title: mRNA and lncRNA profiling of radiation-induced gastric injury in mouse model

status: Public on May 10 2018

city: suzhou

first: zhang

middle: shu

last: yu

state: Jinagsu

address: 199 Ren'ai Rd

department: Radiation Medicine

institute: soochow University

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

summary:
In this study, we measured mRNA and lncRNA profiles of gastric tissues following 0, 6 and 12 Gy irradiation. The stomach of C57 mice were exposed to 0, 6 and 12 Gy X-ray irradiation at a dose rate of 2 Gy/min. The mice were sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified.
mRNA and lncRNA profilings of each groups were analyzed by microarray.

overall_design: The stomach of C57 mice were exposed to 0, 6 and 12 Gy X-ray irradiation at a dose rate of 2 Gy/min. The mice were sacrificed 7 days after irradiation and gastric tissues were collected. mRNA and lncRNA profilings of each groups were analyzed by microarray.

first: Shuyu

first: Guangxia


title: Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions [GFP cells RNA-Seq]

status: Public on May 22 2018

city: Cleveland

first: Donny

last: Licatalosi

state: OH

address: 2109 Adelbert Rd

country: USA

institute: Case Western Reserve University

type: Expression profiling by high throughput sequencing

summary: Dazl (deleted in azoospermia like) is a member of the DAZ family of germ cell-restricted RNA binding proteins required for gametogenesis from worm to human.  The direct RNA targets and functions of these essential proteins are poorly understood.  Here, we generated high-resolution, transcriptome-wide maps of Dazl-RNA interactions in mouse testes.  These maps provide important insights into the mechanism of Dazl recruitment to mRNA and reveal Dazl binding to thousands of mRNAs predominantly through sequence-specific interactions near the polyA tail.  Using transgenic mice and fluorescence activated cell sorting (FACS), we isolated DAZL knockout germ cells and used RNA-Seq to identify mRNAs sensitive to DAZL-ablation.  Intersecting the RNA-Seq and Dazl-RNA interaction datasets revealed that Dazl enhances expression of a subset of directly-bound transcripts, namely mRNAs for a network of essential cell cycle regulatory genes.  Collectively, our integrative analysis delineates a Dazl-dependent post-transcriptional gene regulatory program essential for mammalian germ cell maintenance.

overall_design: RNA-seq libraries generated Dazl WT and Dazl KO GFP+ germ cells

middle: D

first: Leah

middle: L

last: Zagore


title: Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions

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

overall_design: Refer to individual Series


title: Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits

status: Public on Apr 25 2018

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Oryza rufipogon
Oryza sativa
Oryza nivara
Oryza sativa Indica Group
Oryza sativa aus subgroup


title: Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [ncRNA-seq]

summary: MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. Analysis of sRNA datasets revealed a surprisingly higher abundance of 22nt sRNAs originating from a loci on Chromosome 2 in wild rice species. This locus codes for a 22 nt miRNA named as miR397. Studies in Arabidopsis and O. sativa japonica nipponbare have shown that miR397 targets a group of proteins called laccases, which are involved in secondary metabolite (lignin) production. The expression of these targets also differs across the species shown through RNA-Seq analysis. Although a functional significance of this interaction between the miRNA and laccase has not been understood. In the current study we attempt to explain the functional relevance of the miRNA in domestication of rice.

platform_organism:
Oryza rufipogon
Oryza sativa
Oryza nivara
Oryza sativa Indica Group
Oryza sativa aus subgroup

overall_design: We have performed sRNA seq analysis using 4-week old seedling, flagleaf and panicle of various rice species. Libraries were prepared from total RNA isolated from the tissues mentioned.

first: Padubidri

middle: V

last: Shivaprasad

first: Swetha

last: Chenna


title: Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [RNA-seq]

overall_design: We have performed RNA seq analysis using reproductive tissues (flagleaf and panicle) of various rice species. Libraries were prepared from total RNA isolated from the tissues mentioned.


title: Expression profiling of shoot apices of 35S::WOX1:GR seedlings transiently treated with DEX

status: Public on May 11 2018

city: Tsukuba

first: Miyuki

middle: T

last: Nakata

state: Ibaraki

address: 1-1-1, Higashi

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary:
The WOX1 transcription factor is a multifunctional regulator of lateral-organ development that acts as a transcriptional repressor. WOX1 promotes lamina growth, controls marginal tissue differentiation and is involved in establishment and maintenance of the adaxial-abaxial pattern from the middle domain of leaf primordia.
To identify the WOX1 downstream genes, we performed a microarray analysis of shoot apices of transgenic Arabidopsis thaliana lines harboring 35S::WOX1:glucocorticoid receptor (GR) in which the WOX1 function was temporarily enhanced by dexamethasone (DEX).

overall_design: The effects of transient enhancement of WOX1 function on shoot apices of seedlings were analyzed by using GR-DEX system. Plants were grown on solid medium contains 0.5x Murashige and Skoog (MS) salts, 1% sucrose, 0.05% MES-KOH (w/v) pH 5.7, 1.2 % purified agar for 6 days and transfer to liquid medium containing 0.5x MS salts, 1% sucrose and 0.05% MES-KOH (w/v) pH 5.7 with or without 10 µM DEX, 10 µM cycloheximide (CHX) and 20 µM IAA. Samples were treated with DEX, CHX and IAA treatments for 6 hours, 6 hours and 3 hours, respectively, before collection. RNA samples were extracted from shoot apices, including leaf primordia, of 6-day post sowing seedlings by using Plant RNeasy Mini Kit (QIAGEN). For analysis of 35S::WOX1:GR plants treated with or without DEX and/or CHX, sampling was performed twice in two independent lines. For analysis of 35S::GFP:GR and of a combined application of DEX and IAA, sampling was performed from two independent lines.

first: Toshiaki

last: Tameshige

first: Kiyotaka

last: Okada


title: Comparative microRNAome analysis of the leaves in doubled haploid and autotetraploid Chinese cabbages

status: Public on Mar 30 2018

city: Tianjin

first: Yiheng

last: Wang

address: 17km Jinjing Road

country: China

institute: Tianjin Academy of Agricultural Sciences

summary: We performed microRNA profiling of doubled haploids and autotetraploids that generated from a Chinese cabbage doubled haploid line ‘FT’ using the Illumina high-throughput sequencing platform and analyzed differentially expressed miRNAs.

overall_design: microRNA levels were examinated in doubled haploid and autotetraploid leaves of Chinese cabbage.

first: Hui

last: Feng


title: GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer [ChIP-seq]

status: Public on Apr 13 2018

city: Durham

first: Jeff

last: Jasper

state: NC

department: Pharmacology and Cancer Biology

institute: Duke University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the development of resistance it is likely that further development of ER-modulators will yield only incremental improvements. Thus, with the view that resistance is inevitable, we undertook the development of a new approach to treat ER-positive breast cancer by identifying and exploiting targetable vulnerabilities that emerge in endocrine therapy resistant disease. Genomic discovery platforms, including DNASeq, ChIPSeq and RNASeq were used to assess the epigenome, targeting global transcription factor binding profile, and transcriptome in cellular models of endocrine therapy sensitive and resistant disease. DNASeq was first used to identify the chromatin state, with a focus on differences, between these two models. Motif enrichment analysis indicated FOXA1 was a candidate transcription factor influencing the chromatin architecture, which was consistent with previously published studies. This led to the examination of the FOXA1 chromatin binding profile in these models. FOXA1 has previously been described to bind at enhancers. Furthermore, the relative transcription activity of specific enhancers has been shown to be indicated by the epigenomic marks on histones flanking transcription factor binding sites. For this reason, we assessed the specific pattern of histone 3 lysine 4 methylation to confirm enhancer status and histone 3 lysine 27 acetylation as an indicator of transcriptional activity. The specific patterns and distribution of FOXA1 binding was then integrated with this epigenomic information to reveal a subset of enhancers that became activated and another subset that gained enhanced activation in the tamoxifen resistant setting relative to the tamoxifen sensitive model from which it was derived. These results were integrated with the differential transcriptome, or genes shown to be differential expressed based on RNASeq, in the TAMR model as compared to its parental cell line, MCF7-WS8, and confirmed that the active enhancers were in fact associated with genes that were expressed more highly, on average, in the TAMR model.  Motif enrichment at these two subgroups of enhancers indicated that another transcription factor, GRHL2, likely interacts with FOXA1 at these active sites. These results were again integrated with the “differential transcriptome” based on RNASeq and confirmed that the active enhancers, and indicated an even stronger enrichment of genes that were expressed more highly, on average, in the TAMR model relative to the MCF7-WS8 model. The GRHL2 transcriptome was then further defined by both GRHL2 ChIPSeq as well as RNASeq by comparing TAMR samples in which downregulation of GRHL2 expression had been achieved via siRNA as compared to control siRNA sequences. The collection of these data defined a subset of genes, the GRHL2 dependent transcriptome, that demonstrated increased expression in TAMR. The results of these cell lines studies were corroborated by assessing the transcriptome of xenograft mouse models of endocrine therapy sensitive and resistant disease. Integrative analysis of these data identified a collateral ER-independent signaling pathway in endocrine therapy resistant tumors that converges upon and modulates the FOXA1 and GRHL2 cistrome/transcriptome.

overall_design: ChIP-Seq profiling of key factors in WS8 and TAMR cells. All samples have triplicate biological replicates.

middle: S

first: Kimberly

middle: J

last: Cocce

first: Logan

last: Everett

first: Suzanne

last: Wardell

first: Thomas

last: Westerling

first: Taylor

last: Krebs

first: Robert

last: Baldi

first: Tricia

middle: M

last: Wright

first: Alex

last: Yllanes

first: Jeremy

last: Blitzer

first: Craig

last: Logsdon

first: Daniel

last: Rakiec

first: David

last: Ruddy

first: Terry

last: Hyslop

first: Allison

last: Hall

first: Jeffrey

middle: R

last: Marks

first: Gregory

middle: E

last: Crawford

first: Myles

last: Brown

first: Donald

middle: P

last: Mcdonnell


title: Comparative transcriptome analysis of the leaves in doubled haploid and autotetraploid Chinese cabbages

first: Yiheng

last: Wang

summary: We performed transcript profiling of doubled haploids and autotetraploids that generated from a Chinese cabbage doubled haploid line ‘FT’ using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level.

overall_design: mRNA levels were examinated in doubled haploid and autotetraploid leaves of Chinese cabbage, in three biological replicates.

first: Hui

last: Feng


title: Next Generation Sequencing Facilitates Quantitative Analysis of Murine Salivary Gland Transcriptomes

status: Public on Feb 28 2018

city: Rochester

first: Catherine

middle: E.

last: Ovitt

state: NY

address: 601 Elmwood Ave, Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular functions. The goal of this study is to compare NGS-derived salivary gland transcriptome profilings (RNA-seq) to better understand the molecular nature of the physiological differences in adult murine salivary glands.
Methods: Major murine salivary gland mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the gene level with STAR followed by Cufflinks. In vivo NaCl reabsorption measurements were performed for validation.
Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the mouse genome (build mm10) and identified 1991 genes that were differentially expressed across three major salivary glands. RNA-seq data provided valuable insights into the nature of the functional differences among the major salivary glands
Conclusions: Our study represents the first detailed analysis of murine salivary gland transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results confirm functions of many genes, identified using genetically modified mice. We conclude that RNA-seq-based transcriptome characterization would offer a comprehensive and sensitive evaluation of the gene expression.

overall_design: Salivary gland mRNA profiles of 12-week old mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: James

last: Melvin


title: A multi-omic analysis reveals a regulatory role of CD180 during the response of macrophages to Borrelia burgdorferi [RNA-Seq]

status: Public on Mar 14 2018

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

summary: Macrophages are cells of the innate immune system with the ability to phagocytose and induce a global pattern of responses that depend on several signalling pathways. We have determined the biosignature of murine bone marrow-derived macrophages and human blood monocytes using transcriptomics and proteomics approaches. We identified a common pattern of genes transcriptionally regulated that overall indicate that the response to B. burgdorferi involves the interaction of spirochetal antigens with several inflammatory pathways corresponding to primary (triggered by pattern recognition receptors) and secondary (induced by proinflammatory cytokines) responses. We also show that the Toll-like receptor family member, CD180 is downregulated by the stimulation of macrophages, but not monocytes, with the spirochete. Silencing Cd180 results in increased phagocytosis while tempering the production of the proinflammatory cytokine, TNF. Cd180-silenced cells produced increased levels of Itgam and surface CD11b, suggesting that the regulation of CD180 by the spirochete initiates a cascade that increases the CR3-mediated phagocytosis of the bacterium while repressing the consequent inflammatory response.

overall_design: Genome-wide changes in gene Expression in mouse bone marrow-derived macrophages stimulated with Borrelia burgdorferi or left unstimulated were generated by RNAseq.

first: Juan

last: Anguita


title: Development of gene expression signatures during fasting and refeeding (compensatory growth) for zebrafish liver

status: Public on Mar 24 2018

city: Guangzhou

first: jirong

last: jia

address: No.135 Xingang West Road

institute: Sun Yat-sen university

summary: Here, we certified zebrafish to be a suitable model for the compensatory growth study. After a 3-weeks fasting, recovered for 3 days, 10 days and 15 days were chose as the initial, middle and late sampling sites for compensatory growth analysis, and liver samples of each time point were chose for the microarray analysis.At the same time, zebrafish fed ad libitum, as well as fasting for 3 weeks were also added to the microarray research.

overall_design: Fasting and refeeding induced gene expression in zebrafish liver was measured when zebrafish were fasted for 3 weeks, and then refed for 3 days, 10 days and 15 days. The control group (continiously fed) have 4 samples, while the other time point have 3 samples.

first: Wensheng

last: Li

first: Caiyun

last: Sun

first: Jirong

last: Jia


title: Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis

status: Public on Mar 27 2018

city: Wageningen

first: Tian

last: Zeng

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

summary: Arbuscular mycorrhizal fungi arguably form the most successful and wide-spread endosymbiosis with plants. In general terms there is very little host-specificity in this interaction, indicating an extremely broad compatibility. However, host preferences as well as varying symbiotic efficiencies have been observed, the molecular basis of which is still largely unknown. Secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host-dependent manner. Therefore, we studied whether AM fungi adjust their secretome in a host- and stage-dependent manner to contribute to their extremely wide host-range. We investigated the expression of SP encoding genes of R. irregularis DAOM197198 in three evolutionary distantly related plant species, Medicago truncatula (Medicago), Nicotiana benthamiana (Nicotiana) and Allium schoenoprasum (Chives). In addition we used laser microdissection in combination with RNAseq to study SP expression at different stages of the symbiotic interaction in Medicago. Our data indicate that the vast majority of 288 expressed SPs show equal expression levels in the interaction with all three host plants. In addition, a subset (~15%) of the SPs show significant differential expression depending on the host plant and/or environmental condition. This host-dependent expression appears to be controlled locally in the hyphal network in response to host metabolic cues. Overall, this study offers a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis.

overall_design: Research about AM fungal secretomes in 3 hosts (Medicago truncatula, Nicotiana benthamiana and Allium schoenoprasum) and 3 developmental stages (arbuscule, intraradical mycelium and extraradical mycelium). 3 biological replicates each.

first: Erik

last: Limpens


title: Comprehensive single cell RNAseq analysis of the kidney reveals novel cell types and unexpected cell plasticity

status: Public on Apr 05 2018

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

summary: We characterized 57,979 cells from healthy mouse kidneys using unbiased single-cell RNA sequencing. We show that genetic mutations that present with similar phenotypes mostly affect genes that are expressed in a single unique differentiated cell type. On the other hand, we found unexpected cell plasticity of epithelial cells in the final segment of the kidney (collecting duct) that is responsible for final composition of the urine. Using computational cell trajectory analysis and in vivo linage tracing, we found that, intercalated cells (that secrete protons) and principal cells (that maintain salt, water and potassium balance) undergo a Notch mediated interconversion via a newly identified transitional cell type. In disease states this transition is shifted towards the principal cell fate. Loss of intercalated cells likely contributes to metabolic acidosis observed in kidney disease.

overall_design: Single cell RNA sequencing for 57,979 cells from 7 healthy mouse kidneys

first: Rojesh

last: Shrestha

first: Chengxiang

last: Qiu

first: Ayano

last: Kondo

first: Shizheng

last: Huang

first: Max

last: Werth

first: Mingyao

first: Jonathan

last: Barasch

first: Katalin

last: Suszták


title: Gene expression profiling of the Tlr2 mutant of zebrafish embryos at 4 days post infection of M. marinum

status: Public on Jan 01 2018

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

summary: We use the Tlr2 mutant of zebrafish embryos model to study the transcriptome response to Mycobacterium marinum infection. We injected M.marinum into the caudal vein at 28 hours post fertilization and took samples at 4 days post infection.

overall_design: This deep sequence study was designed to determine the gene expression profile in the Tlr2 mutant and heterozygote by M.marinum infection. RNA was isolated at 4 days post infection. Tlr2 mutants and heterozygotes zebrafish embryos were micro-injected into the caudal vein with 150CFU M.marinum, or PBS as a control at 28 hours post fertilization. After injections embryso were transerred into fresh egg water and incubated at 28 degree. At 4 days post infection triplicateds of 10 embryos per condition were snapfrozen in liquid nitogen, and total RNA was isolated using TRIZOL reagent.

first: Shuxin

last: Yang


title: Expression data from CTL and Tc17 cell

status: Public on Feb 09 2018

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerwein-Str. 2

country: Germany

institute: Institute of Medical Microbiology

summary:
Goal of this study was to compare transcriptional changes in CTL cells compared to Tc17 cells
We used microarray to detail the global programme of gene expression underlying CTL and Tc17 cell differentiation and identified distinct classes of upregulated genes thereby

overall_design: WT naive CD8+ T cells were isolated and differentiated for 2 days towards CTL or Tc17 phenotype. Thereafter RNA was isolated and hybridised on Affymetrix microarrays.

first: Christina

last: Lückel


title: The molecular basis of essential fatty acid limitation in Daphnia magna: A transcriptomic approach

status: Public on Jan 22 2018

city: Düsseldorf

first: Heidrun

middle: Sigrid

last: Windisch

state: NRW

address: Universitätsstrasse 1

department: Cell Biology and Zoology

institute: Heinrich-Heine-University

summary: It is widely accepted that in many food webs, the trophic transfer efficiency among primary producers and herbivores is determined by the nutritional value of primary producers. In pelagic freshwater and marine ecosystems, secondary production by herbivorous crustacean zooplankton is often limited by the seston's content of essential ω3 polyunsaturated fatty acids (ω3 PUFAs). However, little is known about the genetic network behind the positive relationship between phytoplankton ω3 PUFA content and zooplankton growth and reproduction. In our experimental study, we analysed gene expression changes of the freshwater cladoceran Daphnia magna under different food regimes differing in their ω3 PUFA composition. To disentangle ω3 PUFA effects from other factors, we fed D. magna with different pure phytoplankton cultures (i.e., algal and cyanobacterial diets) with or without supplementing the essential ω3 PUFA eicosapentaenoic acid (EPA). As hypothesized, we observed enhanced growth on diets supplemented with EPA. We applied an Illumina RNA-seq approach to D. magna from different diet treatments to find and monitor genes that are regulated dependent on EPA availability. Of 26,646 potential protein products (mapped to the D. magna genome), we identified transcriptomic signatures driven by the different food sources. Further analyses revealed specific candidate genes involved in EPA metabolism, irrespective of the basal food source. This allows a first functional annotation of previously uncharacterized genes involved in the EPA-specific response of D. magna and may finally provide a link to molecular processes connected to ω3 PUFA metabolism and conversion and thus trophic transfer efficiency in pelagic food webs.

overall_design: We conducted a feeding experiment in Daphnia magna with strictly controlled diets to address EPA-dependent expression profiles. Two different EPA-free basis food sources were used in the experiment: the green alga (GA) Acutodesmus obliquus and the Cyanobacterium (CY) Synechococcus elongatus. The PUFA EPA was added via liposomes to half of the experimental groups fed with GA or CY to provide a comparable design for monitoring effects of EPA availability. In addition, we also monitored Daphnia magna fed with Cryptomonas ssp. (CRY), serving as a natural positive control (contains naturally EPA). We analysed animals that were exposed to the defined food conditions from hatch until they reached maturity. In total, 5 treatment groups were prepared for sequencing with 3 replicates each. Replicate sample pools consisted of 5 mature specimens to ensure appropriate amounts for RNA extraction and comparability. Using the Illumina HiSeq 4000 platform in paired-end mode we gathered ~ 52.9 million reads per single replicate for transcriptomic analyses.

first: Patrick

last: Fink


title: In vivo molecular signatures of severe dengue infection revealed by viscRNA-Seq

status: Public on Nov 19 2018

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

summary: Dengue virus infection can result in severe symptoms including shock and hemorrhage, but an understanding of the molecular correlates of disease severity is lacking. Bulk transcriptomics on blood samples are difficult to interpret because the blood is composed of different cell types that may react differently to virus infection. Dengue virus RNA can be detected in human plasma, however identifying the cells carrying dengue virus through the bloodstream in vivo has proven challenging. Here we used our recently developed viscRNA-Seq approach to profile transcriptomes of thousands of single blood peripheral mononuclear cells from 6 human subjects with dengue fever and severe dengue, as well as to characterize the cell types associated with dengue virus in the human blood. We found that although no bulk transcriptome marker for severe dengue exists, the expression of MX2 in naive B cells, of CD163 in CD14+/CD16+ monocytes and of other genes in specific cell types is highly predictive for severe dengue. We detected virus-associated cells in the blood of two severe dengue patients with high viral load and discovered the majority of these to be B cells expressing germline IgM or IgD immunoglobulin chains and naive markers but also showing signs of activation and expression of CD69, CXCR4, and other surface receptors. In bystander B cells we detected signs of strong immune activation, parallel hypersomatic evolution and, in one severe degue subject, an anomalously large clone of highly mutated, IgG1 plasmablasts that could be reactive to dengue virus. This study presents a high-resolution molecular exploration into dengue virus infection in humans and can be generalized to any RNA virus.

overall_design: Blood cells from dengue virus infected human patients were subjected to virus-inclusive single cell RNA-Seq.

first: Makeda

last: Robinson

first: Derek

last: Croote

first: Malaya

middle: K

last: Sahoo

first: Ana

last: Sanz

first: Eliana

last: Ortiz-Lasso

first: Ludwig

last: Albornoz

first: Fernando

last: Suarez

first: Jose

middle: G

last: Montoya

first: Leslie

last: Goo

first: Benjamin

middle: A

last: Pinsky

first: Stephen

last: Quake

first: Shirit

last: Einav


title: Load-Dependent Changes in Left Ventricular Gene Expression in a Pathophysiologically Relevant Murine Model of Reversible Heart Failure

status: Public on Dec 14 2017

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company


title: miRNA expression profiling of prostate cancer (PCa) and normal prostatic samples

status: Public on Dec 31 2017

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: MicroRNAs (miRNAs) play important roles in cell differentiation and self-renewal controlling post-transcriptional processing of mRNAs and attenuating production of the encoded proteins. Here, we unveil a novel oncogenic pathway leading to activation of STAT3 signaling through miRNA-mediated silencing of the E3 ubiquitin ligase COP1. miRNA profiling showed that miR-424 was upregulated in prostate cancer compared to normal prostate and specifically associated with reduced level of the ETS factor ESE3/EHF in an aggressive subgroup of tumors. MiR-424 was significantly elevated also in other epithelial cancers and amplified in 1-3% of various cancers. In normal prostate epithelial cells miR-424 was repressed by ESE3/EHF and when upregulated promoted oncogenic and cancer stem cell (CSC) properties. Conversely, ablation of miR-424 in metastatic prostate cancer cells reduced CSC self-renewal and prevented in vivo tumour initiation and metastatic spread. miR-424 targeted the 3' UTR of COP1 mRNA and reduced COP1 protein level. COP1 induced STAT3 ubiquitylation and degradation by the ubiquitin-proteasome system (UPS). Therefore, reduced levels of COP1 in prostate cancer cells, resulted in accumulation and increased STAT3 signaling. COP1 knockdown and over-expression phenocopied the effects of miR-424 deregulation on oncogenic phenotypes and STAT3 signalling, while STAT3 knockdown prevented the transforming effects of miR-424. Consistently, expression of EHF/ESE3 and RFWD2/COP1 were highly correlated in human prostate cancers and other epithelial tumors. Furthermore, miR-424 induced genes were enriched of STAT3 targets, converged with those induced by COP1 loss in mouse embryos and were associated with adverse prognosis in prostate and other epithelial cancers. In primary prostate tumours, low COP1 and high STAT3 protein level were also significantly associated and predictive of biochemical relapse. Collectively, this study reveals a novel miRNA-activated oncogenic axis in prostate cancer. Targeting miR-424 or miR-424 dependent pathways may represent a unique approach to attack a key node in tumorigenesis.

overall_design: 21 samples from normal prostate and 56 from prostate cancer were analyzed for miRNA expression profiling.

first: Giovanna

last: Chiorino

first: Maurizia

last: Mello-Grand

first: Viajy

last: Singh


title: Load-Dependent Changes in Left Ventricular Gene Expression in a Pathophysiologically Relevant Murine Model of Reversible Heart Failure (2 weeks heart failure, 4 weeks reversal)

summary:
Wild type, female, C57BL/6 mice were subjected to sham (n=6) surgery, or TAC + MI to cause progressive LV remodeling (n=12). At 2wks post-TAC, one group of mice underwent de-banding (HF-DB, n=6), whereas in a second group of mice the band remained intact (HF; n = 6).  LV remodeling was evaluated by 2D echocardiography at 14 days post-TAC+MI , and 4 wks  post-debanding.  At 6 wks the hearts were excised and analyzed for changes in gene expression using transcriptional profiling.
e-banding in the HF-DB mice resulted in normalization of LV volumes and LV mass, and normalization of cardiac myocyte hypertrophy at 6wks, without significant changes in myofibrillar collagen in the HF and HF-DB mice. Both LV ejection fraction (LVEF) and LV radial strain improved numerically following de-banding; however, both measurements remained significantly depressed in the HF-DB mice compared to sham, and were not significantly different from HF mice at 6wks. Reverse LV remodeling in the HF-DB mouse hearts was accompanied by a partial (80%) normalization of the genes that became dysregulated during LV remodeling, whereas 20% of genes remained persistently dysregulated following reverse LV remodeling.

overall_design: Gene expression in mouse cardiac left ventricular samples was measured after 6 wk of sustained transverse aortic constriction + small apical myocardial infarction (TAC+MI) (HF group), after 2 wk of TAC+MI with 4 wk of de-banding (HF_DB), and in time-matched animals subjected to sham surgeries both for TAC+MI initiation and for de-banding.  6 individual mice were used per group.

first: Douglas

last: Mann


title: GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer [DNase hypersensitivity]

status: Public on Dec 16 2017

first: Jeff

last: Jasper

summary: The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the development of resistance it is likely that further development of ER-modulators will yield only incremental improvements. Thus, with the view that resistance is inevitable, we undertook the development of a new approach to treat ER-positive breast cancer by identifying and exploiting targetable vulnerabilities that emerge in endocrine therapy resistant disease. Genomic discovery platforms, including DNASeq, ChIPSeq and RNASeq were used to assess the epigenome, targeting global transcription factor binding profile, and transcriptome in cellular models of endocrine therapy sensitive and resistant disease. DNASeq was first used to identify the chromatin state, with a focus on differences, between these two models. Motif enrichment analysis indicated FOXA1 was a candidate transcription factor influencing the chromatin architecture, which was consistent with previously published studies. This led to the examination of the FOXA1 chromatin binding profile in these models. FOXA1 has previously been described to bind at enhancers. Furthermore, the relative transcription activity of specific enhancers has been shown to be indicated by the epigenomic marks on histones flanking transcription factor binding sites. For this reason, we assessed the specific pattern of histone 3 lysine 4 methylation to confirm enhancer status and histone 3 lysine 27 acetylation as an indicator of transcriptional activity.  The specific patterns and distribution of FOXA1 binding was then integrated with this epigenomic information to reveal a subset of enhancers that became activated and another subset that gained enhanced activation in the tamoxifen resistant setting relative to the tamoxifen sensitive model from which it was derived. These results were integrated with the differential transcriptome, or genes shown to be differential expressed based on RNASeq, in the TAMR model as compared to its parental cell line, MCF7-WS8, and confirmed that the active enhancers were in fact associated with genes that were expressed more highly, on average, in the TAMR model.   Motif enrichment at these two subgroups of enhancers indicated that another transcription factor, GRHL2, likely interacts with FOXA1 at these active sites. These results were again integrated with the “differential transcriptome” based on RNASeq and confirmed that the active enhancers, and indicated an even stronger enrichment of genes that were expressed more highly, on average, in the TAMR model relative to the MCF7-WS8 model. The GRHL2 transcriptome was then further defined by both GRHL2 ChIPSeq as well as RNASeq by comparing TAMR samples in which downregulation of GRHL2 expression had been achieved via siRNA as compared to control siRNA sequences.  The collection of these data defined a subset of genes, the GRHL2 dependent transcriptome, that demonstrated increased expression in TAMR. The results of these cell lines studies were corroborated by assessing the transcriptome of xenograft mouse models of endocrine therapy sensitive and resistant disease. Integrative analysis of these data identified a collateral ER-independent signaling pathway in endocrine therapy resistant tumors that converges upon and modulates the FOXA1 and GRHL2 cistrome/transcriptome.

overall_design: In total, 12 samples were analyzed to assess open chromatin using DNase-Seq. This study has 3 cell lines (MCF7, WS8, and TAMR) with two replicates each. Samples were grown in hormone-free media for 24 hours and then treated with either Vehicle or 4-hydroxytamoxifen (4-OHT) for 24 hours.

first: Kimberly

last: Cocce

first: Logan

last: Everett

first: Suzanne

last: Wardell

first: Thomas

last: Westerling

first: Taylor

last: Krebs

first: Robert

last: Baldi

first: Tricia

last: Wright

first: Alex

last: Yllanes

first: Jeremy

last: Blitzer

first: Craig

last: Logsdon

first: Daniel

last: Rakiec

first: David

last: Ruddy

first: Terry

last: Hyslop

first: Allison

last: Hall

first: Jeffrey

last: Marks

first: Gregory

last: Crawford

first: Myles

last: Brown

first: Donald

last: Mcdonnell


title: Hormone Therapy Use and Breast Tissue DNA Methylation: Analysis of Epigenome Wide Data from the Normal Breast Study

status: Public on Dec 19 2017

city: Research Triangle Park

first: Zongli

last: Xu

address: 111 tw alexander Dr.

institute: NIH/NIEHS

summary: Genome wide DNA methylation profiling of fresh frozen, histologically normal-appearing breast tissue from the Normal Breast Study (NBS). The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles for 90 samples, including “current”, “former” and never users of HRT.

overall_design: Bisulphite converted DNA from the 85 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Sophia

last: Harlid

first: Erin

last: Kirk

first: Lauren

last: Wilson

first: Melissa

last: Troester

first: Jack

last: Taylor


title: Bazedoxifene and conjugated estrogen combination improves gut-liver axis health

status: Public on Feb 15 2018

city: Urbana

first: Karen

last: Chen

state: IL

address: 1201 W Gregory St

department: Division of Nutritional Sciences

institute: University of Illinois at Urbana-Champaign

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

sample_organism:
Mus musculus
mouse gut metagenome

platform_organism:
Mus musculus
mouse gut metagenome

overall_design: Refer to individual Series


title: The effect of Schisandra chinensis fruit extract (SCE) and Schisandrin B (SchB) on gene expression profile in TGF-β1-treated A7r5 rat aortic smooth muscle cell

status: Public on Dec 20 2017

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

institute: Seoul National University College of Medicine

summary: Schisandra chinensis fruit extract (SCE) and its active ingredient Schisandrin B (SchB), which are effective in the treatment of vascular diseases, have been known to suppress transforming growth factor β1 (TGF-β1)-mediated Smad activation and myosin light chain (MLC) phosphorylation in vascular smooth muscle cells (VSMCs). However, it is still largely unknown about the pharmacologic effects and mechanisms of SCE and SchB on  TGF-β1-induced intracellular signaling pathways in vascular smooth muscle cells (VSMCs).

overall_design: To investigate gene expression profile alteration and pharmacological actions of SCE and SchB on TGF-β1-treated VSMCs, we performed microarray experiment.

first: Soonbum

last: Park

first: JungNyeo

last: Chun

first: Sanghoon

last: Lee


title: Molecular anatomy of the developing human retina

status: Public on Dec 07 2017

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Clinical and genetic heterogeneity associated with retinal diseases makes stem cell-based therapies an attractive strategy for personalized medicine. However, we have limited understanding of the timing of key events in the developing human retina, and in particular the factors critical for generating the unique architecture of the fovea and surrounding macula. Here we define three key epochs in the transcriptome dynamics of human retina from fetal day (D) 52 to 150. Coincident histological analyses confirmed the cellular basis of transcriptional changes and highlighted the dramatic acceleration of development in the fovea compared to peripheral retina. Human and mouse retinal transcriptomes show remarkable similarity in developmental stages, though morphogenesis was greatly expanded in humans. Integration of DNA accessibility data allowed us to reconstruct transcriptional networks controlling photoreceptor differentiation. Our studies provide insights into human retinal development and serve as resource for molecular staging of human stem cell-derived retinal organoids.

overall_design: Whole human fetal retina samples [spanning 12 time points: D52/54, D53, D57, D67, D80, D94 (2 samples), D105, D107, D115, D125, D132 and D136] or dissected retinal regions [at four time points: D59 (periphery and central, 2 samples each), D73 (periphery and fovea/macula), D96 (periphery, fovea/macula, and nasal central) and D132 (periphery, fovea/macula, and nasal central)] were used to generate RNA-seq libraries.

first: Akina

last: Hoshino

first: Rinki

last: Ratnapriya

first: Vijender

last: Chaitankar

last: Wilken

first: Chi

last: Zhang

first: Margaret

last: Starostik

first: Linn

last: Gieser

first: Anna

last: La Torre

first: Mario

last: Nishio

first: Olivia

last: Bates

first: Ashley

last: Walton

last: Bermingham-McDonogh

first: Ian

last: Glass

first: Rachel

last: Wong

first: Anand

last: Swaroop

first: Thomas

last: Reh


title: Developmental Transcriptome Dynamics of the Murine Retina and iPSC Retina organoid

last: Brooks


title: Developmental Transcriptome Dynamics of Induced Pluripotent Stem Cell Retina Organoid

summary: This study provides analysis of developing mouse retina organoids derived from induced pluripotent stem cells . RNA-seq profiling was performed on 10 time points during retinal organoid development. Alignment, transcript and gene quantitation, and normalization was performed.

overall_design: Retina organoids were collected in triplicate at 10 time points during differentiation (day (D) 0, 4, 7, 10, 12, 15, 18, 22, 25, and 32).

first: Holly

middle: Y

last: Chen

first: Lina

last: Zelinger

first: Alexa

last: Boleda


title: Developmental Transcriptome Dynamics of the Murine Retina

first: Matthew

summary: This study provides a comprehensive transcript analysis of the developing mouse retina with a focus on normalization, differentially expression, cell-type specific gene expression, transcription factor co-expression, alternative splicing, and novel transcript discovery. RNA-seq profiling was performed on four embryonic and eight postnatal time points during mouse retinal development and maturation. Alignment, transcript quantitation, normalization and differential expression, alternative splice usage, and novel transcript discovery was performed. Quantitative analysis revealed that 25,901 total transcripts encoding for 13,714 genes were expressed in the mouse retina between embryonic day 11 and postnatal day 28. Of these expressed transcripts, 12,075 were significantly differentially expressed (10,069 genes) at some point during development corresponding to ~73% of the expressed genes.

overall_design: RNA-seq was performed in duplicate on developing and mature mouse retina from 12 stages comprising four embryonic time points (E11, E12, E14, and E16) and eight postnatal time points (P0, P2, P4, P6, P10, P14, P21, and P28).

last: Chaitankar

first: Koray

last: Kaya


title: GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer (RNA-Seq data set 2)

status: Public on Nov 20 2017

first: Jeff

last: Jasper

overall_design: In total, 18 samples were analyzed for transcript expression profiles. This study compares depletion of GRHL2 by siRNA vs siCtrl. Independent biological triplicates and two technical replicates were used for each siRNA (siCtrl, SiGRHL2-A, siGRHL2-C).

first: Kimberly

last: Cocce

first: Logan

last: Everett

first: Suzanne

last: Wardell

last: Westerling

first: Taylor

last: Krebs

first: Robert

last: Baldi

first: Tricia

last: Wright

first: Alex

last: Yllanes

first: Jeremy

last: Blitzer

first: Craig

last: Logsdon

first: Daniel

last: Rakiec

first: David

last: Ruddy

first: Terry

last: Hyslop

first: Allison

last: Hall

first: Jeffrey

last: Marks

first: Gregory

last: Crawford

first: Myles

last: Brown

first: Donald

last: Mcdonnell


title: Whole genome RNA-seq analysis of Wild type or Elf4-/- peritoneal macrophages and whole genome RNA-seq analysis of 293T cells transfected with miR-221 or empty vector.

status: Public on Nov 21 2017

city: Beijing

first: lili

last: Cao

address: Xueyuan road, haidian district

institute: Peking university health science center

summary:
Wild type or Elf4-/- peritoneal macrophages were infected with VSV, followed by whole genome RNA-seq analysis. 293T cells were transfected with miR-221 or empty vector, followed by whole genome RNA-seq analysis.
Conclusions:Overexpression of miR-221 in cells facilitated viral infection and  inhibited the production of IFNβ.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Wild type or Elf4-/- peritoneal macrophages were infected with VSV for 4 hours. Cells were harvested followed by whole genome RNA-seq analysis. 293T cells were transfected with miR-221 or empty vector. 6 hours later the cells were were harvested followed by whole genome RNA-seq analysis.

first: Lili

first: Fuping

last: You


title: Global control of carbon flux in Bifidobacterium breve UCC2003

status: Public on Mar 09 2018

city: Cork

first: Noreen

last: Lanigan

state: Cork

address: Biosciences Institute, University college Cork, cork, ireland.

department: Microbiology

country: Ireland

institute: University college cork

summary: In this paper, two predicted lac I type transcription factors (TFs) were characterised and shown to be involved in the regulation of the central metabolic pathways of B. breve UCC2003. Although, genetically different, these TF were functionally very similar. When first identified these TFs were named AraQ and MalR1, due to their predicted associations with arabinose and maltose metabolism, respectively. Now, however they have been renamed as BifR1 and BifR2 respectively, due to their control of the central metabolic pathways including the bifid shunt.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Emer

last: Kelly

first: Douwe

last: van Sinderen


title: GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer (RNA-Seq data set 1)

city: Durham

first: Jeff

last: Jasper

institute: Duke University

overall_design: In total, 12 samples were analyzed for transcript expression profiles. This study has 3 cell lines(MCF7, WS8, and TAMR) with two replicates each. Samples were grown in hormone-free media for 24 hours and then treated with either Vehicle or 4-hydroxytamoxifen for 24 hours.

first: Kimberly

last: Cocce

first: Logan

last: Everett

first: Suzanne

last: Wardell

first: Thomas

last: Westerling

first: Taylor

last: Krebs

first: Robert

last: Baldi

first: Tricia

last: Wright

first: Alex


title: GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer

summary:
The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the development of resistance it is likely that further development of ER-modulators will yield only incremental improvements. Thus, with the view that resistance is inevitable, we undertook the development of a new approach to treat ER-positive breast cancer by identifying and exploiting targetable vulnerabilities that emerge in endocrine therapy resistant disease. Genomic discovery platforms, including DNASeq, ChIPSeq and RNASeq were used to assess the epigenome, targeting global transcription factor binding profile, and transcriptome in cellular models of endocrine therapy sensitive and resistant disease. DNASeq was first used to identify the chromatin state, with a focus on differences, between these two models. Motif enrichment analysis indicated FOXA1 was a candidate transcription factor influencing the chromatin architecture, which was consistent with previously published studies. This led to the examination of the FOXA1 chromatin binding profile in these models. FOXA1 has previously been described to bind at enhancers. Furthermore, the relative transcription activity of specific enhancers has been shown to be indicated by the epigenomic marks on histones flanking transcription factor binding sites. For this reason, we assessed the specific pattern of histone 3 lysine 4 methylation to confirm enhancer status and histone 3 lysine 27 acetylation as an indicator of transcriptional activity.  The specific patterns and distribution of FOXA1 binding was then integrated with this epigenomic information to reveal a subset of enhancers that became activated and another subset that gained enhanced activation in the tamoxifen resistant setting relative to the tamoxifen sensitive model from which it was derived. These results were integrated with the differential transcriptome, or genes shown to be differential expressed based on RNASeq, in the TAMR model as compared to its parental cell line, MCF7-WS8, and confirmed that the active enhancers were in fact associated with genes that were expressed more highly, on average, in the TAMR model.   Motif enrichment at these two subgroups of enhancers indicated that another transcription factor, GRHL2, likely interacts with FOXA1 at these active sites. These results were again integrated with the “differential transcriptome” based on RNASeq and confirmed that the active enhancers, and indicated an even stronger enrichment of genes that were expressed more highly, on average, in the TAMR model relative to the MCF7-WS8 model. The GRHL2 transcriptome was then further defined by both GRHL2 ChIPSeq as well as RNASeq by comparing TAMR samples in which downregulation of GRHL2 expression had been achieved via siRNA as compared to control siRNA sequences.  The collection of these data defined a subset of genes, the GRHL2 dependent transcriptome, that demonstrated increased expression in TAMR. The results of these cell lines studies were corroborated by assessing the transcriptome of xenograft mouse models of endocrine therapy sensitive and resistant disease. Integrative analysis of these data identified a collateral ER-independent signaling pathway in endocrine therapy resistant tumors that converges upon and modulates the FOXA1 and GRHL2 cistrome/transcriptome.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
MCF7-WS8 and TAMR cells were treated analyzed in duplicate (for DNASeq) or triplicate (for ChIPSeq, RNASeq) following various treatments. For DNASeq, MCF7-WS8 and TAMR cells were grown in hormone free media for 2 days, followed by 1 day of 4-hydroxytamoxifen treatment. For RNASeq of MCF7-WS8 and TAMR cells at baseline, cells were grown in hormone free media for 2 days, followed by 1 day of 4-hydroxytamoxifen treatment. For ChIPSeq, MCF7-WS8 and TAMR cells were grown in hormone free media for 3 days, following 45 min of vehicle or hormone treatment (estradiol or 4-hydroxytamoxifen). For RNASeq following siRNA treatment, TAMR cells were transfected with various siRNA to GRHL2 or control siRNA for 72 hours in hormone free media. For RNASeq of xenograft tumors, MCF7-WS8 and TAMR tumors were analyzed in quadruplicate following various hormone treatments. For all tumors, female nu/nu mice (~6 weeks in age) were ovariectomized under isoflurane anesthesia; a slow release estradiol pellet (0.72mg/60 days from Innovative Research of America) or tamoxifen treatment pellet (5mg/60 days from Innovative Research of America) was implanted in the scapular region during the same procedure. The next day an approximate 8 mm3 of tumor issues (derived from a sectioning a freshly harvested tumor of 0.8 – 1cm3 volume) was engrafted orthotopically (right axial mammary fatpad) under anesthesia. Tumors were measured 3X weekly, concurrent with weight and behavior monitoring. For MCF7-WS8 tumors, tumors were grown for 30 days when they reached a size of ~0.15-0.2 cm3 volume ( l x w2 x 0.5) animals were then randomized to treatment with vehicle (0.1cc corn oil sc 3x weekly) or tamoxifen (40mg/kg 3x weekly). Animals were euthanized and tissues preserved following a total of 6 weeks of tumor growth. For TAMR tumors, tamoxifen treated animals were randomized to vehicle (0.2cc corn oil sc weekly), or fulvestrant (200mg/kg sc weekly). Animals were euthanized and tissues preserved following a total of 8 weeks of tumor growth.

Refer to individual Series


title: Ectopic expression of RAD52 and dn53BP1 improves homology-directed repair during CRISPR/Cas9 genome editing

status: Public on Nov 23 2017

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

summary:
Gene disruption by CRISPR/Cas9 is highly efficient and relies on the
error-prone non-homologous end-joining (NHEJ) pathway. Conversely, precise gene editing requires homology-directed repair (HDR), which occurs at a lower frequency than NHEJ in mammalian cells. Here, by testing whether manipulation of DNA repair factors would improve HDR efficacy, we show that transient ectopic co-expression of RAD52 and a dominant-negative 53BP1 (dn53BP1) synergize to enable efficient HDR using a single-stranded oligonucleotide DNA donor template at multiple loci in human cells, including patient-derived induced pluripotent stem (iPS) cells. Co-expression of RAD52 and dn53BP1 improves multiplexed HDR-mediated editing, whereas expression of RAD52 alone enhances HDR with Cas9 nickase. Our data show that the frequency of NHEJ-mediated DSB repair in the presence of these two factors is not suppressed, and suggest that dn53BP1 competitively antagonizes 53BP1 to augment HDR in combination with RAD52. Importantly, co-expression of RAD52 and dn53BP1 does not alter Cas9 off-target activity. These findings support the use of RAD52 and dn53BP1 co-expression to overcome bottlenecks that limit HDR in precision genome editing.

overall_design: Examination of genome-wide on- and off-target activity of CCR5 D and Q gRNAs using the Cas9 RAG1B gRNA universal bait and 3 biological replicates for each experiment.  File name abbreviations:  52 = RAD52, 53 = dn53BP1, 523 = Rad52+dn53BP1

first: Bruna

last: Paulsen

first: Pankaj

last: Mandal

first: Frederick

middle: W

last: Alt

first: Derrick

last: Rossi


title: Identification of differentially methylated BRCA1 and CRISP2 DNA regions as blood surrogate markers for cardiovascular disease

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

type: Methylation profiling by genome tiling array

summary: Genome-wide Illumina InfiniumMethylation 450 K DNA methylation analysis was performed on blood samples from clinical atherosclerosis patients (n = 8) and healthy donors (n = 8) in the LVAD study (NCT02174133, NCT01799005). Multiple differentially methylated regions (DMR) could be identified in atherosclerosis patients, related to epigenetic control of cell adhesion, chemotaxis, cytoskeletal reorganisations, cell proliferation, cell death, estrogen receptor pathways and phagocytic immune responses. Furthermore, a subset of 34 DMRs related to impaired oxidative stress, DNA repair, and inflammatory pathways could be replicated in an independent cohort study of donor-matched healthy and atherosclerotic human aorta tissue (n = 15) and human carotid plaque samples (n = 19). Upon integrated network analysis, BRCA1 and CRISP2 DMRs were identified as most central disease-associated DNA methylation biomarkers. Differentially methylated BRCA1 and CRISP2 regions were verified by MassARRAY Epityper and pyrosequencing assays and could be further replicated in blood, aorta tissue and carotid plaque material of atherosclerosis patients. Moreover, methylation changes at BRCA1 and CRISP2 specific CpG sites were consistently associated with subclinical atherosclerosis measures (coronary calcium score and carotid intima media thickness) in an independent sample cohort of middle-aged men with subclinical cardiovascular disease in the Aragon Workers' Health Study (n = 24). Altogether, BRCA1 and CRISP2 DMRs hold promise as novel blood surrogate markers for early risk stratification and CVD prevention.

overall_design: Bisulfite converted DNA from whole blood of 8 atherosclerotic patients and 8 healthy subjects were hybridised to the Illumina Infinium HumanMethylation450 BeadChip.

first: Geoffrey

last: Istas

first: Maria

last: Pudenz

first: Katarzyna

last: Szarc vel Szic

first: Veronica

last: Lendinez-Tortajada

first: Montserrat

last: Leon-Latre

first: Karen

last: Heyninck

first: Guy

last: Haegeman

first: Jose

last: Casasnovas

last: Tellez-Plaza

first: Clarissa

last: Gerhauser

first: Christian

last: Heiss

first: Ana

last: Rodriguez-Mateos

first: Wim

last: Vanden Berghe


title: High throughput single-cell whole transcriptome analysis of induced cardiomyocytes during direct cardiac reprogramming [RNA-seq]

status: Public on Oct 25 2017

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

summary: Direct lineage conversion offers a new strategy for tissue regeneration and disease modeling. Despite recent success in directly reprogramming fibroblasts into a wide spectrum of cell types, the precise changes that fibroblasts undergo as they progress to target cell fates remain unclear. The inherent heterogeneity and asynchronous nature of the reprogramming process make it difficult to study using bulk genomic techniques. Therefore, a fundamental and detailed understanding of global transcriptome changes at the single cell level is necessary to better optimize reprogramming for therapeutic purposes and to advance the understanding of cell plasticity and cell identity acquisition. Here, we applied single-cell RNA-seq to analyze global transcriptome changes at early stages of induced cardiomyocyte (iCM) reprogramming. Using unsupervised dimensionality reduction and clustering algorithms, we identified molecularly distinct subpopulations of cells along the reprogramming process from fibroblasts to iCMs, including a novel intermediate state that exhibited molecular signatures of both fibroblast and cardiomyocyte. In summary, our single cell transcriptomics approaches enabled us to construct a reprogramming trajectory and uncover the intermediate cell populations, regulatory pathways and genes putatively involved in iCM induction.

overall_design: Neonatal mouse cardiac fibroblasts were isolated and reprogrammed with Mef2c, Gata4, and Tbx5. Single cells were captured on day 3 with the microfluidic system C1 in seven separate experiments including two plates of control cells (C1 and C2, uninfected and retroviral transduction control), three plates of reprogramming cells (M1, M2 and M3) and two plates of half-to-half mixed reprogramming cells and retroviral-infected control cells (M4 and M5). External RNA-spike in were added before lysis and used to calculate technical size factor during normalization. Lysate from 574 wells containing single cells (four zero-cell control were included in four of the seven plates) were selected for mRNA sequencing (574 raw data files) and a total of 513 high-quality single-cell transcriptomes were analyzed (513 processed data).

first: Ziqing

last: Liu

first: Li

last: Wang

last: Qian


title: RNA-seq gene expression profiling in resting murine B cells from WT or KMT2D knockout mice, before and after stimulation with LPS, IL4, and anti-CD180

status: Public on Aug 28 2017

city: New York

first: Yanwen

last: Jiang

institute: Weill Cornell Medical College

summary: Resting B cells were isolated from WT or KMTD KO mice by immunomagentic depletion of with anti-CD43 beads. Gene expression use determined by RNAseq in resting B cells or B cells stimulated with LPS, IL4, and anti-mouse CD180 for 3 days.

overall_design: RNAseq was used to profile unstimulated resting B cells (n=3) and B cells stimulated for 3 days (n=3).

first: Andres

last: Canela

first: Isaac

last: Boss

first: Heng

last: Pan

first: Ari

last: Melnick

first: Andre

last: Nussenzweig


title: Analysis of obesity-induced DNA methylation in visceral adipose tissue

status: Public on Oct 08 2017

city: Washington

first: Matthew

middle: David

last: Barberio

state: District of Columbia

address: 111 Michigan Avenue

department: Exercise and Nutrition Sciences

institute: George Washington University

summary: The purpose of this study was to use global gen expression to identify obesity-induced changes in gene expression profiles of lean and obese adolescent females. Visceral adipose tissue was extracted during abdominal surgeries on Lean and Obese adolescent females of african-americam, caucasian, and hispanic descent.

overall_design: Genomic DNA was extracted from visceral adipose tissue of lean and obese adolescent females. Illumina Infinium Human Methylation 450k BeadChips were utilized global methylation profiles in visceral adipose tissue.

first: Monica

last: Hubal

middle: D

first: Evan

last: Nadler


title: Load-Dependent Changes in Left Ventricular Gene Expression in a Pathophysiologically Relevant Murine Model of Reversible Heart Failure (2 weeks heart failure, 2 weeks reversal)

first: Scot

middle: J

last: Matkovich

summary: Wild type, female, C57BL/6 mice were subjected to sham (n=6) surgery, or TAC + MI to cause progressive LV remodeling (n=13). At 2wks post-TAC, one group of mice underwent de-banding (HF-DB, n=6), whereas in a second group of mice the band remained intact (HF_shDB; n = 7).  LV remodeling was evaluated by 2D echocardiography at 14 days post-TAC+MI , and 2 wks  post-debanding.  At 4 wks the hearts were excised and analyzed for changes in gene expression using transcriptional profiling.

overall_design: Gene expression in mouse cardiac left ventricular samples was measured after 4 wk of sustained transverse aortic constriction + small apical myocardial infarction (TAC+MI) (HF_shDB group), after 2 wk of TAC+MI with 2 wk of de-banding (HF_DB), and in time-matched animals subjected to sham surgeries both for TAC+MI initiation and for de-banding.  6 individual mice were used per group, except for HF_shDB which used 7 mice.

first: Douglas

last: Mann


title: Gene expression profile in breast cancer cell lines using RNA sequencing

status: Public on Aug 09 2017

city: Suwon-si,

first: Seong-Jin

last: Kim

address: 145 Gwanggyo-ro, Yeongtong-gu,

institute: Nano-Bio Medicine Research Center

summary: In order to identify novel molecular targets associated with TNBC progression, we initially performed transcriptome analysis using RNA sequencing in breast cancer cell lines, classified as either the luminal subtype (MCF-7, T47D, ZR-75B) or basal-like subtype (MDA-MB-231, MDA-MB-435, Hs578T).

overall_design: Total RNAs of each cell were isolated using the TRIzol reagent for RNA sequencing following manufacturer’s instructions. The total RNAs were treated with DNase I, purified with miRNeasy Mini Kit and subsequently quality checked using an Agilent 2100 Bioanalyzer. An Illumina platform was used to analyze transcriptomes with 90 bp paired-end library. Samples were paired-end sequenced with the Illumina HiSeq 2000 using HiSeq Sequencing kits.


title: Analysis of obesity-induced gene expression changes in visceral adipose tisssue

summary: The purpose of this study was to use global gene expression to identify obesity-induced changes in gene expression profiles of lean and obese adolescent females. Visceral adipose tissue was extracted during abdominal surgeries on Lean and Obese adolescent females of african-americam, caucasian, and hispanic descent.

overall_design: Total RNA extracted from human visceral adipose of obese and lean adolescent females. GeneChip Human Genome U133 Plus 2.0 arrays were utilized to explore gene expression profiles.

first: Monic


title: The Drosophila Embryo at Single-Cell Transcriptome Resolution

status: Public on Sep 01 2017

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

institute: Max Delbrück Center for Molecular Medicine

summary: By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express distinct gene combinations. Here, we used single-cell sequencing of precisely staged embryos and devised DistMap, a computational mapping strategy to reconstruct the embryo and to predict spatial gene expression approaching single-cell resolution. We produce a virtual embryo with about 8000 expressed genes per cell. Our interactive “Drosophila-Virtual-Expression-eXplorer” (DVEX) database generates three-dimensional virtual in situ hybridizations and computes gene expression gradients. We used DVEX to uncover patterned expression of transcription factors and long noncoding RNAs, as well as signaling pathway components. Spatial regulation of Hippo signaling during early embryogenesis suggests a mechanism for establishing asynchronous cell proliferation. Our approach is suitable to generate transcriptomic blueprints for other complex tissues.

sample_organism:
Drosophila melanogaster
Drosophila virilis

overall_design: Single cell transcriptomics of the early Drosophila embryo were generated using Drop-seq

first: Philipp

last: Wahle

first: Christine

last: Kocks

first: Nikolaus

last: Rajewsky

first: Robert

last: Zinzen


title: RRBS and RNA-seq profiling of maize shoot and tassel primordium

status: Public on Aug 07 2017

city: Los Angeles

first: Fei-Man

last: Hsu

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: Profiling the methylation and gene expression between vegetative (coleoptile-stage shoots) and reproductive (tassel primordium) tissues with RRBS and RNA-seq

overall_design: MseI-RRBS are promoter-enriched and CviQI-RRBS are genebody-enriched libraries.  RNA-Seq of shoots and tassels.

first: Ming-Ren

last: Yen

first: Chi-Ting

last: Wang

first: Chieh-Yu

last: Lin

first: Chung-Ju

first: Pao-Yang

last: Chen


title: Human Transcriptome Array 2.0 (HTA) in matched colorectal cancer and normal colonic mucosa.

status: Public on Mar 31 2017

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

institute: University of Catania

summary: We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis.

overall_design: 9 tumoral bioptic samples, deriving from 6 patients, were collected directly after surgical resection. The mean age was 72 years (SD 13.73) for 5 female patients and the only male patient was 73 years-old. In 3 patients, two samples were taken at arbitrary positions in the tumor area, separated by at least 1 cm (double-sampling pairs, indicated as tumoral sample 1 or 2). In 6 cases biopsies of adjacent normal mucosa (at distance of 3-6 cm from the tumor) were also collected (matched tumor/mucosa pairs).

first: Vincenza

last: Barresi

first: Angela

last: Trovato

first: Giorgia

last: Spampinato

first: Giovanna

last: Valenti

first: Nicolo

last: Musso


title: Transcriptome analysis of CPSF5 dependent starvation response

status: Public on Jun 01 2017

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary:
Purpose: transcriptome analysis of CPSF5 dependent starvation response
Methods: Total RNA was extracted from larval fat body using TRIzol® reagent (Invitrogen). After assessing RNA quality with an Agilent Bioanalyzer, libraries constructed with an Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold were sequenced using an Illumina HiSeq 4000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center).
Results: Using an optimized data analysis workflow, we identified 1933 genes responding to starvation and 585 genes were found to be CPSF5-dependent.  The gene set enrichment analyses and qPCR confirmation further suggested autophagy, changes of lipid, protein and energy metabolism is requlated by CPSF5 during starvation.
Conclusions: our study identified the regulatory role of CPSF5 in autophagy and metabolisms during starvation.

overall_design: Analysis the transcriptome changes in the fat body of the CPSF5 mutant or wild-type flies under fed or starvation condition

first: Hong-Wen

last: Tang

first: Norbert

last: Perrimon


title: High throughput quantitative whole transcriptome analysis of individual macrophages 7 days post-sham thoracotomy in B6 CSF1R-GFP mice

status: Public on Jun 19 2017

city: South San Francisco

first: Ian

last: Driver

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

summary: Using fluorescence activated cell sorting, we isolated CD45+, CSF1R-GFP+, F4/80+, Ly6G- mouse lung monocytes and macrophages at 7 days after sham thoracotomy procedures. We then used microfluidic single cell RNA-sequencing to transcriptional profile unique myeloid subsets.

overall_design: After sequencing 31 single cell transcriptomes were analyzed. Hierarcical and k-means clustering reveals several populations of macrophages are present in the lung.

first: Jason

last: Rock


title: RNA-seq analysis of SLIRP knockdown with 1nM DHT in LNCaP cells

status: Public on Mar 01 2017

city: Chapel Hill

first: Young

last: Whang

address: 22-016 Lineberger Cancer Ctr

department: UNC School of Medicine, Clinical Research, Urologic Oncology Program

institute: University of North Carolina at Chapel Hill

summary:
The purpose of this study was to profile gene expression changes that could occur with the loss of co-repressor SLIRP. In addition, we wanted to investigate how DHT could further alter gene expression.
Methods: LNCaP cells were transfected with custom nonsense control siRNA or a pool of SLIRP siRNA (HSS130109, HSS188666, HSS188667 Invitrogen, Carlsbad, CA) at 40nM for 24hrs. Cells were washed once with PBS and replaced with SFM containing EtOH or 1nM/ml DHT for another 24hrs.  Two biological replicates were collected from 2 different experiemnts for total of 4 replicates. RNA collected  was sequenced using Illumia HiSeq2000 single read 50 bp by the HTSF core at UNC and aligned and normalized by the Bioinformatics core at UNC.
Results: We found a differential gene expression pattern between our control and SLIRP knockdown samples. We also identified a 176 AR gene signature with 3 subclasses and a large SLIRP gene signature (~1700).

overall_design: Examination of control (NS) vs. SLIRP siRNA treated with 1nM DHT in the prostate cancer cell line LNCaP

first: Dinuka

last: De Silva


title: Differentially expressed miRNAs in sepsis-induced acute kidney injury target oxidative stress and mitochondrial dysfunction pathways

status: Public on Feb 10 2017

city: shanghai

first: chunmei

last: huang

address: No. 1665 Rd. Kongjiang

department: Department of Emergency

institute: Department of Emergency, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China

summary: Using the highly sensitive miRNA array, we screened 40 miRNAs were differentially expressed among the three groups and we explored the functions of these miRNAs in the serum by Gene Ontology and Kyoto Encyclopedia of Genes annotation. The enrichment results indicated that these miRNAs mainly participated in the oxidative stress and mitochondrial dysfunction pathways. Furthermore, the quantitative real-time polymerase chain reaction showed the different expression of miRNA might potentially be used to discriminate septic AKI from sepsis-non AKI and they were correlated with the regulation of mitochondrial oxidative stress and dysfunction, including PGC-1α, SIRT1, mTOR, OXSR1 and NOX5.

overall_design: In this study, 15 blood samples, including 6 patients with G- sepsis-induced AKI, 6 patients with G- sepsis-non AKI and 3 healthy controls were used to acquire the miRNA expression profiling and the function of the abudant miRNAs in the serum were analyzed by bioinformatic methods,finally, the different expression of miRNA might potentially be used to discriminate septic AKI from sepsis-non AKI and they were correlated with the regulation of mitochondrial oxidative stress and dysfunction, including PGC-1α, SIRT1, mTOR, OXSR1 and NOX5.

first: Ge

last: Qin-Min

first: Pan

last: Shu-Ming


title: Hormone-dependent control of developmental timing through regulation of chromatin accessibility

status: Public on Jun 06 2017

first: Spencer

last: Nystrom

address: 250 Bell Tower Drive

department: Curriculum in Genetics and Molecular Biology

institute: UNC-Chapel Hill

summary: We identify a temporal cascade of ecdysone-inducible transcription factor gene expression during Drosophila wing development. This temporal cascade corresponds with dynamic changes in chromatin accesibility during wing development. We hypothesized that these temporally regulated transcription factors may coordinate these dynamic open chromatin changes. To test this, we investigate the ecdysone-inducible transcription factor, E93, which we determine is required for coordinating transitions in developmental stage by regulating chromatin accesibility of cis-regulatory elements.

overall_design: FAIRE-Seq in Triplicate during wild-type drosophila wing development timecourse (3LW, 24hAPF, 44hAPF). RNAseq in duplicate in wild-type wings (3LW, 24hAPF, 44hAPF). FAIRE-seq from E93-mutant wings (3LW, 24hAPF, 44hAPF) in duplicate. ChIP-seq for E93-GFSTF from 24hAPF wings.

first: Christopher

middle: M

last: Uyehara

first: Matthew

last: Niederhuber

first: Mary

last: Leatham-Jensen

first: Yiqin

last: Ma

first: Laura

last: Buttitta

first: Daniel

last: McKay


title: The Drosophila Dosage Compensation Complex activates target genes via chromosome looping within the active compartment

status: Public on Jul 01 2017

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: X chromosome dosage compensation in Drosophila requires chromosome-wide coordination of gene activation. The male-specific-lethal dosage compensation complex (DCC) identifies X chromosomal High Affinity Sites (HAS) from which it reaches out to boost transcription. A recently discovered sub-class of HAS, PionX sites, represent first contacts on the X. We explored the chromosomal interactions of representative PionX sites by high-resolution 4C methodology and determined the overall chromosome conformation by Hi-C in sex-sorted embryos. X chromosomes from male and female cells display similar nuclear architecture, concordant with clustered, constitutively active genes. PionX sites, like HAS, are evenly distributed in the active compartment and engage in short- and long-range interactions beyond compartment boundaries. De novo induction of DCC in female cells allowed monitoring the reach of activation surrounding PionX sites. Remarkably, DCC not only activates genes in linear proximity, but also at megabase distance if close in space, suggesting that dosage compensation profits from chromosome folding.

overall_design:
Hi-C: female and male embryos (2 biological replicates).
4C-seq: S2 (male) cells GFP or MSL2 RNAi; Kc (female) cells GFP or SXL RNAi (2 biological replicates) at various viewpoints.
ChIP-seq (Covaris): S2 cells: Input, H4K16ac (replicate: GSM929157) or MSL2 (4 biological replicates); Kc cells: Input and H4K16ac (2 biological replicates). ChIP-seq (MNase): S2 and Kc cells: Input and H3K36me3 (2 biological replicates).
RNA-seq: S2 cells: GFP RNAi (2 biological replicates); Kc cells: GFP, SXL #1 (DRSC21490), SXL#2 (DRSC28896) RNAi after 3, 6 and 9 days.

first: Yad

last: Ghavi-Helm

first: Tom

last: Sexton

first: Christian

last: Albig

first: Catherine

last: Regnard

first: Giacomo

last: Cavalli

first: Eileen

middle: E

last: Furlong

first: Peter

middle: B

last: Becker


title: High throughput quantitative whole transcriptome analysis of individual macrophages 7 days post-pneumonectomy in a B6 CSF1R-GFP mouse

first: Ian

last: Driver

summary: Using fluorescence activated cell sorting, we isolated CD45+, CSF1R-GFP+, F4/80+, Ly6G- mouse lung monocytes and macrophages at 7 days after pneumonectomy procedure. We then used microfluidic single cell RNA-sequencing to transcriptional profile unique myeloid subsets. Using the pneumonectomy dataset, we identified 6 cell groups and 4 gene groups that marked several regenerative macrophage subsets including CCR2+, Ly6C+ monocytes and CD206+, Chil3+ M2-like macrophages.


title: Independent validation of human CD4+ T-cell transcriptome in early arthritis

status: Public on Apr 03 2018

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

type:
Expression profiling by array
Third-party reanalysis

summary: An exploration of the peripheral blood CD4+ T-cell transcriptome of early arthritis clinic attendees, (i) to provide validation of previously published observations, and (ii) to facilitate an eQTL analysis.

overall_design:
Ex-vivo CD4+ T-cell RNA was obtained following first early arthritis clinic attendance from 178 patients. Four diagnostic categories were confirmed at median 28 months follow-up. The key outcome categories are RA and non-RA.
The complete dataset representing 71 re-analyzed samples (from GSE20098) and 178 new samples.
[1] The 'Gene_Expression_Raw_DetP.txt' contains raw data for all 249 samples, [2] the 'normalized_re-analysis.txt' contain re-analyzed normalized data for the GSE20098 samples, [3] the complete metadata is provided as metadata_all.xls.

first: Andrew

last: Skelton


title: Altered gene expression associated with thermo-sensitive male sterility in rapeseed (Brassica napus) mutant SP2S

status: Public on Jan 01 2017

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

summary: To reveal the possible molecular mechanism underpinning the temperature sensitive male sterility, a comparative transcriptome analysis of the SP2S line and its NIL SP2F was conducted. Transcriptome differences between fertile and sterile plants were analyzed by using digital gene expression (DGE) tag profiling, and numerous differentially and specifically expressed transcripts were identified. By quantitative RT-PCR, expression levels of 10 genes randomly selected showed consistent expression patterns with the DGE data. A total of 827 up-regulated and 757 down-regulated expression transcripts in SP2S were identified, indicating  the complex responses to temperature in the SP2S line. Some genes in important pathways including ubiquitin mediated proteolysis, phenylpropanoid biosynthesis, endocytosis, apoptosis, oxidative phosphorylation, purine metabolism, MAPK signaling, spliceosome,  and ribosome were up-regulated in SP2S while other genes in the pathways of aminoacyl-tRNA biosynthesis, basal transcription factors, nucleotide excision repair, mismatch repair, and CO2 fixation were down-regulated. Some genes involved in photosynthesis, citrate cycle (TCA cycle), pentose phosphate, and stress-responsive were also differentially expressed.

overall_design: Two lines named TGMS SP2S and the wild-type SP2F were used in this study. SP2S was bred after consecutive generations of selfing from spontaneous mutation of partially male-sterile plants found in an inbred line, SP2, in 2007. The fertile NIL (near-isogenic line) SP2F had the same genetic background with SP2S. The seeds of SP2S and SP2F were sown in field in September and the seedlings were transplanted into a greenhouse in December after vernalization under field condition. The temperature was kept at 22°C and photoperiod was longer than 14h. Young floral buds from SP2S and SP2F were collected, put into RNAlater, and stored at −80°C until further processing. Total RNAs were extracted using the Trizol® Reagent (Invitrogen), and purified using TRK1001 Kit (LC Science, Houston, TX). The total RNA quantity and purity were analyzed by using of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, USA). The cDNAs were amplified according to the Illumina RNA-Seq protocol and sequenced on Illumina Hiseq2500 platform. Two groups of DGE libraries, each in three biological replicates, were constructed using total RNA of young floral buds of SP2S and SP2F grown at 22 Celsius degree with Illumina’s Digital Gene Expression Tag Profiling Kit according to the manufacturer’s protocol. We performed the single end sequencing on an Illumina Hiseq2500 following the vendor's recommended protocol. The raw data containing adaptor sequences, tags with low quality sequences and unknown nucleotides N were filtered to obtain clean reads with 36 nt in length. Clean reads were then conducted for quality assessment. All clean tags were mapped to the unigenes of our assembled transcripts dataset and JGI Brassica rapa genome by Bowtie 2 software, only 1 bp mismatch is allowed. For monitoring the mapping events on both strands, both the sense and the complementary antisense sequences were included in the data collection. The number of perfect clean reads corresponding to each gene was calculated and normalized to the number of Reads Per Kilobase of exon model per Million mapped reads (RPKM). Based on the expression levels, the significant DETs (Differentially expressed transcripts) among different samples were identified with the 3rd quartile of counts in all samples ≥ 10, p value ≤0.05, and log2 fold-change≥1. Gene ontology (GO) analysis was conducted for functional classification of DGTs and pathway analysis was carried out by using KEGG.

first: Jungang

last: Dong


title: RNAseq profiling of FACS-sorted zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures

status: Public on Aug 11 2017

city: Wageningen

first: Julien

last: Rougeot

state: Gerlderland

address: Droevendaalsesteeg 1  Building 107

department: Plant Science Group

institute: Wageningen University and Research

summary: We used different zebrafish transgenic lines to sort macrophages, neutrophils and immature lymphoid cells from 5-6 day old zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature.

overall_design: Embryos were grown into egg water refresh every day and incubated for 5 or 6 days at 28°C. 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) was added after 1 day to prevent melanisation. After the incubation period, embryos were dissociated into single cell suspension by Trypsin treatment and fluorescent cells were sorted by FACS. RNA extraction and library preparation were performed as previously described. (Rougeot et al., 2014, Methods Mol Biol 1197:41-66). For infection experiments, zebrafish embryos were manually dechorionated at 24 hours post fertilization (hpf) and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Infected larvae were collected for FACS sorting 5 day post infection.

first: Ania

last: Zakrzewska

first: Vincenzo

last: Torraca

first: Zakia

last: Kanwal

first: Hans

last: Jansen

first: Herman

middle: P

last: Spaink

first: Annemarie

middle: H

last: Meijer


title: Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA Methylation by dCas9 methyltransferases (CRISPRme) [WGBS]

status: Public on Dec 14 2016

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

summary: Fusion of active protein domains to the nuclease-deficient clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 9 (dCas9) has been widely used for epigenome editing, but the specificities of these engineered proteins have still not been fully investigated. Targeted methylation of specific gene loci offers a direct approach to perturb DNA methylation-associated biological processes. In this study, we generated and validated the global off-target characteristics of CRISPR-guided DNA methyltransferases (CRISPRme) by fusing the catalytic domain of DNMT3A or DNMT3B to the C terminus of the dCas9 protein from S. pyogenes. Using targeted quantitative bisulfite pyrosequencing and whole genome bisulfite sequencing (WGBS), we prove that CRISPRme can efficiently methylate the CpG dinucleotides flanking its target sites in genomic loci (uPA and TGFBR3) in human cells (HEK293T) with CpG-methylation levels exceeding 70% for some target sites. Using qPCR, fluorescent reporter cells, and RNA sequencing, we found that CRISPRme can mediate transient inhibition of gene expression which appears to result from Cas9-mediated interference with transcription rather than de novo DNA methylation. Analyses of whole genome methylation did not identify global methylation changes, however a substantial number of CRISPRme off-target differentially methylated regions (DMR, over 6000) were still identified. The majority of these DMRs were hypermethylated both in cells expressing CRISPRme alone and cells expressing CRISPRme together with gRNAs. These off-target hypermethylated sites were enriched in gene bodies, introns, 5’UTR, CGI shores, Alu sequences, open chromatin and PAM rich regions, but not correlated with off-target binding sites predicted by ChIP-seq. Our results prove that CRISPRme allows for efficient RNA-guided methylation of endogenous CpGs, however with high frequencies of off-target methylation indicating that further improvements of the specificity of CRISPR-dCas9 based DNA methylation modifiers are still required.

overall_design: Nine samples transfected with pUC19, or dCas9 methyltransferases with or without gRNAs were analyzed by WGBS.

first: Lin

last: Lin

first: Yong

last: Liu

first: Fengping

last: Xu

first: Jinrong

last: Huang

first: Tina

last: Daugaard

first: Trine

middle: S

last: Petersen

first: Bettina

last: Hansen

first: Lingfei

last: Ye

first: Qing

last: Zhou

first: Fang

last: Fang

first: Shengting

last: Li

first: Lasse

last: Fløe

first: Ellen

last: Shrock

first: Huanming

last: Yang

first: Jian

last: Wang

first: Xun

first: Lars

last: Bolund

first: Anders

last: Nielse


title: Next Generation Sequencing Transcriptomes of breast cancer

status: Public on Sep 06 2017

city: Harbin

first: shipeng

last: shang

address: XueFu Road 194, NanGang District

institute: Department of Breast Surgery, Harbin Medical University Cancer Hospital

summary: We performed high throughput transcriptome of breast cancer and normal tissues, identifying lincRNA associated molecular subtype with powerful capacity to distinct breast cancer population and predict prognosis. We also identified subtype-specific lincRNAs that may be a useful complement to intrinsic molecular subtype classification when divergence emerges among pathologists.Paired-end transcriptome sequencing were carried out on a cohort of 33 breast tissues from 11 groups including five breast cancer subtypes including luminal A (LA), luminal B (HER2 negative)(LB, HER2-), luminal B (HER2 positive) (LB, HER2+), HER2 and tripple negative breast cancer (TNB), adjacent noncancerous breast tissue (ANT, three samples for each subtype) and the complete normal breast tissues (three samples)

overall_design: Examination of transcriptomes in 15 breast cancer and 18 normal tissues.

first: Da

last: Pang

first: Shouping


title: Characterization of gene expression associated with the adaptation of the nematode C. elegans to hypoxia and reoxygenation stress

status: Public on May 09 2017

city: San Francisco

first: Binyamin

last: Zuckerman

institute: UCSF

summary: Oxygen (O2) is a double-edged sword to cells for while it is vital for energy production in all aerobic animals and insufficient O2 (hypoxia) can lead to cell death, the reoxygenation of hypoxic tissues may trigger the generation of reactive oxygen species (ROS) that can destroy any biological molecule. Indeed, both hypoxia and hypoxia-reoxygenation (H/R) stress are harmful, and may play a critical role in the pathophysiology of many human diseases such as myocardial ischemia and stroke. Therefore, understanding how animals adapt to hypoxia and H/R stress is critical for developing better treatments for these diseases. Previous studies showed that the neuroglobin GLB-5(Haw) is essential for the fast recovery of the nematode Caenorhabditis elegans (C. elegans) from H/R stress. Here, we characterize the changes in neuronal gene expression during the adaptation of worms to hypoxia and recovery from H/R stress. Our analysis show that innate immunity genes are differentially expressed during both adaptation to hypoxia and recovery from H/R stress.

overall_design: To explore the changes in neuronal gene expression occurring during the adaptation of worms to hypoxia and recovery from H/R stress, we used mRNA tagging (Kunitomo et al., 2005; Von Stetina et al., 2007; Petersen et al., 2011). Briefly, we created npr-1(ad609) and glb-5(Haw);npr-1(ad609) transgenic worms expressing a pan-neuronal poly(A)-binding protein 1 (PAB-1) with an N-terminal FLAG affinity tag (these strains were created using the parental strain SD1241 (Von Stetina et al., 2007)). Moreover, we created glb-5(Haw);npr-1(ad609) transgenic worms expressing intestinal FLAG-PAB-1 to control for the efficiency of neuronal mRNA purification (this strain was created using the parental strain SD1084 (Pauli et al., 2006)). We purified mRNA from Prgef-1::FLAG-PAB-1 and Pges-1::FLAG-PAB-1 animals at time-points in which the bordering recovery of worms from H/R stress was previously characterized (as specified in the introduction and in (Gross et al., 2014; Abergel et al., 2016)), namely the 0, 3, 6, 24.5 and 28 h time points.  The mRNA, from each time-point, was amplified and labeled for application to an Agilent microarray chip representing ~95% of the predicted C. elegans genes. We used 12 Agilent chips to compare the expression of genes between time 0 and 3 (the 0-3 h pair), 3 and 6 (the 3-6 h pair), 6 and 24.5 (the 6-24 h pair), and 24.5 and 28 (the 24.5-28 h pair) . In addition, we used two chips were to compare the expression of genes between npr-1(ad609) and glb-5(Haw);npr-1(ad609) neurons in times 3 and 24.5 h. Finally, we used two chips to compare the expression of neuronal and intestinal genes of glb-5(ad609);npr-1(ad609) worms in times 3 and 24.5 h. The microarray data were extracted using the Agilent's Feature Extraction 10.7 software, and further analyzed using a custom written MATLAB program.

first: Zohar

last: Abergel

first: Veronica

last: Zelmanovich

first: Leonor

last: Romero

first: Rachel

first: Leonid

last: Livshits

first: Yoav

last: Smith

first: Einav

last: Gross


title: miR-424 induces COP1 silencing and STAT3 activation in prostate cancer: a novel miRNA-dependent axis driving tumor progression

status: Public on Mar 09 2017

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

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

overall_design: Refer to individual Series


title: Mutant p53R273H regulated microRNA profiling in presence and absence of DNA damage in H1299 cells

status: Public on Apr 28 2017

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

institute: Indian Statistical institute

summary: In the present study, we used a high-throughput small RNA deep sequencing followed by a systematic computational analysis to identify genome wide mutant p53R273H regulated miRNAs in both DNA damage dependent and independent context. Several miRNA-mRNA regulatory networks have been predicted that might contribute to mutant p53 GOF properties. Differentially regulated miRNA signature profile has been validated in the lung cancer patients harboring wildtype and mutant p53. We identified specific miRNA signatures for lymph node metastasis associated with p53 mutation in lung adenocarcinoma and also predicted the possible contribution of two mutant p53 regulated miRNAs in EMT process. Furthermore, this study identified a hitherto unknown miRNA in human which might act as one of the crucial downstream targets of GOF mutant p53 to confer oncogenic properties.

overall_design: Determination of mutant p53R273H regulated microRNAs H1299 cells.

first: Susanta

last: Roychoudhury


title: Gene expression profiling of continuous growth hormone infused (cGH) adult male mouse liver by RNA-seq analysis of polyA-selected liver RNA. [G88_G96]

status: Public on Jul 14 2017

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: PolyA-selected RNA isolated from livers of adult male mice treated with a continuous infusion of growth hormone for either 10 hr or 14 days was analyzed by RNA-seq

overall_design: Liver RNA was isolated from 8 week old male mice treated with a continuous GH infusion (cGH) for either 10 hr or 14 day. For the 10 hour time point, n=9-10 individual liver RNA samples were pooled for each of 2 biological replicate libraries. For the 14 day time point, 2-3 individual RNA samples were pooled to make each of 3 biological replicate libraries. The sequencing data for the sham-treated controls is found in GEO series GSE66140, together with polyA-selected cGH infusions for 1 day, 4 day and 7 days from the same study as this study.

first: Dana

last: Lau-Corona

first: Alexander

last: Suvorov