title: ChIRP_seq data for Rrp6 project analysis in malaria (Plasmodium falciparum)

summary: We adopted the technique of Chromatin Isolate by RNA Purification combined with high-throughput sequencing (ChIRP-seq) to gain mechanistic insight into the transcriptionally regulatory role of the trans-acting RUF6 ncRNA in detail

overall_design: We performed the ChIRP-seq assay with the parasite lines PfRrp6-DD-1C and WT 3D7-G7, and the probe pool were designed on the antisense strand of RUF6 ncRNAs while the probes from the sense strand  were designed as complementary control.


title: Defined p16High senescent cell types are indispensable for mouse healthspan

status: Public on Jan 01 2020

city: Nice

first: Dmitry

last: Bulavin

address: 28 Av Valomdrose

country: France

institute: IRCAN

type: Expression profiling by high throughput sequencing

summary: The accumulation of senescent cells can drive many age-associated phenotypes and pathologies. Consequently, it has been proposed that removing senescent cells might extend lifespan. Here we generated two knock-in mouse models targeting the best-characterized marker of senescence, p16Ink4a. Using a genetic lineage tracing approach, we found that age-induced p16High senescence is a slow process that manifests around 10-12 months of age. The majority of p16High cells were vascular endothelial cells mostly in liver sinusoids (LSECs), and to lesser extent macrophages and adipocytes. In turn, continuous or acute elimination of p16High senescent cells disrupted blood–tissue barriers with subsequent liver and peri-vascular tissue fibrosis and health deterioration. Our data show that senescent LSECs are not replaced after removal and have important structural and functional roles in the aging organism. In turn, delaying senescence or replacement of senescent LSECs could represent a powerful tool in slowing down aging.

overall_design: CD31-positive cells were purified from the livers of 1-yeal-old p16-Cre/Rosa26-mTmG mice and subsequently FACS-sorted to get GFP-positive and GFP-negative fractions. These fractions were used for RNA-Seq analysis.

first: Laurent

last: Grosse


title: Rrp6-mediated heterochromatin surveillance secures antigenic variation and sexual commitment of human malaria parasites

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

country: China

institute: Tongji University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptomic Characterization of Human Beige Adipocyte Differentiated From Adipose Mesenchymal Stem Cells

city: Athens

first: Liang

last: Zhang

state: GA

address: 325 Riverbend Road

department: Biochemistry and Molecular Biology, Center for Molecular Medicine

country: USA

institute: University of Georgia

summary: Beige adipocytes are a distinct type of thermogenic fat cells in human. Since beige adipocytes are distributed sporadically within white adipose, characterization of human beige adipocytes has long been a problem. In this study, we reported a rapid and roboust method in generating human beige adipocyte with chemically defined medium and RNA-Seq was perfomed to reveal the molecular characterization of derived human beige adipocytes.

overall_design: mRNA profiling of adipose derived mesenchymal stem cells and in vitro differentiated beige adipocytes were generated by RNA-Seq, in duplicate, using illumina NextSeq platform. mRNA profile of in vitro differentiated white adipocytes were also generated by same method and serve as control.

first: Amar

last: Singh

first: Stephen

last: Dalton


title: Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence

status: Public on Jan 02 2020

city: Aglantzia

first: Vasilis

middle: J

last: Promponas

state: Nicosia

address: 1 Panepistimiou Avenue

department: Department of Biological Sciences

country: Cyprus

institute: University of Cyprus

summary: Gene expression analysis of highly vs. lowly pathogenic P. aeruginosa strains identifies many virulence factors and only a few metabolism genes related to virulence. Functional transcriptomics re-analysis of core metabolism at the pathway level, reveals amino-acid, succinate, citramalate, and chorismate biosynthesis and beta-oxidation as important for full virulence and expression of these pathways indicative of virulence in various strains.

overall_design: Highly pathogenic Pseudomonas aeruginosa strains (PA14, MTB-1 and B136-33) were compared with lowly pathogenic ones (CF5, C3719 and PACS2) via RNAseq using  RNA isolated from LB cultures at OD600nm 1 and 3 in 2 biological replicates each.

first: Yiorgos

last: Apidianakis


title: RNA_seq data for Rrp6 project analysis in malaria (Plasmodium falciparum)

summary: We carried out strand-specific RNA-seq libraries followed by deep sequencing (RNA-seq) to explore the transcriptional profile of the PfRrp6-DD-1C,PfRrp6-DD-1B,PfRrp6-DD-4C,WT 3D7-G7, WT NF54 and PfMaf1-OE lines.

overall_design: The RNA-seq assay was carried out to detect the transcriptional profiles in PfRrp6-DD three clones and PfMaf1-OE line  with WT 3D7-G7, NF54 and vector lines as control.

first: Yanting

last: Fan

first: Guiying

last: Wei

first: Cizhong

last: Jiang

first: Qingfeng


title: Functional specification of CCK+ interneurons by alternative isoforms of Kv4.3 auxiliary subunits

status: Public on Dec 31 2019

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: CCK-expressing interneurons (CCK+INs) are crucial for controlling hippocampal activity. We found two firing phenotypes of CCK+INs in rat CA3 area; either possessing a previously undetected membrane potential-dependent firing or regular firing phenotype, due to different low-voltage-activated potassium currents. These different excitability properties destine the two types for distinct functions, because the former is essentially silenced during realistic 8-15 Hz oscillations. The general excitability, morphology and gene-profiles of the two types were surprisingly similar. Even the expression of Kv4.3 channels were comparable, despite evidences showing that Kv4.3-mediated currents underlie the distinct firing properties. Instead, the firing phenotypes were correlated with the presence of distinct isoforms of Kv4 auxiliary subunits (KChIP1 vs. KChIP4e and DPP6S). Our results reveal the underlying mechanisms of two previously unknown types of CCK+INs and demonstrate that alternative splicing of few genes, which may be viewed as a minor event in the cells’ whole transcriptome, can underlie distinct cell-type identity.

overall_design: mRNA profiles of 17 CCK+/CNR1+ CA3 interneurons, 8 showing rectifying firing (TOR type),  9 showing regular firing (RS type)

first: Viktor

last: Oláh

first: David

last: Lukacsovich

first: Jochen

last: Winterer

first: Andrea

last: Lörincz

first: Zoltan

last: Nusser

first: János

last: Szabadics


title: Late recurrence-associated long non-coding RNA NR2F1 antisense 1 (NR2F1-AS1) II

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National cancer center research institute

summary: Long non-coding RNA NR2F1 antisense RNA1 (lncRNA NR2F1-AS1) was identified as the main candidate associated to late recurrence in ER-positive breast cancer clinical samples. Gain-of-function of NR2F1-AS1 induced the expression of dormancy-inducers BMP4 and DEC2, and upregulated pluripotency markers NANOG and OCT4. Representative pathways entailed to metastatic events such as HER2/Neu, hypoxia, EMT and inflammatory-response were also found enriched.

overall_design: We identified the lncRNA NR2F1 antisense RNA1 (NR2F1-AS1) as the main candidate associated to late recurrence in ER-positive breast cancer. We conducted in vitro gain-of-function of NR2F1-AS1 variant1 and variant 4 in breast cancer BT474 cell line and applied microarray-based analysis.

first: Anna

middle: S

last: Calle

first: Yumi

last: Kawamura

first: Ai

last: Mitsuhashi-Hironaka

first: Makiko

last: Ono

first: Fumitaka

last: Takeshita

first: Takahiro

last: Ochiya


title: RIP_seq data for Rrp6 project analysis in malaria (Plasmodium falciparum)

first: Shijun

last: Shen

summary: We carried out RNA Immunoprecipitation followed by deep sequencing (RIP-seq) to explore the difference of direct target substrates of PfRrp6 and RNA exosome core

overall_design: We carried out RIP-seq assay to detect specific recognition of Rrp6 by PfRrp6 line with PfRrp4 and GFP as control

first: Yanting

last: Fan

first: Guiying

last: Zhang


title: Microarray expression profile analysis of long non-coding RNAs and mRNAs in A Rat Carotid Artery Balloon Injury Model

city: Guangzhou

first: Yu

last: Zhou

state: Guangdong

address: No 58, Zhongshan 2nd street

department: Division of Vascular Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

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

summary: Restenosis after angioplasty or stent is a major clinical problem. While long noncoding RNAs (lncRNAs) are implicated in a variety of diseases, their role in restenosis is not well understood. This study aims to investigate how dysregulated lncRNAs and mRNAs contribute to restenosis.

overall_design: The differentially expressed lncRNAs and mRNAs between 3 sham control carotid arteries and 3 balloon-injuried carotid arteries(14days) were examined using Arraystar Rat LncRNA microarray v2.0 system.

first: Zuojun

last: Hu


title: Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome.

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

summary: During stress, while global mRNA translation is reduced, specific stress-responsive transcripts are translated. How stress-responsive mRNAs are selectively translated is unknown. Ribosome modifications may facilitate selective translation of specific transcripts in different cell types under differing conditions.  Here we identify METL-5 as a C. elegans N6-adenosine methyltransferase that methylates adenosine 1717 on 18S rRNA. METL-5 specifically enhances ribosomal binding and selective translation of a cytochrome P450 mRNA, cyp-29A3, whose protein product oxidizes the omega-3 polyunsaturated fatty acid (PUFA) eicosapentaenoic acid to eicosanoids, important signaling molecules in stress responses. In fact although mutant metl-5 C. elegans grow normally under homeostatic conditions, they are resistant to a variety of stresses, including heat shock, cold, oxidants and UV irradiation. metl-5 mutant worms have reduced overall lipid levels and of bioactive lipid eicosanoids. Moreover, dietary supplementation of eicosanoid products of CYP-29A3 restores stress sensitivity of metl-5 mutant worms. Thus methylation of a specific residue of 18S rRNA by METL-5 selectively enhances translation of cyp-29A3, to increase production of eicosanoids that increase stress-related death.

overall_design: Comparing transcriptomes and ribosome profiles of adult nematode worms. Two strains (WT and DMETL-5), two temperatures (20 and 37 ⁰C), 3 replicates in each group.

first: Noa

last: Liberman-Isakov

first: Eric

last: Greer


title: High resolution and allelic-specific annotation of preimplantation embryo transcriptome using long-read sequencing

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: We used an combination of long-read and short-read sequencing data to explore the transcriptome of preimplantation embryo

overall_design: We selected 7 stage of early embryo including sperm and oocyte from ♂DBA/2J and ♀C57/BL6J and sequenced using Pacbio and Illumina

first: Huang

last: Shisheng

first: Ren

last: Chao

first: Yuan

last: Jie

first: Qiao

last: Yunbo

first: Liu

last: Zhen

first: Shu

last: Wenjie


title: Comparison of transcriptome in gonads and somatic tissues in mice

city: Dresden

first: Attila

last: Toth

state: Saxony

address: Fiedlerstr. 42

department: Faculty of Medicine

country: Germany

institute: TU Dresden

summary: RNA from female gonads (C57/BL6xDBA/2 background) at different developmental stages (11.5dpc, 12.5dpc, 14.5dpc, 16.5dpc, 18.5dpc, 20.5dpc – dpc: days post coitum) together with RNA from adult testes and 17 different somatic tissues was used for transcriptome comparison.

overall_design: For each developmental stage from female gonads RNA was extracted from at least a pool of 34 ovaries. Total RNA samples from different mouse somatic tissues were purchased via Ambion (liver, brain, thymus, heart, lung, spleen and kidney) and Zyagen (mammary gland, pancreas, placenta, salivary gland, skeletal muscle, skin, small intestine, spinal cord, tongue and uterus)


title: Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize

city: Fort Pierce

first: Joshua

last: Voss

state: FL

address: 5600 N US Highway 1

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

summary: Variation in transciptomic patterns between shallow and mesophotic corals was assessed using tag-based RNA-Seq (Tag-Seq) through analysis of natural populations across four regions in the Gulf of Mexico. Additionally, colonies were fate-tracked and repeatedly sampled to assess changes in gene expression through time in a transplant experiment between shallow and mesophotic depth zones at West and East Flower Garden Banks. This repository contains the raw .fastq.gz files for all sequenced samples.

overall_design:
Examination of gene expression between shallow and mesophotic depths across four sites for natural populations. Examination of gene expression through time between depth tratements for manipulative experiment.

Please note that the isogroup notations (in the processed data files, e.g. Mcavernosa00001, Cladocopium100036 etc.) correspond to uniprot database annotations for the coral host (Montastraea cavernosa) and the dominant algal symbiont (Cladocopium sp.). Mcavernosa_Cladocopium_iso2geneName.tab is the corresponding isogroup-to-gene lookup table used for downstream analyses

first: Michael

last: Studivan

middle: D


title: Late recurrence-associated long non-coding RNA NR2F1 antisense 1 (NR2F1-AS1)

first: Yusuke

last: Yamamoto

overall_design: Applied microarray-based analysis to 24 ER-positive breast cancer clinical specimens. The clinical specimens were selected from  ER-positive breast cancer patients who did not receive any treatment previously to the needle-biopsy and developed distant metastases 10 years after the initial diagnosis. Same criteria were applied for ER-positive breast cancer specimens from patients with no signs of distant metastases after 10 years. We successfully identified the lncRNA NR2F1 antisense RNA1 (NR2F1-AS1) as a main lncRNA linked to recurrence. Clinical samples were gifted from the National Cancer Center Hospital of Japan (Tsukiji, Tokyo, Japan).

first: Anna

last: Calle

first: Yumi

last: Kawamura

first: Ai

last: Mitsuhashi-Hironaka

first: Makiko

last: Ono

first: Fumitaka

last: Takeshita

first: Takahiro

last: Ochiya


title: Gene expression of splenocytes in collagen-induced arthritis (CIA)  model between Wildtype and Stinggt/gt mice.

status: Public on Dec 27 2019

city: Ratchathewi

first: Mookmanee

last: Tansakul

state: Bangkok

country: Thailand

institute: Mahidol university

summary: To explore the effect of sting molecule in CIA model, we decided to performed microarray for study at how the difference in gene expression profiles between wildtype and Stinggt/gt mice.

overall_design: We injected chicken collagen type II plus CFA intradermally to the mice. After two weeks of injection, mice were euthanasia and spleen were collected to perform microarray.

first: Prapaporn

last: Pisitkun


title: Directed Remodeling of the Mouse Gut Microbiome Inhibits the Development of Atherosclerosis

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome


title: Directed Remodeling of the Mouse Gut Microbiome Inhibits the Development of Atherosclerosis [bacteria]

summary: The gut microbiome is a malleable microbial community that can remodel in response to various factors, including diet, and contribute to the development of several chronic diseases, including atherosclerosis. We devised an in vitro screening protocol of the mouse gut microbiome to discover molecules that can selectively modify bacterial growth. This approach was used to identify cyclic D,L-α-peptides that remodeled the Western diet (WD) gut microbiome toward the low-fat-diet microbiome state. Daily oral administration of the peptides in WD-fed LDLr-/- mice reduced plasma total cholesterol levels and atherosclerotic plaques. Depletion of the microbiome with antibiotics abrogated these effects. Peptide treatment reprogrammed the microbiome transcriptome, suppressed the production of pro-inflammatory cytokines (including interleukin-6, tumor necrosis factor-α and interleukin-1β), rebalanced levels of short-chain fatty acids and bile acids, improved gut barrier integrity and increased intestinal T regulatory cells. Directed chemical manipulation provides an additional tool for deciphering the chemical biology of the gut microbiome and might advance microbiome-targeted therapeutics.

overall_design: We examined the transcriptional profile of gut microbiome in the mice on regular chow diet (CHD) or high-fat diet (HFD) after the lead peptide treatment

first: P

middle: B

first: M

middle: R

last: Ghadiri

first: L

last: Leman


title: Directed Remodeling of the Mouse Gut Microbiome Inhibits the Development of Atherosclerosis [mouse tissue]

overall_design: We examined the transcriptional profile in the liver and ileum from the mice on regular chow diet (CHD) or high-fat diet (HFD) after the lead peptide treatment


title: Glioneuronal tumor with CLIP2-MET fusion: A case report

status: Public on Dec 28 2019

city: Seoul

first: Jongil

last: Kim

address: Daehak-ro 103

country: South Korea

institute: Seoul National University

type: Genome variation profiling by high throughput sequencing

summary: Glioneuronal tumor (GN) is one type of biphasic central nervous system (CNS) tumor that exhibits both glial and neuronal immunohistological characteristics. We report a case of glioneuronal tumor (GN) with a discovery of novel gene fusion of CLIP2-MET resulting from aberrant chromosome 7 abnormalities. The tumor exhibited typical characteristics on histological examinations. We executed an elaborate genomic study on this case including whole-exome sequencing and RNA sequencing. Genomic analysis of the tumor revealed aberrations in chromosomes 1 and 7 and a CLIP2-MET fusion. Further analysis of the upregulated genes revealed substantial connections with MAPK pathway activation. We concluded that the chromosome 7 abnormalities prompted CLIP2-MET gene fusion which successively leads to MAPK pathway activation. We deliberated that MAPK pathway activation is responsible for the oncogenesis of GN based on our case and other previously reported ones.

overall_design: Whole exome seq, RNA seq and methyl-seq

first: Chul-Kee

last: Park

first: Jong-Il

first: Tamrin

last: Chowdhury

first: Yeajina

last: Lee


title: Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility

status: Public on Dec 21 2019

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

type: Methylation profiling by high throughput sequencing

summary: Predicting dairy bull fertility is a current challenge for the dairy industry. The goal of this study was to integrate DNA methylation data with previously published RNA sequencing results in order to identify candidate markers for sire fertility.

overall_design: Five high-fertility bulls and five low-fertility bulls were used for this study. Sperm samples were subjected to DNA extraction and subsequent whole-genome bisulfite sequencing.

first: Hasan

last: Khatib

last: Peñagaicano


title: Transcriptional regulation of arogenate dehydratase genes linked to lignin biosynthesis in maritime pine [11PP17]

status: Public on Dec 17 2019

city: MALAGA

first: FERNANDO

last: DE LA TORRE

state: MALAGA

address: CAMPUS DE TEATINOS SN

department: BIOLOGIA MOLECULAR Y BIOQUIMICA

country: Spain

institute: UNIVERSIDAD MALAGA

summary:
Microarray analysis of Pinus pinaster plantlets (stem) downregulated for the PpMYB8 transcription factor.
Transgenic 11PP17 vs control plants

overall_design: Total RNA was extracted from 16 month old transgenic plants (downregulated for PpMYB8) and controls. RNA was extracted from stems.

first: Fernando

last: de la Torre

first: Jorge

last: El-Azaz

middle: M

last: Canovas


title: Identification of GLYMA.08G357600 binding sites in soybean mid-maturation embryos II.

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.08G357600 in mid-maturation embryos using ChIP-seq.

overall_design: Identification of Glyma.08G357600 binding sites in soybean embryos at the mid-maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates, with two technical replicates (sequencing lanes) for each sample.  A total of 4 samples were sequenced using the Illumina HiSeq2500 platform.

first: Julie

last: Pelletier

first: Russell

last: Baden

first: Leonardo

last: Jo

first: Min

first: Robert

last: Golberg


title: Human interleukin-4 treated regulatory macrophages promote epithelial wound healing and reduce colitis in an mouse model

status: Public on Dec 16 2019

city: Calgary

first: Matthew

last: Workentine

state: Alberta

address: 3280 Hospital Drive NW

country: Canada

institute: University of Calgary

summary: Murine alternatively activated macrophages can exert anti-inflammatory effects.  Expanding upon this, we sought to determine the ability of human IL-4-treated macrophages (i.e. hM(IL4)) to promote epithelial wound repair and serve as a novel anti-inflammatory cell transfer treatment for inflammatory bowel disease (IBD).   Blood monocytes from healthy volunteers and patients with Crohn’s disease or ulcerative colitis (active and inactive disease) were converted to macrophages and treated with IL-4.  Subsequently, cells were assessed by qPCR, in in vitro epithelial wounding and permeability models, and for anti-colitic capacity in dinitrobenzene sulphonic acid (DNBS)-treated Rag1-/- mice. IL-4 treatment of blood-derived macrophages from healthy volunteers and patients with inactive IBD resulted in a characteristic CD206+CCL18+CD14low/- phenotype (RNA-seq revealed IL-4 affected expression of 996 genes). Conditioned media from freshly generated or cryopreserved hM(IL4)s were equally effective in promoting wound healing, and reducing cytokine-driven loss of epithelial barrier function in vitro.  Systemic delivery of hM(IL4) to DNBS-treated Rag1-/- mice significantly reduced disease as assessed my macroscopic disease and histopathology scores.  Remarkably, the anti-colitic effect of hM(IL4) transfer was still apparent when mice were challenged with DNBS one month after receiving hM(IL4)s. Positing that hM(IL4)s would be anti-colitic, this study demonstrates the capacity of M(IL4)s from healthy volunteers and patients with inactive IBD to promote epithelial recovery after injury and to suppress colitis.  These novel findings with hM(IL4), provide proof-of-concept support for the development of autologous M(IL4) transfer as a cellular immunotherapy for IBD.

overall_design: 3 samples of IL4-treated blood derived macrophages were compared to 3 sample of untreated macrophages

first: Derek

last: McKay

first: Timothy

last: Jayme

middle: L


title: Transcriptional regulation of arogenate dehydratase genes linked to lignin biosynthesis in maritime pine

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

overall_design: Refer to individual Series


title: Transcriptional regulation of arogenate dehydratase genes linked to lignin biosynthesis in maritime pine [11PP16A]

summary:
Microarray analysis of Pinus pinaster plantlets (stem) downregulated for the PpMYB8 transcription factor.
Transgenic 11PP16 vs control plants


title: Analysis and comprehensive comparison of Pacbio and Nanopore-based RNA-sequencing in Arabidopsis transcriptome

status: Public on Dec 15 2019

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: Rapidly increased studies by third-generation sequencing [Pacific Biosciences (Pacbio) and Oxford Nanopore Technologies (ONT)] have been used in all kinds of research areas. Among them, the plant full-length single-molecule transcriptome studies were most used by Pacbio while ONT was rarely used. Therefore, in this study, we developed ONT RNA-sequencing methods in plants. We performed a detailed evaluation of reads from Pacbio and Nanopore PCR cDNA (ONT Pc) sequencing in plants (Arabidopsis), including the characteristics of raw data and identification of transcripts. We aimed to provide a valuable reference for applications of ONT in plant transcriptome analysis.

overall_design:
Sequencing the Arabidopsis cDNA samples from overall ground parts at the same growth stage by Pacbio and Nanopore platform repectively. And then, we compared the advantages and disadvantages between Pacbio and Nanopore RNA-seq.
Please note that the Sample 1 RNA-seq is to generate a transcriptome assembly and the rest of the samples are to quantify the gene expression.

first: Jiawen

last: Cui


title: A Central Role for PRC1 in Shaping the 3D Nuclear Landscape

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary:
1. Loss of RING1B substantially disrupts nuclear architecture.
2. PRC1 mediated looping can occur at a Mb scale and is independent of CTCF.
3. Polycomb mediated looping is driven by canonical PRC1 complexes.
4. Trimeric PRC1-mediated interactions occur in vitro and in vivo.
5. Gene up-regulation does not directly lead to the loss of PRC1 loops.

overall_design: Hi-C analysis of WT, RING1B I53A and RING1B KO E14 mouse ES cells; 4 replicates for WT and 2 replicates each, for both mutants.

first: Shelagh

last: Boyle

first: Iain

last: Williamson

first: Dipta

last: Sengupta

first: Wendy

middle: A

last: Bickmore

last: Illingworth


title: Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (scRNA-seq)

status: Public on Dec 12 2019

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Here we characterize microglia transcriptional program across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, while humans express significant microglia heterogeneity. In addition, we observed notable differences in complement, phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders, including Alzheimer’s and Parkinson’s disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia-based therapies in humans.

sample_organism:
Danio rerio
Gallus gallus
Callithrix jacchus
Macaca fascicularis
Homo sapiens
Ovis aries
Mesocricetus auratus
Mus musculus
Rattus norvegicus
Nannospalax galili

overall_design: Single cell and bulk RNA-seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3-6.

first: Laufey

last: Geirsdottir

first: Eyal

last: David

first: Assaf

last: Weiner

first: Hadas

last: Keren-Shaul

first: Igor

last: Ulitsky


title: WaGa single cell RNA sequencing of the MCC cell line WaGa under HDAC inhibitor treatment compared to untreated WaGa control cells

city: Essen

first: Jan

last: Gravemeyer

address: Universitätstraße 1

institute: DKZF

summary: The Merkel cell carcinoma cell line (MCC) WaGa was sequenced without and under HDAC inhibitor treatment using the 10x Genomics 3' Chromium v2.0 platform. The treatment induced changes were analysed on a single cell level.

overall_design: scRNAseq of the MCC cell line WaGa under HDAC inhibitor treatment compared to untreated WaGa control cells

first: Fan

last: Kaiji

first: Becker

last: Jürgen

first: Gravemeyer

last: Jan


title: Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program

platform_organism:
Danio rerio
Gallus gallus
Callithrix jacchus
Macaca fascicularis
Homo sapiens
Ovis aries
Mesocricetus auratus
Mus musculus
Rattus norvegicus
Nannospalax galili


title: The global gene expression profiling of the earliest phase of the differentiation of human embryonic stem cells into classical brown adipocytes

status: Public on Dec 10 2019

city: Sinjuku-ku

first: Kumiko

last: Saeki

address: 1-21-1 Toyama

institute: National Center for Global Health and Medicine

summary: Although brown adipocyte (BA) is known to be derived from Myf5-positive myoblasts, its earlier developmental process remains unknown. To understand its pre-myoblastic developmental pathway, human embryonic stem cells (KhES-3) were subjected to a directed differentiation into BA using multiple culture dishes at a time. Cells were harvested from each dish with an interval of 2 to 6 hours and total RNA was extracted for the analyses.

overall_design: RNA samples were collected totally at 19 time points during the 72-hour differentiation culture. All samples were subjected to microarray analyses.

first: Norihiko

last: Kobayashi

first: Miwako

last: Nishio


title: Expression data for patients with myocardial infarction (MI) vs healthy patients

status: Public on Dec 06 2019

city: Moscow

first: German

last: Osmak

address: 3-ya Cherepkovskaya

country: Russia

institute: National Medical Research Center for Cardiology

summary:
Myocardial infarction (MI) is one of the most severe manifestations of coronary artery disease (CAD) and the leading cause of death from non-infectious diseases worldwide. It is known, that the central component of CAD pathogenesis is a chronic vascular inflammation. However, the mechanisms underlying the changes that occur in T, B and NK-lymphocytes, monocytes and other immune cells during CAD and MI are still poorly understood. One of those pathogenic mechanisms might be the dysregulation of intracellular signaling pathways in the immune cells.
In the present study we performed a transcriptome profiling in peripheral blood mononuclear cells of MI patients and healthy individuals. The machine learning algorithm was then used to search for  MI-associated signatures, that could reflect the dysregulation of intracellular signaling pathways and be assisted in MI diagnosis and/or prognosis.
ADAP2, KLRC1, MIR21, PDGFD and CD14 genes were identified as the most important signatures for the classification model with L1-norm penalty function. The classifier output quality was equal to 0.911 by Receiver Operating Characteristic metric on test data. These results were validated on two independent open GEO datasets.

overall_design: 6 patients with myocardial infarction (MI) were analyzed vs 6 healty patients

first: Natalia

last: Baulina

first: Philipp

last: Koshkin

first: Olga

last: Favorova


title: Expression data from 18-month old rats

status: Public on Dec 03 2019

first: Yujie

last: Wang

address: 49 North Garden Road, Haidian District

department: Department of Anesthesiology

institute: Peking Universtity Third Hospital

summary:
Multiple mechanisms and pathophysiological changes after anesthesia, such as brain aging and neurodegenerative diseases. And the gene transcription patterns and modulation networks after general anesthesia remains to be elucidated.
We used microarrays to detail the global programme of gene expression in rats after sevoflurane anesthesia and identified distinct classes of changed.

overall_design: Eighteen-month old male Sprague-Dawley rats were subjected to 2.5% sevoflurane (case group) or 100% oxygen (control group) exposure for 4 h. The hippocampus was selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Cheng

last: Ni


title: Genome-wide profiling of transcription, H3K27me3 and RING1B occupancy in mouse ESCs following EZH1/2 inhibition

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

summary: Mouse embryonic stem cells (mESCs) were treated with DMSO (control) or EPZ-6438 (EPZ; a potent inhibitor of the EZH1/2) for 24 h. ChIP-seq was used to determine the impact of this treatment on the level and distribution of H3K27me3 and RING1B genome-wide. In parallel, gene expression was assessed by deep sequencing of both total RNA (RNA-seq) and 4-thiouridine metabolically labelled RNA (4sU-seq). Calibrated ChIP-seq, utilizing Drosophila chromatin as an exogenous control, demonstrated a marked global depletion of H3K27me3 following 24 h of EPZ treatment concomitant with a substantial reduction in RING1B occupancy. A rather modest change in the levels of total and nascent transcripts allowed us to identify a direct contribution of the polycomb system in controlling chromatin architecture and 3D nuclear organization.

overall_design: Following 24 h of treatment with either DMSO or EPZ-6438, mESCs were processed for ChIP-seq (calibrated H3K27me3 and non-calibrated RING1B), RNA-seq and 4sU-seq. Two independent replicate experiments were prepared for each sample.

first: Shelagh

last: Boyle

first: Ilya

last: Flyamer

first: Iain

last: Williamson

first: Dipta

last: Sengupta

first: Wendy

last: Bickmore

first: Robert


title: Single cell RNA sequencing of total peritoneal cells from Beclinf/f-Lyz2cre mice

status: Public on Dec 02 2019

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

summary: In Beclinf/f-Lyz2cre mice, we observed proinflammatory activation of tissue-resident peritoneal macrophages. These mice were resistent to lethal bacterial infection with Listeria. It is important to understand how the peritoneal immunity is affected by Beclin deletion in myeloid cells. To characterize the immune cells in the peritoneum, we performed single cell RNA sequencing of total peritoneal cells from Beclinf/f-Lyz2cre and littermate control Beclinf/f mice. The single cell RNA-seq analyses revealed profound changes in both the myeloid compartment and bystander cells.

overall_design: Total peritoneal cells from Becn1f/f-LysMcre and Becn1f/f mice, n=4 each, age 8 wks

first: Ya-Ting

first: Konstantin

last: Zaitsev

first: Qun

last: Lu

first: Shan

last: Li

first: W

middle: T

last: Schaiff

first: Ki-Wook

last: Kim

first: Lindsay

last: Droit

first: Craig

last: Wilen

first: Chandni

last: Desai

first: Dale

last: Balce

last: Orchard

first: Anthony

last: Orvedahl

first: Sunmin

last: Park

first: Darren

last: Kreamalmeyer

first: Scott

last: Handley

first: John

last: Pfeifer

first: Megan

last: Baldridge

middle: N

first: Christina

last: Stallings

first: Herbert

middle: W

last: Virgin


title: The landscape of alternative splicing in aggressive prostate cancers

city: Los Angeles

middle: W.

last: Phillips

state: California

address: 675 Charles E Young Drive South

department: MIMG

institute: UCLA

summary: We sought to define the landscape of alternative pre-mRNA splicing in prostate cancers and the relationship of exon choice to known genetic driver alterations. To do so, we compiled a meta-dataset comprised of RNA-Seq samples from publicly available sources representing a range of phenotypes from normal tissue to drug resistant metastases. We subjected these samples to exon-level analysis with purpose-built software. We then correlated transcriptional signatures of cancer driver pathways with these alternative splicing events and discovered that Myc signaling was correlated with incorporation of a set of cassette exons found in RNA binding proteins. We experimentally verified this finding in a human prostate cell transformation assay. Our results connect changes in alternative pre-mRNA splicing to oncogenic alterations common in prostate and many other cancers. We also establish a role for Myc in regulating RNA processing by controlling the incorporation of nonsense mediated decay-determinant exons in RNA binding proteins.

overall_design: Whole transcriptome sequencing of three independent cell lines derived from the prostate epithelium of three different human specimens. c-Myc was withdrawn over a time course and mRNA was collected at 0 and 24 hours. Also includes processed data files that represent RNA expression values and exon inclusion data (percent spliced in, PSI) for a prostate meta-dataset that includes de-identified normal prostate tissue and cancer samples combined from previously-published studies and presented here as part of a unified analysis.

first: Yang

last: Pan

first: Brandon

last: Tsai

first: Zhijie

last: Xie

first: Levon

last: Demirdjian

first: Wen

last: Xiao

first: Harry

last: Yang

first: Yida

last: Zhang

first: Chia

middle: H

last: Lin

first: Donghui

last: Cheng

first: Douglas

last: Black

first: Owen

last: Witte

first: Yi

last: Xing


title: Dual RNA-seq on pneumococcal infection to murine lung

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

country: Netherlands

institute: University of Groningen

summary: Tropism is a very important factor in pneumococcal infection. Previous study has shown that clinical isolate showed niche preference in model organism. In particular, ear isolate showed particular tropism in nasopharyngeal carriage while blood isolate survives better in the murine lung. We have detected a SNP located inside rafR, repressor of sugar metabolism regulon, that contributes to strain tropism. We then perform a swap mutation between the rafR ear and blood isolates and perform intranasal infection using the four strains: original ear and blood isolates, ear isolate with rafR blood isolate and blood isolate with rafR ear isolate. We harvested the lung six hours into infection and exploited the recently described dual RNA-seq to reconstruct transcriptomics landscape during host-pathogen interaction.

sample_organism:
Streptococcus pneumoniae
Mus musculus

platform_organism:
Streptococcus pneumoniae
Mus musculus

overall_design: Twelve samples are analysed, categorized into four conditions with three replicates each

first: Jan-Willem

last: Veening

first: Vikrant

middle: V

last: Minhas

first: Lauren

last: McAllister

first: Claudia

middle: C

last: Trappetti

first: James

last: Paton


title: MYT1 attenuates neuroblastoma cell differentiation by inhibiting retinoic acid signaling pathway

status: Public on Dec 01 2019

city: Shanghai

first: Kai

last: Chen

address: NO.1665, Kongjiang Road

institute: Xinhua hospital

summary: This study first reveals that MYT1 is a potential oncogene in neuroblastoma, which is significantly correlated with poor prognosis and represses cellular differentiation via interrupting retinoic acid signaling pathway.

overall_design: MYT1 knockout was performed in neuroblastoma cell line SK-N-BE(2)

first: Zhixiang

last: Wu


title: A Quantitative Method for Proteome Reallocation Using Minimal Regulatory Interventions

status: Public on Nov 30 2019

city: Cuernavaca

first: José

last: Utrilla

state: Morelos

address: Av. Universidad sn

department: Centro de Ciencias Genómicas

country: Mexico

institute: Universidad Nacional Autónoma de México

summary: Engineering resource allocation in biological systems is an ongoing challenge. Organisms allocate resources for ensuring survival, reducing the productivity of synthetic biology functions. Here we present a novel approach for engineering the resource allocation of Escherichia coli by rationally modifying its transcriptional regulatory network. Our method (ReProMin) identifies the minimal set of genetic interventions that maximises the savings in cell resources. To this end, we categorized Transcription Factors according to the essentiality of its targets and we used proteomic data to rank them. We designed the combinatorial removal of TFs that maximise the release of resources. Our resulting strain containing only three mutations, theoretically releasing 0.5% of its proteome, had higher proteome budget, increased production of an engineered metabolic pathway and showed that the regulatory interventions are highly specific. This approach shows that combining proteomic and regulatory data is an effective way of optimizing strains using conventional molecular methods.

overall_design: Examination of 3 different KO in two E. coli strains by duplicate

first: Gustavo

last: Lastiri-Pancardo

first: J

last: Mercado-Hernandez

first: Juhyun

last: Kim

middle: I

last: Jiménez


title: Relationship between cell cycle and diel transcriptomic changes in metabolism in a unicellular red alga

status: Public on Nov 26 2019

city: Mishima

first: Takayuki

last: Fujiwara

state: Shizuoka

address: Yata 1111

institute: National institute of genetics

summary: Metabolism, cell cycle stages, and related transcriptomes in eukaryotic algae change with the diel cycle of light availability. In the unicellular red alga Cyanidioschyzon merolae, the S and M phases occur at night. To examine how diel transcriptomic changes in metabolic pathways are related to the cell cycle and to identify all genes, for which mRNA levels change depending on the cell cycle, we examined diel transcriptomic changes in C. merolae. In addition, we compared transcriptomic changes between the wild type and transgenic lines, in which the cell cycle was uncoupled from the diel cycle by the depletion of either cyclin-dependent kinase A (CDKA) or retinoblastoma-related (RBR) protein. Of 4,775 nucleus-encoded genes, the mRNA levels of 1,979 genes exhibited diel transcriptomic changes in the wild type. Of these, the periodic expression patterns of 454 genes were abolished in the transgenic lines, suggesting that the expression of these genes is dependent on cell cycle progression. The periodic expression patterns of most metabolic genes, except those involved in starch degradation and de novo dNTP synthesis, were not affected in the transgenic lines, indicating that the cell cycle and transcriptomic changes in most metabolic pathways are independent of the diel cycle. Approximately 40% of the cell–cycle–dependent genes were of unknown function, and approximately 19% of these genes of unknown function are shared with the green alga Chlamydomonas reinhardtii. The dataset presented in this study will facilitate further studies on the cell cycle and its relationship with metabolism in eukaryotic algae.

overall_design: The C. merolae wild type, G1-arrested HA-CDKA-conditional knockdown (cKD) and RBR-KO cells cultured in the 12-h light and dark cycle at 42°C. The algal cells were collected every four hours (8 samples through the diurnal LD cycle). To obtain two replicates of the data sets, pairs of LD cultures of the wild type and HA-CDKA-cKD were performed twice 1 month apart as biological replicates [WT1 vs. HA-CDKA-cKD1 (rep. 1) and WT2 vs. HA-CDKA-cKD2 (rep.2)] and  pairs of LD cultures of the wild type and RBR-KO were performed twice 1 month apart as biological replicates [WT3 vs. RBR-KO1 (rep.1) and WT4 vs. RBR-KO2 (rep.2)].

first: Shunsuke

last: Hirooka

first: Ryudo

last: Ohbayashi

first: Ryo

last: Onuma

first: Shin-ya

last: Miyagishima


title: RNA sequencing analysis of shControl and shSASH1 in MDA-MB-468 cells

status: Public on Nov 23 2019

city: Dalian

first: dapeng

last: Liang

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

summary: We performed RNA-seq to determine the impact of SASH1 depletion on global gene expression profile.The results reveal that dysregulated genes were enriched for genes related to cell adhesion, extracellular matrix (ECM) organization and cell migration, suggesting SASH1 may play a critical role in determining the invasion and metastasis phenotype in breast cancer cells.

overall_design: Investigate transcriptomic difference between control and SASH1-depleted cells.

first: Ke

last: Jiang

first: Songshu

last: Meng

first: Dapeng


title: In vitro and in vivo epigenome-wide CRISPR screens in mouse KrasG12D/P53-/- (KP) lung adenocarcinoma model

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: To systematically study the functions of epigenetic genes in controlling tumor progression and regulating anti-tumor immunity, we performed a series of in vitro and in vivo epigenome-wide CRISPR screens in mouse KP lung adenocarcinoma model.  We constructed an epigenetic-focused sgRNA library, established KP-Cas9-library pools, and then performed in vitro and in vivo CRISPR screens. For in vitro screens, we compared the cell pools harvested at week 4 with the cells pools harvested at week 2 to check the functions of epigenetic genes in tumor cell proliferation. For in vivo screens, we compared the IgG treated tumors in Rag1-/- mice or WT mice with the input cell pool to check the functions of epigenetic genes in tumor growth; we compared the IgG treated tumors in WT mice with the IgG treated tumors in Rag1-/- mice to check the functions of epigenetic genes in regulating anti-tumor immunity; we compared the anti-PD-1 treated tumors in WT mice with IgG treated tumors in WT mice to check the functions of epigenetic genes in modulating sensitivity to anti-PD-1 treatment.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Examination of sgRNA abundance in library, cultured cell pools, input cell pool  and tumors with different treatments.

first: Fei

last: Li

first: Kwok

middle: K

last: Wong


title: Integrated analyses of early responses to radiation in glioblastoma identify new alterations in RNA processing and candidate targets to improve treatment outcomes

city: San Antonio

first: David

last: Kadosh

state: Texas

address: 7703 Floyd Curl Dr., MC: 7758

department: Department of Microbiology, Immunology & Molecular Genetics

institute: University of Texas Health Science Center at San Antonio

summary: High-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation.

overall_design: Expression and Ribosome profilling of U251 and U343 glioblastoma cell lines at three time points T0, T1, and T24. U251 RNA-seq: T0 (2 replicates); T1 (3 replicates); T24 (3 replicates). U343 RNA-seq: T0 (3 replicates); T1( 3 replicates); T24 (3 replicates). U251 Ribo-seq: T0 (2 replicates); T1 (3 replicates); T24 (3 replicates). U343 Ribo-seq: T0 (3 replicates); T1( 3 replicates); T24 (3 replicates).

first: Luiz

middle: O

last: Penalva

first: Saket

last: Choudhary


title: Paralog-specific phenotypes of ribosomal protein mutants identify translational control mechanisms in the cell cycle and replicative longevity

status: Public on Nov 20 2019

city: College Station

first: Rodolfo

last: Aramayo

address: Room 412, Biological Sciences Building West (BSBW)

department: Biology

institute: Texas A&M University

summary: The translational efficiency of mRNAs of cells progressing synchronously through the mitotic cell cycle has been interrogated by ribosome profiling.

overall_design: Ribosome Profiling (RP) and Transcriptional Profiling (TP) samples corresponding to a cell-size series, for the following Saccharomyces cerevisiae ribosome protein mutants: RPL22A, RPL22B, RPL34A, and RPL34B

first: Michael

last: Polymenis


title: In vitro transcriptomic responses to thioacetamide-S-oxide exposure in Sprague-Dawley rat primary hepatocytes, renal tube epithelial, and cardiomyocytes

status: Public on Nov 19 2019

city: Frederick

first: Patric

last: Schyman

state: Maryland

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

summary: In this study we tested the ability to predict organ injury endpoints from in vitro transcriptomics responses at early time points (9 and 24 hours) after to thioacetamide-S-oxide treatment, the toxic metabolite of thioacetamide. Thioacetamide, an organosulfur compound, have been extensively used in animal studies as a hepatotoxin and carcinogen for its ability to cause acute liver damage.

overall_design: We treated three-cell types from Sprague-Dawley rats, primary hepatocytes (vehicle, low (0.025 mM), or high (0.125 mM) dose), renal tube epithelial cells (vehicle, low (0.125 mM), or high (0.500 mM) dose), and cardiomyocytes (vehicle, low (0.50 mM), or high (1.50 mM) dose) with thioacetamide-S-oxide. RNA-seq data were collected 9 and 24 hours after application of vehicle or thioacetamide-S-oxide.

first: Richard

last: Printz

first: Shanea

last: Estes

first: Tracy

middle: P

last: O’Brien

first: Masakazu

last: Shiota

first: Anders

last: Wallqvist


title: Prediction of novel non-coding RNAs relevant for the growth of Pseudomonas putida in a bioreactor

city: Oeiras

first: Cecilia

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

summary:
Pseudomonas putida is a microorganism with great potential for industry due to its stress-endurance traits and easy manipulation of the metabolism. However, optimization is still required to improve production yields. In the last years, manipulation of bacterial small non-coding RNAs (ncRNAs) has been recognized as an effective tool to improve the production of industrial compounds. So far, very few ncRNAs are annotated in P. putida beyond the generally conserved.
In the present study, P. putida was cultivated in a two-compartment scale-down bioreactor that simulates large-scale industrial bioreactors. We performed RNA-Seq of samples collected at distinct locations and time-points to predict novel and potentially important ncRNAs for the adaptation of P. putida to bioreactor stress conditions. Instead of using a purely genomic approach, we have rather identified regions of putative ncRNAs with high expression levels using two different programs (Artemis and sRNA detect). Only the regions identified with both approaches were considered for further analysis and, in total, 725 novel ncRNAs were predicted. We also found that their expression was not constant throughout the bioreactor, showing different patterns of expression with time and position. This is the first work focusing on the ncRNAs whose expression is triggered in a bioreactor environment. This information is of great importance for industry, since it provides possible targets to engineer more effective P. putida strains for large-scale production.

overall_design: RNA-Seq of P. putida KT2440 grown in bioreactor was done with Illumina Hi-Seq platform.

first: V

last: Pobre

first: G

last: Graça-Lopes

first: M

last: Saramago

first: A

last: Ankenbauer

first: R

last: Takors

first: C

first: S

last: Viegas


title: RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting

status: Public on Nov 16 2019

city: Pasadena

first: Paul

last: Sternberg

address: 1200 E California Blvd

department: BBE

institute: Caltech

summary: RNA Polymerase II contains a disordered C-terminal domain (CTD) whose length enigmatically correlates with genome size. The CTD is crucial to eukaryotic transcription, yet the functional and evolutionary relevance of this variation remains unclear. Here, we use smFISH, live imaging, and RNA-seq to investigate how CTD length and disorder influence transcription. We find that length modulates the size and frequency of transcriptional bursting. Disorder is highly conserved and mediates CTD-CTD interactions, an ability we show is separable from protein sequence and necessary for efficient transcription. We build a data-driven quantitative model, simulations of which recapitulate experiments and support CTD length promotes initial polymerase recruitment to the promoter but slows down its release from it, and that CTD-CTD interactions enable promoter recruitment of multiple polymerases. Our results reveal how these tunable parameters provide access to a range of transcriptional activity, offering a new perspective for the mechanistic significance of CTD length and disorder in transcription across eukaryotes.

overall_design: We measured the transcriptional phenotype of CTD mutants and their response to galactose using RNA-seq, comparing wild-type with strains of 10 CTD repeats (CTDr), 10CTDr fused to FUS low complexity domain (LCD), and 10CTDr fused to TAF LCD.

first: Porfirio

last: Quintero-Cadena

first: Tineke

last: Lenstra


title: RNA sequence reveal gene expression mechanism of sugar beet in response to alkaline stress

status: Public on Nov 13 2019

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

country: China

institute: Shanxi Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Here, we first systematically identified and characterized responsive lncRNAs and mRNAs expressed in leaves of sugar beet at a genome-wide scale, focusing on alkaline-responsive lncRNAs and mRNAs.

overall_design: Five-week-old seedlings were treated with Hoagland solution, containing 75 mM mixed alkaline solution (Na2CO3:NaHCO3, 1:2) for 0 day (control, designated as C), 3 days (short-term treatment, designated as ST) and 7 days (long-term treatment, designated as LT). Fresh leaves from the same position of seedlings at different treatments were collected, and three biological replicates were sampled.

first: Caifeng

last: Li


title: RNA-seq analysis of colorectal cancer cell lines HT29-POLR1D-silenced and SW480-POLR1D-silenced

status: Public on Nov 12 2019

city: Graz

first: Samantha

last: Perakis

address: Neue Stiftingtalstraße 6

country: Austria

institute: Diagnostic & Research Institute of Human Genetics; MedUniGraz

summary:
Purpose: To explore the effect of POLR1D on colorectal cancer cell lines HT29 and SW480.
Methods: Whole transcriptome profiles of POLR1D knock down and AllStars Negative Control transfected colorectal cancer cell line (ie. HT29 and SW480) were generated by whole transcriptome sequencing, in replicate, using the Illumina NextSeq 550. The sequence reads that passed quality filters were analyzed at the gene level with Kallisto followed by DESeq2.
Results: 45 genes showed consistent change after silencing of POLR1D, which included 2 genes that are well-known to be involved in the cell growth-related pathway, ie. VEGFA and EREG.
Conclusions: POLR1D can infulence cell proliferation through VEGFA and EREG related pathway.

overall_design: Whole transcriptome profiles of POLR1D-silenced and AllStars Negative Control transfected colorectal cancer cell lines  HT29 and SW480 in replicate, using Illumina NextSeq 550.

first: Qing

last: Zhou

first: Ellen

last: Heitzer

first: Michael

last: Speicher


title: Oncogenic MYC Activates a Feedforward Regulatory Loop Promoting Essential Amino Acid Metabolism and Tumorigenesis

status: Public on Nov 11 2019

city: Wuhan

first: Ming

last: Yue

address: Hangkong Road 13, Qiaokou District

institute: Tongji Medical College, Huazhong University of Science and Technology

summary:
Oncogenic MYC selectively activates Slc7a5 and Slc43a1 transcription and thus promotes essential amino acids (EAAs) uptake in Daudi cells. Elevated EAAs in turn stimulate Myc mRNA translation, prompting us to investigate whether Slc7a5/Slc43a1 inhibition affects MYC-dependent transcription.
We performed microarrays to profile global gene expression and to identify Slc7a5-regulated genes.

overall_design: Daudi cells were infected with control shRNA, Slc7a5 shRNA or C-Myc shRNA, respectively. C-Myc shRNA-treated cells were used as a positive control.

first: Jue

last: Jiang

first: Guoliang

last: Qing


title: Functional interactions between Mi-2β and AP1 complexes control response and recovery from barrier disruption

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

country: USA

institute: Harvard Medical School

summary: Keratinocytes respond to environmental signals by eliciting induction of genes that preserve skin’s integrity.  Here we show that the transcriptional response to stress signaling is supported by short-lived epigenetic changes. Comparison of chromatin accessibility and transcriptional changes induced by barrier disruption or by loss of the nucleosome remodeler Mi-2β identified their striking convergence in mouse and human keratinocytes. Mi-2β directly repressed genes induced by barrier disruption by restricting AP1-enriched promoter-distal sites, occupied by Mi-2β and JUNB at steady state and by c-JUN after Mi-2β depletion or stress signaling.  Barrier disruption led to a modest reduction in Mi-2β expression and a further selective reduction of Mi-2β localization at stress response genes possibly through competition with activated c-JUN. Consistent with a repressive role at stress response genes, genetic ablation of Mi-2β did not prevent re-establishment of barrier integrity but was required for return to homeostasis. Thus a competition between Mi-2β repressive and activating AP1 complexes may permit rapid transcriptional response to and resolution from stress signaling.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 24 mRNA-seq, 8 ATAC-seq, 22 ChIP_seq samples

first: Sayaka

last: Shibata

first: Mariko

last: Kashiwagi


title: Comparative gene expression in response to various inflammatory stimuli in vitro: infection-mediated versus systemic inflamamtion

status: Public on Nov 15 2019

city: Tezpur

first: Rupak

last: Mukhopadhyay

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

address: Napaam, Sonitpur, Assam

department: Department of Molecular Biology and Biotechnology

country: India

institute: Tezpur University

summary: To unedrstand the global gene expression profile depending upon origin of inflammation, we have employed microarray analysis in vitro. We have treated THP-1 macrophage like cells with TNFα, IL-6 to mimic inflammatory milieu similar to systemic inflammation while bacterial LPS treatment represented for infectious inflammation.

overall_design: THP-1 macrophage like cells were treated with TNFα (10 ng/ml), IL-6 (50 ng/ml) and LPS (100 ng/ml) for 2 hours. Cells were treated with PBS served as control

first: Anindhya

last: Sundar Das


title: Cell specific profiling of neurons expressing differnet neurotransmitters during Drosophila development

status: Public on Nov 05 2019

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

summary: In order to gain a greater understanding of neurotransmitter specification we profiled the transcription state of cholinergic, GABAergic and glutamatergic neurons in vivo at multiple developmental time points. We identified 86 differentially expressed transcription factors that are uniquely enriched, or uniquely depleted, in a specific neurotransmitter subtype. Some transcription factors show a similar profile across development, others only show enrichment or depletion at specific developmental stages. Profiling of acj6 (cholinergic enriched) and Ets65A (cholinergic depleted) binding sites in vivo reveals that they both directly bind the ChAT locus, in addition to a wide spectrum of other key neuronal differentiation genes.

overall_design: Profiling of RNA Polymerase II occupancy in different neurotransmitter populations of neurons in Drosophila, at different developmental stages. Also profiling of acj6 and Ets65A-RA genomic binding in the Drosophila brain.

middle: D

first: Alicia

last: Estacio-Gómez


title: Long noncoding RNA SAM promotes myoblast proliferation and skeletal muscle regeneration through stabilizing Sugt1 and facilitating kinetochore assembly

status: Public on Nov 08 2019

city: HONG KONG

first: Jie

last: Yuan

state: HONG KONG

address: Prince of Wales Hospital

department: Orthopaedics and Traumatology

institute: The Chinese University of Hong Kong

summary: Long non-coding RNAs (lncRNAs) are novel family of gene regulators but the study of lncRNAs in satellite cell lineage progression is still at the infancy stage. Here we identified a novel lncRNA, SAM (Sugt1 associated muscle lncRNA) that was enriched in the proliferation myoblast cells but decreased as the cells progress to differentiation. Gain- or loss- of function of SAM in muscle satellite cells altered myogenic proliferation and differentiation. The above phenotypical changes in cells were also substantiated when RNAseq was performed to assess transcriptomic changes caused by SAM loss. Gene Ontology (GO) cluster analysis of up- or down-regulated genes is in line with the pro-proliferative function of SAM and the precocious differentiation upon SAM loss.

overall_design: siRNA targeting SAM (siSAM) or negative control (siNC) treated myoblasts were subjected to transcriptome analysis by RNA-seq

first: Huating

last: Wang

first: Hao

last: Sun

first: Yuying

first: Leina

last: Lu


title: Analysis of long noncoding RNA expression profile in the whole blood of neonatal Hypoxic Ischemic Encephalopathy

city: Shanghai

first: xiaohua

last: dong

address: 1111 XianXia Road

institute: Tongren Hospital, Shanghai Jiao Tong University School of Medicine,

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

summary: Long noncoding RNAs (lncRNA) have been proved to participate in many biological processes. To investigate the expression profile of lncRNAs and their potential functions in neonatal hypoxic ischemic encephalopathy (HIE). We detected the lncRNA and mRNA expression in the peripheral blood samples in HIE and relative control using microarray. A total of 376 lncRNAs and 126 mRNAs were detected to be differentially expressed between HIE and the non-HIE samples (fold change>2). Quantitative real-time PCR were used to validation of microarray data. Gene ontology (GO) enrichment and KEGG pathway analysis were used to determine the gene function. Furthermore, the co-expression network of lncRNA-mRNA were conducted to predicted the potential the targets of lncRNAs. In conclusion, our study first demonstrated the differentially expression profile of lncRNAs in the whole blood of neonatal HIE and may provide a new view of distinct lncRNAs functions in HIE.

overall_design: 6 human whole blood samples were collected for lncRNA microarray profiling, including 3   HIE samples and 3 non-HIE samples

first: Xiaohua

last: Dong


title: Genome-wide maps of Zc3h10 in mouse brown adipose tissue

status: Public on Nov 01 2019

city: Berkeley

first: Danielle

last: Yi

address: 220 Morgan Hall

institute: UC Berkeley

summary: Using high throughput sequencing, we report Zc3h10 enrichment in promoter regions of of thermogenic genes.

overall_design: Examination of Zc3h10 in mouse brown adipose tissue

first: Hei

middle: S

last: Sul


title: OncoScan CNV SNP array data for MNG/PTC samples

city: Ulm

first: Rabea

last: Wagener

address: Albert-Einstein-Allee 11

department: Ulm University and Ulm University Medical Center

institute: Institute of Human Genetics

summary: Genome-wide copy number analysis using SNP-arrays (OncoScans) in multinodular goitres from individuals with the c.1552G>A;p.E518K mutation in DGCR8 show allelic imbalance at Chr22 in all samples. Likewise this event is confirmed in papillary thyroid tumors harboring the same alteration somatically.  The only alteration common in all MNG and FvPTC samples was the allelic imbalance at the Chr22 in line with all samples showing an homozygous genotype at the DGCR8 locus

overall_design:
OncoScan CNV arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved blood and FFPE tumor samples.
Copy number analysis of OncoScan CNV array data was performed.

first: Reiner

last: Siebert


title: Nuclear Parkin Regulates Transcriptional Response during Hypoxia

status: Public on Nov 06 2019

city: San Diego

first: Justin

middle: Michael

last: Quiles

address: 9500 Gilman Drive

department: Skaggs School of Pharmacy & Pharmaceutical Sciences

institute: University of California San Diego

summary:
Purpose: The E3 ubiquitin ligase Parkin is a well-characterized regulator of mitochondrial autophagy (mitophagy); however, it is becoming increasingly appreciated to perform additional roles in various compartments of the cell. Our laboratory confirmed the presence of Parkin in the nucleus of various tissues (biochemical fractionations) and cell types (immunofluorescent imaging). Hypoxia-induced nuclear translocation of Parkin occured independent of the mitophagy regulator PINK1, and Parkinson's disease-associated mutants were restricted from the nuclueus. Accordingly, we inserted a nuclear localization sequence (NLS) at the n-terminus of Parkin and overexpressed both NLS Parkin and the wild-type protein in HeLa cells cultured at normoxia and hypoxia. Next-generation RNA-sequencing (RNA-seq) was used to determine the effect of nuclear Parkin on cellular transcription.
Methods: mCherry-tagged NLS and wild-type Parkin were overexpressed in HeLa cells. Differential expression analyses were performed on Parkin vs. mCherry control cells and NLS Parkin vs. mCherry control cells at normoxia and following 12hr of hypoxia (n=3/group/condition). Paired-end sequencing was performed using the HiSeq4000. FastQC v0.11.3 was used for quality control, Trimmomatic v0.36 was used to trim reads which were aligned to the human genome (GRCh37.p13) using the STAR aligner v2.5.3a. Read quantification was performed with RSEM v 1.3.0 and the Gencode release 19. The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis.
Results: During normoxia, Parkin had no effect on basal transcription; however, overexpression of NLS Parkin was associated with 168 differentially expressed genes (DEGs: fold-change </= 1.5, FDR < 0.05) relative to mCherry control cells. Following hypoxia, the transcriptome associated with the overexpression of wild-type Parkin more closely resembled that of NLS Parkin. Along these lines, Parkin overexpression during hypoxia coincided with a total of 158 DEGs, 37% of which were shared with NLS Parkin. Overlapping and shared DEGs among Parkin and NLS Parkin were implicated in cellular metabolism, HIF1 signaling and survival. Our follow up co-immunoprecipitation and real-time quantitative PCR studies demonstrated that Parkin interacts with the Estrogen Related Receptor Alpha (ERRa) to promote the induction of its downstream target genes.
Conclusions: Nuclear translocation of Parkin is a novel means by which this cytoprotective protein contributes to cellular homeostasis and especially critical during hypoxia.

overall_design: HeLa cells were infected with adenovirus encoding: 1) mCherry-tagged wild-type Parkin, 2) mCherry-tagged nuclear-localized Parkin (NLS) or 3) mCherry alone and were cultured at A) normoxia or B) hypoxia (12hr). Three biological replicates from each group and condition were used for RNA-seq and differential expression analysis.

middle: M

first: Sarah

middle: E

last: Shires

first: Asa

middle: B

last: Gustafsson


title: Reconstituted Rela-/- MEF

city: LOS ANGELES

first: Pinghui

last: Feng

department: Section of Infection and Immunity

institute: Herman Ostrow School of Dentistry, University of Southern California

summary: Protein deamidation is emerging as a post-translational modification that regulates protein function. The general role of protein deamidation is emerging asn fundamental to biological processes, yet remains is poorly understood. Here, we report that the rate-limiting enzyme of pyrimidine synthesis, a trifunctional enzyme containing activity of carbamoyl phosphate synthetase, aspartyl transcarbamoylase and dihydroorotase (CAD), deamidates the RelA subunit to inactivate NF-κB and promote glycolysis. Functional screening and identified CAD as a negative regulator of NF-κB activation, and biochemical analysis demonstrated that CAD deamidatesd RelA in vitro and in cellsto negate NF-κB activation. D eamidated RelA, though failed to activate the expression of NF-κB-dependent genes, thoughbut it up-regulated that of key glycolytic enzymes to promote glycolysis and cell proliferation. In proliferating cells, CAD is activated and catalyzes de novo pyrimidine synthesis to meet the metabolic need during S phase. CAD-mediated RelA deamidation and NF-κB inactivation and glycolytic gene expression paralleled in a cell cycle-dependent mannerdriven by CAD-mediated RelA deamidation are necessary for cell proliferation. In addition, CAD promoted glycolysis via deamidated RelA that up-regulated the expression of key glycolytic enzymes. Stratification of cancer cell lines by CAD-mediated RelA deamidation predicted their sensitivity to inhibitors of glycolytic enzymes, while a subset of mutations predisposed RelA to deamidation and promoted glycolysis to enable cell proliferation. This work describes a process of metabolic reprogramming enabled by CAD-mediated RelA deamidation that underpins cell proliferation and tumorigenesis.

overall_design: mRNA profile of RelA mutant stable cell line compared to wide type cell line upon SeV infection

first: Jun

last: Zhao


title: Expression profile and potential functions of circulating long noncoding RNAs in acute ischemic stroke in the Southern Chinese Han population

city: Nanning

first: shenghua

last: Li

state: China

address: The First Affiliated Hospital of Guangxi Medical University

summary:
Background: Long noncoding RNAs (lncRNAs) have been confirmed to be associated with ischemic stroke (IS); however, their involvement still needs to be extensively explored. Therefore, we aimed to study the expression profile of lncRNAs and the potential roles and mechanisms of lncRNAs in the pathogenesis of acute ischemic stroke (AIS) in the Southern Chinese Han population.
Methods: lncRNA and mRNA expression profiles in AIS were analyzed using high-throughput RNA sequencing (RNA-Seq) and validated using quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and network analyses were performed to predict the functions and interactions of the aberrantly expressed genes. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value of lncRNAs in AIS.
Results: RNA-Seq analysis showed that 428 lncRNAs and 957 mRNAs were significantly upregulated, while 791 lncRNAs and 4263 mRNAs were downregulated in patients with AIS when compared with healthy controls. GO enrichment and KEGG pathway analyses of differentially expressed genes showed that the apoptosis, inflammatory, oxidative and calcium signaling pathways were potentially implicated in AIS pathology. The PCR results showed that the selected lncRNA-C14orf64 and lncRNA-AC136007.2 were significantly downregulated in AIS. ROC curve analysis showed that the area under the ROC curve (AUC) values of lncRNA-C14orf64 and lncRNA-AC136007.2 between AIS and healthy controls were 0.74 and 0.94, respectively.
Conclusion: This study provides evidence of altered expression of lncRNAs and their potential functions in AIS. Our findings may facilitate pathological mechanistic studies of lncRNAs in AIS and provide potential diagnostic biomarkers and therapeutic targets for AIS.

overall_design: lncRNA and mRNA expression profiles of acute ischemic stroke were generated by high-throughput RNA sequencing, using Illumina HiSeqTM 2500.

first: Shenghua

last: li

first: Jingli

last: Liu


title: TRANSCRIPTIONAL RESPONSES IN CHILDREN WITH SICKLE CELL

city: Columbus

first: Benjamin

middle: T.

last: Kopp

state: Ohio

address: 700 Children’s Drive

department: Section of Pediatric Pulmonology

institute: Nationwide Children’s Hospital

summary: To date, little is known about lung disease pathogenesis in patients with sickle cell disease (SCD). Acute chest syndrome (ACS) is a significant cause of morbidity and premature.mortality in SCD, but preventative, diagnostic, and therapeutic options are limited. Further, ACS and acute vasoccclusive pain crises (VOC) can have overlapping features such as chest pain, which causes a diagnostic dilemma for clinicians.  We aimed to explore changes in gene expression profiles in patients with SCD at baseline and during hospitalization for VOC or ACS in order to better understand ACS disease pathogenesis.

overall_design: Whole blood RNA-Seq was performed using the Illumina HiSeq4000 platform for 26 patients who had matched baseline and hospitalization blood samples for ACS or VOC.

first: Susan

last: Creary

first: Chandra

middle: L

last: Shrestha

first: Kavitha

last: Kotha

first: Abena

last: Minta

first: James

last: Fitch

first: Lisa

last: Jaramillo

first: Shuzhong

last: Zhang

first: Swaroop

last: Pinto

first: Rohan

last: Thompson

first: Octavio

last: Ramilo

first: Peter

last: White

first: Asuncion

last: Mejias

middle: T


title: Collateral fitness effects of mutations

status: Public on Oct 28 2019

city: Baltimore

first: Marc

last: Ostermeier

state: MD

address: 3400 N. Charles St.

department: Chemical & Department of Chemical & Biomolecular Engineering

institute: Johns Hopkins University

summary: We performed RNA-seq experiments to compare the gene expression profiles of cells expressing TEM-1 beta-lactamase with single-codon substitutions in the absence of beta-lactam antibiotics. Mutations with deleterious fitness effects in the absense of antibiotics also caused significant changes in gene expression, primarily in the induction of specific outer envelope stress response pathways and, in some cases, the mild-induction of a few genes in the heat-shock response pathway.

overall_design: E. coli cells harboring single-codon substitutions to the TEM-1 gene were grown in monoculture growth assays. Controls consisted of cells with the wildtype TEM-1 allele that were not induced with IPTG as well as cells containing a ΔTEM-1 gene deletion that were induced with IPTG. Growth was halted at about 330 minutes to ensure the cells were still in exponential growth phase based on OD measurements. Total RNA was extracted from pelleted cell cultures. mRNA was enriched and used to synthesize double-stranded cDNA. The double-stranded cDNA was end prepped and purified. Illumina adaptor sequences were ligated to the double stranded cDNA and PCR enriched before being purified and pooled for Illumina Tru-Seq (2 x 75 bp reads).

first: Jacob

last: Mehlhoff


title: Investigating Global Changes in Gene Expression in a Murine Model of Cherubism

status: Public on Oct 26 2019

city: Farmington

last: Maye

state: Connecticut

address: 263 Farmington Avenue

department: Reconstructive Sciences

institute: UConn Health

summary:
Purpose: To identify the mechanistic changes that lead to impaired osteogenesis and spontaneous osteoclast formation in both the hematopoietic and mesenchymal cell populations the makeup bone marrow cultures derived from cherubism mice (Sh3bp2KI/KI).
Methods: Bone marrow cultures derived from wild type and cherubism mice were grown for seven days.  On day seven, hematopoietic and mesenchymal cell types were sorted using CD45 and Sca1 cell surface markers.  CD45+Sca1+ identified the hematopoietic population. CD45-Sca1+ identified the mesenchymal population. Total RNA was prepared from cell sorted populations. RNA quality was confirmed, ribosomal RNAs were depleted, libraries were prepared, and paired-end sequencing was performed on a illumina platform.  We performed this study using six biological replicates.
Results: Gene expression differences were identified
Conclusions: Our study, for the first time, identifies the impact of a cherubism mutation on the global transcriptome of hematopoietic and mesenchymal cells extracted from murine bone marrow stromal cultures. With this study, we have found novel molecular signatures that are consistent with the cherubism phenotype (inflammation, bone loss, and fibrosis).

overall_design: mRNA profile of cherubism hematopoietic and mesenchymal cells extracted from day 7 murine bone marrow stromal cultures

first: Tulika

last: Sharma


title: MicroRNA 1253 regulation of WAVE2 and its relevance to health disparities in hypertension

status: Public on Oct 23 2019

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The prevalence of hypertension among African Americans (AAs) in the US is among the highest of any demographic and affects over two-thirds of AA women. Previous data from our laboratory suggests substantial differential gene expression of mRNAs and microRNAs (miRNAs) in peripheral blood mononuclear cells (PBMCs) isolated from AA and white women with or without hypertension. We hypothesized that differential gene expression by race may contribute to racial differences in hypertension. We found that the Wiskott-Aldrich syndrome protein Verprolin homologous-2 (WAVE2) is differentially-expressed in AA women with hypertension, along with several other members of the actin cytoskeleton signaling pathway that plays a role in cell shape and branching of actin filaments. We performed an in silico miRNA target prediction analysis that suggested miRNA miR-1253 regulates WAVE2. Transfection of miR-1253 mimics into human umbilical vein endothelial cells (HUVECs) and human aortic endothelial cells (HAECs) significantly repressed WAVE2 mRNA and protein levels (P<0.05), and a luciferase reporter assay confirmed that miR-1253 regulates the WAVE2 3’ UTR (P<0.01). miR-1253 over-expression in HUVECs significantly increased HUVEC lamellipodia formation (P<0.01), suggesting the miR-1253/WAVE2 interaction may play a role in endothelial cell shape and actin cytoskeleton function. Together, we have identified novel roles for miR-1253 and WAVE2 in a hypertension-related disparities context. This may ultimately lead to the discovery of additional actin-related genes which are important in the vascular-related complications of hypertension and influence the disproportionate susceptibility to hypertension among AAs in general and AA women in particular.

overall_design: Primary human endothelial aortic cells (HAECs) were transfected with either pre-miR miRNA precursors for hsa-miR-103a-2-5p, miR-585-5p, miR-1253 or scrambled negative control (Control), and the transcriptional changes examined by gene expression microarray analysis using three biological repeats of each experimental condition.

first: Mercy

middle: A

last: Arkorful

first: Nicole

last: Noren Hooten

first: Yongqing

first: Amirah

middle: N

last: Hewitt

first: Lori

last: Barrientos Sanchez

first: Michele

last: Evans

first: Douglas

middle: F

last: Dluzen


title: Synaptopathy in Kii ALS/PDC, a disease concept based on transcriptome analyses of human brains

city: Shinjuku-ku

first: Mitsuru

last: Ishikawa

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

summary:
Amyotrophic lateral sclerosis (ALS) and parkinsonism-dementia complex (PDC) (ALS/PDC) is a unique endemic neurodegenerative disease, with high-incidence foci in the Kii Peninsula, Japan. Although ALS/PDC presents with multiple proteinopathies, the genetic and environmental factors that influence disease onset remain unknown. We performed transcriptome analyses of patients’ brains, which may provide new insights into the pathomechanisms underlying Kii ALS/PDC.
We prepared frozen brains from 3 healthy controls (frontal lobe and temporal lobe), 3 patients with Alzheimer’s disease (AD) (frontal lobe and temporal lobe) as tauopathy-disease controls, and 21 patients with Kii ALS/PDC (frontal lobe and/or temporal lobe). We acquired microarray data from the cerebral gray and white matter tissues of Kii ALS/PDC patients.
Microarray data revealed that the expression levels of genes associated with neurons, heat shock proteins (Hsps), DNA binding/damage, and senescence were significantly changed in Kii ALS/PDC brains compared with those in control brains. The RNA expression pattern observed for Kii ALS type brains was similar to that for Kii PDC type brains and unlike those of control and AD brains.
Additionally, pathway and network analyses indicated that the molecular pathogenic mechanism underlying Kii ALS/PDC may be associated with the oxidative phosphorylation of mitochondria, ribosomes, and the synaptic vesicle cycle; in particular, upstream regulators of these mechanisms may be found in synapses and during synaptic trafficking. Therefore, we propose the novel disease concept of “synaptopathy” for Kii ALS/PDC. Furthermore, phenotypic differences between Kii ALS type and Kii PDC type were observed, based on the human leukocyte antigen (HLA) haplotype.
We performed exhaustive transcriptome analyses of Kii ALS/PDC brains, for the first time, and revealed new insights indicating that Kii ALS/PDC may be a synaptopathy. Determining the relationship between synaptic dysfunction and the pathogenesis of ALS/PDC may provide a new step toward understanding this mysterious disease.

overall_design: Total RNA was extracted with an RNeasy Kit (Qiagen, Hilden, Germany), and RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Total RNA (100 ng) was reverse transcribed, labeled with biotin, using a TargetAmp-Nano Labeling kit (Epicentre, Madison, WI, USA), and hybridized to a HumanHT-12 v4 Expression BeadChip (Illumina, San Diego, CA, USA). The arrays were washed and stained, using Cy3-Streptavidin, and then scanned with the BeadChip Scanner iScan System (Illumina, San Diego, CA, USA), according to the manufacturer’s instructions. The raw probe intensity data were normalized [RMA normalization (85th percentile), Low signal cutoff (cut off value: 100), Log transformation (Base 2), Ratio to control samples (mean)] by using the transcriptome data analysis software Subio Platform (Subio, Kagoshima, Japan).

first: Satoru

last: Morimoto

first: Hirotaka

last: Watanabe

first: Miho

last: Isoda

first: Masaki

last: Takao

first: Shiho

last: Nakamura

first: Fumiko

last: Ozawa

first: Yoshifumi

last: Hirokawa

first: Shigeki

last: Kuzuhara

first: Hideyuki

last: Okano

first: Yasumasa

last: Kokubo


title: Neuronal transcriptome analyses reveal novel neuropeptide modulators of excitation and inhibition imbalance in C. elegans

status: Public on Oct 22 2019

city: La Jolla

first: Yishi

last: Jin

institute: University of California, San Diego

summary: Neuropeptides are secreted molecules that have conserved roles modulating many processes, including mood, reproduction, and feeding.  Dysregulation of neuropeptide signaling is also implicated in neurological disorders such as epilepsy. However, much is unknown about the mechanisms regulating specific neuropeptides to mediate behavior. Here, we report that the expression levels of dozens of neuropeptides are up-regulated in response to circuit activity imbalance in C. elegans. acr-2 encodes a homolog of human nicotinic receptors, and functions in the cholinergic motoneurons. A hyperactive mutation, acr-2(gf), causes an activity imbalance in the motor circuit. We performed cell-type specific transcriptomic analysis and identified genes differentially expressed in acr-2(gf), compared to wild type. The most over-represented class of genes are neuropeptides, with insulin-like-peptides (ILPs) the most affected. Moreover, up-regulation of neuropeptides occurs in motor neurons, as well as sensory neurons.  In particular, the induced expression of the ILP ins-29 occurs in the BAG neurons, which are previously shown to function in gas-sensing. We also show that this up-regulation of ins-29 in acr-2(gf) animals is activity-dependent.  Our genetic and molecular analyses support cooperative effects for ILPs and other neuropeptides in promoting motor circuit activity in the acr-2(gf) background. Together, this data reveals that a major transcriptional response to motor circuit dysregulation is in up-regulation of multiple neuropeptides, and suggests that BAG sensory neurons can respond to intrinsic activity states to feedback on the motor circuit.

overall_design:
4 total samples. Two replicates each of isolated cholinergic neurons from either wild type(strain CZ631 control) or acr-2(gf)(strain CZ5808 experimental) strain in C. elegans. Syncronized populations  were collected at 72hr.
-------------------------------
Authors state "We did not include FPKM data for CZ5808 in our manuscript, but compared the sequence to CZ631 data in DESeq2. The FPKM data for CZ631 was just used as a comparison to previous studies."

first: Katherine

last: McCulloch

first: Kingston

last: Zhou


title: mRNA and lncRNA profiling by array of astrocytic tumors

status: Public on Oct 17 2019

city: Changsha

first: Chen-Xue

last: Mao

address: Xiangya road 110

department: Departments of Clinical Pharmacology

institute: Xiangya Hospital, Central South University

summary: Astrocytoma is a common pathologic type of glioma, its survival and prognosis remain poor.

overall_design: We performed mRNA and lncRNA expression analyses of 33 astrocytic tumor tissues and 9 non-tumor brain tissues.

first: Zhao-Qian

last: Liu


title: RNA-sequencing and ChIP-sequencing in murine mesenchymal stem cells treated with Ezh2 inhibitor GSK126 or β-catenin siRNA

city: Rochester

first: Andre

middle: J

last: van Wijnen

state: MN

address: 200 First Street SW

department: Orthopedic Surgery & Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: During mesenchymal stem cell (MSC) differentiation, both Wnt signaling and the development of a rigid cytoskeleton promote commitment to the osteoblastic over adipogenic lineage. β-catenin  is thought to play a critical role in Wnt effects. We show that β-catenin  was additive with cytoskeletal signals to prevent adipogenesis, and β-catenin  knockdown promoted adipogenesis even when the actin cytoskeleton was depolymerized. β-catenin  also prevented osteoblast commitment in a cytoskeletal-independent manner, with β-catenin  knockdown enhancing lineage commitment. Chip-seq showed that β-catenin associated with the promoter of EZH2, a key component of the PRC2 complex that governs genome methylation. Knocking down β-catenin  lowered EZH2 levels and H3K27me3 at osteogenic loci. Further, when EZH2 was inhibited, β-catenin ’s anti-differentiation effects were lost. These results indicate that regulating EZH2 activity is key to β-catenin effects on MSC to preserve MSC multipotentiality.

overall_design: RNA-sequencing of 3 groups (non-targeting siRNA,  β-catenin siRNA, and GSK126 treated) each with 3 biological replicates. ChIP-sequencing for H3K27me3 in one biological replicate from each group (non-targeting siRNA,  β-catenin siRNA, and GSK126 treated).

first: Janet

last: Rubin


title: miRNA profiling by array of astrocytic tumors

status: Public on Oct 12 2019

overall_design: We performed microRNA expression analyses of 33 astrocytic tumor tissues and 9 non-tumor brain tissues.


title: β-catenin preserves the stem state of murine mesenchymal stem cells through activation of EZH2

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

overall_design: Refer to individual Series


title: Transcriptome-wide maps of mouse interneurons after chronic stress

status: Public on Oct 10 2019

city: New Haven

first: Matthew

last: Girgenti

state: CT

address: 34 Park St

institute: Yale School of Medicine

summary: Using Sst and parvalbumin subtype-specific fluorescence activated cell sorting (FACS) and RNA sequencing we identify distinct transcriptome profiles for these interneuron subtypes in the medial PFC. Chronic stress causes significant dysregulation of several key pathways, including sex specific differences in the SST interneuron profiles.

overall_design: Examination of sex-specific transcriptomic profiles in two interneuron subtypes

first: Sameet

last: Mehta


title: Target genes of miR-361-3p in human oral squamous cell carcinoma cells, GFP-SAS

status: Public on Oct 09 2019

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary:
Inhibition of miR-361-3p by locked nucleic acid (LNA)/DNA antisense oligonucleotide markedly suppressed the growth of GFP-SAS cells.
We explored the target genes of miR-361-3p in GFP-SAS cells using microarray analysis.

overall_design: We compared the gene expression profiles of GFP-SAS cells treated with anti-miR-361-3p and non-target LNA/DNA antisense oligonucleotide.


title: Gene and miRNA expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples

status: Public on Oct 07 2019

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

platform_organism:
Homo sapiens
synthetic construct


title: SMARCB1 knockdown in IMR90 and ARPE19

status: Public on Oct 04 2019

city: seoul

first: SungKyung

last: Choi

address: 120, Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea

institute: Konkuk university

summary:
Identifying the mechanism action of SMARCB1 in totally different cell lines.

Determine whether it is general role or context dependent role.

overall_design: Generating stable SMARCB1 knockdown cells using shRNA in IMR90 and ARPE19

first: Jueng-Soo

last: You

first: Sung-Kyung


title: Transcriptome profiles of antibody-producing CHO cells across different amplification strategies

status: Public on Oct 01 2019

first: Nathan

last: Lewis

state: CA

address: 9500 Gilman Dr

institute: UCSD

summary: The mechanism of action behind the increased secretion capacity of the amplified progeny of CHO cells is investigated in this study through comparative transcriptomic analysis

overall_design: The amplified DG-44 CHO cells, taken at both exponential and stationary growth phase were compared to non-amplified CHO DG-44 cells. Non-producing CHO-S samples were used as negative controls.


title: Analysis of signaling moelculs induced by UNE-C1 treatment

status: Public on Oct 08 2019

first: seongmin

last: cho

institute: Seoul national university

summary: To investigate the mechanism on stimulation of BMDCs by UNE-C1, we performed RNA-Seq after treating UNE-C1 on BMDCs. Genes related with pro-inflammation such as IL-6, iNOS, IL-12, CD40, CD80, and CD86 were increased by UNE-C1 treatment. KEGG pathway analysis was performed using top 100 up-regulated genes indcued by UNE-C1 and found out that genes related with Toll-like signaling pathway is up-regulated by UNE-C1.

overall_design: BMDCs were treated with UNE-C1 and samples were analyzed by RNA-Seq

first: Seongmin

last: Cho


title: RelA mutants 'reconstituted' and cell cycle synchronized HCT116 Colorectal Cancer Cells

first: Pinghui

last: Feng

overall_design: mRNA profiles of RelA mutant stable cell line compared to wide type cell line, and mRNA profiles of S phase and G1 phase HCT116 cells.

first: Jun

last: Zhao


title: Hematopoietic stem cell-restricted Cdx2 expression induces transformation to myelodysplasia and acute leukemia [RNASeq_Cdx2_4weekspost_Tamoxifen]

status: Public on Sep 30 2019

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

summary: The caudal-related homeobox transcription factor CDX2 is ectopically expressed in the majority of patients with acute myeloid leukemia (AML). We generated an inducible transgenic mouse model whereby Cdx2 was specifically activated in HSCs. Cdx2 mice developed myelodysplastic syndrome (MDS) with progression to acute leukemia associated with stepwise acquisition of additional driver mutations.

overall_design: To gain insight into the mechanism underlying Cdx2-mediated transformation of HSCs, we examined RNA-Seq gene expression on Scl-CreERT, Scl-CreERTxCdx2, Scl-CreERT x FLT3 ITD/+ and Scl-CreERT x Cdx2 x FLT3 ITD/+ 4 weeks after tamoxifen induced Cre-Recombinase excision leading to ectopic Cdx2 expression

first: Therese

last: Vu

first: Steven

middle: W

last: Lane


title: Hematopoietic stem cell-restricted Cdx2 expression induces transformation to myelodysplasia and acute leukemia


title: Pregnancy-associated changes of peroxisome proliferator-activated receptor delta (PPARD) and cytochrome P450, family 21, subfamily A, polypeptide 2 (CYP21A2) expression in the bovine corpus luteum

status: Public on Sep 22 2019

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: To evaluate functional changes of the corpus luteum (CL) during early pregnancy in cows, gene expression profiles of the CL at the time of maternal recognition were investigated. Microarray analysis, using a 15 K bovine oligo DNA microarray, demonstrated 30 and 266 differentially expressed genes in the CL on days 15 (P15) and 18 (P18) of pregnancy compared with the CL on day 15 (NP15) of non-pregnancy (n=4 for each group, >2-fold change relative to NP15; P<0.05).

overall_design: Bovine corpus luteum were obtained from Japanese-Black cows in the institute ranch within 10-30 min of exsanguination. Tissue samples were collected from cows on 15 day of the estrous cycle (NP15) and 15 and 18 days of the gestation (P15 and P18)(n=4 animals/each day). The day of artificial insemination was designated as day 1.

first: Ryosuke

last: Sakumoto


title: Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays

status: Public on Sep 25 2019

city: Los Angeles

first: Jessica

middle: Elizabeth

last: Davis

address: 607 Charles E Young Dr E

department: CHEMISTRY AND BIOCHEMISTRY

institute: UCLA

summary: We designed and assayed synthetic regulatory elements varying c-amp response element number, affinity, distance to the promoter, spacing between multiple CREs, and surrounding sequence content. Using 5 massively-parallel reporter assays, we measured the expression of 17,406 unique sequences when placed upstream of a minimal promoter using next-generation sequencing of barcodes associated with synthesized elements. We then determine how the varied c-amp response element architectures influence expression when these variants are assayed in an episomal and genomic context across a range of forskolin concentrations, an inducer of c-amp response element activity. Included here are all sequences designed and analyzed in the assay. Assay results from certain library designs were not insightful and not included in the main text but are additionally included here in the barcode-mapping and MPRA sequencing datasets.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: We associated barcodes to variants using next-generation sequencing, then analyzed variant expression using barcode next-generation sequencing on amplified cDNA and DNA samples per assay condition.

first: J

first: K

last: Insigne

first: E

last: Jones

first: Q

last: Hastings

first: W

last: Boldridge

first: S

last: Kosuri


title: Cdx2 driven acute myeloid leukemia is sensitive to therapy used in myeloid disease [RNASeq_Cdx2_AML_Azacitidine]

summary: The caudal-related homeobox transcription factor CDX2 is ectopically expressed in the majority of patients with acute myeloid leukemia (AML). We generated an inducible transgenic mouse model whereby Cdx2 was specifically activated in HSCs . Cdx2 mice developed myelodysplastic syndrome (MDS) with progression to acute leukemia associated with stepwise acquisition of additional driver mutations.

overall_design: RNA profiles of Cdx2-expressing LKS+ cells from mice transplanted with Cdx2 AML, generated after treatment with vehicle, short intermittent high dose or prolonged low dose Azacitidine, in triplicate.


title: Hematopoietic stem cell-restricted Cdx2 expression induces transformation to myelodysplasia and acute leukemia [RNASeq_Cdx2_secondaryAML]

overall_design: Scl-CreERT BM cells or Scl:Cdx2 leukemic BM cells (CD45.2) were transplanted into lethally irradiated wild-type recipients (CD45.1). Once engraftment/leukemia was established, BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells were sorted for RNA extraction.