Weis

first: Michael

last: McCann

first: Christopher

last: Stock

first: Roberta

last: Kahn

first: Erin

last: Iturriaga

first: Elmer

last: Yu

first: Ahmed

last: Elkashef

first: B

last: Johnson


title: Single cell RNA-seq of basal, luminal and total epithelial cells from the mammary glands of female mice

first: Gordon

last: Smyth

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

Mammary glands were collected from female mice of various ages: pre puberty (2 weeks), pubescent (5 weeks), adult (10 weeks) and pregnant (12.5 days mid-pregnancy). Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. In some cases, cells were further sorted into basal and luminal subsets. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were sequencing on an Illumina HiSeq 2000 to achieve 100bp paired-end reads or on an Illumina NextSeq to achieve 75bp paired-end reads.

overall_design: Refer to individual Series


title: Post-transcriptional 3’UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

summary:
Here, using genome wide analysis, we demonstrate that canonical mRNA is processed post-transcriptionally through an alternative cleavage and polyadenylation mechanism. As a result of this process, the downstream cleavage fragment of the 3′UTR remains uncapped and stable
This finding indicates that different parts of gene mRNA are separate and independent, by re-annotating the human transcriptome using this model, we provide a new overview of the function and impact of microRNA (miRNA)
Our results shed new light on the mammalian transcriptome and show that what were considered as 3′UTRs are in fact autonomous RNA fragments.

overall_design: Examination of mRNA levels and cleavage across transcripts in U2OS and 293 cell types (3 replicates each)

first: Yuval

last: Malka

first: Avital

last: Steiman-Shimony

first: Eran

last: Rosenthal

first: Liron

last: Argaman

first: Leonor

last: Cohen-Daniel

first: Eliran

last: Arbib

first: Hanah

last: Margalit

last: Berger


title: The impact of lncRNA LAST knockdown on gene expression profile in HCT116 cells

status: Public on Nov 16 2017

city: Hefei

first: Pengfei

last: Zhang

address: 443 Huang-Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: High-throughput sequencing was employed to analyze the genes whose expression are altered when lncRNA LAST is downregulated by shRNA in HCT116 cells. The Gencode Gene ID of lncRNA LAST is ENSG00000254682.1.

overall_design: In order to identify the genes whose expression levels were changed under the condition of LAST knockdown,  we performed High-throughput sequencing and mRNA expression profile data analyzing.

first: Mian

last: Wu

first: Limian

last: Cao


title: Metabolic regulation of filamentous fungi is tailored for secondary secondary metabolite production

city: Hørsholm

first: Jens Christian

last: Nielsen

address: Hørsholm Kongevej

country: Denmark

institute: Gubra

summary: We investigated the metabolism of six secondary metabolite producing fungi of the Penicillium genus, during nutrient depletion in the stationary phase of batch fermentations and assessed conserved metabolic responses across species using genome-wide transcriptional profiling. Coexpression analysis revealed that expression of secondary metabolite biosynthetic genes correlates with expression of genes associated with pathways responsible for generation of precursor metabolites for secondary metabolism. Our results highlight the main metabolic routes for precursor supply of the secondary metabolism during nutrient depletion, and suggests that regulation of fungal metabolism is tailored to meet the demands for secondary metabolite production. These findings can aid in identifying wild type species, which are optimized for production of specific secondary metabolites, and therefore can be utilized as high yielding cell factories.

sample_organism:
Penicillium coprophilum
Penicillium polonicum
Penicillium nalgiovense
Penicillium decumbens
Penicillium flavigenum
Penicillium steckii

overall_design: Controlled bioreactor fermentations were carried out for six different Penicillium species in defined and complex medium. A sample for transcriptome analysis was collected in the stationary phase several hours after the CO2 exhaust had peaked

first: Jens

middle: C


title: Integrative genome-wide analysis in non-small cell lung cancer cells

city: Shanghai

first: Dan

last: Li

address: Siping 1239

department: Life science and Technology department

institute: Tongji University

summary:
We used complementing high-throughput sequencing technologies, including RNA-seq, DNase I-seq, and ChIP-seq, to examine the distribution of DNase I hypersensitive sites and H3K4me2 histone marks, to infer transcription factor binding sites, to identify key pathways in Gefinitib resistant and sensitive cell lines, PC9R and PC9 respectively, and to verify that some of up-regulated genes in PC9R can be found in Gefinitib resistant patients, which indicated that our study has valid clinical relevance.
Total mRNA profiles of PC9 and PC9R cell lines were generated by deep sequencing, in duplicate, using Illumina Hiseq2000.The mapping results of RNA-seq reads by the TopHat algorithm (version 1.1.4) to the hg19 reference genome were used to count the number of reads per gene with the hgseq-count algorithm. Then, DESeq was used to detect the genes differentially expressed between the PC9 and PC9R samples, with a p-value of 0.05 as the threshold. DNase-Seq and ChIP-Seq raw reads were aligned with Bowtie0.12.9 to hg19. MACS2 (https://github.com/taoliu/MACS/downloads) was employed to call PC9-specific regions using PC9 cells as the treatment and PC9R cells as the control, with a q-value threshold (DNase-Seq: 10-2; ChIP-Seq: 10-3) to minimise false positives; then, the process was repeated with the treatment and control cell lines switched.

overall_design: All methodes used in 2 cell lines including drug sensitive and resistant cells

first: Fan


title: Gene expression profiling of mouse macrophages following long noncoding RNA Malat1 knockdown

city: Birmingham

first: Huachun

last: Cui

state: Alabama

institute: University of Alabama at Birmingham

summary: We applied next-generation sequencing to investigate the gene expression profiles in mouse bone-marrow derived macrophages with or without long noncoding RNA-Malat1 knockdown. We identified a number of differentially regulated genes in cells with Malat1 knockdown.

overall_design: Mouse bone-marrow derived macrophages were transfected with Antisense LNA™ GapmeRs against Malat1 or Negative Control oligos (Exiqon). 48h after transfection, total RNA was isolated and subjected to high-throughput sequencin (RNA-seq), using Illumina GAIIx. Gene expression profiles were compared between two groups.

first: Gang

last: Liu


title: Polycomb Repressive Complex 2 methylates Elongin A to tune transcript levels of targeted genes [ChIP-seq]

city: Boston

first: Behfar

last: Ardehali

state: Massachusetts

address: Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN7250

department: Molecular Biology

institute: MGH, Harvard Medical School

summary: Polycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27). PRC2 is required to maintain gene repression during development and differentiation and misregulation of PRC2 is linked to a range of neoplastic malignancies, activities that are believed to involve H3K27 methylation. The full spectrum of non-histone substrates of PRC2, however, is not known, and it is not known which other substrates might also contribute to the biological functions of PRC2.  We characterized the target recognition specificity and substrate diversity of PRC2, and identified more than one hundred potential novel nuclear targets of PRC2. The RNA polymerase II (Pol II) transcription elongation factor, Elongin A (EloA), is an in vivo target of PRC2. Mutation of the EloA residue that is methylated by PRC2 decreases repression of numerous PRC2 target genes. We propose that this functional crosstalk between PRC2 and EloA tunes the level of repression of targeted genes and contributes to the biological functions of PRC2.

overall_design: We examined the genome-wide distribution of PRC2 catalytic subunit, EZH2, in mES cell by ChIP-seq

first: M

middle: B

first: Anthony

last: Anselmo


title: Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function [RNA-seq]

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

summary: Polycomb repressive complex 1 (PRC1) plays essential roles in cell fate determination. Recent studies have found that the composition of mammalian PRC1 is particularly varied and complicated, whereas the function of such variant PRC1 complexes on cell fate determination remains unknown. Here we show that Kdm2b, which recruits a variant PRC1 complex (PRC1.1) to CpG islands (CGIs), elevates Oct4 induced somatic reprogramming. Interaction with PRC1 is critical for Kdm2b’s promotion on the process of induced pluripotency. Furthermore, we find that bone morphogenetic proteins (BMPs) repress Oct4/Kdm2b induced somatic reprogramming selectively. Mechanistically, BMP-Smad pathway attenuates PRC1.1 occupation and H2AK119 ubiquitination on development genes, resulting in the release of meso-endoderm factors such as Sox17 and suppression of somatic reprogramming. These observations reveal that PRC1.1 participates in the establishment of pluripotency as well as cellular differentiation and identify BMP signal as a modulator of PRC1.1 function.

overall_design: We analyzed the gene expression profiles and PRC1.1 occupation on chromatin  during the Oct4/Kdm2b induced reprogramming process by RNA-seq and ChIP-seq


title: Exploring the transcriptomic pattern in two kind of sheep skin with remarkable phenotype differences on wool

city: Gongzhuling

first: Lichun

state: Jilin

address: 186 Dongxinhua St

department: Branch of Animal Husbandry

institute: Jilin Academy of Agricultural Science

summary: We report the application of High throughout sequencing to explore the differences of skin between Super Merino sheep(SM) and Small Tail Han sheep, which have remarkable phenotype differences on wool and hair follicle traits. We analysed the expression data by CLC genomic workbench 9.0 software. We find there are 435 differential expressional genes (DEGs) (127 were up-regulated and 308 were down-regulated) when STH sheep as control group. Some hair follicle KRTs, KAPs genes and hair follicle stem cells marker genes, were up-regulated in SM sheep. However, some of mammalian epidermal development complex (EDC) family genes were up-regulated in STH sheep. The GO and gene network analysis shown high expression genes in SM sheep enriched on type I interferon, lipid/fatty acid synthesis metabolism. This study provide more details in skin which control the development of follicle and wool in sheep.

overall_design: Examination of 2 different transcript profiles of skin.

first: Aaron

last: Ingham


title: Single cell RNA-seq of 278 epithelial cells from the mammary glands of pregnant and non-pregnant mice

first: Gordon

last: Smyth

department: Bioinformatics

country: Australia

summary: Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 non-pregnant adult (10 week old) female mice. Epithelial cells were FACS sorted from the pregnant mice. Cells from the adult mice were FACS sorted as basal or luminal. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve 75 bp paired-end reads.

overall_design: 112 basal cells and 43 luminal cells were profiled from the adult mice. 123 total epithelial cells were profiled from the pregnant mice.

first: Yunshun

last: Chen

first: Bhupinder

last: Pal

first: Jane

last: Visvader


title: Harnessing BET inhibitor sensitivity reveals AMIGO2 as a melanoma survival gene.

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: We utilize the transcriptional effects of BETi in melanoma and identify AMIGO2 as a direct target gene essential for melanoma cell survival both in vitro and in vivo. We further map the enhancer landscape of NHM and melanooma and show that genes regulated by super enhancers are expressed in higher levels, exihibit higher sensitivity to BETi, and over expressed in melanoma relative to NHM. In melanoma, AMIGO2 is regulated by super enhancers, which upon BETi lose their BRD2/BRD4 enrichment, resulting in AMIGO2 silencing.

overall_design: We interogate two NHM culures and four melanoma cell lines for transcriptional changes upon BET inhibition and correlate those wiith changes in enhancer landscape and BRD2/4 occupancy at regulatory regions.

first: Barbara

last: Fontanals-Cirera

last: Hasson

first: Chiara

last: Vardabasso

first: Eva

last: Hernando


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and OsAFB6 overexpression mutant Transcriptomes

city: Wuhan

first: Qin

address: shizishan street

institute: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transgene-derived OsAFB6 overexpression mutant transcriptome profiling (RNA-seq) to microarray
Methods: young panicle(<1mm) mRNA profiles of 80 individual plants of OsAFB6 overexpression mutants and the correspondinng negative plants during the same transgenic event as control were generated by deep sequencing, in two replicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we found 59 genes were upregulated and 229 genes were down regulated in OsAFB6 overexpression mutant.
Conclusions: Our study represents the first detailed analysis of young panicle transcriptomes of OsAFB6 overexpression mutant, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.  We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: young panicle(<1mm) mRNA profiles of 80 individual plants of OsAFB6 overexpression mutants and the correspondinng negative plants during the same transgenic event were generated by deep sequencing, in two replicate,, using Illumina HiSeq 2000.

first: Yongzhong

last: Xing


title: RNA-sequencing of Adult Zebrafish Inner Ear Hair Cells

city: Omaha

first: David

state: Nebraska

address: 2500 California Plaza

department: Department of Biomedical Sciences

institute: Creighton University

summary: To understand the basic biological properties of inner ear hair cells (HCs) from non-mammalian vertebrates, we examined the transcriptome of adult zebrafish auditory and vestibular HCs.  GFP-labeled HCs were isolated from inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish.  One thousand HCs and 1,000 non-sensory surrounding cells (nsSCs) were separately collected for each biological replicate, using the suction pipette technique.  RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs, which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution.

overall_design: One thousand HCs and 1,000 nsSCs were separately collected for each biological replicate, using the suction pipette technique.  RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs, which may underlie HC specialization.

first: Cody

last: Barta

first: Huizhan

first: Lei

first: Yi

last: Li

first: Kim

last: Giffen

first: Kenneth

last: Kramer

first: Kirk

middle: W

last: Beisel

last: He*


title: Identification of CNBP binding mRNA and the binding sites/motifs in HCT116 cells

first: Pengfei

last: Zhang

summary: High-throughput RNA-IP sequencing was employed to identify the CNBP binding mRNAs and their binding sites in HCT116 cells.

overall_design: In order to identify the CNBP binding mRNAs and their binding sites,  we performed CNBP RIP and High-throughput sequencing.

first: Mian

last: Wu

first: Limian

last: Cao


title: Non-monotonic changes in Progenitor Cell Behavior and Gene expression during aging of the Adult Neural Stem Cell Niche

city: Rensselaer

first: Thomas

last: Kiehl

address: One Discovery Drive

institute: Neural Stem Cell Institute

summary: Neural stem cell activity in the ventricular-subventricular zone (V-SVZ) decreases with aging, thought to occur by a unidirectional decline. However, by analyzing the V-SVZ transcriptome of male mice at 2, 6, 18 and 22 months, we found that most of the genes that change significantly over time show a reversal of trend, with a maximum or minimum expression at 18 months. In vivo, MASH1+ progenitor cells decrease in number and proliferation between 2-18 months, but these increased between 18-22 months. Time-lapse lineage analysis of 944 V-SVZ cells showed that age-related declines in neurogenesis were recapitulated in vitro in clones. However, activated type B/type C cell clones divide slower from 2-18 months, then unexpectedly faster at 22 months, with impaired transition to type A neuroblasts. Our findings indicate that aging of the V-SVZ involves significant non-monotonic changes that are programed within progenitor cells, and observable independent of the aging niche.

overall_design: RNA extracted from Mouse SVZ, in triplicate, from ages 2, 6, 18 and 22 months.

first: Maria

last: Apostolopoulou

first: Sally

last: Temple


title: Pigment producing melanocytes as the cells of origin of BRAFV600E-induced mouse cutaneous melanoma

first: Sara

last: Aibar

address: Herestraat 49

department: Center for Brain & Disease Research

institute: VIB-KU Leuven

summary:
To investigate whether cutaneous melanoma originates from a resident adult melanocyte stem cell (MSC) or a mature melanocyte, we created a model that recapitulates key histopathological features of human melanomagenesis by inducing a BRafV600E-driven melanomagenic program in interfollicular (IF) melanocytes located in mouse tails.
To this end, we sequenced the transcriptome of FACS-sorted individual IFE reporter-positive cells from BRaf/Pten/tdTomato mice, the tails of which had been painted with 4-HT for 31 and 72 days, respectively. These time points were chosen as melanoma cells are exclusively found in the IF epidermis at day 31 (d31) and in both epidermis and dermis at day 72 (d72). Normal IF melanocytes from Tyr::CreERT2/+; ROSA26RLSL-tdTomato/+ were also isolated and profiled
These data indicated that loss of differentiation markers occurs in a subset of targeted epidermal melanoma cells before the onset of dermal invasion and that this event may, at least partly, be a consequence of induction of Zeb1 expression.

overall_design: scRNAseq (SMARTseq2) of epidermal melanocytes and melanoma cells at different stages of melanomagenesis in a tail melanoma mouse model.

first: Florian

last: Rambow