title: Mechanisms of in utero cortisol effects on the newborn heart revealed by transcriptomic modeling

city: Gainesville

first: Elaine

middle: Mary

last: Richards

state: FL

department: Pharmacodynamics

institute: University of Florida

summary: We have identified effects of elevated maternal cortisol on fetal cardiac maturation and function in an ovine model.  Whereas short term exposure, produced by maternal infusion (1 mg/kg/d) from 115-130d gestation increased fetal heart wall thickness and weight, myocyte proliferation and Purkinje fiber apoptosis, when cortisol exposure continued until term (~145 days of gestation), there was a profound increase in perinatal stillbirth.  Further study indicated increases in P-R and R-R interval of the ECG and increased incidence of arrhythmias at birth, suggesting that these changes in the fetal heart contribute to the stillbirth. We have used systems biology to statistically model the transcriptomic changes in hearts at 130 days and near term. In the current study, we used this approach to test for effects on pathways related to metabolism and cardiac structure in the left ventricle and septum from newborn lambs. Cortisol altered genes in pathways involved in cardiac architecture in the left ventricle, including SMAD and BMP; cortisol also increased collagen deposition. Genes in pathways involved in metabolism and actin filament assembly were affected within the septum. Comparison of the effects of cortisol to the effects of normal maturation from day 140 to birth revealed that only 1% of the genes changed by cortisol in the LV and 18% in the septum were consistent with the normal maturational changes in gene expression. These results indicate that chronic in utero exposure to elevated cortisol concentrations alters the normal maturation of the fetal myocardium, adversely impacting perinatal cardiac function.

overall_design: Singleton newborn sheep were used. Pregnant ewes were infused with cortisol 1mg/kg/day (Cortisol) or vehicle (Control) from 115 days gestation until birth (n=5/group). Cortisol and Control lambs were euthanized between 10 minutes and 480 minutes after birth. Data from these lambs were also compared to data previously collected from term fetuses from cortisol-or vehicle-treated ewes (GSE54237).

first: Andrew

last: Antolic

first: Celia

middle: W

last: Curtis

first: Charles

last: Wood

first: Maureen

last: Keller-Wood


title: Global effects of SUPT4H1 RNAi on gene expression of primary human fibroblasts

status: Public on Jan 01 2019

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

country: USA

institute: Denali Therapeutics

type: Expression profiling by high throughput sequencing

summary: SUPT4H1 is a transcription elongation factor comprising part of the RNA polymerase II complex. Recent studies propose a selective role for SUPT4H1 in transcription of repeat-containing transcripts; the translated products of which being a hallmark of neurodegeneration in disorders such as Huntington’s Disease and C9orf72-amyotrophic lateral sclerosis. To investigate the potential of SUPT4H1 as a therapeutic target in repeat-associated neurodegeneration, we depleted SUPT4H1 by RNA interference in order to mimic pharmacological loss of function. Using RNA sequencing we assessed SUPT4H1-knockdown induced changes is both immortalized cells (HEK293t) as well as primary human fibroblasts. Diminished SUPT4H1 leads to a global reduction in cellular RNA.

overall_design: siRNA-mediated knockdown of SUPT4H1 in fibroblasts cells was performed.  Control experiments (treatment with non-targeting siRNA) was compared to knockdown conditions for the assessement of global modulatory effects on cell RNA abundances after SUPT4H1 depletion. Gene expression was assessed using 3' tag sequencing of poly-adenylated RNA (QuantSeq, Lexogen, Vienna, Austria).

first: Adam

last: Naguib

first: William

middle: E

last: Dowdle

first: Joe

last: Lewcock


title: NanoString nCounter Human HCC expression analysis

city: Berlin

first: Henrik

last: Seidel

address: Muellerstr. 178

country: Germany

institute: Bayer AG

summary: Archival tumor tissues from HCC patients recruited in the Ph 3 RESORCE trial were analysed with the pan Cancer immune profiling panel

overall_design: Baseline mRNA expression from archival tumor tissue (FFPE) of 46 patients

first: Michael

last: Teufel


title: Comparative Analysis of Gammaherpesvirus Circular RNA

status: Public on Jan 07 2019

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: Recent studies have identified circular RNAs (circRNAs) expressed from the Epstein-Barr virus (EBV) and Kaposi’s sarcoma herpesvirus (KSHV) human DNA tu- mor viruses. To gain initial insights into the potential relevance of EBV circRNAs in virus biology and disease, we assessed the circRNAome of the interspecies homologue rhesus macaque lymphocryptovirus (rLCV) in a naturally occurring lymphoma from a simian immunodeficiency virus (SIV)-infected rhesus macaque. This analysis revealed rLCV orthologues of the latency-associated EBV circular RNAs circRPMS1_E4_E3a and circEBNA_U. Also identified in two samples displaying unusually high lytic gene expres- sion was a novel rLCV circRNA that contains both conserved and rLCV-specific RPMS1 exons and whose backsplice junctions flank an rLCV lytic origin of replication (OriLyt). Analysis of a lytic infection model for the murid herpesvirus 68 (MHV68) rhadinovirus identified a cluster of circRNAs near an MHV68 lytic origin of replication, with the most abundant of these, circM11_ORF69, spanning the OriLyt. Lastly, analysis of KSHV la- tency and reactivation models revealed the latency associated circRNA originating from the vIRF4 gene as the predominant viral circRNA. Together, the results of this study broaden our appreciation for circRNA repertoires in the Lymphocryptovirus and Rhadinovirus genera of gammaherpesviruses and provide evolutionary support for vi- ral circRNA functions in latency and viral replication.

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Murid herpesvirus 68

overall_design: RNA-sequencing of Ribodepleted + RNase R treated, and Poly-A selection libraries of gammaherpesviral samples


title: RNA-seq: WT under proteotoxic stress conditions

city: Cologne

first: Thorsten

last: Hoppe

address: Joseph-Stelzmann-Str. 26

department: Institut für Genetik

institute: CECAD Cologne and Institute for Genetics

summary: In order to elucidate on mRNA changes upon various proteotoxic stress conditions, synchronized WT (N2) worms were treated from L4 to day 1 of adulthood and collected for RNA extraction in the following

overall_design: mRNA profile under proteotoxic stress in WT (N2) worms, done in triplicates

first: Alexander

last: Springhorn

first: Lucie

last: Proksch


title: RNA-seq data from human lymphoma cell lines

city: Lausanne

first: Giovanni

last: Ciriello

address: Rue du Bugnon 27

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

summary: RNA-seq experiments were performed on OCI-Ly19 EZH2-wild type cell line (LY19WT) and a syngenic OCI-Ly19 cell line expressing the mutated protein EZH2-Y646F (LY19Y646F). We investigated the transcriptome changes between the two conditions.

overall_design: RNA-seq was performed for two cell lines (LY19WT and LY19Y646F). For each of sample, data for three biological replicates were generated.

first: Maria

middle: C

last: Donaldson

first: Stephanie

last: Sungalee

first: Marie

last: Zufferey

first: Daniele

last: Tavernari

first: Natalya

last: Katanayeva

first: Elena

last: Battistello

first: Marco

last: Mina

first: Kyle

middle: M

last: Douglass

first: Timo

last: Rey

first: Franck

last: Raynaud

first: Suliana

last: Manley

first: Elisa

last: Oricchio


title: ChIP-seq data for H3K27me3 from human lymphoma cell lines

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq experiments for H3K27me3 histone mark were performed on OCI-Ly19 EZH2-wild type cell line (LY19WT) and a syngenic OCI-Ly19 cell line expressing the mutated protein EZH2-Y646F (LY19Y646F). We investigated the genome-wide changes in H3K27me3 levels between the two conditions.

overall_design: ChIP-seq was performed for H3K27me3 for two cell lines (LY19WT and LY19Y646F). For each sample, data for one input and three biological replicates were generated.


title: Role of TAF5L and TAF6L in controlling the mouse ESC state

city: Melbourne

first: Partha

last: Das

state: Victoria

address: 211 Wellington Road

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

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

overall_design: Refer to individual Series


title: Characterizing the transcriptomic profile of the cortex within the long-term window of ischemic tolerance mediated by resveratrol preconditioning

city: Palo Alto

first: Nathalie

last: Khoury

state: CA California

address: 3801 Miranda Avenue Blvd. 100 VAPA D3-111 - Neurology

institute: Stanford University

summary: To identify novel genes and adaptations induced by resveratrol preconditioning that could promote long-term cerebral ischemic tolerance. After analyzing the results, we identified only 155 differentially expressed genes among which the majority of genes consisting of 126  were downregulated and only 29 genes were upregulated. The downregulated genes clustered into biological processes involved in regulating the memebrane potential, gene expression regulation, and neurotrasmitter transport secrection. While the upregulated gene  included immediate early genes and genes involved in antioxidant defense.

overall_design: Mice were subject to an intraperitoneal injection of vehicle or resveratrol (10mg/kg) (n=3 per group), two weeks later their cerebral cortex was collected, RNA was  extracted and then sent for sequencing

first: Miguel

middle: A

last: Perez-Pinzon

first: Juan

middle: I

last: Young


title: Expression data from myeloid progenitors derived from control and antibiotic-treated wild-type C57BL/6 mice

city: Philadelphia

first: Lehn

last: Weaver

state: PA

address: 3615 Civic Center Boulevard

department: Pediatric Rheumatology

institute: The University of Pennsylvania / The Children's Hospital of Philadelphia

summary:
Myeloid progenitors derived from antibiotic-treated mice have cell-intrinsic functional defects. In this microarray dataset, the transcriptomes of bone marrow myeloid progenitors from antibiotic-treated and control mice are compared.
Myeloid progenitors from antibiotic-treated mice have a reduced interferon gene expression signature. These data suggest that tonic interferon signaling is sensed by myeloid progenitors and such signals are reduced in antibiotic-treated mice.

overall_design: A total of 16 samples were analyzed comparing myeloid progenitors (CMPs, GMPs, and cMoPs) from control and antibiotic-treated mice.  Differentially expressed genes were identified between myeloid progenitors from antibiotic-treated mice and control mice using a two-way ANOVA statistical test in Partek Genomics Suite software and corrected for multiple testing using the Benjamini-Hochberg procedure to calculate a false discovery rate (FDR) of <0.2.

first: Edward

last: Behrens


title: Conserved miRNA discovery in switchgrass

city: Newark

first: Karl

last: Franke

state: Delaware

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: University of Delaware

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA libraries were constructed, sequenced, and analyzed with our Sequence Homology Pipeline for miRNA discovery (Jeong et al. 2013) to identify 59 unique conserved miRNA sequences from 199 precursors in switchgrass.

overall_design: Eight samples in total were analyzed. Three were tissue samples. The remaining 5 samples included drought and cold stress conditions along with controls.  Switchgrass  (AP13)  was  grown  under  greenhouse  conditions  with  an  average  day  temperature  of  26°C  and  an  average  night  temperature  of  20°C.    Stress  treatments  were  carried  out  two  months  after  propagation  from  cuttings  and  the  second  and  third  leaf  blades  from  the  top  were  sampled. Cold  treatments  at  4°C  were  performed  for  24  hours.  For  drought  experiments,  the  drought  sample  was  harvested  11  days  after  watering  was  stopped.  Plants  subjected  to  recovery  were  then  watered,  and  on  the  12th  day  they  were  sampled.

middle: R

first: Skye

last: Schmidt

first: Sunhee

last: Park

first: Dong-Hoon

last: Jeong

first: Monica

last: Accerbi

first: Pamela

middle: J

last: Green


title: Analysis of Brachypodium miRNA targets: Evidence for diverse control during stress and conservation in bioenergy crops

summary:
Background: Since the proposal of Brachypodium distachyon as a model for the grasses over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass, are completely absent from the miRBase database. While a significant number of miRNAs have been identified which are highly conserved across plants, little research has been done with respect to the conservation of miRNA targets. Plant responses to abiotic stresses are regulated by diverse pathways many of which involve miRNAs; however, it can be difficult to identify miRNA guided gene regulation when the miRNA is not the primary regulator of the target mRNA.
Results: To investigate miRNA target conservation and stress response involvement, a set of PARE (Parallel Analysis of RNA Ends) libraries totaling over 2 billion reads was constructed and sequenced from Brachypodium, switchgrass, and sorghum representing the first public release of degradome data from the latter two species. Analysis of this data provided not only PARE evidence for miRNA guided cleavage of over 7,000 predicted target mRNAs in Brachypodium, but also evidence for miRNA guided cleavage of over 1,000 homologous transcripts in sorghum and switchgrass. A pipeline was constructed to compare RNA-seq and PARE data made from Brachypodium plants exposed to various abiotic stress conditions. This resulted in the identification of 44 miRNA targets which exhibit stress regulated cleavage. Time course experiments were performed to reveal the relationship between miR393ab, miR169a, miR394ab, and their respective targets throughout the first 36 hours of the cold stress response in Brachypodium.
Conclusions: Knowledge gained from this study provides considerable insight into the degradomes and the breadth of miRNA target conservation among these three species. Additionally associations of a number of miRNAs and target mRNAs with the stress responses have been revealed which will aid researchers in developing stress tolerant transgenic crops.

sample_organism:
Sorghum bicolor
Brachypodium distachyon
Panicum virgatum

overall_design: Libraries were constructed from tissue samples from Brachypodium, sorghum, and switchgrass plants as well as above ground tissue which had been exposed to various stress conditions. Two biological replicates were constructed for each library type. Control libraries were constructed in addition to stress samples. Brachypodium  Bd21  seeds  were  germinated  in  soil  and  the  plants  were  grown  in  a  growth  chamber  at  a  constant  20°C,  under  a  20  h  light  350  μE⋅m−2⋅s−1,  4  h  dark  cycle.  On  day  21,  10  hours  after  light  started,  plants  were  subjected  to  various  stress  treatments.  For  heat  stress,  plants  were  placed  at  40°C.  For  drought  stress,  plants  were  removed  from  soil  and  the  roots  were  dried  with  paper  towels.  For  submergence  stress,  plants  were  submerged  completely  with at  least  5  cm  of  tap  water  covering  the  top  of  the  plants.  For  cold  stress,  plants  were  placed  at  4°C.  For  stress  libraries,  above  ground  tissue  was  sampled  after  12  hours  of  stress;  for  the  cold  stress  time  courses,  samples  were  taken  at  0,  1,  2,  3,  6,  12,  24,  and  36  hours.  Switchgrass  (AP13)  was  grown  under  greenhouse  conditions  with  an  average  day  temperature  of  26°C  and  an  average  night  temperature  of  20°C.    Stress  treatments  were  carried  out  two  months  after  propagation  from  cuttings  and  the  second  and  third  leaf  blades  from  the  top  were  sampled.  After  germination,  Sorghum  bicolor  (BTx623)  seedlings  were  transferred  to  soil  in  a  growth  chamber.  After  14  days  of  growth  (12  hours  light  at  28°C,  12  hours  dark  at  25°C),  cold  treatments  were  carried  out  and  the  above-ground  tissue  was  harvested.  Switchgrass  and  sorghum  cold  treatments  at  4°C  were  performed  for  24  hours.  For  switchgrass  drought  experiments,  the  drought  sample  was  harvested  11  days  after  watering  was  stopped.  Plants  subjected  to  recovery  were  then  watered,  and  on  the  12th  day  they  were  sampled.


title: Proteolytic cleavage by taspase1 and the regulation of the stability of MLL1

status: Public on Jan 02 2019

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Chromosomal translocations of the Mixed-lineage leukemia 1 (MLL1) gene generate MLL-chimeras that drive pathogenesis of acute myeloid and lymphoid leukemia.  The untranslocated MLL1 is a substrate for proteolytic cleavage by the endopeptidase, taspase1, however, the biological significance of MLL1 cleavage by this endopeptidase remains unclear. Here, we demonstrate that taspase1-dependent cleavage of MLL1 results in the destabilization of full-length MLL.  Upon loss of taspase1, MLL1 association with chromatin is markedly increased due to the stabilization of its unprocessed version and this stabilization of the uncleaved MLL1 can result in the displacement of MLL-chimeras from chromatin in leukemic cells. Casein kinase II (CKII) phosphorylates MLL1 proximal to the taspase1 cleavage site, facilitating its cleavage, and pharmacological inhibition of CKII blocks taspase1-dependent MLL1 processing, increases MLL1 stability, and results in the displacement of the MLL-chimeras from chromatin. Furthermore, inhibition of CKII in MLL-AF9 mouse model of leukemia delayed leukemic progression in vivo. This study provides insights into the direct regulation of the stability of MLL1, which can be harnessed for targeted therapeutic approaches for the treatment of aggressive MLL leukemia.

overall_design: To characterize the functions of MLL1 cleavage by taspase1 using taspase1 knockout human cancer cell lines

first: Zibo

last: Zhao

first: Elizabeth

last: Bartom


title: Global gene expression analysis of human monocyte-derived dendritic cells (DCs) treated with HMGN1 (N1) and R848 alone or in combination.

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: RNA-seq data demonstrate that N1 plus R848 at the global gene expression level synergistically promotes DC maturation and subsequent upregulation of many genes in DCs that are involved in the polarization of CD4+ T cells into Th1-type effectors.

overall_design: DCs sham-treated or treated with N1, R848, or N1 plus R848 for 4 hours.

first: Md

last: Alam

first: De

last: Yang

first: Anna

last: Trivett

first: Joost

last: Oppenheim


title: Role of TAF5L and TAF6L in controlling the mouse ESC state [RNA-seq]

first: Partha

last: Das

summary: Self-renewal and pluripotency of the embryonic stem cell (ESC) state is established and maintained by multiple regulatory networks that comprise transcription factors and epigenetic regulators. Although many studies have been performed, the function of epigenetic regulators in these networks is incompletely defined. We conducted a CRISPR-Cas9 mediated loss-of-function genetic screen to target 323 epigenetic and ESC-specific transcription factor genes. This screen identified two new epigenetic regulators—TAF5L and TAF6L—with high confidence for the mouse ESC state. TAF5L and TAF6L are also essential for the efficient somatic reprogramming. In-depth analyses demonstrate that TAF5L and TAF6L belong to and establish a regulatory circuitry with MYC and CORE networks. Moreover, detailed molecular studies reveal TAF5L and TAF6L predominantly regulate their target genes through the c-MYC and MYC regulatory network to control self-renewal of mouse ESCs. Our findings illuminate the multi-layered regulatory networks of TAF5L and TAF6L for gene regulation to maintain the ESC state.

overall_design: RNA-seq gene expression comparison between WT mouse embryonic stem cells and Taf5l/Taf6l knockouts, as well as between c-Myc knockout and WT.


title: The mircoRNA expression profiles of human temporal lobe epilepsy in HS ILAE type 1

city: Harbin

first: Zhiguo

last: Lin

state: Heilongjiang

address: No.23 Youzheng street

department: Neurosugery

country: China

institute: First affiliated hospital of Harbin medical university

summary: Temporal lobe epilepsy (TLE) is associated with neurodegeneration, often leading to hippocampal sclerosis (HS). The type 1 HS, which is characterized by severe neuronal cell loss and gliosis predominantly in regions CA1 and CA4, is the most common subtype and is associated with best prognosis according to ILAE classification system. MiRNAs are participate in the biological processes underlying many nervous system diseases including epilepsy. However, the miRNA expression profile of HS ILAE type 1 is not completely understood. A total of 14 patients were identified as having the ILAE subtype, as determined by NeuN immunohistochemistry (ILAE type 1=7; no-HS=7). Next-generation sequencing and reverse transcription polymerase chain reaction technology was used to validate the dysregulated miRNAs. Bioinformatics analysis of the predicted target gene was conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. In total, 1643 mature miRNAs were detected in this study, along with 5 miRNAs were upregulated and 2 miRNAs were downregulated expression in the type 1 group. Bioinformatics analysis showed that 1545 target genes were predicted using miRDB and Targetscan databases, and these predicted genes showed enrichment in the pathway associated with nucleic acid binding, intracellular and cellular macromolecule metabolic processes, and the PI3K-Akt signaling pathway. This study is the first to report the miRNA expression profile of HS ILAE type 1 compared with no-HS. These results provide new insights into the neuron loss pathology and offer fundamental evidence as to why there is a good prognosis among patients with type 1 HS.

overall_design: MicroRNA profile of 3 hippocampus section of ILAE type I  and No-HS type in each group were generated by next-generation sequencing, using Illumina Hiseq 2500 platform.

first: Chongyang

last: Tang


title: Oligogalacturonomics of plant-fungus interactions

city: VERSAILLES

first: Samantha

last: VERNHETTES

address: route de saint Cyr

country: France

institute: INRA

summary: Despite an ever-increasing interest for the use of pectin-derived oligogalacturonides (OGs) as biological control agents in agriculture, very little information exists, mainly for technical reasons, on the nature and activity of the OGs that accumulate during pathogen infection. Here we developed a sensitive OG profiling method, which revealed unsuspected features of the OGome generated during infection of Arabidopsis thaliana with the fungus Botrytis cinerea. Indeed, most OGs were acetyl- and methylesterified, and 80 % of them were produced by fungal pectin lyases (PNL), not polygalacturonases (PG). PG products did not accumulate as larger size OGs but were converted into oxidized GalA dimers. Finally, the comparison of the OGomes and transcriptomes of leaves infected with B. cinerea mutants with reduced pectinolytic activity but with decreased or increased virulence respectively, identified novel candidate OG elicitors. In conclusion, OGome analysis provides new insights into the enzymatic arms race between plant and pathogen and facilitates the identification of novel defense elicitors.

overall_design: Affymetrix four-arrays strips (Arabidopsis Gene 1,1 ST Array strip) were used from three replicates of  leaves infected by the pathogen

first: Aline

last: Voxeur

first: Olivier

last: Habrylo

first: Stéphanie

last: Guénin

first: Fabien

last: Miart

first: Marie-Christine

last: Soulié

first: Christophe

last: Rihouey

first: Corinne

last: Pau-Roblot

first: Jean-Marc

last: Domon

first: Laurent

last: Gutierrez

first: Jérôme

last: Pelloux

first: Grégory

last: Mouille

first: Mathilde

last: Fagard

first: Herman

last: Höfte

last: Vernhettes


title: Effect of BMP2 on B16F10 melanoma cells

city: Epalinges

first: Tatiana

last: Petrova

state: VD

address: 155, Chemin des Boveresses

department: Oncology

summary: BMP2 treatment significantly reduces growth of B16F10 melanoma spheroids. This experiment analyses the transcriptome changes in B16F10 cells treated with or without BMP2.

overall_design: B16F10 cell spheroids in Matrigel were treated with control PBS or 100 ng/ml BMP2 for 10 days. The experiment was performed three times (batches 1-3), yielding three replicates for each group.

first: Stefanie

last: Hendrikx

first: Sina

last: Nassiri

middle: V


title: Investigation of downstream genes regulated by ACOT12 in HCC cells [Huh7]

city: Shanghai

first: Ming

last: Lu

address: No. 12, Middle Urumqi Road

department: Huashan hospital

institute: Fudan university

summary: Huh7 cell, a human hepatocellular carcinoma (HCC) cell line, was stably overexpressed with scramble shRNA or shRNA against ACOT12. These cells were then used for gene expression profiles analysis.

overall_design: In the study presented here, to investigation of downstream genes regulated by ACOT12 in HCC cells, Huh7 cells were stably overexpressed with scramble shRNA or shRNA against ACOT12. These stable cells were obtained by puromycin selection for 1 week. After validations by western boltting and other functional assays, these cells were then used for gene expression profiles analysis.


title: C5aR1 regulates T-follicular-helper differentiation and chronic graft-versus-host disease bronchiolitis obliterans

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: The goal of the study was to determine the effect of T cell expressed C5ar1 on transcriptional profiles of in vivo generated allogeneic T follicular helper cells

overall_design: 10 million CD8 depleted spleen cells from WT or C5aR1-deficient donors were injected into (bxd)F1 recipients and 7 days later donor CXCR5, PD1hi cells were flow sorted and sequenced. Side by side control samples of naïve WT and C5ar1 deficient CD4 cells were included

first: Zhengzi

last: Yi

first: Peter

middle: S

last: Heeger


title: Exploration of gene expression signature for human coronary artery endothelial cells in response to inhibition of myocyte enhancer factor 2A

city: Guangzhou

first: Liu

last: Benrong

address: No.250 Changgang Dong Road

institute: Guangzhou institute of cardiovascular disease

summary: Myocyte enhancer factor 2A (MEF2A) is a crucial transcritional activator which plays diverse roles in the control of cell growth, survival, apoptosis and inflammation etc. To expore the gene expression signature of human coronary artery endothelial cells (HCAEC) in reponse to inhibition of MEF2A， we have employed whole genome microarray expression profiling as a discovery platform to identify genes with important functional role in HCAEC. Three independent groups of HCAEC transfected with MEF2A specific siRNA were separately performed. Three MEF2A specific siRNA groups were indicated as 1527-1, 1527-2 and 1527-3, and the mixed control group was designated as NC.

overall_design: Alteration in gene expression in response to inhibition of MEF2A was measured at 72 hours after transfection with MEF2A specific siRNA and negative control siRNA.

first: Xiong

last: Yujuan

last: Shi-Ming


title: Investigation of downstream genes regulated by ACOT12 in HCC cells


title: RNA-seq analyisis of PUM2 knockout cells

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

institute: EPFL

summary: Expression analysis in HeLa stable cell clones expressing a control shRNA (SCR) or two independent shRNAs targeting PUM2

overall_design: HeLa cells were trasduced with lentivirus expressing SCR, PUM2sh#1 or PUM2#2 and stable clones were selected with puromycin

first: Davide

last: D'Amico


title: Identification of molecular signatures of cystic fibrosis disease status using plasma-based functional genomics

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: The complex milieu of inflammatory mediators associated with many diseases is often too dilute to directly measure in the periphery, necessitating development of more sensitive measurements suitable for mechanistic studies, earlier diagnosis, guiding selection of therapy, and monitoring interventions.  Previously, we determined that plasma of recent-onset (RO) Type 1 diabetes (T1D) patients induce a proinflammatory transcriptional signature in fresh peripheral blood mononuclear cells (PBMC) relative to that of unrelated healthy controls (HC).  Here, using an optimized cryopreserved PBMC-based protocol, we compared the signature found between unrelated healthy controls and non-diabetic cystic fibrosis patients possessing Pseudomonas aeruginosa pulmonary tract infection.

overall_design: UPN727 cells were stimulated with unrelated healthy control (uHC) plasma (n=31), or plasma from patients with cystic fibrosis (CF) possessing Psuedomonas aeruginosa pulmonary tract infection (n=103). Gene expression analysis was perfromed in order to evaluate the transcriptional signature associated with cystic fibrosis.

first: Hara

last: Levy

first: Shuang

last: Jia

first: Aurélien

last: Mazurie

first: Christophe

last: Lambert

first: Melodee

middle: L

last: Nugent

first: Melissa

last: Reske

first: Rachel

last: Bersie

first: Michael

last: Renda

last: Quasney

first: Mary

last: Dahmer

first: Ellis

last: Avner

first: Philip

last: Farrell

first: Pippa

last: Simpson


title: Genome-wide expression analysis of wild type, hda6, hdc1, and hda19 in short day conditions [RNA-seq]

status: Public on Dec 31 2018

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: To investigate how HDC1, HDA6, and HDA19 regulate gene transcription and flowering time in short day conditions, we performed RNA deep sequencing (RNA-seq) to compare the transcriptomes of wild type, hdc1, hda6, and hda19 mutants grown in short day conditions with two biological repeats.

overall_design: Transcriptomes of wild type, hda6, hdc1, and hda19 grown in short day conditions for 18 days were generated by deep sequencing, using Illumina HiSeqXTen.

first: Yongqiang

last: Ning

first: Rongnan

last: Lin

first: Xinjian


title: Assessing the effect of SUPT4H1 RNAi on the transcription of a repeat-containing reporter construct

city: South San Francisco

first: Thomas

last: Sandmann

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: SUPT4H1 is a transcription elongation factor comprising part of the RNA polymerase II complex. Recent studies propose a selective role for SUPT4H1 in transcription of repeat-containing transcripts, the translated products of which are a hallmark of neurodegeneration in disorders such as Huntington’s Disease and C9orf72-amyotrophic lateral sclerosis. To investigate the potential of SUPT4H1 as a therapeutic target in repeat-associated neurodegeneration, we engineered a reporter containing 71 hexanucleotide repeats (HNRs) encoding for pDi-amino acid repeats (DARPs) fused to EGFP. To approximate endogenous expression levels, the reporter also incorporated human C9orf72 intronic DNA immediately 5' of the hexanucleotide repeats. The reporter construct was integrated into the genome of HEK293t cells. We assessed the effect of depleting SUPT4H1 by RNAi interference on the transcriptome as a whole and on the DARP-EGFP reporter.

overall_design: HEK293 cells stably expressing the intron-DARP-EGFP reporter were transfected with pools of siRNAs targeting SUPT4H1 or with scrambled control siRNAs. Starting from the same culture, six independent transfections were performed for each treatment side by side. A 3'-end tag library was generated using the Quant-seq (Lexigen) 3'-polyA library preparation kit and analyzed by Illumina sequencing.

first: Adam

last: Naguib

first: William

last: Dowdle

first: Joe

last: Lewcock


title: Deep single-cell RNAseq of Gpnmb+Clec7a+ microglia from postnatal day 7 cerebellum

city: Stanford

first: Qingyun

last: Li

state: CA

address: 299 Campus Drive

department: Neurobiology

summary: We generated single-cell RNAseq profiles of 143 microglia, sorted in the gate CD45lowCD11+Gpnmb+Clec7a+, from postnatal day 7 cerebellum to validate the newly identified “proliferative region-associated microglia (PAM)” (Gpnmb and Clec7a are PAM surface markers). Single cells were FACS index sorted followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). These cells showed characteristic PAM gene expression and clustered together with other PAM cells sequenced in the same study.

overall_design: Single microglia were FACS sorted from pooled male animal samples (C57BL/6N) into 96-well plates. Libraries were prepared with a semi-automated Smart-seq2 protocol. All 143 cells passed the three QC criteria (Y=passed).

first: Ben

last: Barres


title: Global effects of SUPT4H1 RNAi on gene expression of HEK293 cells

summary: SUPT4H1 is a transcription elongation factor comprising part of the RNA polymerase II complex. Recent studies propose a selective role for SUPT4H1 in transcription of repeat-containing transcripts; the translated products of which being a hallmark of neurodegeneration in disorders such as Huntington’s Disease and C9orf72-amyotrophic lateral sclerosis. To investigate the potential of SUPT4H1 as a therapeutic target in repeat-associated neurodegeneration, we depleted SUPT4H1 by RNA interference in order to mimic pharmacological loss of function. Using RNA sequencing we assessed SUPT4H1-knockdown induced changes is both immortalized cells (HEK293t) as well as primary human fibroblasts. Diminished SUPT4H1 leads to a global reduction in cellular RNA.

overall_design: siRNA-mediated knockdown of SUPT4H1 in HEK293 cells was performed.  Control experiments (HEK293 treatment with non-targeting siRNA) was compared to knockdown conditions for the assessement of global modulatory effects on cell RNA abundances after SUPT4H1 depletion. Ribosomal RNA was depleted before library preparation using Illumina's RiboZero Gold kit.  Three disitnct clonal cell lines were engineered and assayed: one expressing EGFP (control) and two expressing di-amino acid (DARP) repeats, fused to EGFP.  DARPs were encoded by an array of 71 G4C2 repeats as a model of C9orf72 ALS.


title: Expression data from bovine bone-marrow derived MSCs following preconditioning (hypoxia and/or transforming growth factor-beta (TGF-β))

first: Lachlan

middle: James

last: Smith

state: Pennsylvania

address: 371 Stemmler Hall, 3450 Hamilton Walk

department: Department of Orthopaedic Surgery

institute: University of Pennsylvania

summary:
The innate repair and regeneration potential of skeletal tissues such as the intervertebral disc and articular cartilage is extremely limited, in part due to their avascularity and low cell density. Despite recent advances in MSC-based disc and cartilage regeneration, key challenges remain, including the sensitivity of these cells to in vivo microenvironmental stress such as low oxygen and nutrient levels. The objective of this study was to investigate whether preconditioning with hypoxia and/or transforming growth factor-beta (TGF-β) can enhance MSC survival and extracellular matrix production in a low oxygen and nutrient-limited microenvironment. Secondarily, the effects of donor variability on the response of MSCs to preconditioning was examined. MSCs from multiple bovine donors were preconditioned in monolayer in normoxia or hypoxia, with or without TGF-β.
The effects of preconditioning on MSC gene expression during monolayer expansion were examined using microarrays.

overall_design: Bone marrow-derived MSCs were isolated from juvenile (age < 6 months) bovine femurs and tibiae. Following the initial isolation, MSCs were expanded to confluence through a single initial passage in standard tissue culture conditions with normal oxygen tension (atmospheric, 21% O2), 5% CO2, in basal medium comprised of high glucose (4.5 g/L) Dulbecco’s Modified Eagle medium (DMEM; ThermoFisher Scientific; Waltham, MA), 10% fetal bovine serum (FBS; ThermoFisher Scientific; Waltham, MA), and 1% penicillin, streptomycin, and fungizone (PSF; ThermoFisher Scientific; Waltham, MA). Following primary expansion and preconditioning (n = 3 donors/biological replicates x 4 expansion conditions for a total of 12 samples), MSCs were harvested and RNA was isolated from each samples. The quality of each RNA sample (RIN > 9) was verified using an Agilent BioAnalyzer and RNA 6000 Pico Kit (Agilent; Santa Clara, CA). Global gene expression was measured using the WTPlus Bovine Gene Chip (Affymetrix, Santa Clara, CA). Gene expression data were normalized using Robust Multi-array Average (Irizarry et al., 2003) and adjusted for false discovery rate to generate adjusted p-values.

first: Sun

middle: H

last: Peck

first: Justin

last: Bendigo

first: John

last: Tobias

first: George

last: Dodge

first: Robert

last: Mauck

first: Neil

last: Malhotra


title: Deep single-cell RNAseq of postnatal day 7 microglia from wild type and Trem2 knockout brains

summary: We generated single-cell RNAseq profiles of 369 microglia (183 from wild type and 186 from Trem2 knock-out), sorted in the gate CD45lowCD11+ or CD45lowCD11+Gpnmb+Clec7a+ (PAM enrichment), to compare gene expression of wild type vs. Trem2 knock-out microglia on the postnatal day 7. Single cells were FACS index sorted from the whole brain followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). A total of 334 cells passed quality control for data analysis. Microglia in the Trem2 knock-out contained a similar PAM population with characteristic gene expression, suggesting that the presence of early postnatal PAM do not depend on TREM2.

overall_design: Single microglia were FACS sorted from male animals (C57BL/6J background) into 96-well plates. Libraries were prepared with a semi-automated Smart-seq2 protocol. Three QC criteria were used (Y=passed, N=not passed), and only cells that passed all three criteria were used for downstream analysis.


title: Bulk RNA-seq of adult homeostatic microglia from 4 brain regions

summary: To compare microglial regional heterogeneity, we generated bulk RNA-seq profiles of postnatal day 60 microglia, sorted by TMEM119+ (also CD45lowCD11b+), from cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR) regions. For each sample, 3000 microglia were FACS sorted into RLT lysis buffer for total RNA extraction, followed by Smart-seq library preparation and Illumina Nextseq (sequence depth 10-20 million per sample). Consistent with our scRNA-seq data, samples from 4 regions were highly correlated (R>0.99), and individual samples did not cluster according to tissue origins, suggesting striking similarities between homeostatic microglia from different brain regions. Moreover, we could not detect any differentially expressed genes (FDR < 0.05) between regions from the bulk samples. These data suggest that classical adult microglia with homeostatic signatures (e.g. Tmem119), as the most dominant microglial population in the healthy brain, have little transcriptomic heterogeneity across brain regions.

overall_design: TMEM119+ microglia (3000 cells each sample) from a given region were FACS sorted from pooled male animal samples (C57BL/6N) into RLT lysis buffer in Eppendorf tubes. Three replicates were done for each region. Libraries were prepared following the Smart-seq protocol (v4 ultra low input RNA kit). All samples were barcoded and pooled together for Illumina Nextseq sequencing.


title: Micro-RNA expression profiles in upper tract urothelial carcinoma differentiate stage and tumor progression

city: Burlington

first: Travis

last: Sullivan

state: MA

address: 41 Mall Rd.

institute: Lahey Hospital & Medical Center

type:
Other
Non-coding RNA profiling by array

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Expression data from CCR2+ and CCR2-  splenic marophages from C57BL6 mouse infected with Listeria Monocytogenes in vivo on day3

first: xiaoqing

last: xu

address: No.5 Dongdan Santiao, Dongcheng District

department: Immunology

institute: Chinese Academy of Medical Sciences

summary: We used microarrays to detail the global gene expression in CCR2+ and CCR2- spenic macrophages (SM) sorted from  C57BL6 mouse infected with Listeria Monocytogenes in vivo on day3

overall_design: CCR2+ and CCR2- spenic macrophages sorted from  the spleen of  C57BL6 mouse infected with Listeria Monocytogenes in vivo on day3   were for RNA extraction and hybridization on Affymetrix microarrays.

first: Xiaoqing

last: Xu

first: Yanmei

last: Han

first: Xujia

last: Xue

first: Tao

last: Cao


title: Micro-RNA expression profiles in upper tract urothelial carcinoma differentiate stage and tumor progression: secondary data set

summary:
Accurate grading and staging of upper tract urothelial carcinoma (UTUC) often proves challenging, and improved knowledge of tumor biology could identify patients who are candidates for minimally invasive therapy rather than nephroureterectomy (NU).  Total RNA was extracted from formalin-fixed, paraffin-embedded NU samples.  Thirty-five samples with diverse pathologies were selected and screened via microRNA RT-qPCR array for 752 unique miRNA. Validation of differentially expressed miRNA was performed on 123 additional NU tissue specimens from two institutions.
The data presented in this series are for the 123 samples analyzed in the validation analysis.  The data were normalized to the average of the insignificant control miRNA detected in all samples: miR-125b-5p and miR-185-5p, which were selected from the screening array dataset using NormFinder©.

overall_design: FFPE nephroureterectomy specimens from 158 patients were analyzed for microRNA expression. 35 of these specimens were initially screened for 752 microRNA.  The candidate microRNA identified in the screening analysis were tested on the remaining 123 samples.  In an effort to develop a diagnostic model, samples in the secondary set were randomly assigned to either a training set to verify miRNA with differential expression, or a validation set to access the diagnostic capability of the training set miRNA signature.  Each sample was only assigned to one of the testing groups.  All microRNA levels were measured using RT-qPCR.  Each of the microRNA tested in the screening analysis were measured once per samples (a single well), whereas the microRNA levels were measured in triplicate for the 123 samples of the secondary analysis.

first: Brendan

last: Browne


title: Developmental heterogeneity of microglia and brain myeloid cells revealed by deep single-cell RNA sequencing

institute: Stanford University


title: Bcl9 and Pygo synergize downstream of Apc to effect intestinal neoplasia in mouse models recapitulating Familial Adenomatous Polyposis (Illumina Beadchip)

city: Cambridge

first: Laurens

middle: Moore

last: van Tienen

state: Cambridgeshire

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

summary: Bcl9 and Pygo function within the Wnt enhanceosome to effect β-catenin-dependent transcription. Whether they also mediate β-catenin-dependent neoplasia is unclear. Here we assess their roles in intestinal tumorigenesis initiated by Apc loss-of-function (ApcMin). Gene expression profiling revealed that loss-of-Bcl9 synergizes with loss-of-Pygo to shift gene expression within Apc-mutant adenomas from stem cell-like to differentiation along Notch-regulated secretory lineages.

overall_design: Total RNA was isolated from EDTA-dissociated crypt epithelium or intestinal ApcMin adenomas of wild type (wt), Bcl9/B9l double knockout (DKO), Pygo 1/2 DKO, or Bcl9/B9l & Pygo 1/2 quadruple knockout (QKO) mice, and analysed for differential gene expression using Illumina MouseWG-6 v2.0 expression beadchips.

first: Ashraf

last: Ibrahim

first: Mariann

last: Bienz


title: lncRNA LINC00844 regulates prostste cancer cell migration and invasion through AR signaling

city: Macau

first: Edwin

last: Cheung

state: Macau

address: Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

summary: The majority of the human genome is transcribed, yielding a rich repository of non-coding transcripts that are involved in a myriad of biological processes including cancer. However, how non-coding transcripts such as Long Non-coding RNAs (lncRNAs) function in prostate cancer is still unclear. In this study, we have identified a novel set of clinically relevant androgen-regulated lncRNAs in prostate cancer. Among this group, we found LINC00844 is a direct androgen regulated target that is actively transcribed in AR-dependent prostate cancer cells. In clinical analysis, the expression of LINC00844 is higher in normal prostate compared to malignant and metastatic prostate cancer samples and patients with low expression demonstrate poor prognosis and significantly increased biochemical recurrence suggesting LINC00844 may function in suppressing tumor progression and metastasis. From in-vitro loss-of-function studies, we showed LINC00844 prevents prostate cancer cell migration and invasion. Moreover, in gene expression studies we demonstrate LINC00844 functions in trans, affecting global androgen-regulated gene transcription. Mechanistically, we provide evidence to show LINC00844 is important in facilitating AR binding to the chromatin. Finally, we showed LINC00844 mediates its phenotypic effects in part by activating the expression of NDRG1, a crucial cancer metastasis suppressor. Collectively, our findings indicate LINC00844 is a novel coregulator of AR that plays an important role in the androgen transcriptional network and the development and progression of prostate cancer.

overall_design: Microarray analysis in LNCaP cells treated with siControl (NC) or siLINC00844#1 and #4 and stimulated with 10nM of DHT or vehicle control for 12 hours. All the experiments are performed in triplicates.


title: Deep single-cell RNAseq of microglia and brain myeloid cells from various brain regions and developmental stages

first: Qingyun

last: Li

summary: We generated single-cell RNAseq profiles of microglia and brain myeloid cells (1922 total; 1816 cells passed quality control) from different developmental stages (E14.5, P7 and P60) to study their heterogeneity. Cells were isolated from either the whole developing brain (for the E14.5 stage) or six separate regions (for P7 and P60 stages): Cortex (CTX), Cerebellum (CB), Hippocampus (HIP), Striatum (STR), Olfactory bulb (OB), Choroid plexus (CP). Single cells were FACS index sorted followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). All 1816 cells were grouped into 15 clusters using Seurat package (Macosko, Basu, Satija et al. Cell. 2015), and manually annotated based on gene expression signatures and meta data. We found that the majority of adult microglia expressing homeostatic genes are remarkably similar in transcriptomes, regardless of brain region. By contrast, postnatal microglia represent a more heterogeneous population. We discovered a proliferative region-associated microglia (PAM) subset, mainly found in developing white matter, that share a characteristic gene signature with degenerative disease-associated microglia (DAM). Such PAM have amoeboid morphology, are metabolically active, and phagocytose newly formed oligodendrocytes. This scRNA-seq atlas will be a valuable resource for dissecting innate immune functions in health and disease.

overall_design: Single microglia or myeloid cells from a given time point and region were FACS sorted from pooled male animal samples (C57BL/6N) into 96-well plates. Libraries were prepared with a semi-automated Smart-seq2 protocol. Each Nextseq sequencing run was done by pooling ~350 cells with the unique Illumina 384 indexes. Three QC criteria were used (Y=passed, N=not passed), and only cells that passed all three criteria were used for downstream analysis.

first: Ben

last: Barres


title: ChIP-seq and RNA-seq from human lymphoma cell lines

city: Lausanne

first: Giovanni

last: Ciriello

address: Rue du Bugnon 27

department: Department of Computational Biology

institute: University of Lausanne


title: Achilles-mediated and sex-specific regulation of circadian mRNA rhythms in Drosophila

city: Saint Louis

first: Jiajia

state: MO

address: 9952 CSRB, 4939 Children's Place.

department: Department of Medicine

institute: Washington University in St. Louis

summary: The circadian clock is an evolutionarily conserved mechanism that drives rhythmic expression of downstream genes. The core circadian clock drives the expression of clock-controlled genes either directly or indirectly, which in turn play critical roles in carrying out many rhythmic physiological processes. Nevertheless, the molecular mechanisms by which clock output genes orchestrate rhythmic signals from the brain to peripheral tissues are largely unknown. Here we explored the role of one rhythmic gene, Achilles, in regulating the rhythmic transcriptome in fly heads. Achilles is a clock-controlled gene in Drosophila that encodes a putative RNA-binding protein. Achilles expression is not detectable in core clock neurons using in-situ hybridization, although its expression is found in neurons throughout the fly brain. Together, these observations argue against a role for Achilles in regulating the core clock. To assess its impact on circadian mRNA rhythms, we performed RNA sequencing (RNAseq) to compare the rhythmic transcriptomes of control flies and those with diminished Achilles expression in all neurons. Consistent with previous observations, we observe dramatic upregulation of immune response genes upon knock-down of Achilles. Furthermore, a subset of circadian mRNAs lose their rhythmicity in Achilles knock-down flies, suggesting that a subset of the rhythmic transcriptome is regulated either directly or indirectly by Achilles. These Achilles-mediated rhythms include many genes involved in immune function and neuronal signaling such as Prosap, Nemy and Jhl-21. Comparison of RNAseq data from control flies reveal that only 42.7% of clock-controlled genes in the fly brain are rhythmic in both males and females. As mRNA rhythms of core clock genes are largely invariant between the sexes, this observation suggests that sex-specific mechanisms are an important, and heretofore under-appreciated, regulator of the rhythmic transcriptome.

overall_design: Achl RNAi and control flies; male and female; 96 samples with no replicates in total. 7-8 heads per sample, sampled every 2 hours for 2 days.

first: Michael

last: Hughes


title: Post-developmental deletion of adipocytes autophagy

city: Slat Lake City

first: Sihem

last: Boudina

institute: University of Utah

summary: Autophagy is a homeostatic cellular process involved in the degradation of long-lived/damaged cellular components. The role of autophagy in adipogenesis is well recognized, but its role in mature adipocyte function is largely unknown.  We show that the autophagy proteins Atg3 and Atg16L1 are required for proper mitochondrial function in mature adipocytes. In contrast to previous studies, we found that post-developmental ablation of autophagy causes peripheral insulin resistance independently of diet or adiposity. Finally, lack of adipocyte autophagy reveals a - cross talk between fat and liver mediated by lipid peroxide-induced Nrf2 signaling. Our data reveal a - role for autophagy in preventing lipid peroxide formation and their transfer in insulin-sensitive peripheral tissues

overall_design: Epididymal adipose tissue from 4 WT and 4 Adiponectin-Cre Atg3f/f male mice fed chow diet

first: Jinjin

last: Cai

first: Karla

last: Pires

first: Maroua

last: Ferhat

first: Bhagirath

last: Chaurasia

first: Márcio

last: Buffolo

first: Rana

last: Smalling

first: Ashot

last: Sargsyan

first: Donald

last: Atkinson

first: Scott

last: Summers

first: Timothy

last: Graham


title: Homoharringtonine deregulates MYC transcriptional expression by directly binding NF-κB repressing factor

city: SHANGHAI

first: Xinjie

last: Chen

state: SHANGHAI

address: RUIJIN ER ROAD

institute: Shanghai Institute of Hematology

summary: Homoharringtonine (HHT), a previously known protein synthesis inhibitor, has anti-myeloid leukemia effect and potentiates the therapeutic efficacy of anthracycline/cytarabine induction regimens for acute myeloid leukemia (AML) with favorable and intermediate prognosis, especially in t(8;21) subtype. Here we provide evidence to show that HHT inhibits the activity of leukemia-initiating cells (Lin-/Sca-1-/c-kit+, LICs) in t(8;21) murine leukemia model and exerts down-regulating effect on MYC pathway genes in human t(8;21) leukemia cells (Kasumi-1). By using biochemistry approach, NF-κB-repressing factor (NKRF) was discovered to be bound directly by HHT via the second double-strand RNA binding motif (DSRM2) domain, which is the nuclear localization signal (NLS) of NKRF. A series of deletion and mutagenesis experiments mapped HHT direct binding site to K479 and C480 amino acids in the DSRM2 domain. HHT treatment shifts NKRF from nucleus (including nucleoli) to cytoplasm through occupying the DSRM2 domain, strengthens p65-NKRF interaction, and interferes with the p65-p50 complex formation, thereby attenuating the transactivation activity of p65 on MYC gene. Moreover, HHT significantly decreases the expression of KIT, a frequently mutated and/or highly expressed gene in t(8;21) AML, in consistence with MYC downregulation. Our work has thus identified a mechanism different to, but in concert with, the classical mode of action of HHT and justifies its further clinical exploration in the treatment of AML.

overall_design: Kasumi-1 cells vehicle; Kasumi-1 cells treated with 20 nM HHT for 24h

first: Xin-Jie

last: CHEN

first: Wei-Na

last: ZHANG

first: Bing

first: Wen-Da

last: XI

first: Ying

last: LU

first: Jin-Yan

last: HUANG

first: Yue-Ying

last: WANG

first: Jun

last: LONG

first: Song-Fang

last: WU

first: Yun-Xiang

first: Shu

first: Si-Xing

last: LI

first: Tong

last: YIN

first: Min

first: Xiao-Dong

first: Jun-Min

first: Kan-Kan

first: Zhu

first: Sai-Juan


title: Expression data from mouse adrenal glands extracted from wild-type and sf1:Cre; Ezh2 Fl/Fl (KO) adrenals

city: Aubiere

first: Pierre

last: Val

address: 24 avenue des Landais

institute: CNRS

summary:
Ezh2 encodes the catalytic subunit of the polycomb repressive complex 2 epigenetic regulator. Its ablation in the adrenal cortex results in profound alterations of adrenal homeostasis.
We used microarrays to analyse gene expression in response to Ezh2 gene ablation.

overall_design: Adrenal glands were dissected from KO (4) and wild-type littermate (3) 2-month-old female mice.


title: AGO2-IP after miR-941 overexpression

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: miRNA sponge, a special class of miRNA target,  has been emerging as a pivotal player in miRNA mediated regulatory network. Currently, the identified miRNA sponge genes mostly act on sequestering conserved miRNAs (e.g. miR-7, miR-145), however, the existence, potential function and evolutionary process of miRNA sponge genes for species-specific miRNA, especially for human specific miRNA, are largely unknown. In this study, we conducted a systematic analysis including sponge gene identification and subsequent function and evolutionary analyses for an authentic human-specific miRNA, miR-941.

overall_design: Ago2 Immunoprecipitation (Ago2-IP) experiments after miR-941 overexpression were conducted in 293T cell line.

first: Zheng

last: Yan

first: Philipp

last: Khaitovich


title: lncRNA LINC00844 regulates prostate cancer cell migration and invasion through AR signaling [ChIP-seq]

first: Edwin

last: Cheung

overall_design: AR ChIP-seq in LNCaP cells treated with siControl (NC) or siLINC00844#1 and #4 and stimulated with 100nM of DHT or vehicle control for 2 hours. All the experiments are performed in duplicates.


title: Profiling and bioinformatics analyses reveal differential expression of circular RNA in tongue cancer revealed by high-throughput sequencing

city: Nantong

first: hao

last: wu

state: Jiangsu

address: XiSi Road,No.20

institute: Affiated hospital of nantong unversity

summary: Circular RNAs (circRNA) are special non-coding RNAs. They are widely present, but with unknown functions. Recent studies have shown that many endogenous circRNAs have sponge function to absorb microRNAs. They can regulate target gene mRNA expression and play important roles in many biological processes. However, expression profile and function of circRNAs in human TSCC haven’t been reported. High-throughput sequencing was performed to identify and annotate from three TSCC tissues and adjacent tissues. A separate set (n=20) of human TSCCs and corresponding adjacent tissues were subjected to RT-PCR for validation of circular RNAs expression profile. GO functional analysis, KEGG pathway analysis, and circRNA–microRNA network analysis were also performed to predict the function of circRNA in TSCC.A total of 12,156 circRNAs were identified and annotated, most of the circRNAs were novel (n=6,231) and exonic (62.09%). Statistical analysis revealed 322 differentially expressed (DE) circRNAs. RT-PCR results showed that circRNA expression in TSCC was higher than that in adjacent tissues. GO functional analysis, KEGG pathway analysis, and circRNA–microRNA network analysis all showed that circRNAs correlated with tumor development and progression to a certain extent. The present study is the first to systematically characterize and annotate circRNA expression in TSCC, the majority were novel circRNAs. Some host genes of the DE circRNAs were involved in tumor signaling pathway and had complicated correlations with tumor-relevant microRNAs, indicating that circRNAs might be promoted development and progression of  TSCC.

first: Hao

last: Wu

first: Qingwen

first: Xiaoxia

last: Qiu

first: Ke

last: Xu


title: Dissection of CD20 regulation in lymphoma using RNAi

city: Heidelberg

first: Mikolaj

last: Slabicki

address: Im Neuenheimer Feld 460

department: Deptartment of Translational Oncology

institute: German Cancer Research Center

summary: mRNA levels after MS4A1, CREM, MBD2 and NTC knockdown

overall_design: Raji cells were infected with indicated shRNAs, selected with puromycin for 48h and total RNA samples were harvested 3 days post-transduction.

first: Mikołaj

last: Słabicki


title: Investigation of downstream genes regulated by ACOT12 in HCC cells [MHCC97H]

city: Shanghai

first: Ming

last: Lu

address: No. 12, Middle Urumqi Road

institute: Fudan university

summary: MHCC97H cell, a human hepatocellular carcinoma (HCC) cell line, was stably overexpressed with empty vector, ACOT12, or ACOT12(RR312,313EE) mutant (ACOT12m). These cells were then used for gene expression profiles analysis.

overall_design: In the study presented here, to investigation of downstream genes regulated by ACOT12 in HCC cells, MHCC97H cells were stably overexpressed with empty vector, ACOT12, or ACOT12 mutant (ACOT12m). These stable cells were obtained by puromycin selection for 1 week. After validations by western boltting and other functional assays, these cells were then used for gene expression profiles analysis.


title: Next-generation sequence analysis for transcriptome of Drosophila melanogaster third instar larval eye discs expressing sevenless-GAL4 directed down or up regulated levels of hsromega lncRNAs levels

city: varanasi

first: subhas chandra

last: lakhotia

state: uttar pradesh

address: cytogenetics lab, department of Zoology BHU

department: Department of Zoology

country: India

institute: Brown University

summary:
Purpose: To compare transcriptomic changes in 3rd instar larval eye discs following sev-GAL4 driven down- or up- regulation of hsrω lncRNAs.
Method: Eye disc total RNA profiles of wandering late third instar larvae of sev-GAL4>UAS-GFP, sev-GAL4>UAS-hsrωRNAi, sev-GAL4>EP3037 were generated by sequencing, in duplicate, using Illumina Hiseq2500 platform using 50bp pair-end reads, 6 samples per lane and each sample run across 2 lanes. This resulted in a sequencing depth of ~20 million reads. The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012).
Result: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the Drosophila genome (dm6) and identified 15,905 transcripts with TopHat workflow in each genotypes studied. The sev-GAL4 driven expression of RNAi for hsromega gene transcripts in eye discs resulted in differential expression of many genes, with 409 genes being down-regulated and 100 up-regulated, when compared with those in sev-GAL4>UAS-GFP eye discs. Compared to control eye discs in case of up regulation of hsrω RNA, 66 gene were up-regulated while 635 were down-regulated. Some of these (11 genes) were validated using qRT-PCR.
Conclusion: Analysis of RNA-seq data revealed that a large proportion of transcripts were indeed similarly affected by down- or up-regulation of hsrω RNA in normal as well as activated Ras expression background. A comparison of transcriptomes of sev-GAL4>hsrωRNAi and sev-GAL4>EP3037 eye discs revealed that in each case the number of genes down regulated was more than those up-regulated. Interestingly, while 319 genes were commonly down regulated and 15 were commonly up-regulated in the two genotypes, only 2 genes showed opposing trends between sev-GAL4>UAS-hsrωRNAi and sev-GAL4>EP3037 eye discs.

overall_design: Eye discs mRNA profiles of wandering late third instar larvae of sev-GAL4>UAS-GFP, sev-GAL4>UAS-hsrωRNAi and sev-GAL4>EP3037 third instar larvae were generated by sequencing, in duplicate, using Illumina Hiseq2500 platform.

first: Subhash

last: Lakhotia

first: Mukulika

last: Ray


title: Single-cell RNA sequencing of E12.5 mouse thalamus

city: Farmington

first: James

middle: YH

last: Li

state: CT

address: 263 Farmington Ave

department: Genetics and Genome Sciences

institute: UCHC

summary: In this study we performed single-cell sequencing of E12.5 mouse diencephalon revealing different newly generated neurons and their associated molecular features.

overall_design: Design: Single-cell suspensions were prepared using Accumax digestion followed by manual trituration using a Pasteur pipette. Cells were processed with the 10X Genomics Chromium Single Cell Kit Version 1


title: IMP2 increases mouse skeletal muscle mass and voluntary activity by enhancing autocrine IGF2 production and optimizing muscle metabolism

city: Boston

first: Ning

last: Dai

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: The Igf2 mRNA binding protein2/Imp2 was selectively deleted from adult mouse muscle; two phenotypes were observed: modestly decreased accrual of skeletal muscle mass after weaning and reduced wheel running activity but normal forced treadmill performance. Reduced voluntary activity occurs when fed a high fat diet but is normalized when consuming standard chow. The reduced muscle mass is due to diminished autocrine Igf2 production, reduced Akt1 activation, disinhibition of Gsk3α and reduced protein synthesis, without altered mTOR complex1 activity. The diet-dependent reduction in spontaneous exercise is accompanied by suboptimal muscle fatty acid oxidation, caused by reduced PPARα mRNA and protein, the former an Imp2 client. Nevertheless, in contrast to global Imp2 deficiency, muscle specific Imp2 inactivation does not alter glucose tolerance or the hypoglycemic effect of insulin. Imp2 deficiency in skeletal muscle reduces autocrine production of Igf2 and fiber growth and disorders nutrient metabolism so as to reduce voluntary physical activity.

overall_design: The function of IMP2 in adult muscle has been investigated by creating the IMP2 muscle specific knockout mice. The metabolism of these mice at the whole body level, cellular lever, molecular level have been studied.

first: Laura

last: Regue

first: Fei

last: Ji

first: Daniel

last: Flicker

first: Dana

last: Kramer

first: William

last: Pierce

first: Teekhon

last: Davidoff

first: Jeffrey

last: Widrick

first: Nicholas

last: Houstis

first: Liliana

last: Minichiello

first: Joseph

last: Avruch


title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome

city: Davis

first: Hong

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

type: Methylation profiling by genome tiling array

summary: Genomewide DNA methylation profiling of saline, diesel exhaust particiles and house dust mite treated human airway epithelial cells. Methylation profiles were generated by the Illumina Infinium MethylationEPIC beadchips.

overall_design: Human bronchial epithelial cells were treated with PBS, diesel exhaust particles (5ug/cm2), and house dust mite (25ug/ml) for 24 hours. Genomic DNA were extracted and treated with or without oxidation following the TrueMethyl® protocol (NuGen) followed by bisulifte conversion before being hybridized to the Illumina Infinium MethylationEPIC beadchips

first: Xue

last: Zhang


title: Genome-wide analysis of wild type, hda6, hdc1, and hda19 in short and long day conditions

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

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

overall_design: Refer to individual Series


title: Expression data from roots of WT and bts-3 plants exposed to either Fe sufficient or Fe deficient conditions for 72 hours

city: Hanover

first: Maria

middle: Noelle

last: Hindt

state: NH

address: 78 College St. Rm 130 HB6044

department: Biology

institute: Dartmouth College

summary:
We wanted to understand at what level BTS acts, i.e. how upstream BTS acts and if BTS misregulation affets only a subset or multiple subsets of Fe regulated genes.  We studied WT and bts-3 mutant roots.
Using microarray analysis, we demonstrated that bts-3 has a consitutitive expression of Fe deficiency response in root.

overall_design: RNA was harvested from root tissues from WT and bts-3 plants grown on B5 for 2 weeks and then transferred to either +Fe or -Fe medium for 3 days. Two biological replicates per condition were used for WT and 3 biological replicates were used for bts-3.

middle: N

first: Mary

last: Guerinot


title: Effect of the Freund's adjuvant on E. tarda FKC vaccination

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

country: Japan

institute: Tokyo University of Marine Science and Technology

summary: Interferon gamma expression was modulated by FCA.

overall_design: Fish were treated with FKC or FKC mixed with FCA and isolation of total RNA from spleen of the fish at 6 hours and 3days after the treatment.

first: Seangmin

last: Chung

first: Ikuo

last: Hirono


title: The effects of AAV-VEGF-B and deletion of endothelial VEGFR1 on heart transcriptome in adult mice

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

summary: We evaluated the effects of vascular endothelial growth factor -B (VEGF-B) and the deletion of its receptor VEGFR1 from endothelial cells on cardiac hypertrophy. Whole-genome transcriptomic analysis showed that overexpression of the ligand had similar effects on the heart transcriptome as deletion of its receptor. Both treatments also induced angiogenesis and mild cardiac hypertrophy. The aim of the study was to identify pathways, which mediate angiogenesis-induced cardiac hypertrophy.

overall_design: 3 wt mice treated with AAV-Scramble, 3 EC-specific VEGFR1 deleted mice with AAV-Scramble, 2 wt mice treated with AAV-VEGF-B, 4 EC-specific VEGFR1 deleted mice treated with AAV-VEGF-B

first: Kari

last: Alitalo


title: Differences in Shewanella algae C6G3 transcriptomes according to nature of electron acceptor (MnIV/NO3)

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

summary: Shewanella algae C6G3 can conduct dissimilative nitrate reduction into ammonium and MnIV reduction. This bacteria have the unusual ability to produce anaerobically nitrite from ammonium in the presence of MnIV. This property may explain NO2/3- accumulation observed in some anaerobic zones of marine sediments. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing with lactate and ammonium as carbon and nitrogen sources and with MnIV or nitrate as electron acceptors. Genes exhibiting higher expression levels in the presence of MnIV belonged to functional categories of carbohydrate, coenzyme, lipid metabolisms and inorganic ion transport. Furthermore, comparative transcriptomic pattern between MnIV and NO3 revealed that the strain presented an ammonium limitation status with MnIV, despite the presence of identical and non-limiting concentration of ammonium in both culture conditions. Regulators ntrB/nrtC, ammonium channel, nitrogen regulatory protein P-II, glutamine synthetase and asparagine synthetase glutamine dependent genes were over-expressed. In nitrate condition, genes involved in synthesis of several amino acids were over expressed. Among the genes associated with the stress response, Kat E was highly expressed particularly under manganese condition

overall_design: Study of Shewanella algae C6G3 Transcriptome in 2  growth conditions: with nitrate as electron acceptor (nitrate reduction into ammonium) and Mn-oxide  (MnIV reduction into MnII). All these cultures have been processed in duplicate.

first: Axel

last: Aigle

first: Patricia

last: Bonin

first: Nicolas

last: Fernandez -Nuñez

first: Béatrice

last: Loriod

first: Sophie

last: Guasco

first: Aurélie

first: Fabrice

last: Armougom

first: Chantal

last: Iobbi-Nivol

first: Jean

last: Imbert

first: Valérie

last: Michotey


title: A serum-induced transcriptome and serum cytokine signature obtained at diagnosis correlates with the development of early pancreatic ductal adenocarcinoma metastasis

city: Milwaukee

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Immune indicators of PDAC progression were obtained from peripheral blood and analyzed in the context of each other by calculating a serum-induced transcriptome index and a serum cytokine index. Significant correlation of the transcriptome index with the inflammatory transcriptome index suggest that inflammtion has a role in PDAC progression. The segregation of   metastatic progressed and not progressed patients when the inflammatory transcriptome index was analyzed in the context of the serum cytokine index suggest that the serum cytokine index may be a systemic biomarker of PDAC progression . Our data illustrates both the transcriptome and cytokine indices have promise as biomarkers of cancer immunity.

overall_design: For the transcriptome analysis, baseline (at diagnosis and before treatment) serum from patients with radiographic evidence of PDAC metastasis (i.e. progressed) and serum from patients without PDAC progression was incubated over peripheral blood mononuclear cells (PBMC) obtained from a normal donor. PBMC cRNA was hybridized to the GeneChip Human Genome U133 plus 2.0 array. Image data were analyzed with Affymetrix Expression Console 1.1.2 software and normalized using Partek Genomics Suite 6.5 to determine signal log intensities/ratios. The statistical significance of differential gene expression and false discovery rates (FDR) was determined through using RankProd Package in Bioconductor (www.bioconductor.org). Hierarchical clustering was conducted with Genesis.

first: Susan

last: Tsai

first: A

last: Mackinnon

first: Bryon

last: Johnson

first: Shuang

last: Jia

first: Mary

last: Kaldunski

first: Mohammed

last: Aldakkak

first: Jenny

last: Grewal

first: Laura

last: McOlash

first: Katie

last: Palen

first: Jill

last: Gershan


title: Genome-wide  analysis of P8 sciatic nerve gene expression of control, Maf mutant and ErbB2 mutant mice

first: Hagen

last: Wende

address: Im Neuenheimer Feld 366

department: Institute of Pharmacology

institute: Heidelberg University

summary: Analysis of genes regulated by Maf and donwstream of ErbB2 in P8 Schwann cells

overall_design: Total RNA from sciativ nerves of P8 control mice was compared to P8 Maf mutant mice and ErbB2 mutant mice

first: Carmen

last: Birchmeier


title: Fission yeast telomeres are packaged into a non-canonical histone-containing chromatin structure dependent on Shelterin and RNA.

city: London

first: Jessica

last: Greenwood

address: 1 Midland Rd

institute: The Francis Crick Institute

summary: Yeast telomeres exist in a distinct protected structure at the chromsome end.  This structure, termed the telosome, has long been thought to be free of histones.  Here we show that this is not the case - telomere repeats are indeed associated with histones.  This finding has implications for telomere function and ultrastructure.

overall_design: ChIP-Seq analysis of H3K9Me2 in Schizosaccharomyces pombe.  2 biological replicates of 1 L wild-type cells grown in YE4S to OD600=0.6 cells used per replicate, crosslinked in formaldehyde.  ChIP carried out with antibodies to H3K9Me2, input and IP DNA purified was purified and processed for sequencing.

first: J

first: H

last: Patel

first: T

last: Cech

middle: P

last: Cooper


title: mRNA expression in liver of adult F2 female rats born to F0-fathers fed a chow or high-fat diet

city: Stockholm

first: Thais

last: de Castro Barbosa

state: Stockholm

address: von Eulers väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary:
The purpose of this study was to investigate whether paternal high-fat diet (HFD) transgenerationally remodeled the hepatic transcriptome of F2 female rats
Liver mRNA expression profiling of F2-female from F0-founders fed either a chow or a chronic HFD challenged. Adult females were challenge or not a high-fat diet for 12 weeks. Liver was dissected at an endpoint experiment. Rats were subjected to 4 hours fasting prior to anesthesia with pentobarbital and tissue collection.

overall_design: F2-females Sprague-Dawley rats from F0 founders fed or not a high-fat diet  were also subjeted to high-fat consumption for 12 weeks. At terminal experiment, liver from 6 to 7 animals per group was collected, prepared and subjected to the gene array analysis.

first: Petter

last: Alm

first: Romain

last: Barres

first: Juleen

last: Zierath

first: Anna

last: Krook


title: Role of TAF5L and TAF6L in controlling the mouse ESC state [ChIP-seq]

city: Melbourne

first: Partha

last: Das

state: Victoria

address: 211 Wellington Road

department: Anatomy & Developmental Biology

institute: Monash University

summary: Self-renewal and pluripotency of the embryonic stem cell (ESC) state is established and maintained by multiple regulatory networks that comprise transcription factors and epigenetic regulators. Although many studies have been performed, the function of epigenetic regulators in these networks is incompletely defined. We conducted a CRISPR-Cas9 mediated loss-of-function genetic screen to target 323 epigenetic and ESC-specific transcription factor genes. This screen identified two new epigenetic regulators—TAF5L and TAF6L—with high confidence for the mouse ESC state. TAF5L and TAF6L are also essential for the efficient somatic reprogramming. In-depth analyses demonstrate that TAF5L and TAF6L belong to and establish a regulatory circuitry with MYC and CORE networks. Moreover, detailed molecular studies reveal TAF5L and TAF6L predominantly regulate their target genes through the c-MYC and MYC regulatory network to control self-renewal of mouse ESCs. Our findings illuminate the multi-layered regulatory networks of TAF5L and TAF6L for gene regulation to maintain the ESC state.

overall_design: ChIP-seq binding comparison between WT mouse embryonic stem cells and Taf5l/Taf6l knockouts for various histone marks and transcription factors.


title: Characteristic energy metabolism in mouse primordial germ cells

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

institute: Tohoku University

summary: Primordial germ cells (PGCs), undifferentiated embryonic germ cells, are the only cells that have the ability to become gametes and to reacquire totipotency upon fertilization. It is generally understood that the development of PGCs proceeds through the expression of germ cell-specific transcription factors and characteristic epigenomic changes. However, little is known about the properties of PGCs at the metabolite and protein levels, which are directly responsible for the control of cell function. Here, we report the metabolic profiles of PGCs through the first comprehensive analyses of the metabolome and proteome, including remarkable activation of oxidative phosphorylation in mitochondria. Moreover, conversion of energy metabolism is involved in the control of PGC reprogramming and differentiation of pluripotential stem cells (PSCs) into PGCs in culture. Our findings about the unique metabolic property of PGCs provide novel insights into our understanding of the importance of distinct energy metabolism for switching PGC and PSC status.

overall_design: Total RNAs (100 ng) from mouse E13.5 male gonadal somatic cells (Somas) and VR15 embryonic stem cells (ESCs) were used for analysis. cRNA samples were prepared using Agilent Low Input Quick Amp Labeling Kit (Agilent 5190-2331). Samples were hybridized onto Mouse GE 4 x 44 K V2 Microarray Kit (Agilent G4846A) according to the manufacturer's instruction. The microarrays were scanned using DNA microarray scanner (Agilent). Each cell type was analyzed in 3 biological replicates. Multiple testing corrections were performed with the Benjamini-Hochberg false-discovery rate correction.

first: Kei

last: Otsuka

first: Masayuki

last: Ebina

first: Kaori

last: Igarashi

first: Asuka

last: Takehara

first: Mitsuyo

last: Matsumoto

first: Akio

last: Kanai

first: Kazuhiko

first: Tomoyoshi

last: Soga

first: Yasuhisa

last: Matsui


title: LRP5 and LRP6 are required for maintaining self-renewal and differentiation of hematopoietic stem cells

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: The canonical Wnt signaling pathway has been demonstrated as a critical role in the self-renewal, proliferation and differentiation of Hematopoietic Stem Cells (HSCs), but the functions are indeterminacy in adult HSCs since the different experimental systems using gain- or loss- functions mice models. Low-density lipoprotein receptor-related proteins 5 and 6 (LRP5 and LRP6) are important co-receptors in the canonical Wnt/β-catenin pathway. In this study, the knockout mice models were established for adult HSC investagation via conditional ablation of LRP5 and LRP6 in adult hematopoiesis by Vav-Cre Loxp system. We found the HSC numbers were diminished due to the decreased proliferation and cell cycle. To investigate the molecular mechanisms, RNA-seq was performed using HSC cells isolated from WT and dKO mice.

overall_design: HSC (CD34-Flt3- Lin-ScaI+C-Kithigh cells) purified by FACS sorting

first: Juanjuan

last: Liu


title: Gene expression of ex vivo cultured osteoclasts during the course of differentiation

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

institute: University Medical Center Hamburg-Eppendorf

summary: The aim of this analysis was to investigate the changes in the gene expression pattern of ex vivo cultured wildtype murine osteoclasts during the course of osteoclastogenic differentiation.

overall_design: Primary osteoclasts were obtained from 12 week old female C57Bl/6J mice. Bone marrow was extracted and cultured in a-MEM including 10 % FBS and 10 nM vitmain-D3 for 3 days. Thereafter they were cultured in a-MEM including 10% FBS, 10 nM Vitamin-D3, 20 ng/ml MCSF and 40 ng/ml RANKL. The expression patterns of these cells was compared at four timepoints during the course of differentiation (day 1, day 4, day 5 and day 7).

first: T

last: Streichert

first: J

last: Albers


title: BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (I)

city: Hannover

first: Antje

last: Prasse

address: Carl-Neubergstrasse 1

department: Pneumology

institute: Medical School Hannover

summary: Background: Based on previous publication and our own data we became interested in the gene expression signature of airway basal cells. Methods: Bronchoscopy with bronchial brushes and bronchoalveolar lavage was performed in healthy donors. Airway basal cells were obtained by brushing segmental bronchi of the right lower lobe and outgrowth of cells in BEGM supplemented with growth factors according to the manufacturer’s instructions. Alveolar macrophages were sorted by flow cytometry. Microarray data of 11 airway basal cell samples, 7 alveolar macrophage samples and 4 samples of bronchial epithelial cells were obtained. The transcriptome of the three different cell types was compared using univariate ANOVA resulting in 8874 genes significantly differently expressed between the three cell types (p<0.0001). The data of these 8874 transcripts were used for a clustering approach applying Cluster 3.0 software. The samples were hierarchically clustered with median normalization of the genes and centroid linkage, and the similarity metric used was Pearson correlation. Results and Conclusion: we obtained an airway basal cell type specific signature consisting out of 961 genes which was used in further studies.


title: BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells


title: Modeling CADASIL vascular pathologies with patient-derived induced pluripotent stem cells

first: Zunpeng

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a rare hereditary cerebrovascular disease caused by a NOTCH3 mutation. However, the underlying cellular and molecular mechanisms remain unidentified. Here, we generated non-integrative induced pluripotent stem cells (iPSCs) from fibroblasts from a CADASIL patient harboring a heterozygous NOTCH3 mutation (c.3226C>T, p.R1076C). Vascular smooth muscle cells (VSMCs) differentiated from CADASIL-specific iPSCs showed transcriptional changes and disease-associated cellular dysfunction, including activation of the NF-kB signaling pathway, cytoskeleton disorganization, and excessive cell proliferation. In comparison, these abnormalities were not observed in vascular endothelial cells (VECs) derived from the patient’s iPSCs. Importantly, the abnormal upregulation of NF-kB target genes in CADASIL VSMCs was diminished by a NOTCH pathway inhibitor, providing a potential therapeutic strategy for CADASIL. Overall, using this iPSC-based disease model, our study identified clues for studying the disease mechanisms of CADASIL and developing treatment strategies for this disease.

overall_design: Transcriptomic analyses of WT and Cadasil specific vascular cells.

first: Guanghui


title: Screens of C. albicans deletion collections in the murine  reveals role for filamentation transcription factors

city: San Francisco

first: Suzanne

last: Noble

address: 513 Parnassus Ave., Box 0414

institute: UCSF

summary: Candida albicans is a human gut commensal and an opportunistic pathogen. The ability to transition from yeasts to invasive hyphae is a central virulence attribute, but it is unclear how these two cell types function during commensal growth.  Using FISH to visualize C. albicans in a murine gut colonization model, we observed the co-occurrence of yeasts and hyphae throughout the gastrointestinal tract. Forward genetic analysis revealed that major transcriptional activators of yeast-to-hypha morphogenesis have unexpected activity as potent inhibitors of commensalism.  In vivo FISH, transcriptomic, and genetic analyses indicate that the morphogenesis program inhibits commensal fitness, not through control of cell shape as expected from in vitro studies, but by activating expression of a hypha-specific pro-inflammatory secreted protease and a hyphal cell surface adhesin. These results reveal a tradeoff between fungal programs supporting commensalism and virulence within the commensal niche in which selection against hypha-specific markers limits the disease-causing potential of this ubiquitous commensal-pathogen.

overall_design: Pooled mutants from isogenic knockout collections were screened for commensal fitness in a mouse model of murine gastrointestinal colonization

first: Jessica

last: Witchley


title: Thrombopoietin metabolically primes hematopoietic stem cells to megakaryocyte lineage differentiation

city: Southampton

first: Patrick

last: Stumpf

state: Hampshire

address: University Road

department: Faculty of Medicine

institute: University of Southampton

summary: During acute myelosuppression or thrombocytopenia, bone marrow (BM) hematopoietic cells respond rapidly to replenish peripheral blood platelets. While the cytokine Thrombopoietin (Thpo) concomitantly regulates platelet production and maintains HSC stem cell potential whether Thpo directly controls Mk-lineage differentiation of HSCs is unclear. Stress hematopoiesis requires quiescent HSCs to proliferate, a process which depends on a higher energy production. However, whether this switch of metabolic state relates to lineage differentiation of HSCs is not known. We here show that Thpo rapidly upregulates mitochondrial activity in HSCs which was accompanied by preferential differentiation to Mk-lineage. During unperturbed hematopoiesis, HSCs with high mitochondrial content and activity exhibit Mk-lineage biased differentiation. Furthermore, Thpo rapidly skewed HSCs to express a tetraspanin molecule, CD9, which expression correlated to mitochondria cell content. While highly proliferative, mitochondrial-rich HSCs were resistant to apoptosis and oxidative stress upon Thpo stimulation. Thpo regulated mitochondrial activity did not associate with high levels of cMpl expression but was influenced by non-nuclear mitochondrial translocation of phosphorylated of STAT3 at serine 727. Our data reveals that HSCs are metabolically heterogeneous and higher mitochondrial activity primes HSCs toward the Mk lineage differentiation. We also uncover a pivotal role of Thpo in regulating the rapid Mk-lineage commitment during stress hematopoiesis. Our findings suggest that mitochondria metabolism primes HSCs not only to exit dormancy but toward direct differentiation to Mk lineage.

overall_design: Single-cell RNA sequencing of mouse hematopoietic stem cells from control mice and from mice treated with Thpo.

first: Toshio

last: Suda

first: Ayako

last: Nakamura-Ishizu


title: Single-cell RNA-seq of NR5A1-eGFP positive cells of the developing mouse ovary from E10.5 to P6

city: Ramat Gan

first: Isabelle

last: Stévant

address: Institute of Nanotechnology and Advanced Materials, Building 206

country: Israel

institute: University of Bar Ilan

summary:
Purpose: We performed a time-course single-cell RNA-seq of the somatic cells of the XX mouse gonads to study the cell population heterogeneity and the genetic program during their differentiation.
Methods: We collected gonads from NR5A1-eGFP transgenic embryos at six embryonic stages: E10.5, E11.5, E12.5, E13.5, E16.5 and P6.
Methods: Cells were capture with the C1 autoprep system and cDNA sequenced with Illumina HiSeq 2000.
Results: One cell population was detected at E10.5 and give rise to both Granulosa and steroidogenic precursor cells. A precursor cell population remains undifferentiated at P6 and are likely to be theca cell precursors.
Conclusion: Our study is, to date, the most granular transcriptomic study of the developing mouse ovary and provide a more complete model of  somatic cell differentiation during female sex determination.

overall_design: 663 cells were collected in total. 71 cells at E10.5, 106 cells at E11.5, 164 cells at E12.5, 106 cells at E13.5, 95 cells at E16.5, and 121 at P6. We performed two independent captures for each embryonic stage to reach a reasonable number of cells except for E10.5 where we capture enough cells in one experiment.

first: Françoise

last: Kühne

first: Andy

last: Greenfield

first: Marie-Christine

last: Chaboissier

first: Emmanouil

middle: T

last: Dermitzakis

first: Serge

last: Nef


title: Bcl9 and Pygo synergize downstream of Apc to effect intestinal neoplasia in mouse models recapitulating Familial Adenomatous Polyposis

city: Cambridge

first: Laurens

last: van Tienen

address: Francis Crick Avenue

department: PNAC

institute: MRC Laboratory of Molecular Biology

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

overall_design: Refer to individual Series


title: Bcl9 and Pygo synergize downstream of Apc to effect intestinal neoplasia in mouse models recapitulating Familial Adenomatous Polyposis (RNA-Seq)

summary: We assessed differential gene expression using RNAseq in intestinal adenomas between Apc loss-of-function (Apcmin) mice, or by Apc1322T mice encoding a partially-functional Apc truncation commonly found in colorectal carcinomas.

overall_design: Total RNA from intestinal adenomas of ApcMin and Apc1322T mice was used to generate single-ended stranded 50 bp reads from cDNA on an Illumina HiSeq 4000.

middle: M

first: Mariann

last: Bienz


title: Dental pulp cell-derived powerful inducer of TNF-alpha comprises PKR containing stress granule rich microvesicles (GFvsDP-1)

status: Public on Dec 30 2018

city: Fukuoka

first: Takao

last: Fukuda

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku,

department: Faculty of dental science

institute: Kyushu University

summary: It is well known that dental pulp tissue can evoke some of the most severe acute inflammation observed in the human body. We found that dental pulp cells secrete a factor that induces tumor necrosis factor-α production from macrophages, and designated this factor, dental pulp cell-derived tumor necrosis factor-α-inducing factor (DPTIF). DPTIF was induced in dental pulp cells and transported to recipient cells via microvesicles. Treatment of dental pulp cells with a PKR inhibitor markedly suppressed DPTIF activity, and weak interferon signals were constitutively activated inside the cells. In recipient macrophages, stimulation with DPTIF-containing supernatants from pulp cells resulted in activation of both nuclear factor-κB and MAP kinases like JNK and p38. Proteomics analyses revealed that many stress granule-related proteins were present in supernatants from dental pulp cells as well as microvesicle marker proteins like GAPDH, β-actin, HSPA8, HSPB1, HSPE1, and HSPD1. Furthermore, giant molecule AHNAK and PKR were detected in microvesicles derived from dental pulp cells, and gene silencing of AHNAK in pulp cells led to reduced DPTIF activity. Thus, it appeared that the core protein of DPTIF was PKR, and that PKR was maintained in an active state in stress granule aggregates with AHNAK and transported via microvesicles. The activity of DPTIF for TNF-α induction was far superior to that of gram-negative bacterial endotoxin. Therefore, we, report for the first time, that active PKR is transported via microvesicles as stress granule aggregates and induces powerful inflammatory signals in macrophages.

overall_design: To determine the differences in gene expression between cells with and without dental pulp cell-derived tumor necrosis factor-α-inducing factor (DPTIF) activity, we compared gene expression profiles between immortalized dental pulp calls (DP-1) with DPTIF activity and gingival tissue-derived fibroblasts without DPTIF activity

first: Shigeki

last: Suzuki

first: Shintaro

last: Nagayasu

first: Jun

last: Nakanishi

first: Kazuma

last: Yoshida

first: Shizu

last: Hirata-Tsuchiya

first: Yuki

last: Nakao

first: Tomomi

last: Sano

first: Akiko

last: Yamashita

first: Satoru

last: Yamada

first: Hideki

last: Shiba

first: Kouji

last: Ohta

first: Fusanori

last: Nishimura


title: Comparison of DNA methyltransferase-1 (Dnmt1) deleted urogenital sinus epithelium compared to wildtype urogenital sinus epithelium

city: Madison

first: Chad

middle: Michael

last: Vezina

state: WI

address: 1656 Linden Drive

department: Comparative Biosciences

institute: University of Wisconsin-Madison

summary: Dnmt1 is an important regulator of tissue development and differentiation. To assess the effects of epithelium Dnmt1 deletion in the developing urogenital sinus (precursor of the urethra and prostate in males), we isolated urogenital sinus epithelial tissue from Dnmt1 deleted mouse embryos and wildtype mouse embryos. The transcriptomes were analyzed by RNA-seq

overall_design: A Shh cre driver was used to achieve Dnmt1 deletion in the epithelium of the developing urogenital sinus. Epithelium of the urogenital sinus of embryonic day 15.5 mouse embryos were isolated by trypsin digestion. Tissues from Dnmt1 mutants (Dnmt1cKO) were compared to wildtype embryos (Control) in this experiment.

first: Diya

middle: B

last: Joseph

first: Li-Fang

last: Chu


title: Next generation sequence analysis for transcriptome of Drosophila melanogaster wandering third instar larva in wt and lncRNA hsromega mutant

city: varanasi

first: subhas chandra

last: lakhotia

address: cytogenetics lab, department of Zoology BHU

institute: Brown University

summary:
Purpose: To compare transcriptomic changes between 3rd instar wild type larvae and those with highly down regulated hsrω lncRNAs levels

Method: Whole third instar larval total RNA profiles of +/+ and +/+;hsromega[66] homozygous were generated by sequencing, in duplicate, on Illumina Hiseq2500 platform using 100bp pair-end reads, which resulted in a sequencing depth of ~20 million reads. The resulting FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples. Cuffdiff 2.1.1 was used (Trapnell et al., 2012) to ascertain differential expression of gene transcripts between different samples, .

Result: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the Drosophila genome (dm6) and identified  21,529 transcripts with TopHat workflow in each genotype studied, with 20,956 having baseline expression. 134 genes were up regulated and 74 downregulated in +/+;hsromega[66] compared to +/+ whereas 201  expressed only in the wild type sample and 164 only in hsromega[66] mutant

Conclusion: Analysis of RNA-seq data revealed that a large proportion of the transcripts affected in larvae with loss of hsromega lncRNA transcripts belonged to innate immune response pathway, mainly those in defense against Gram positive bacteria.  Many of these genes are part of proteolysis pathway having endopeptidase activity with predominence of serine-threonine endopeptidases. Kegg pathway analysis revealed that metabolism, especially that of Drugs, was indicated to be affected. Genes showing differential expression belonged to ascorbate and aldarate metabolism,retinol metabolism, pentose and glucoronate interconversion, metabolism of xenobiotics by cytochrome P450

overall_design: total RNA profiles of wandering late third instar larvae of +/+ and +/+;hsromega[66]  were generated by sequencing, in duplicate, using Illumina Hiseq2500 platform.

first: Subhash

middle: C

last: Lakhotia

first: Mukulika

last: Ray