title: Single-Cell RNA-Sequencing of Human Embryonic Stem Cell Differentiation Delineates Adverse Effects of Nicotine on Embryonic Development

status: Public on Jan 22 2019

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: Nicotine, the main constituent of tobacco, is highly detrimental to the developing fetus by increasing the risk of gestational complications and organ disorders. The effects of nicotine on human embryonic development and related mechanisms, however, remain largely unresolved. Here, we performed single-cell RNA-sequencing (scRNA-seq) of human embryonic stem cell (hESC)-derived embryoid body (EB) in the presence or absence of nicotine. Nicotine induced lineage-specific responses and dysregulated cell-to-cell communication in EBs, shedding light on the adverse effects of nicotine on human embryonic development. Additionally, nicotine reduced cell viability, increased reactive oxygen species (ROS), and altered cell cycling in EBs. Abnormal Ca2+ signaling was found in muscle cells upon nicotine exposure and verified in hESC-derived cardiomyocytes. Consequently, our scRNA-seq data suggests direct adverse effects of nicotine on hESC differentiation at the single-cell level and offers new method for evaluating drug and environmental toxicity on human embryonic development in utero.

overall_design: Differential expression was quantified from microdroplet-based scRNA-seq on day 21 control and nicotine-exposed embryoid bodies (EBs)

first: Hongchao

last: Guo

first: Joseph

last: Wu


title: Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral DDT Exposure

status: Public on Jan 19 2019

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

country: USA

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: In previous studies, the pesticide DDT was shown to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs), also called epimutations, which can mediate this epigenetic inheritance. In the current study, the developmental origins of the transgenerational DMRs during gametogenesis have been investigated. Male control and DDT lineage F3 generation rats were used to isolate embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, adult pachytene spermatocytes, round spermatids, caput epididymal spermatozoa, and caudal sperm. The DMRs between the control versus DDT lineage samples were determined at each developmental stage. The top 100 statistically significant DMRs at each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed.

overall_design: F3 generation control and DDT lineage male rats were used in this experimental design to isolate various germ cell stages for epigenetic analysis. The F0 generation gestating female rats at 90 days of age were transiently exposed to DDT or a vehicle control during embryonic days 8-14 when the PGCs were migrating to colonize the indifferent gonad during early stage of gonadal sex determination. The F1 generation offspring were obtained and when they reached 90 days of age they were bred within the control and DDT lineages to generate the F2 generation (grand offspring) which were then bred at 90 days of age to obtain the transgenerational F3 generation for each control and DDT lineage. No cousin or sibling breeding were used to avoid any inbreeding artifacts. Only the F0 generation gestating females were exposed to DDT, which also directly exposed the F1 generation fetus and the germline within the F1 generation fetus that will generate the F2 generation. Therefore, the F3 generation is the first transgenerational generation not directly exposed and was used to study the developmental origins of the sperm epimutations. The F3 generation control and DDT lineage male rats were aged to the embryonic day 16 (E16) fetal stage for prospermatogonia cell isolation, to postnatal day 10 (P10) for spermatogonial cell isolation, and to 120 days of age for pachytene spermatocyte isolation, round spermatid isolation, caput spermatozoa isolation, and cauda epididymal sperm isolation. Three different pools each with different individual sets of animals were obtained from 5-6 males per pool for the E16 stage, 6-7 males per pool for the P10 stage, 3 adult males per pool for the adult stage. Therefore, 3-7 different males were used in the analysis within the three different pools analyzed for both the control and DDT lineages. Genomic DNA was isolated from each pool and from individual animals for caput and cauda sperm for subsequent epigenetic analysis. The analysis of differential DNA methylation regions (DMRs) was performed with a methylated DNA immunoprecipitation (MeDIP) procedure followed by next generation sequencing for an MeDIP-Seq protocol.

first: Millissia

last: Ben Maamar

first: Eric

last: Nilsson

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

first: John

middle: R

last: McCarrey


title: Prostate Cancer Cell RNA-Seq (PC3E and GS689.Li)

status: Public on Jan 18 2019

city: Los Angeles

first: Zijun

last: Zhang

state: CA

address: 650 Charles E. Young Drive South

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: Two prostate cancer cell lines. PC3E and GS689.Li

overall_design: High-throughput RNA sequencing of PC3E and GS689, each cell line with 3 replicates.

first: Samir

last: Adhikari

first: Yi

last: Xing


title: Comparison of cortical grey matter from Rasmussen Encephalitis patients and age-matched epileptic controls

city: Linz

first: Anna

middle: Regina

last: Tröscher

address: Krankenhausstraße 5

department: Center for Medical Research

country: Austria

institute: Johannes Kepler University Linz

summary: We performed whole-genome transcriptome analysis of Rasmussen Encephalitis of the early disease stages for an overview of differentially expressed pathways leading to widespread neuroinflammation and degeneration.

overall_design: This study was done on FFPE surgical resection material from patients suffering from Rasmussen Encephalitis and epileptic controls (age matched tumour patients). We included patients from Rasmussen Encephalitis stage 0 - 2 (no inflammation - acute inflammation). Controls (n=7), RE stage 0 (n= 5), RE stage 1 (n= 6), RE stage 2 (n=6)

first: A


title: sRNA sequencing of miRNAs exported to HDL from primary human islets

status: Public on Jan 16 2019

city: Nashville

first: Leslie

middle: Roteta

last: Sedgeman

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNAs are exported to high density lipoproteins (HDL). This study aimed to understand what miRNAs are exported from primary islets to HDL in vitro.

overall_design: Examination of miRNAs exported from primary islets to HDL

first: Kasey

last: Vickers


title: Genome wide analysis of upper spinal cords with training after spinal cord hemisection injury

status: Public on Jan 15 2019

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

summary: The goal of this study is to elucidate the influence of treadmill training on transcriptome of the upper lumbar spinal cord after thoracic spinal cord hemisection. mRNA profiles of spinal cords at 23 days-post injury with/without treadmill training were generated. The expression levels of 650 genes in the trained animal were increased ( > 2-fold) compared to untrained animals. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion after treadmill training, with biologic replicates, generated by RNA-seq technology.

overall_design: The effect of training after spinal cord injury (T9) on the transcriptome of intact upper spinal cord was investigated.

first: Kazu

last: Kobayakawa

first: Reggie

last: Edgerton

first: Akihito

last: Harada

first: Jumpei

last: Nogami


title: EXPORTIN 1A Prevents Transgene Silencing in Arabidopsis through Modulating the Nucleo-cytoplasmic Partitioning of HDA6

status: Public on Jan 12 2019

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: In eukaryotic cells, nucleo-cytoplasmic trafficking of macromolecules across the nuclear envelope is an essential process that ensures a rapid exchange of different cellular components, including proteins and RNAs, between the nucleus and cytoplasm. The significance of the nucleo-cytoplasmic trafficking of chromatin regulators in regulating DNA methylation and gene silencing is not well understood. Here, using a genetic screen, we identified XPO1A, one of the nuclear export receptors in Arabidopsis, as an anti-silencing factor that protects transgenes from transcriptional silencing. Loss-of-function of XPO1A leads to locus-specific DNA hypermethylation at transgene promoters and some endogenous loci. We found that XPO1A directly interacts with histone deacetylase HDA6 in vivo and the xpo1a mutation causes increased nuclear retention of HDA6 protein, resulting in reduced histone acetylation and enhanced transgene silencing. Our results revealed a new mechanism of epigenetic regulation through the modulation of XPO1A-dependent nucleo-cytoplasm partitioning of a chromatin regulator.

overall_design: MethylC-Seq: 1 sample examined: xpo1a-4 mutant (with 35S::SUC2 transgene)

first: Guohui

first: Kai

last: Tang

first: Cheng-Guo

last: Duan


title: Mitoprotein-induced stress launches a global transcriptional fail-safe program

city: Kaiserslautern

first: Johannes

last: Herrmann

address: Erwin-Schrodinger-Strasse 13

department: Cell Biology

country: Germany

institute: University of Kaiserslautern

summary: Most mitochondrial proteins are synthesized as cytosolic precursor proteins before being imported into mitochondria. Cytosolic accumulation of mitochondrial precursors hazards cellular fitness and is associated with a growing number of diseases, but is not observed under physiological conditions. Individual mechanisms how cells avoid precursor accumulation outside mitochondria have recently been discovered, but their interplay and regulation have remained elusive. Here we show that cells rapidly launch a global transcriptional program to restore cellular proteostasis after induction of a “clogger” protein that reduces the number of available mitochondrial import sites. Cells upregulate the protein folding and proteolytic systems in the cytosol and downregulate both the cytosolic translation machinery and many mitochondrial metabolic enzymes, presumably to relieve the workload of the overstrained mitochondrial import system. We show that this transcriptional remodeling is a combination of a “wideband” core response regulated by the transcription factors Hsf1 and Rpn4 and a unique mitoprotein-induced downregulation of the OXPHOS components, the most abundant group of precursors. These findings not only depict the first comprehensive model of adaptations to mitochondrial import impairment, but also reveal their regulation, connecting so far isolated stress response mechanisms into a coordinated network of cellular reactions.

overall_design: Examination of expression over time (timepoints 0, 10, 30, 90, 270 min after clogger induction) in 4 independent biological replicates, 2 strains expressing different clogger variants (b2-DHFR, b2delta-DHFR) and 2 reference strains expressing no clogger (empty vecgtor) or cytosolic DHFR

first: Felix

last: Boos

first: Lena

last: Krämer

first: Carina

last: Groh

first: Ferris

last: Jung

first: Adrian

last: Gackstatter

first: Eva

last: Zöller

first: Vladimir

last: Benes

middle: M


title: Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2 [III]

status: Public on Jan 17 2019

city: Houston

first: James

last: Lupski

state: TX

address: One Baylor Plaza Room #604B

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. Our data indicate an increased rate of clustered single nucleotide variant mutation in cis that is not present with recurrent rearrangement of the genome at the same locus. Indel and single nucleotide mutations are associated with both copy number gains and losses of 17p11.2, occur up to ~1 Mb away from the breakpoint junctions, and favor C>G transversion substitutions; results suggesting that single stranded DNA is formed during the genesis of the SV and providing compelling support for a microhomology-mediated break-induced replication mechanism for SV formation.

overall_design: To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the 17p11.2 chromosomal region to query the genomic DNA of 55 individuals and their parents. This allowed us to discern the extent of the rearrangements, the copy number, and the de novo status of each rearrangement.

first: Christine

last: Beck


title: A microRNA-inducible CRISPR-Cas9 platform serves as microRNA sensors and cell type specific genome regulation tools

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

country: China

institute: Peking University

summary: microRNAs (miRNAs) are an important class of small regulatory noncoding RNAs expressed by plants, animals and viruses. However, measuring miRNA activity in vivo remains a big challenge. Using a miRNA-mediated sgRNA releasing strategy and dCas9-VPR to drive a transgene RFP expression, we create a miRNA sensor that can faithfully measure miRNA activity at cellular levels and show that it can be used to monitor the differentiation status of stem cells. When sgRNAs are designed to target endogenous locus, we show this system can be adopted to achieve cell type specific activation of endogenous genes. Furthermore, when dCas9 is fused with a transcriptional repressor or a base editor, we show this system can be used to repress the expression of endogenous genes or mutate specific DNA bases of chromosome depending on the expression of cell type-specific miRNAs. Finally, by a miRNA sensor library screening, we discovered a previously undefined layer of heterogeneity associated with miR-21a activity in mouse embryonic stem cells. Together, these results highlight the utility of a miRNA-induced CRISPR-Cas9 system as miRNA sensors and cell type-specific genome regulation tools.

overall_design: Examination of differential expressed genes between sorted RFP low and RFP high mouse embryonic stem cells by poly(A)+ RNA-Seq. Two independently prepared mouse ESCs samples were used for RNA-seq.

first: Y

first: X

first: L

last: Hu

first: J

last: Hao

last: Liao

last: Chiu

first: M

last: Shi


title: Human renal fibroblasts are strong immunomobilizers during a urinary tract infection mediated by uropathogenic Escherichia coli

status: Public on Jan 11 2019

city: örebro

first: isak

last: demirel

address: campus usö

country: Sweden

institute: örebro University

summary: To prevent the onset of urosepsis and reduce mortality, a better understanding of how uropathogenic Escherichia coli (UPEC) manages to infiltrate the bloodstream through the kidneys is needed. The present study elucidates if human renal interstitial fibroblasts are part of the immune response limiting a UPEC infection, or if UPEC has the ability to modulate the fibroblasts for their own gain. Microarray results showed that upregulated genes were associated with an activated immune response. We also found that chemokines released from renal fibroblasts upon a UPEC infection could be mediated by LPS and triacylated lipoproteins activating the TLR2/1, TLR4, MAPK, NF-κB and PKC signaling pathways. Furthermore, UPEC was also shown to be able to adhere and invade renal fibroblasts, mediated by the P-fimbriae. Furthermore, it was found that renal fibroblasts were more immunoreactive than renal epithelial cells upon a UPEC infection. However, both renal fibroblasts and epithelial cells were equally efficient at inducing neutrophil migration. In conclusion, we have found that human renal fibroblasts can sense UPEC and mobilize a host response with neutrophil migration. This suggests that renal fibroblasts are not only structural cells that produce and regulate the extracellular matrix, but also highly immunoreactive cells.

overall_design: Uropathogenic E.coli (CFT073) induced gene expression in primary human renal fibroblasts was measured at 6 hours after exposure at MOI 10. Three independent experiments were perfomed.

first: Isak

last: Demirel

first: Boxi

last: Zhang

first: Kristin

last: Klarström Engström


title: Overlapping and differential functions of ATF6α versus ATF6β in the mouse heart

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: We used microarrays to generate differentially expressed gene profiles upon cardiomyocyte-specific overexpression of transcriptionally-active N-termini of either ATF6α or ATF6β

overall_design: Total RNA was extracted from control and experimental ventricles, processed for, and analyzed using Affymetrix microarrays.

first: Robert

middle: N

last: Correll

first: Jeffery

middle: D

last: Molkentin


title: Nucleomorph small RNAs in cryptophyte and chlorarachniophyte algae

status: Public on Jan 09 2019

city: Uppsala

first: Anna

last: Åsman

address: PO Box 7080

department: Molecular Sciences

institute: Swedish University of Agricultural Sciences (SLU)

summary: The regulation of gene expression and RNA maturation underlies fundamental processes such as cell homeostasis, development and stress acclimation. The biogenesis and modification of RNA is tightly controlled by an array of regulatory RNAs and nucleic acid-binding proteins. While the role of small RNAs (sRNAs) in gene expression has been studied in-depth in select model organisms, little is known about sRNA biology across the eukaryotic tree of life. We used deep sequencing to explore the repertoires of sRNAs encoded by the miniaturized, endosymbiotically-derived ‘nucleomorph’ genomes of two single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. A total of 32.3 and 35.3 million reads were generated from G. theta and B. natans, respectively. In G. theta, we identified nucleomorph U1, U2 and U4 spliceosomal RNAs (snRNAs) as well as 11 C/D box small nucleolar RNAs (snoRNAs), five of which have potential plant and animal homologs. The snoRNAs are predicted to perform 2’-O methylation of rRNA (but not snRNA). In B. natans, we found previously undetected RNA components of the nucleomorph spliceosome (U4 snRNA) and ribosome (5S rRNA), along with six orphan sRNAs. Analysis of chlorarachniophyte snRNAs shed light on the removal of the miniature 18-21 nt introns found in B. natans nucleomorph genes. Neither of the nucleomorph genomes appears to encode RNA pseudouridylation machinery, and U5 snRNA cannot be found in the cryptophyte. Considering the central roles of U5 snRNA and RNA modifications in other organisms, cytoplasm-to-nucleomorph RNA shuttling in cryptophyte algae is a  distinct possibility.

sample_organism:
Guillardia theta
Bigelowiella natans

platform_organism:
Guillardia theta
Bigelowiella natans

overall_design: In total twelwe samples were analyzed. Six samples  from Guillardia theta: duplicates from light treatment, duplicates from dark treatment and one sample each from light and dark treatment where the RNA had been incubated with Terminator Exonuclease. Six samples from Bigelowiella natans: triplicates from light treatment and triplicates from dark treatment.

first: Bruce

middle: A

last: Curtis

first: John

last: Archibald


title: Detection of RNA–DNA binding sites in long noncoding RNAs

city: Aachen

first: Ivan

middle: G.

last: Costa

state: NRW

address: Pauwelsstr. 19

department: RWTH Aachen Medical Faculty

institute: Institute for Computational Genomics

summary:
Triple helix is a potential mechanism how lncRNAs interact with the genome. Our in silico method (Triplex Domain Finder) is able to predict the binding sites of lncRNA MEG3 and GATA6-AS in the genome. In order to validate these predictions, we develop DBD-Capture-Seq to capture the DNA loci where the given RNA oligo binds to via triplex.
Method: Different RNA oligos  are used The biotinylated RNA oligos (MEG3 TFR1, MEG3 TFR2, and GATA6-AS TFR1) were incubated with sheared genomic DNA to allow for triplex formation. After binding to streptavidin-coated beads, RNA-associated DNA was eluted and subjected to deep sequencing.
Control experiments were conducted in the absence of biotinylated RNA oligos.

overall_design: We have used 3 RNA oligos (MEG3 TFR1, MEG3 TFR2 and GATA6-AS TFR1) for capturing their triplex-forming loci (all in duplicates). Input and control experiments were tested as well.

middle: G

first: Chao-Chung

last: Kuo

first: Nevcin

last: Sentürk Cetin


title: Xist RNA antagonizes the chromatin remodeler, BRG1, from the inactive X chromosome

status: Public on Jan 14 2019

city: Boston

first: Jeannie

middle: T

last: Lee

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Harvard University / MGH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The noncoding Xist RNA recruits silencing factors to the inactive X (Xi) and facilitates re-organization of Xi structure. Here, we examine the epigenomic landscape of the Xi and assess how Xist alters chromatin accessibility. Interestingly, Xist deletion propels selective chromatin re-accessibility on the Xi, affecting various Xi regions differentially. Re-accessibility is regulated by BRG1, an ATPase subunit of SWI/SNF chromatin remodeling complex. In vitro, RNA binding inhibits the nucleosome remodeling and ATPase activities of BRG1. In vivo, Xist directly interacts with BRG1 and expels BRG1 from the Xi. Xist ablation leads to a selective return of BRG1 in cis, emanating from pre-existing BRG1 sites that are Xist-free. BRG1's return correlates with cohesin re-binding and restoration of topologically associated domains (TADs), and results in formation of de novo Xi "superloops." Thus, Xist RNA binding inhibits BRG1's nucleosome remodeling activity and results in expulsion of the SWI/SNF complex from the Xi.

overall_design: The role of Xist RNA as a safeguard of the Xi chromsome during X-chromosome inactivation (XCI) was explored by performing DNA accessibility assay (ATAC-seq) in WT and Xist-KO fibroblast cells. Xist's role in repulsion of the catalytic subunit of SWI/SNF complex, BRG1, was determined by native chromatin immunoprecipitation (ChIP-seq) in these cells. Xist's role on gene regulation during XCI maintenance was investigated by genome-wide expression profiling (RNA-seq).

first: Teddy

last: Jégu

first: Roy

last: Blum

first: Jesse

middle: C

last: Cochrane

first: Lin

last: Yang

first: Chen

middle: Y

last: Wang

first: Maud

middle: E

last: Gilles

first: David

last: Colognori

first: Attila

last: Szanto

first: Sharon

last: Marr

last: Kingston


title: ANRIL siRNA Microarray Data in HUVECs

city: Cleveland

first: QING

last: WANG

state: Ohio

address: 9500 Euclid Ave

department: Molecular Cardiology

institute: Cleveland Clinic

summary:
Coronary artery disease (CAD) is the most common cardiovascular disease and the leading cause of death worldwide.  To date, the 9p21.3 locus is the most robust and frequently replicated risk locus of CAD among >90 CAD risk loci identified by GWAS. More than 50 CAD-associated genomic variants were identified at the 9p21.3 CAD locus and many of them are located within a long non-coding gene ANRIL, which was initially referred to as Antisense Non-coding RNA in INK4 Locus.  The causal role of ANRIL in CAD and the underlying molecular mechanism are unknown.
We used gene expression microarray to identify the downstream target genes of ANRIL and to explore molecular mechanisms by which ANRIL might contribute to the risk development of CAD.

overall_design: Three sets of human umbilical vascular endothelial cells (HUVECs) were transfected with ANRIL-specific siRNA or control scrambled siRNA. Global gene expression of each transfected cell sample was profiled by Affymetrix GeneChip Human Genomic U133 Plus 2.0 array.  Differential expression analysis was conducted between ANRIL siRNA transfected and scrambled siRNA transfected cells.  Top-ranked downstream genes of ANRIL were confirmed by independent semi-quantitative RT-PCR experiments and real-time RT-qPCR.  Gene set enrichment analysis was performed to explore biological pathways or processes highly enriched with ANRIL downstream genes.

first: Qing

first: Qiuyun

last: Chen


title: Targeted DamID reveals Fuss as a pivotal element in bitter gustatory neurons

status: Public on Jan 10 2019

city: Regensburg

first: Mathias

last: Rass

address: Universitätsstraße 31

department: Developmental Biology

institute: University of Regensburg

summary: To find differentially expressed genes by comparing Fuss neurons and mutant Fuss neurons we utilised targeted DamID in Drosophila melanogaster. This not only predicts many genes expressed and nonexpressed in adult Fuss neuron populations, but also reveals Fuss being expressed in gustatory neurons, especially bitter gustatory neurons. Comparison of control and mutant datasets reveals a reduced expression of gustatory receptor gene Gr66a. Gr66a is an important component of the gustatory receptors compounds responsible for toxic compound sensation. Behaviourial tests reveal an impaired toxic compound sensation of adult Fuss mutant flies.

overall_design: Examination of Dam-PolII binding sites in adult Fuss neurons and Fuss mutant neurons

first: Stephan

last: Schneuwly


title: ERK2-dependent gene expression

city: Peoria

first: Sejeong

last: Shin

state: Illinois

address: 1 illini drive

institute: University of Illinois at Chicago

summary: ERK is a key coordinator of the epithelial to mesenchymal transition (EMT). However, the mechanisms by which ERK controls the EMT program are not well understood. We used microarray to determine global changes of gene expression mediated by ERK2.

overall_design: Vector control, D319N ERK2, and Y261A ERK2 expression was induced by doxycycline in Tet-on MCF10A cell systems. Cells were grown for 7 days, and RNAs were purified from three individual replicates of each condition and microarray was performed.

first: Sang-Oh

last: Yoon

first: John

last: Blenis


title: Molecular profiles in red drum (Sciaenops ocellatus) larvae exposed to Deepwater Horizon oil

city: Riverside

first: Genbo

last: Xu

address: 900 University Ave

institute: University of California, Riverside

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

overall_design: Refer to individual Series


title: Arid1a loss drives non‐alcoholic steatohepatitis in mice via epigenetic dysregulation of hepatic lipogenesis and fatty acid oxidation

city: shanghai

first: Xuxu

last: Sun

address: 227 south chongqing road

department: school of medicine

institute: shanghai jiao tong university

summary: ARID1A, a DNA-binding component of the SWI/SNF ATP-dependent chromatin-remodeling complex, contributes to nucleosome repositioning and access by transcriptional regulators. Liver-specific deletion of Arid1a (Arid1a LKO) caused the development of age-dependent fatty liver disease in mice. Transcriptome analysis revealed upregulation of lipogenesis and down-regulation of fatty acid oxidation genes.

overall_design: Livers of P90-day-old mice were collected, and transcriptomic analysis performed via RNA-seq.

first: Austin

last: Moore

first: Hao

last: Zhu

first: Xin

last: Luo


title: The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans [RNA-seq]

city: Worcester

first: Read

last: Pukkila-Worley

state: Massachusetts

address: 55 N Lake Ave

department: Medicine

institute: University of Massachusetts Medical School

summary: Germline-encoded pattern recognition receptors (e.g. Toll-like receptors) play key roles in innate immune activation. However, some metazoans, such as C. elegans, do not have canonical mechanisms of pattern recognition, yet they are able to mount anti-pathogen immune defenses. Here, we demonstrate that a nuclear hormone receptor (NHR), a ligand-gated transcription factor, functions in immune activation and pathogen defense. NHRs have expanded dramatically in C. elegans compared to other metazoans. Because NHRs often function redundantly, it has been challenging experimentally to characterize the biology of individual NHRs. Here, we use genetic epistasis experiments, transcriptome profiling analyses and chromatin immunoprecipitation to show NHR-86 is sufficient to activate protective immune defenses against the bacterial pathogen Pseudomonas aeruginosa. Interestingly, NHR-86 drives the transcription of immune effectors whose basal regulation requires the canonical p38 MAPK PMK-1 immune pathway. However, NHR-86 functions independently of PMK-1 and directly induces the transcription of infection response genes in a manner that confers protection from bacterial infection. Importantly, we found that nhr-86 does control immune gene expression and is necessary for host defense against a different pathogen, Enterococcus faecalis. Our findings characterize an ancient role of an NHR in innate immunity, and suggest that the expansion of the NHR protein family in C. elegans has been fueled in part by the need to activate immune defenses in response to pathogen attack.

overall_design: Transcriptional profiles of C. elegans animals treated with immunostimulator molecule R24 in wild-type and nhr-86 loss of function animals

first: Nicholas

last: Peterson


title: The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans [ChIP-seq]

overall_design: DNA binding profile of NHR-86 in C. elegans animals treated with immunostimulator molecule R24 in NHR-86::GFP transgenic animals


title: Dose-responsive transcriptomic profiles in red drum (Sciaenops ocellatus) larvae exposed to Deepwater Horizon oil

summary:
Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for estuary fish exposed to different concentrations of Deepwater Horizon (DWH) oil, transcriptomic profiles in  red drum (Sciaenops ocellatus) embryos exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated  using High Throughput Sequencing (HTS).
Methods:Total mRNA profiles of 48 hpf red drum larvae after slick (1.25%, 2.5%, and 5%)  and source/mass oil (0.135%, 0.27% and 0.54%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2.
Results:To determine the potential biological impact of oil exposure at system level, a gene ontology (GO) term analysis on biological processes (BPs) was conducted by analyzing the DEGs using DAVID. After exposure to source oil, the top enriched biological processes were terms associated with oxidation-reduction process, metabolic process (e.g. steroid), and organism development.  Similar biological processes were also among the most significant biological processes by slick oil exposure.  Among the top biological process list a significant number of nervous system related terms were highly enriched by both source and slick oil exposure, including midbrain development, motor neuron axon guidance, nervous system development, eye development, neuron development, neuron differentiation etc.

overall_design: Total mRNA profiles of 48hpf red drum larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Elvis

first: Alex

middle: J

last: Khursigara

first: Edward

last: Mager

first: Andrew

last: J. Esbaugh

first: Martin

last: Grosell

first: Daniel

last: Schlenk


title: Comparative analysis of gene expression of SLC3A2 monoallelic knockout and wild type clones

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

institute: OncoRay

summary: By employing a global gene expression profiling, we performed analysis of the molecular pathways which are deregulated in SLC3A2 monoallelic knockout clone generated from the head-and-neck cancer cell line Cal33 via CRISPR/Cas9 approach. Both non-irradiated and irradiated with 4Gy samples were compared.

overall_design: SLC3A2 monoallelic knockout and wild type clones were compared, both non-irradiated and irradiated with 4Gy X-ray dose. Each of 4 samples has been prepared in 3 replicates.

first: Anna

last: Dubrovska

first: David

last: Digomann


title: Serine metabolism supports macrophage IL-1β production.

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

summary: Serine is a substrate for nucleotides, NADPH and glutathione (GSH) synthesis. Previous studies in cancer cells and lymphocytes have shown that serine-dependent one-carbon units are necessary for nucleotide production to support proliferation.  Presently, it is unknown whether serine metabolism impacts the function of non-proliferative cells, such as inflammatory macrophages. We find that in macrophages, serine is required for optimal lipopolysaccharide (LPS) induction of IL-1β mRNA expression, but not inflammasome activation. The mechanism involves a requirement for glycine, which is made from serine, to support macrophage glutathione (GSH) synthesis. Cell-permeable GSH, but not the one-carbon donor formate, rescues IL-1β mRNA expression. Pharmacological inhibition of de novo serine synthesis in vivo decreased LPS induction of IL-1β levels and improved survival in an LPS-driven model of sepsis in mice. Our study reveals that serine metabolism is necessary for GSH synthesis to support IL-1β cytokine production.

first: Arianne

last: Rodriguez

first: Gregory

middle: S

last: Ducker

first: Leah

last: Billingham

first: Carlos

last: Martinez

first: Nello

last: Mainolfi

first: Vipin

last: Suri

first: Adam

last: Friedman

first: Mark

last: Manfredi

first: Samuel

last: Weinberg

first: Joshua

last: Rabinowitz


title: Histone methylation landscape in response to short hypoxic exposure

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

country: United Kingdom

institute: University of Liverool

summary: H3K4me3 and H3K36me3 ChIP seq in HeLa cells exposed to 0H (normoxia) or 1H of 1%O2 (hypoxia)

overall_design: 3 biological replicates, H3K4me3 ChIP seq and H3K36me3 ChIP seq in HeLa cells exposed to 0H (normoxia) or 1H of 1%O2 (hypoxia)

first: Michael

last: Batie


title: Uncoupling of transcription and cytodifferentiation in mouse spermatocytes with impaired meiosis

city: Bar Harbor

last: Carter

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

summary: We use the cytologically well-defined Prdm9 mutant mouse as a model of developmental arrest to demonstrate that parallel programs of cellular differentiation and transcription can become dis-associated. By comparing cytological phenotype markers and transcriptomes in wild-type and mutant spermatocytes, we identified multiple instances of cellular and transcriptional uncoupling in Prdm9-/- mutants.

overall_design: Transcript abundance from mouse spermatocytes with wild-type, heterozygous, and homozygous mutant alleles of Prdm9, collected at three time points with replicates.

first: Alexander

last: Fine

first: Robyn

middle: L

last: Ball

first: Yasuhiro

last: Fujiwara

first: MaryAnn

last: Handel

middle: W


title: Genome-wide RNA sequencing of sequential TLR agonist stimulation in C57Bl6/J macrophages

status: Public on Jan 08 2019

city: New Haven

first: Andrew

last: Wang

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University School of Medicine

summary: We report the genome-wide RNA sequencing of bone marrow derived macrophages after sequential TLR agonist stimulation.

overall_design: Examination of sequential TLR agonist stimulation.  Bone marrow derived macrophages (BMDMs) were prepared from male animals 6-12 weeks of age. Cells were isolated from femurs and tibias. The bone marrow cells were and grown in macrophage growth medium (RPMI 1640 supplemented with 10% FBS (Gibco), 1% penicillin-streptomycin (Gibco), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco), 0.01 M HEPES (AmericanBio), and 30% L929-conditioned media as a source of CSF-1), and plated on petri dishes. Macrophage growth medium was supplemented on day 3. Cells were plated for use on day 6. For sequential stimuli, cells were first stimulated with, PBS, 100 ng/mL Poly I:C (InvivoGen), or 5 ng/mL LPS derived from Escherichia coli 055:B5 (Sigma-Aldrich). 24 hours after the initial stimulation, the media was removed and cells were washed twice with warmed macrophage growth media, and then the media was replaced with Poly I:C or LPS.

first: Ruslan

last: Medzhitov

first: Scott

last: Pope


title: The dynamic landscape of coding and non-coding RNAs in the innate immune response to microbial pathogens

city: La jolla

first: Qiong

last: Zhang

state: California

address: 9500 Gilman Dr.

department: Pediatrics

institute: UCSD

summary: We performed a systematic analysis of the coding and non-coding transcriptomes of human macrophages after stimulation with ligands to TLR2/6  (FSL), TLR 1/2  (Pam3CSK4), and TLR4 (LPS)

overall_design: Transcriptome of THP1 derived macrophages without and with treatment with 3 different TLR ligands for 8hrs

first: Veena

last: Patil


title: MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network with PRC2 [iCLIP]

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We performed iCLIP for AGO2 to identify AGO2-interacting mRNAs in T98G glioblastoma multiforme cells.

overall_design: iCLIP for AGO2.

first: Haridha

last: Shivram


title: MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network with PRC2 [ChIP-seq]

summary: We performed ChIP-seq for EZH2 and its associated histone mark, H3K27me3, in T98G Glioblastoma multiforme cells.

overall_design: ChIP-seq for EZH2, H3K27me and Input in T98G cells.


title: The study of the role of POU3F2 in response to UVB treatment

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

summary: siRNA KD of POU3F2 directly effect DNA-damage repair and apoptosis genes

overall_design: 501mel melanoma cell line was treated with either siCTR or siPOU3F2 prior to UVB treatment. The samples were collected at the indicated time

first: Katharine

last: Herbert

first: Colin

middle: R

last: Goding


title: A Combined Approach Reveals a Regulatory Mechanism Coupling Src's Kinase Activity, Localization, and Phosphotransferase-Independent Functions

city: Seattle

first: Douglas

last: Fowler

address: 3720 15th Ave NE, Foege Building, S041

department: Genome Sciences

institute: University of Washington

summary: Protein kinases are subject to multiple layers of regulation that modulate their activity, localization and substrate specificity. However, the details of kinase regulation are incompletely understood, even for some of the most well-characterized kinases. Here, we measure the functional effect of thousands of single amino acid mutants of Src kinase's catalytic domain to identify residues involved in novel regulatory interactions.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae

overall_design: A barcoded plasmid library of Src variants was expressed in S. cerevisiae and timepoints were sampled throughout growth. Plasmids were extracted and barcodes amplified and counted with Illumina sequencing. Barcodes were related back to their cognate variant using barcode-variant map.

first: Dustin

last: Maly


title: Directed endocytosis mediates immune communication between an epithelial commensal microbe and the host

city: New York

first: Leandro

middle: Pires

last: Araujo

state: New York

address: 701 W 168th St, 9th floor

department: Microbiology and Immunology

institute: Columbia University

summary: Commensal bacteria influence host physiology, including immune responses, without invading host tissues. We show that proteins from segmented filamentous bacteria (SFB), which are immunomodulatory commensal microbes, are transferred into intestinal epithelial cells by adhesion-directed endocytosis that is distinct from the clathrin-dependent endocytosis of invasive pathogens. SFB transfer microbial cell wall-associated proteins, including an antigen that stimulates mucosal Th17 cell differentiation, into the cytosol of epithelial cells. Removal of CDC42 activity in vivo led to disruption of endocytosis induced by SFB, decreased epithelial antigen acquisition with consequent loss of immune modulation by SFB-specific CD4 T cells and mucosal Th17 cells.  Our findings indicate direct communication between a resident gut microbe and the host and show that intestinal epithelial cells acquire antigens from commensal bacteria for generation of T-cell responses to the resident microbiota.

overall_design: Intestinal epithelial cells from WT and IECΔCDC42 mice were isolated to performed RNAseq.

first: Ivaylo

last: Ivanov


title: Translocation of Pyoverdine into Host Cells Mediates Iron Removal and Activates a Specific Host Immune Response

city: Houston

first: Natalia

middle: V

last: Kirienko

address: 6100 Main St. MS140

department: BioSciences

institute: Rice University

summary: Pseudomonas aeruginosa is a re-emerging opportunistic pathogen with broad antimicrobial resistance. We have previously reported that the major siderophore pyoverdine from this pathogen disrupts mitochondrial networks and induces a lethal hypoxic response in model host Caernorhabditis elegans. However, the mechanism of such cytotoxicity remained unclear. Here, we demonstrate that pyoverdine translocates into host cells, binding to host ferric iron sources. The reduction of host iron content disrupts mitochondrial function such as NADH oxidation and ATP production and activates mitophagy. This activates a specific immune response that is distinct from colonization-based pathogensis and exposure to downstream pyoverdine effector Exotoxin A. Host response to pyoverdine resembles that of a hypoxic crisis or iron chelator treatment. Furthermore, we demonstrate that pyoverdine is a crucial virulence factor in P. aerguinosa pathogenesis against cystic fibrosis patients; ΔF508 mutation in human CFTR increases susceptibility to pyoverdine-mediated damage.

overall_design: There are 9 samples total that comprise three biological replicates of glp-4 animals exposed to S basal media or pyoverdine in liquid for 12 hours at 25°C, or left untreated on original agar plates. Each biological replicate consists of glp-4 C. elegans animals in the young adult developmental stage.


title: MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network


title: The NSL complex–mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise

status: Public on Jan 13 2019

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: We report that the Drosophila Non-Specific Lethal (NSL) complex is necessary to maintain this stereotypical nucleosomal organization at promoters. Upon NSL1 depletion, nucleosomes invade the NDRs at TSSs of NSL-bound genes. NSL complex member NSL3 binds to TATA-less promoters in a sequence-dependent manner.  We showed that the NSL complex is necessary and sufficient to recruit NURF chromatin remodeling complex to target promoters. The NSL complex is not only essential for transcription but is required for accurate TSS selection for genes with multiple TSSs. Further, loss of NSL complex leads to an increase in transcriptional noise. Thus, the NSL complex establishes a canonical nucleosomal organization that enables transcription and determines TSS fidelity.

overall_design: We performed (in 2-3 replicates) Mnase-seq (GST control, NSL1, INO80, NURF-301), ChIP-seq (NSL1, NURF-301 with Input control), MAPCap (upon knockdown of NSL1, with GST control), RNA-seq (upon knockdown of NSL1, with GST control), gDIP (genomic-DNA immunopurification, with GFP control, Input control, GST control, MCRS2, NSL1 and NSL3) and scRNAseq (upon knockdown of NSL1, with GST control) to systematically analyze how the NSL complex regulates transcription.

first: Kin

last: Lam

first: Ho-Ryun

last: Chung

first: Giuseppe

last: Semplicio

first: Vivek

last: Bhardwaj

first: Herbert

last: Holz

first: Plamen

last: Georgiev


title: Gene expression profiling of human iPS cell-derived podocytes and sorted human adult podocytes

city: Kumamoto

first: Yasuhiro

last: Yoshimura

state: Japan

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: Podocytes play an important filtration role in the kidney. We examined culture condition for efficient podocyte induction and established a method to selectively induce podocytes from human iPS cells. To understand how expression profiles of human iPS cell-derived podocytes were close to that in vivo, we isolated human adult podocytes for human adult kidney. Purified RNAs from human iPS cells, nephron progenitor cells, human immortalized podocyte cell line, human iPS cell-derived podocytes, and sorted human adult podocytes were analyzed by RNA-seq.

overall_design: Nephron progenitor cells from human iPS cells by the defined protocol, followed by the induction of podocytes by the newly established protocol. Human adult podocytes were sorted as Nephrin/Podocalyxin-positive population from the normal part of human adult kidney of nephrectomy patients with normal kidney function, whereas human non-podocytes were sorted as Nephrin/Podocalyxin-negative population. The immortalized human podocyte cell line were purchased from Bristol University and cultured under their published protocol. Podocyte mRNA profiles of these cells were examined.

first: Ryuichi

last: Nishinakamura


title: Mapping the molecular signatures of diet-induced NASH and its regulation by the hepatokine Tsukushi

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

summary:
OBJECTIVE: Nonalcoholic steatohepatitis (NASH) is closely associated with metabolic syndrome and increases the risk for end-stage liver disease, such as cirrhosis and hepatocellular carcinoma. Despite this, the molecular events that influence NASH pathogenesis remain poorly understood. The objectives of the current study are to delineate the transcriptomic and proteomic signatures of NASH liver, to identify potential pathogenic pathways and factors, and to critically assess their role in NASH pathogenesis.
METHODS: We performed RNA sequencing and quantitative proteomic analyses on the livers from healthy and diet-induced NASH mice. We examined the association between plasma levels of TSK, a newly discovered hepatokine, and NASH pathologies and reversal in response to dietary switch in mice. Using TSK knockout mouse model, we determined how TSK deficiency modulates key aspects of NASH pathogenesis.
RESULTS: RNA sequencing and quantitative proteomic analyses revealed that diet-induced NASH triggers concordant reprogramming of the liver transcriptome and proteome in mice. NASH pathogenesis is linked to elevated plasma levels of the hepatokine TSK, whereas dietary switch reverses NASH pathologies and reduces circulating TSK concentrations. Finally, TSK inactivation protects mice from diet-induced NASH and liver transcriptome remodeling.
CONCLUSIONS: Global transcriptomic and proteomic profiling of healthy and NASH livers revealed the molecular signatures of diet-induced NASH and dysregulation of the liver secretome. Our study illustrates a novel pathogenic mechanism through which elevated TSK in circulation promotes NASH pathologies, thereby revealing a potential target for therapeutic intervention.

overall_design: RNA-seq on healthy vs nonalcoholic steatohepatitis (NASH) mouse liver; RNA-seq on liver sinusoid endothelial cells of healthy vs NASH mouse liver.

first: Xuelian

last: Xiong

first: Henry

last: Kuang

first: Sahar

last: Ansari

first: Tongyu

last: Liu


title: Blimp1 is required to repress Foxp3+ regulatory T cell pathogenic activity in mice

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

summary: Foxp3+Tregcells are essential modulators of immune responses but under specific conditions can acquire inflammatory properties and potentially contribute to disease pathogenesis. Here we show that the transcription factor Blimp1 is a critical regulator of Foxp3+Treg functional plasticity. The intrinsic expression of Blimp1 was required to prevent Treg from producing Th17-associated cytokines and acquiring an inflammatory phenotype while preserving Foxp3 expression. Mechanistically, Blimp1 acts as a direct repressor of the Il17a/Il17f genes in Foxp3+Treg and binding of Blimp1 at this locus is associated with altered chromatin status, reduced binding the co-activator p300, unaltered binding of the Th17-asssociated transcription factor RORt and more abundant binding of IRF4, which was required for the production of IL17A in Blimp1-deficient Foxp3+Tregcells, as shown by IRF4 siRNA-mediated knockdown. Consistent with their capacity to produce inflammatory cytokines, Blimp1-deficient Foxp3+Treg exacerbate Th17-mediated inflammation in vivo indicating that Blimp1 is required to prevent Treg cells from acquiring pathogenic properties

overall_design: Total RNA from sorted Ctrl and Blimp1 CKO Foxp3 GFP+ pTreg cells

first: Rashmi

last: Bankoti

first: Chihiro

last: Ogawa

first: Jordan

last: Brown

first: Vincent

last: Funari

first: Gislâine

last: Martins


title: Expression analysis of T-ALL cell lines TALL-1, RPMI-8402, SUPT11 and P12-ICHIKAWA after treatment with NVS-ZP7-3

city: Cambridge

first: Joseph

last: Loureiro

address: 181 Massachusetts Ave

department: CBT

institute: Novartis

summary: Identification of a NVS-ZP7-3 response signature in T-ALL cell lines to understand the transcriptional response in both Notch pathway active cell lines and Notch pathway inactive lines.

overall_design: Four cell lines treated with DMSO control or NVS-ZP7-3 in triplicate for a total of 24 samples.

first: Christy

last: Fryer

first: Sara

last: Gans

first: Somnath

last: Bandyopadhyay

first: Nicole

last: Hartmann

first: Clarisse

last: Wache-Mainier

first: Frank

last: Staedtler


title: Genome-wide map of RNA polymerase II enrichment in Wild-Type and Ipa1-1 mutant samples

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

summary: We report on a comparison of ChIP-seq comparison of wild-type (BY4741) and Ipa1-1 mutant yeast, using duplicate samples of each genotype.  Our analysis shows that loss of Ipa1 function leads to loss of 3'-end formation, and specifically shows a distinct gain of occupancy immediately downstream of polyA sites, suggesting that inefficient cleavage is causing PolII to remain attached ot the genomic DNA for relatively longer periods of time.

overall_design: Examination of Ipa1-1 mutation induced changes in polII occupancy

first: Claire

last: Moore


title: Cell type specific profiling of alternative translation identifies novel protein isoforms in the mouse brain

city: St Louis

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: Translation canonically begins at a single AUG and terminates at the stop codon, generating one protein species per transcript. However, some transcripts may use alternative initiation sites or sustain translation past their stop codon, generating multiple protein isoforms. Through other mechanisms such as alternative splicing, both neurons and glia exhibit remarkable transcriptional diversity, and these other forms of post-transcriptional regulation are impacted by neural activity and disease. Here, using ribosome footprinting, we demonstrate that alternative translation is likewise abundant in the central nervous system and modulated by stimulation and disease. First, in neuron/glia mixed cultures we identify hundreds of transcripts with alternative initiation sites and confirm the protein isoforms corresponding to a subset of these sites by mass spectrometry. Many of them modulate their alternative initiation in response to KCl stimulation, indicating activity-dependent regulation of this phenomenon. Next, we detect several transcripts undergoing stop codon readthrough thus generating novel C-terminally-extended protein isoforms in vitro. Further, by coupling Translating Ribosome Affinity Purification to ribosome footprinting to enable cell-type specific analysis in vivo, we find that several of both neuronal and astrocytic transcripts undergo readthrough in the mouse brain. Functional analyses of one of these transcripts, Aqp4, reveals readthrough confers perivascular localization, indicating readthrough can be a conserved mechanism to modulate protein function. Finally, we show that AQP4 readthrough is disrupted in multiple gliotic disease models. Our study demonstrates the extensive and regulated use of alternative translational events in the brain and indicates that some of these events alter key protein properties. [NOTE: this GEO series only contains in vivo data]

overall_design: For in vivo experiments (4 samples in total): 2 replicates were prepared from P21 Snap25::eGFP-RpL10a mouse brains for profiling neurons, 2 replicates from Aldh1l1:: eGFP-RpL10a mouse brains for profiling astrocytes. All samples were uniquely indexed and pooled across two lanes.  For each sample, the uploaded fastq files are union of both lanes.

first: Darshan

last: Sapkota

first: Allison

middle: M

last: Lake

first: Wei

last: Yang

first: Chengran

first: Hendrik

last: Wesseling

first: Amanda

last: Guise

first: Ceren

last: Uncu

first: Jasbir

last: Dalal

first: Andrew

last: Kraft

first: Jin-Moo

last: Lee

first: Mark

last: Sands

first: Judith

last: Steen


title: RNAseq of rim cells and retinal neuroepithelial cells of zebrafish optic cup at 18-20ss stage

city: Dresden

first: Jaydeep

last: Sidhaye

state: Sachsen

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

summary: This data set was generated with the aim to identify a comprehensive list of genes expressed in the rim cells and the RNE cells during zebrafish optic cup morphogenesis. GFP expressed under vsx2 locus was used as a reporter to isolate the rim cells (with low GFP expression) and retinal neuroepithelial cells (with high GFP expression).

overall_design: Comparison of LowGFP (vsx2::GFP) vs HighGFP (vsx2::GFP) cells of 18-20 ss zebrafish optic cup; experiment was done in quadruplets per condition (for details, see PhD thesis J.Sidhaye: http://tud.qucosa.de/landing-page/?tx_dlf[id]=http%3A%2F%2Ftud.qucosa.de%2Fapi%2Fqucosa%253A30746%2Fmets)

first: Caren

last: Norden


title: N-cadherin expressing bone and marrow stromal progenitor cells maintain reserve hematopoietic stem cells

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Regulation of hematopoietic stem cells (HSCs) by bone marrow (BM) niches has been extensively studied; however, whether and how HSC subpopulations are distinctively regulated by BM niches remain unclear. Here, we functionally distinguished reserve HSCs (rHSCs) from primed HSCs (pHSCs) based on their response to chemotherapy and examined how they are dichotomously regulated by BM niches. Both pHSCs and rHSCs supported long-term hematopoiesis in homeostasis; however, pHSCs were sensitive but rHSCs were resistant to chemotherapy. Surviving rHSCs restored the HSC pool and supported hematopoietic regeneration after chemotherapy. The rHSCs were preferentially maintained in the endosteal region that enriches N-cadherin+ (Ncad+) bone-lining cells in homeostasis and post-chemotherapy. N-cad+ cells were functional bone and marrow stromal progenitor cells (BMSPCs), giving rise to osteoblasts, adipocytes, and chondrocytes in vitro and in vivo. Finally, ablation of Ncad+ niche cells or deletion of SCF from N-cad+ niche cells impaired rHSC maintenance during homeostasis and regeneration.

overall_design: Transcriptome analysis of HSPCs and niche cells in homeostasis and chemotherapeutic stress.  HSPCs include reserve HSCs, primed HSCs, ST-HSCs, MPPs.  Niche cells were isolated from both central marrow and endosteal region.

first: Linheng

last: Li

first: Meng

last: Zhao

first: Fang

last: Tao

first: Aparna

last: Venkatraman

first: Zhenrui

first: Sarah

last: Smith

first: Jay

last: Unruh

first: Christina

last: Ward

first: Pengxu

last: Qian

first: John

last: Perry

first: Heather

last: Marshall

first: Jinxi

last: Wang

first: Xi

last: He


title: small RNA-Seq of miR-181 deficient Treg cells

status: Public on Jan 04 2019

city: Frankfurt am Main

first: Nikita

middle: Aaron

last: Verheyden

state: Hessen

address: Sandhofstr. 2-4

institute: Institute for Molecular Medicine

summary: The interdependence of selective cues during development of regulatory T (Treg) cells in the thymus and their suppressive function remains incompletely understood. Here we analyzed this interdependence by taking advantage of highly dynamic changes of miR-181a/b-1 during late T-cell development with very high levels of expression during thymocyte selection followed by massive downregulation in the periphery. Loss of miR-181a/b-1 resulted in inefficient de novo generation of Treg cells in the thymus, but simultaneiously permitted homeostatic expansion in the periphery in the absence of competition. Modulation of T-cell receptor (TCR) signal strength in vivo indicated that miR-181a/b-1 controlled Treg cell formation via establishing adequate signaling thresholds. Unexpectedly, miR-181a/b-1-deficient Treg cells displayed elevated suppressive capacity in vivo, in line with elevated levels of CTLA-4 protein, but not mRNA, in thymic and peripheral Treg cells. Therefore, we propose that intrathymic miR-181a/b-1 controls development of Treg cells and imposes a developmental legacy on their peripheral function.

overall_design: miR-181a-1/b-1 deficient Treg cells were sorted and sequenced for small RNA. Wild type Treg cells were used as a control. Results were then analyzed for differential expression of micro RNAs. Three biological replicates were analyzed

middle: A

first: Samantha

last: Winter

first: Andreas

last: Krueger


title: Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation

status: Public on Jan 07 2019

first: Christopher

middle: Mitsuo

last: Uyehara

state: NY

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

summary: Modifications of histone H3 lysine 27 (H3K27) are strongly correlated with gene activation and gene repression. The histones bearing these modifications are encoded by both the replication-dependent H3 genes, and the replication-independent H3.3 genes. To examine the role that K27 modification of the H3.3 genes plays during development, we use CRISPR/Cas9 to mutate the endogenous H3.3 genes to a non-modifiable residue and performed RNAseq. We find that H3.3K27 is required for Polycomb target gene silencing, but this requirement is at a later stage of development than the requirement for replication-dependent H3K27. Notably, we find no evidence of transcriptional defects in H3.3K27 mutants, despite the strong correlation between H3.3K27 acetylation and active transcription.

overall_design: Total-RNAseq from whole, male pharates in wildtype, H3.3B K27R single mutants, and H3.3A K27R; H3.3B K27R double mutants.

first: Mary

last: Leatham-Jensen

first: Brian

middle: D

last: Strahl

first: Alan

middle: G

last: Matera

first: Robert

last: Duronio

first: Daniel

last: McKay


title: ENT1 and cell proliferation in the IVD

status: Public on Jan 05 2019

city: London

first: Matthew

last: Veras

state: ON

address: 1151 Richmond St.

country: Canada

institute: Western University

summary: Mice lacking equilibrative nucleoside transporter 1 demonstrate progressive calcification of spinal tissues including the annulus fibrosus (AF) of the intervertebral disc (IVD). To identify cellular pathways altered by loss of ENT1, we conducted microarray analysis of AF tissue from wild-type (WT) and ENT1-null mice before calcification (2 months) and associated with calcification (6 months).

overall_design: There are 2 timepoints in this data set, each with a respective WT control. Thus, there are 4 groups total: 2 month WT, 2 month ENT1-null, 6 month WT, and 6 month ENT1-null

first: Cheryle

last: Séguin


title: miRNA profiling of urinary exosomes to assess the progression of acute kidney injury

city: Augusta

first: Sang-Ho

last: Kwon

state: GA

address: 1460 Laney Walker Blvd  CB2820

department: Cellular biology and Anatomy

institute: Augusta University

summary: Using renal ischemia-reperfusion injury as a model of acute kidney injury, we deteremined temporally-released miRNAs released in urinary exosomes during the injury

overall_design: Examination of miRNAs released in urinary exosomes day 1, day 2, day 3, day 7, and day 14 post ischemia-reperfusion kidney injury


title: sRNA sequencing of HDL from human donors

status: Public on Jan 03 2019

city: Nashville

first: Leslie

middle: Roteta

last: Sedgeman

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

summary: miRNAs and other small RNAs have been found associated with high-density lipoproteins (HDL). The aim of this study was to investigate the miRNA signature on human HDL from 10 donors.

overall_design: Examination of miRNAs on human HDL

first: Kasey

last: Vickers


title: The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans

city: Worcester

first: Read

last: Pukkila-Worley

state: Massachusetts

address: 55 N Lake Ave

department: Medicine

institute: University of Massachusetts Medical School

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

Keywords: Expression profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Stem cell gene expression profiling of primary mammary tumors derived from orthotopic xenograft tumors treated with Sulforaphane (SFN) or control I

city: Bethesda

first: Anand

last: Merchant

address: 41 Center Dr

institute: NIH

type:
Expression profiling by array
Other

summary: In this study, we explored stem cell markers profile of mammary tumor initiation and growth derived from a human breast cancer cell line (MDA-MB-231 D3H1 Luci). In this dataset, we include expression data from primary mammary tumors pre-treated with Sulforaphane for 2 weeks (daily i.p. injection of 50mg SFN/kg) and kept treatment after cell injection for more 3 weeks and Saline 0.9% as a Control.

overall_design: In total, 36 samples were analyzed. We built a customized NanoString nCounter® Gene Expression Codeset of 107 genes and controls that contained significant embryonic core stem cell genes and epithelial-mesenchymal transition (EMT)-Mesenchymal Epithelial Transition (MET) markers.  We generated the following pairwise comparison using nSolver version 2.070: SFN vs. Saline.  Genes  with  a p-value < 0.05 and an absolute fold-change of 1.5 were selected.

first: Nadia

last: Pereira de Castro

first: David

last: Salomon


title: miRNA expression profiles and molecular networks in resting and LPS-activated BV-2 microglia - Effect of cannabinoids

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Cannabinoids are known to exert immunosuppressive activities. However, the mechanisms which contribute to these effects are unknown. Using lipopolysaccharide (LPS) to activate BV-2 microglial cells, we examined how Δ9-tetrahydrocannabinol (THC), the major psychoactive component of marijuana, and cannabidiol (CBD) the non-psychoactive component, modulate the inflammatory response through miRNA expression

overall_design: Sequencing analysis of mRNA and miRNA levels was performed using Illumina platform and the resulting expression patterns analyzed using the Ingenuity Pathway Analysis to identify functional subsets of genes, and the Ingenuity System Database to denote the gene networks regulated by CBD and THC.

first: Ana

last: Juknat

first: Fuying

last: Gao

first: Zvi

last: Vogel

first: Ewa

last: Kozela


title: The cell type resolved mouse transcriptome in neuron-enriched brain tissues from the hippocampus and cerebellum during prion disease

city: WInnipeg

first: Sarah

last: Medina

state: Manitoba

address: 1015 Arlington Street

department: One Health

institute: Public Health Agency of Canada

summary: Multiple cell types and complex connection networks are an intrinsic feature of brain tissue. In this study we used expression profiling of homogeneous cell populations from specific microscopic regions of heterogeneous tissue sections isolated by laser capture microdissection (LCM) to determine insights into the molecular basis of brain pathology in prion disease. Temporal profiles in two mouse models of prion disease, bovine spongiform encephalopathy (BSE) and a mouse-adapted strain of scrapie (RML) were performed in microdissected regions of the CA1 and cerebellar granular that are enriched in neuronal cell bodies. We noted that during clinical disease the number of activated microglia and astrocytes that occur in these areas are increased, thereby likely diluting the neuronal gene expression signature. We performed a comparative analysis with gene expression profiles determined from isolated populations of neurons, microglia and astrocytes to identify transcripts that are enriched in each of these cell types. Although the incubation periods of these two models are quite different, over 300 days for BSE and ~160 days for RML scrapie, these regional microdissections revealed broadly similar profiles. Microglial and astrocyte-enriched genes contributed a profound inflammatory profile consisting of inflammatory cytokines, genes related to phagocytosis, proteolysis and genes coding for extracellular matrix proteins. CA1 pyramidal neurons displayed a net upregulation of transcription factors and stress induced genes at pre-clinical stages of disease while all tissues showed profound downregulation of overlapping genes related to neuronal function, in particular transcripts related to neuronal communication including glutamate receptors, phosphatase subunits and numerous synaptic-related markers. Of note we found a small number of genes expressed in neurons that were upregulated during clinical disease including, COX6A, FZD9, RXRG and SOX11, that may be useful biomarkers of neurodegeneration.

overall_design: Biological replicates were compared between infected and control cells at each time point. A total of 5 time points were investigated (60, 140, 200, 300 DPI, and end point post-inoculation). Dye swaps were performed for each condition.

first: Anna

last: Majer

first: Debra

last: Sorensen

last: Martin

first: Kathy

last: Frost

first: Clark

last: Phillipson

last: Manguiat

first: Stephanie

last: Booth


title: Stem cell gene expression profiling of primary mammary tumors derived from orthotopic xenograft tumors treated with Sulforaphane (SFN) or control

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


title: Impaired TNFa-driven dendritic cell activation limits LPS-induced protection from asthma in infants.

city: Birmingham

first: Beatriz

last: Leon Ruiz

state: Alabama

address: 1825 University Blvd

department: Microbiology

institute: University of Alabama at Birmingham

summary: We found that approximately 200 genes were differentially expressed between CD11b+ lung-migratory dendritic cells (CD11b+ mDCs) from adult and infant mice treated with house dust mite allergen + LPS, and that the TNFa-via NFkB signaling pathway was significantly enriched in CD11b+ mDCs from adults relative to those from infants. Specifically, out of the 200 genes in the hallmark TNFa-via NFkB signaling pathway that were analyzed, 31 genes were significantly downregulated in CD11b+ mDCs from infants compared to CD11b+ mDCs from adults.

overall_design: We conducted an RNA-seq analysis on sorted CD11b+ lung-migratory dendritic cells (CD11b+ mDCs: B220-CD64-CD103-CD11c+MHCIIhiCD11b+) from adult (7wks-old) and infant (2-3wks-old) mice obtained from the mediastinal lymph node (mLN) 24 hours after house dust mite allergen (HDM) +LPS intranasal sensitization. This analysis was performed to identify and quantify differentially expressed genes and differentially enriched signaling pathways between CD11b+ mDCs from adults and infants.

first: Kamaljeet

last: Kaur

first: Holly

last: Bachus

first: Tatiana

middle: T

last: Marquez-Lago

first: Amber

last: Papillion

first: André

last: Ballesteros-Tato

last: León


title: MARCKS and lnc-MARCKS act as inflammation regulators

city: La jolla

first: Qiong

last: Zhang

state: California

address: 9500 Gilman Dr.

department: Pediatrics

institute: UCSD

summary: The goals of this study are to reveal the target transcriptome of MARCKS and lnc-MARCKS in TLR2 signaling pathway. We knocked down MARCKS, or over-expressed lnc-MARCKS in THP1-derived macrophages stimulated with Pam3CSK4 for 8 hours. And compared the transcriptomes of the editing cells with control cells

overall_design: Transcriptome in MARCKS knock-down or lnc-MARCKS overexpressed cells

first: Ti-chun

last: Chao


title: MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network with PRC2 [miRNA-seq]

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We performed miRNA-seq to test for global loss of miRNA in response to VP55 overexpression.

overall_design: miRNA-seq in WT and EZH2-/- T98G cells and VP55 overexpressed WT and EZH2-/- T98G cells.

first: Haridha

last: Shivram


title: mRNA Expression Data from murine Medial Prefrontal Cortex and Hippocampus at baseline, 64 hours post-MI, and 8 weeks post-MI in Clock∆19/∆19 and WT C57Bl/6 mice

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

state: Ontario

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

institute: University of Guelph

summary:
Male Clock∆19/∆19 and WT C57Bl/6 mice were randomized into 3 groups: i) baseline, ii) short-term post-myocardial infarction (MI; 64h post-MI), iii) long-term post-MI (heart failure, HF; 8 weeks post-MI). Medial prefrontal cortex (mPFC) and hippocampus brain regions were collected at ZT19 (waketime).
The microarray approach allows the investigation of transcriptome-wide gene expression changes in brain regions from Clock∆19/∆19 and WT mice at baseline, post-MI, and in HF.

overall_design: There are a total of 48 samples: i) 4 Clock∆19/∆19 HF mPFC , ii) 4 WT HF mPFC, iii) 4 Clock∆19/∆19 MI mPFC , iv) 4 WT MI mPFC, v) 4 Clock∆19/∆19 baseline mPFC , vi) 4 WT baseline mPFC, vii) 4 Clock∆19/∆19 HF hippocampus , viii) 4 WT HF hippocampus, ix) 4 Clock∆19/∆19 MI hippocampus , x) 4 WT MI hippocampus, xi) 4 Clock∆19/∆19 baseline hippocampus , xii) 4 WT baseline hippocampus. Animals were sacrificed at 7 hours into the dark phase (ZT19).

first: Tami


title: Investigation of gene expression profiles in a rat adjuvant arthritis model

city: Hangzhou

first: Weifeng

last: Hu

address: NO.318, chaowang road

institute: The second affiliated hospital of Zhejiang Chinese medical university

summary: In order to study the molecular biological mechanism underlying the inhibition of RA synovial pannus by triptolide, differentially expressed genes in synovial tissues from an adjuvant arthritis (AA) rat model with and without triptolide treatment were detected and verified by gene transcripts produced by Agilent Technologies.

overall_design: An AA model was established by injecting 0.1 ml Freund's complete adjuvant (i.p.) daily for 18 days and scored by arthritis index assessment. Triptolide (0.4 mg/kg) or an equivalent amount of saline was administered daily for 14 days. Subsequently, synovial tissues from the ankle joints of the rats' hind legs were obtained. Total RNA was extracted and purified, and microarray hybridization was used to investigate the effect of triptolide on the gene expression profile in RA.

first: Yang

last: Zou


title: lncRNA-PCAT1 knockdown effect on the gene expression of androgen independent LNCaP (LNCaP-AI) cell line

status: Public on Jan 01 2019

city: Tianjin

first: Yuanjie

last: Niu

address: Pingjiang Road 23

institute: Tianjin Institute of Urology

summary: We generated and characterized an androgen-independent LNCaP-AI cell line by long-term culture of androgen-dependent LNCaP cells in RPMI-1640 medium containing charcoal-stripped serum. This approach used to generate the line mimics the castration resistant condition for treating prostate cancer, supporting the relevance of the LNCAP-AI cell line to Castration Resistant Prostate Cancer.

overall_design: LNCaP-AI cells transfected with lncRNA PCAT1 shRNA and the scramble shRNA were used for the RNA-seq.

first: Zhiqun

last: Shang

first: Qian

last: Dong

first: Libin

last: Sun

first: Jianpeng

last: Yu


title: Randomized PAM depletion of AsCas12a

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: We report the PAMs of AsCas12a using a cell-free TXTL-based cleavage assay. By adding randomized PAM library and AsCas12a-gRNA in vitro, functional PAM sequences were cleaved, while non-functional PAMs remained. By amplifying the non-cleaved DNA, we use next-generation sequencing to analyze the depletion of functional PAMs of AsCas12a.

overall_design: Uncleaved DNA from the randomized PAM library was amplified using Illumina Nextera Indices

first: Thomas

last: Jacobsen


title: Divergent biological response to neoadjuvant chemotherapy in muscle-invasive bladder cancer

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

institute: GenomeDx

summary: Despite cisplatin-based neoadjuvant chemotherapy (NAC) 60% of patients with muscle-invasive bladder cancer still have residual invasive disease at radical cystectomy (RC). The NAC-induced biological alterations in these cisplatin-resistant tumors remain largely unstudied. We analyzed gene expression from 133 patients with residual invasive disease after cisplatin-based NAC. H&E and immunohistochemistry were used to confirm tissue sampling and gene expression analysis. Established molecular subtyping models proved to be inconsistent in their classification of the post-NAC samples. Unsupervised consensus clustering revealed four distinct consensus clusters (CC). The CC1-Basal and CC2-Luminal subtypes expressed genes consistent with a basal-like and a luminal-like phenotype, respectively. The CC3-Immune subtype had the highest immune activity, including T-cell infiltration and checkpoint molecule expression, but lacked both basal and luminal markers. The CC4-Scar-like subtype expressed genes associated with wound-healing/ scarring and was associated with favorable prognosis.

overall_design: RC samples were available for gene expression analysis from 133 patients with residual invasive disease after cisplatin-based NAC. Unsupervised consensus clustering (CC) was performed and the CC were investigated for their biological and clinical characteristics. H&E and immunohistochemistry on tissue microarrays were used to confirm tissue sampling and gene expression analysis.

first: Roland

last: Seiler

first: Ewan

last: Gibb

first: Natalie

middle: Q

last: Wang

first: Htoo

middle: Z

last: Oo

first: Hung-Ming

last: Lam

first: Kim

middle: E

last: van Kessel

first: Charlotte

middle: S

last: Voskuilen

first: Brian

last: Winters

first: Mandeep

last: Takhar

first: Nicholas

last: Erho

first: James

last: Douglas

first: Funda

last: Vakar-Lopez

first: Simon

middle: J

last: Crabb

first: Bas

last: van Rhijn

first: Elisabeth

last: Fransen van de Putte

first: Ellen

middle: C

last: Zwarthoff

first: George

middle: N

last: Thalmann

first: Joost

last: Boormans

first: Marc

last: Dall'Era

first: Michiel

last: van der Heijden

first: Jonathan

last: Wright

first: Peter

last: Black


title: Muscle stem cells give rise to rhabdomyosarcomas in severe model of Duchenne muscular dystrophy

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

summary: We identified muscles as cells of origin of rhabdomyosarcoma in dystrophic mice

overall_design: We compared expression profiling from 6 different muscles population immediately after isolation through cell sorting

middle: B

last: Sesillo

first: Alessandra

last: Sacco


title: MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network with PRC2 [RNA-seq]

first: Vishy

last: Iyer

summary: We performed RNA-seq to identify differentially expressed genes in response to knockout of EZH2 and global miRNA knockdown (VP55 overexpressed) in T98G Glioblastoma multiforme cells.

overall_design: RNA-seq in WT and EZH2-/- T98G cells and VP55 overexpressed WT and EZH2-/- T98G cells.

first: Haridha

last: Shivram


title: Shift work disrupts circadian regulation of the transcriptome in hospital nurses

first: Karen

middle: L.

last: Gamble

address: 1720 7th Ave S

department: Psychiatry

summary: In the present study, we sought to determine the degree of circadian misalignments of hormonal and transcriptional rhythms with the timing of sleep-wake behavior on days off in day-shift and night-shift hospital nurses. We conducted a genome-wide microarray analysis on RNA isolated from PBMCs to examine individual variability of transcriptional rhythms.

overall_design: Total RNA obtained from isolated PBMCs every three hours from night-shift and day-shift nurses on a day off, in controlled laboratory conditions (isocaloric, and time-matched meals and low dim red light).


title: Relation between biofilm and virulence in Vibrio tapetis, a transcriptomic study

city: Evreux

first: Sophie

last: Rodrigues

state: ---US State---

address: 55 rue saint germain

country: France

institute: Université de Rouen

summary: The aim of this study is to compare the transcriptomic profiles of V. tapetis in biofilm culture vs. In planktonic culture and to understand the relation between biofilm and virulence.

overall_design: V. tapetis mRNA profiles of 48h planktonic culture (Liquid) and biofilm culture (Biofilm) were generated by deep sequencing, in triplicate, using Illumina HiSeq.

first: Christine

last: Paillard

first: Sabine

last: Van Dillen

first: Ali

last: Tahrioui

first: Jean-Marc

last: Berjeaud

first: Alain

last: Dufour

first: Alexis

last: Bazire


title: Genome-wide maps of Trim33, Ctcf and H3K27ac binding in embryoid bodies

city: Ann Arbor

first: Vesa

middle: Matti

last: Kaartinen

state: MI

address: 1011 N. University

department: BMS

institute: University of Michigan

summary: We report high throughput profiling and co-occupancy of Trim33, Ctcf and H3K27ac in differentiating embryoid bodies derived from mouse embryonic stem cells. An average of ~37 million reads were generated for each of the described samples and input sample generating 4,426, 52,446, 30,047 peaks respectively for Trim33, CTCF and H3K27ac. Motif enrichment analyses for Trim33 ChiP-Seq data returned CTCF and BORIS (CTCF analog) motifs as best matches. Of the merged peaks, 723 were shared by Trim33, CTCF as well as H3K27ac. In addition, 1299 peaks were shared by Trim33 and CTCF, 1131 were shared by Trim33 and H3K27ac and  3321 were shared by CTCF and H3K27ac.

overall_design: Examination of genome-wide binding of Trim33, Ctcf and H3K27ac in differentiating embryoid bodies at day 6 in culture in vitro.

first: Sudha

last: Rajderkar

middle: M


title: Micro-RNAs secreted through astrocyte-derived extracellular vesicles cause neuronal network degeneration in C9orf72 ALS

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
Background: Astrocytes regulate neuronal function, synaptic formation and maintenance partly through secreted extracellular vesicles (EVs). In amyotrophic lateral sclerosis (ALS) astrocytes display a toxic phenotype that contributes to motor neuron (MN) degeneration.

Methods: We used human induced astrocytes (iAstrocytes) from 3 ALS patients carrying C9orf72 mutations and 3 non-affected donors to investigate the role of astrocyte-derived EVs (ADEVs) in ALS astrocyte toxicity. ADEVs were isolated from iAstrocyte conditioned medium via ultracentrifugation and resuspended in fresh astrocyte medium before testing ADEV impact on HB9-GFP+ mouse motor neurons (Hb9-GFP+ MN). We used post-mortem brain and spinal cord tissue from 3 sporadic ALS and 3 non-ALS cases for PCR analysis.

Findings: We report that EV formation and miRNA cargo are dysregulated in C9ORF72-ALS iAstrocytes and this affects neurite network maintenance and MN survival in vitro. In particular, we have identified downregulation of miR-494-3p, a negative regulator of semaphorin 3A (SEMA3A). We show here that by restoring miR-494-3p levels through expression of an engineered miRNA mimic we can downregulate Sema3A levels in MNs and increases MN survival in vitro. Consistently, we also report lower levels of mir-494-3p and higher levels of SEMA3A in cortico-spinal tract tissue isolated from sporadic ALS donors, thus demonstrating the pathological importance of this pathway in MNs and its therapeutic potential.

Interpretation: ALS ADEVs and their miRNA cargo are involved in MN death in ALS and we have identified miR-494-3p as a potential therapeutic target.

overall_design: Gene expression profiling utilised total RNA extracted from extracellular vesicles derived from astrocytes directly reprogrammed from human C9ORF72 ALS patient (n=3) and control fibroblasts (n=3).

first: Andre

last: Varcianna

first: Monika

middle: A

last: Myszczynska

first: Lydia

last: Castelli

first: Brendan

last: O’Neill

first: Yeseul

last: Kim

first: Jordan

last: Talbot

last: Nyberg

first: Immanuelle

last: Nyamali

middle: R

first: Matthew

last: Stopford

first: Guillaume

last: Hautbergue

first: Laura

last: Ferraiuolo


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

city: Burlington

first: Travis

last: Sullivan

state: MA

address: 41 Mall Rd.

institute: Lahey Hospital & Medical Center

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 35 samples analyzed in the screening analysis.  The data was normalized to the global mean of each sample using microRNA detected in all samples with a Cq<37.

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.

last: Browne


title: Effect of lactation and location relative to the corpus luteum on the transcriptome of the bovine oviduct epithelium

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

summary: Lactation and associated metabolic stresses during the post-partum period have been shown to impair fertility in dairy cows. The oviduct plays key roles in  embryo development and the establishment of pregnancy in cattle. The aim of this study was to investigate the effects of lactation and location relative to the corpus luteum (CL) on the transcriptome of the bovine oviduct epithelium.

overall_design: An original animal model was used. At 60 days post-partum, Holstein lactating (n=4) and non-lactating (i.e. never milked after calving; n=5) cows, as well as control nulliparous heifers (n=5), were slaughtered on Day 3 following induced œstrus, and epithelial samples from the ampulla and isthmus ipsilateral and contralateral to the corpus luteum (CL) were recovered for RNA sequencing. Differentially expressed genes (DEGs) were identified between heifers compared with both postpartum groups.

first: Yann

last: Locatelli

first: Niamh

last: Forde

first: Helmut

last: Blum

first: Benoît

last: Piegu

first: Pascal

last: Mermillod

first: Eckhard

last: Wolf

first: Patrick

last: Lonergan

first: Marie

last: Saint-Dizier


title: MicroRNA profiles in red drum (Sciaenops ocellatus) larvae exposed to Deepwater Horizon oil

city: Riverside

first: Genbo

last: Xu

address: 900 University Ave

institute: University of California, Riverside

summary:
Purpose:To help identify molecular regulatory mechanisms of developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, microRNA profiles in red drum larvae exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated  using High Throughput Sequencing (HTS).
Methods:Total microRNA profiles of 48 hpf red drum larvae after source oil (0.135%, 0.27%, and 0.54%)  and slick oil (1.25%, 2.5% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq 500.
Results: Source and slick oil significantly dysregulated the expression of miR-18a, miR-27b, and miR-203a across all exposure concentrations. The target genes of these miRNAs were predominantly involved in the neuro-cardio system development processes and associated key signaling pathways such as axonal guidance signaling, CREB signaling in neurons, synaptic long-term potentiation pathway, calcium signaling and role of NFAT in cardiac hypertrophy.

overall_design: Total microRNA profiles of 48hpf red drum larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Elvis

middle: G

first: Alex

last: Khursigara

first: Andrew

last: Esbaugh

first: Martin

last: Grosell

first: Daniel

last: Schlenk


title: Affymetrix human DMET Plus array in GIST patients treated with imatinib

city: Bologna

first: Gloria

last: Ravegnini

state: BO

address: via irnerio 48

department: PHARMACY AND BIOTECHNOLOGY

country: Italy

institute: UNIVERSITY OF BOLOGNA

summary: To understand the contribution of germline DNA polymorphisms discriminating between imatinib clinical outcome and toxicity, 38 GIST patients (all with KIT exon 11 mutation) treated with imatinib were analyzed through Affymetrix human DMET Plus array.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples of imatinib responder and non responder patients. Analysis of 38 patients

first: Sabrina

last: Angelini

first: Maria

last: Pantaleo


title: The tumor suppressor PTEN regulates negatively Sertoli cell proliferation, testis size and sperm production in vivo

status: Public on Jan 02 2019

city: Geneve

first: Chloe

last: MAYERE

address: Michel Servet, 1

country: Switzerland

institute: UNIGE

summary: Single cell data from E16.5 SF1-GFP mouse testis

overall_design: Two captures of testis cells from E16.5 male embryos using 10X chromium device

first: Yasmine

last: Neirijnck

first: Chloé

last: Mayère

first: Serge

last: Nef

first: Pauline

last: Sararols

first: Françoise

last: Kühne


title: Circulating microRNAs from HCC patients recruited in the Ph3 RESORCE trial

city: Berlin

first: Henrik

last: Seidel

address: Muellerstr. 178

institute: Bayer AG

summary: Micro RNAs are deregulated in a variety of human cancers.In this study we analayzed baseline expression levels of circulating human micro RNAs from patients of the Ph 3 RESORCE trial for predictive value of overall survival and time to progression.

overall_design: Plasma samples from 343 patients.

first: Michael

last: Teufel


title: Transcriptomic response to mild rhizotoxic ion stresses: Comparison of gene expression responses to mild concentration of rhizotoxic ions (Al, Cu, Cd and NaCl) in Arabidopsis roots.

city: Gifu

first: Kazutaka

last: Kusunoki

state: Gifu

address: 1-1 Yanagido

department: Faculty of Applied Biological Sciences

institute: Gifu University

summary: Transcriptional profiling of genes recoverd by Arabidopsis Col-4 line. The roots were exposed to Al, Cd, Cu and NaCl stressed conditions, then genes recovered expression were analyzed. Goal is identification of the genes worked for milder rhizotoxic ion stresses.

overall_design: Two-condition experiment, rhizotoxic ion treatment v.s. control. Biological replicates: 3 of Al treatments replicates, 3 Cd treatment replicates, 3 Cu treatment replicates, 3 NaCl treatment replicates.

first: Yasufumi

last: Kobayashi

first: Yuriko

first: Hiroyuki

last: Koyama


title: Stem cell gene expression profiling of primary mammary tumors derived from orthotopic xenograft tumors treated with Sulforaphane (SFN) or control II

city: Bethesda

first: Anand

last: Merchant

address: 41 Center Dr

institute: NIH

summary: In this study, we explored stem cell markers profile of mammary tumor initiation and growth derived from a human breast cancer cell line (MDA-MB-231 D3H1 Luci). In this dataset, we include expression data from primary mammary tumors pre-treated with Sulforaphane for 2 weeks (daily i.p. injection of 50mg SFN/kg) and kept treatment after cell injection for more 3 weeks and Saline 0.9% as a Control.

overall_design: In total, 36 samples were analyzed. We used a commercially available NanoString nCounter Human Stem Cell.  We generated the following pairwise comparison using nSolver version 2.070: SFN vs. Saline.  Genes  with  a p-value < 0.05 and an absolute fold-change of 1.5 were selected.

first: Nadia

last: Pereira de Castro

first: David

last: Salomon


title: Identification of fatty acid regulatory genes using in silico analysis from Ovary and Hepatopancreas ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon)

city: Khlong Luang

first: Wananit

last: Wimuttisuk

state: PATHUM THANI

address: 113 Thailand Science Park

country: Thailand

institute: National Center for Genetic Engineering and Biotechnology

summary: Comparisons of gene expression profiles in hepatopancreas and ovary of domesticated broodstock at different ovarian maturation stages were made through a cDNA microarray in the black tiger shrimp (Penaeus monodon).   Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR.  Selected genes were further characterized.

overall_design: A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 6826 features. RNA samples were extracted from both hepatopancreas and ovaries of pooled mature broodstock (11 month-old, pooled from n=10 ), individual broodstocks from Surath Thani Provice in Thailand. The RNA from ovaries and hepatopancreases of shrimp at week 0 (before the experiment began) were labeled with Cy3 dye as a reference and those of ovaries and hepatopancreas after treatment (4 weeks of feeding with polychaetes and unilateral eyestalk ablation) were labeled with Cy5 dye.

first: Pacharawan

last: Deenarn

first: Punsa

last: Tobwor

first: Rungnapa

last: Leelatanawit

first: Somjai

last: Wongtripop

first: Jutatip

last: Khudet

first: Nitsara

last: Karoonuthaisiri

first: Vanicha

last: Vichai


title: Gene expression data from atopic dermatitis induced NC/Nga mouse model skin

city: Seoul

first: Kwang Hoon

last: Lee

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Dermatology

country: South Korea

institute: Yonsei University College of Medicine

summary:
We identified zinc-alpha-2-glycoprotein (ZAG), a 41-kDa adipokine that regulates body weight, lipid, and mobilization, as a novel biomarker for AD. ZAG levels were consistently decreased in sera, T cells, and skin in human AD patients compared with healthy controls.
We used microarrays to obtain the change of signaling molecules by topical treatment of recombinant ZAG using atopic dermatitis induced mouse model.

overall_design: Atopic dermatitis induced NC/Nga mice skin was collected for RNA extraction and hybridization on Affymetrix microarrays. We compared two groups:  1) Atopic dermatitis induced NC/Nga mice using house dust mice ointment (n=3), 2) Atopic dermatitis induced NC/Nga mice treated with 1 μg/mL of recombinant ZAG (n=3).

first: Ji-Yeon

last: Noh

first: Jung-U

last: Shin

first: Kwang-Hoon


title: mRNA changes in mir-71(n4115) Caenorhaditis elegans

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 assess mRNA changes in mir-71(n4115) compared to wildtype (N2) we performed a Microarray analysis with 4 biological replicates at day 1 of adulthood.

overall_design: Synchronized day 1 C. elegans were collected for RNA extraction and subsequent hybridization on an Affymetrix microarray.

first: Fabian

last: Finger


title: A genome-wide framework for mapping gene regulation via cellular genetic screens

city: SEATTLE

first: Molly

last: Gasperini

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Over one million candidate regulatory elements have been identified across the human genome, but nearly all are unvalidated and their target genes uncertain. Approaches based on human genetics are limited in scope to common variants, and in resolution by linkage disequilibrium. We present a multiplex, eQTL-inspired framework for mapping enhancer-gene pairs by introducing random combinations of CRISPR/Cas9-mediated perturbations to each of many cells, followed by single-cell RNA-seq. Across two experiments, we used dCas9-KRAB to perturb 5,920 candidate enhancers with no strong a priori hypothesis as to their target gene(s), measuring effects by profiling 254,974 single-cell transcriptomes. We identified 664 (470 high-confidence) cis enhancer-gene pairs, which were enriched for specific transcription factors, non-housekeeping status, and genomic and 3D conformational proximity to their target genes. This framework will facilitate the large-scale mapping of enhancer-gene regulatory interactions, a critical yet largely uncharted component of the cis-regulatory landscape of the human genome.

overall_design: Three scRNA-seq datasets of a low multiplicity-of-infection (MOI) pilot gRNA screen, high MOI pilot, and at-scale screen, in addition to bulkRNA-seq used to validate individual enhancer-gene pairs from the screens.