title: Single cell RNAseq data from A2058 cell line (Melanoma)

status: Public on Jun 22 2020

city: perth

first: Carlos

last: Aya-bonilla

address: 32 kinship street

institute: Telethon Kids Institute

summary: The goal of this study was to unlock the cellular diversity of A2058, a melanoma cell line known to be resistant to BRAF inhibition, by performing single cell RNAseq profiling using a 10X genomics platform. This approach allowed us to study the transcriptional programming of every single melanoma cell, particularly of those cells expressing ABCB5, a cell surface protein involved in invasiveness and resistance to BRAF inhibition. Findings from this study revelaed that ABCB5-expressing cells also expressed melanocytic genes (MITF) but with a distinct transcriptional program to those expressing AXL. We also used this data to identify the expresion of commonly studied drug efflux pumps in melanoma cells.

overall_design: Viable A2058 cells were encapsulated and uniquely barcoded using Chromium Single Cell 3’ Reagent Kit v2 on a Chromium platform (10X Genomics). Single cell libraries were prepared as recommended by 10X Genomics and sequenced at 30,000 raw reads per cell in a NextSeq500 High Output flow cell (2x150 bp reads). Bioinformatic analyses including alignment, transcript count and cell clustering were performed using the Cell Ranger™ 2.0 software (10X Genomics). Visualization of cell clustering and gene expression analyses were performed on Loupe Cell Browser (10X Genomics).

last: Aya-Bonilla

first: Lokeswari

last: Tangella

first: Elin

last: Gray

first: Mel

last: Ziman


title: Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [GeoMx human protein]

status: Public on Nov 01 2020

city: Seattle

first: Jason

middle: W

last: Reeves

state: WA

address: 530 Fairview Blvd

department: R&D

country: USA

institute: Nanostring

summary:
The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We analyzed specimens from 24 autopsies from patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter- and intra- patient heterogeneity of pulmonary virus infection.  There was a spectrum of high and low virus cases that was associated with duration of disease and activation of interferon pathway genes.  Using a digital spatial profiling platform, the intra-pulmonary spatial heterogeneity of the virus corresponded to focal expression of interferon response genes and association with immune checkpoint genes
In this dataset, we capture the GeoMx DSP protein profiling work done in conjunction with this study. The files here represent SARS-CoV-2 infected rapid autopsy patients (n = 6) which were profiled with the following nanoString GeoMx protein panels: Immune Cell Profiling Core v1.0, IO Drug Target Module v1.0, Immune Cell Typing Module v1.0, Immune Activation Status Module v1.0, PI3K/AKT Signaling Module v1.0, MAPK Signaling Module v0.9, and Cell Death Module v0.9. These panels were then read out using Nanostring nCounter quantification following standard HybCode panel profiling protocols. For access to high resolution (single channel, composite, or ROI) images please contact the corresponding author or GeoMxSupport@nanostring.com. RNA sequencing data and results for bulk RNA profiling can be accessed in study GSE150316.

overall_design: This dataset contains expression from localized sampling within 6 SARS-CoV-2 infected patient FFPE samples collected during rapid autopsy, with 3 non-infected control samples. Up to 48 segments were collected within each patient sample. RNA Scope on serial sections was used to guide ROI selection, and ROI ISH staining by RNA Scope is noted in the sample annotations.

first: Niyati

last: Desai

first: Azfar

last: Neyaz

first: Annamaria

last: Szabolcs

first: Angela

last: Shih

first: Jonathan

middle: H

last: Chen

first: Vishal

last: Thapar

first: Linda

middle: T

last: Nieman

first: Alexander

last: Solovyov

first: Arnav

last: Mehta

first: David

middle: J

last: Lieb

first: Anupriya

middle: S

last: Kulkarni

first: Christopher

last: Jaicks

last: Pinto

first: Dejan

last: Juric

first: Ivan

last: Chebib

first: Robert

middle: B

last: Colvin

first: Arthur

middle: Y

last: Kim

last: Monroe

first: Sarah

middle: E

last: Warren

first: Patrick

last: Danaher

first: Jingjing

last: Gong

first: Erroll

last: Rueckert

first: Benjamin

middle: D

last: Greenbaum

first: Nir

last: Hacohen

first: Stephen

middle: M

last: Lagana

first: Miguel

middle: N

last: Rivera

first: Lynette

last: Sholl

first: James

middle: R

last: Stone

last: Ting

first: Vikram

last: Deshpande


title: Single cell Transcriptome profiling of Human first trimester placenta.

status: Public on May 29 2020

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

type: Expression profiling by high throughput sequencing

summary: Single cell RNA sequencing of human first trimester placenta were generated by deep sequencing using the 10x Genomics Chromium Single Cell Gene Expression Solution (10xgenomics.com).

first: Paul

last: Soumen

first: Ganguly

last: Avishek

first: Home

last: Pratik

first: Ghosh

last: Ananya

first: Gunewardena

last: Sumedha


title: Regional different regulations in development of human cortex and pons revealed by single cell transcriptome

status: Public on Aug 25 2020

city: Beijing

first: Yuanyuan

last: Fu

address: 5 Yiheyuan Road

country: China

institute: BIOPIC, Peking University

summary: Neurons showed both spatial and temporal distinctions while glial cells were much uniform among the regions. We captured the developmental course of oligodendrocytes and found human specific cell state comparing to that in mouse. A new subcluster of NPCs were identified in particular embryonic weeks from GW11 to GW14, which destinated to deeper layers. We specified the progress of human deeper layer, upper layer and mature neuron genesis along the time and their intrinsic regulations. Regional characters was revealed both for cortical regions and the pons. With the systematic single cell analysis, we uncovered human embryonic neural development on both temporal and spatial scale, which offered deeper insights into the human neurogenesis and cortical development.

overall_design: Here we did single cell transcriptome profiling on the four cortical lobes along the human embryonic development. Moreover, to interpret the evolution level of the cerebral cortex, we also compared the neuronal developmental processes in the cortex to those in the pons, which is evolutionarily more conserved in human.

first: Xiaoying

last: Fan


title: Single cell RNA-seq of mouse megakaryocytes from wild type and Nf-e2 knock out mice

status: Public on Jul 15 2020

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: Fetal livers from 8X E13.5 wildtype and 6X Nf2-/- mutant embryos were mechanically dissociated, pooled by genotype and stained for CD41, CD42d, LIN (Ter119,B220). LIN- CD41high CD42d+ Cells were sorted on an Aria Cell Sorter (Becton Dickinson), centrifuged and counted.  Fetal livers of 5X E13 wildtype or Nf2-/- embryos were prepared as above and transplanted into UBC-GFP+ recipients subjected to 2X 550cGrays irradiations (0.37 embryonic equivalent/recipient). Mice were screened at 4 weeks for blood platelet content and their GFP status. Bone marrow from the femurs, tibias, hips and humeri of 4 transplanted mice (2X WT donor, 2X Nf2-/- donor) was dissociated, pooled by genotype, filtered and stained for CD41, CD42d, LIN (Ter119, B220). GFP- LIN- CD41high CD42d+ Cells were sorted on an Aria Cell Sorter (Becton Dickinson), centrifuged and counted.

overall_design: 3.9K (Adult) and 6.9K (Fetal Liver) cells were loaded onto a Chromium Controller (10X Genomics). Single cell 3' v2 transcriptome libraries were obtained following manufacturer's instructions. Samples were pooled and sequenced on NextSeq (Illumina) (75bp kit, paired end, where 98bp were sequenced for genomic read).

first: Christine

last: Biben

first: Samir

last: Taoudi


title: Comprehensive Expression Analysis of mRNA and microRNA for Investigation of Compensatory Mechanisms in the Rat Kidney after Unilateral Nephrectomy (Female_mRNA)

status: Public on Apr 01 2020

city: Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa, JAPAN

first: Kohei

last: Matsushita

country: Japan

institute: National Institute of Health Sciences

summary: Compensation is a physiological response that occurs during chemical exposure to maintain homeostasis. Because compensatory responses are not usually considered adverse effects, it is important to understand compensatory mechanisms for chemical risk assessment. Although the kidney is a major target organ for toxicity, there is controversy over whether hyperplasia or hypertrophy contributes to the compensatory mechanism, and there is limited information to apply for chemical risk assessment. In the current study, compensatory mechanisms of the kidney were investigated in a unilateral nephrectomy (UNx) model using adult male and female rats. In residual kidneys of male and female rats after UNx, 5-bromo-2'-deoxyuridine-labeling indices and mRNA expression of cell cycle-related genes were increased, although there were no fluctuations in mRNA expression of transforming growth factor-β1, which contributes to hypertrophy in renal tubules. Pathway analysis using mRNA expression data from a cDNA microarray revealed that canonical pathways related to cell proliferation were mainly activated and that forkhead box M1 (FOXM1) was an upstream regulator of compensatory cell proliferation in residual kidneys of male and female rats. cDNA microarray for microRNAs (miRNAs) demonstrated that 9 miRNAs were downregulated in residual kidneys, and mRNA/miRNA integrated analysis indicated that miRNAs were associated with the expression of factors downstream of FOXM1. Overall, these results suggested that FOXM1-mediated hyperplasia rather than hypertrophy contributed to compensatory mechanisms in the kidney and that miRNAs regulated downstream FOXM1 signaling. These results will be beneficial for evaluating nephrotoxicity in chemical risk assessment and for developing new biomarkers to predict nephrotoxicity.

overall_design: Female rats (F344/NSlc, 10-weeks-olds) were performed to unilateral nephrectomy sham operation (n=4). After 2 days, residual kidney samples were supplied for mRNA microarray analysis.


title: Comprehensive Expression Analysis of mRNA and microRNA for Investigation of Compensatory Mechanisms in the Rat Kidney after Unilateral Nephrectomy (Male_mRNA)

overall_design: Male rats (F344/NSlc, 10-weeks-olds) were performed to unilateral nephrectomy sham operation (n=4). After 2 days, residual kidney samples were supplied for mRNA microarray analysis.


title: Comprehensive Expression Analysis of mRNA and microRNA for Investigation of Compensatory Mechanisms in the Rat Kidney after Unilateral Nephrectomy

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

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

overall_design: Refer to individual Series


title: Massively parallel reporter assays combined with cell-type specific eQTL identified a functional melanoma risk variant in HIV-1 restriction gene, MX2 [MX2_overexpress]

status: Public on Apr 20 2020

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

summary: Genome-wide association studies (GWAS) have identified twenty melanoma susceptibility loci. To identify susceptibility genes and variants simultaneously from multiple GWAS loci, we integrated massively-parallel reporter assays (MPRA) with melanocyte-specific expression quantitative trait locus (eQTL) profiling. We identified thirty-nine candidate functional variants displaying allelic transcriptional activity, of which nine from four loci were also correlated with local gene expression in melanocytes (CTSS, CASP8, MX2, and MAFF). Among these, we further characterized the locus in MX2 gene on chromosome band Chr21q22.3 and validated a functional variant, rs398206. The functional variant mediates allelic transcriptional activity via binding of the transcription factor, YY1. This allelic transcriptional regulation largely accounts for a significant cis-eQTL of the HIV-1 restriction gene, MX2, in primary melanocytes, where the melanoma risk-associated A allele is correlated with higher MX2 levels. Melanocyte-specific transgenic expression of human MX2 in a zebrafish model demonstrated an accelerated melanoma formation in a BRAFV600E background. Thus, using an efficient scalable approach to streamline GWAS follow-up functional studies, we uncovered a pleiotropic function of MX2 in melanoma susceptibility.

overall_design: To identify genes that are differentially expressed upon MX2 over-expression in primary human melanocytes, we performed RNA-seq of total of 27 samples (melanocyte cultures from 3 individuals, in 3 conditions, and 3 biological replicates). Three conditions include 1) MX2 control (with 0 doxycycline treatment on the cells transduced with MX2 cDNA under the control of tetracycline-inducible promoter), 2) MX2 over-expression (with 100ng/ml doxycycline treatment resulting in 2-10 fold increase of MX2 levels), and 3) Doxycycline control (with 100ng/ml doxycycline treatment on the cells transduced with empty pINDUCER20 vector). We identified differentially expressed genes in MX2 over-expression samples compared to MX2 control samples for pathway analysis. Same type of analysis was performed to identify doxycycline-induced genes by comparing Doxycycline control samples (100ng/ml treatment on Empty vector) to MX2 control samples (no treatment) for pathway analysis.

first: Jiyeon

last: Choi

first: Kevin

last: Brown


title: Genetic analysis of the modern Australian labradoodle dog breed reveals strong selection for poodle traits

status: Public on Jul 17 2020

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Allele frequency analysis reveals that the breed is enhanced for genes controlling traits associated with the poodle-type coat, which are perceived to have an association with hypoallergenicity, with no strong signatures of selection for Labrador retriever (LAB) traits. This study provides a blueprint for understanding how dog breeds are formed, highlighting the limited scope of trait selection in defining seemingly new breeds.

overall_design: 47 canid samples representing 3 breeds

first: Muhammad

last: Ali

first: Jacquelyn

last: Evans

first: Heidi

middle: G

last: Parker

first: Jaemin

last: Kim

first: Susan

last: Pearce-Kelling

first: D

last: Whitaker

first: Jocelyn

last: Plassais

first: Qaiser

last: Khan

first: Elaine

last: Ostrander


title: Massively parallel reporter assays combined with cell-type specific eQTL identified a functional melanoma risk variant in HIV-1 restriction gene, MX2 [MX2_overexpress_time]

status: Public on Apr 23 2020

overall_design: To identify genes that are differentially expressed upon MX2 over-expression in primary human melanocytes, we performed RNA-seq of total of 27 samples (melanocyte cultures from 1 individual (C23), in 2 conditions, 2 time point (6hr and 72hr) and 3 biological replicates). Two conditions include 1) MX2 control (with 0 doxycycline treatment on the cells transduced with MX2 cDNA under the control of tetracycline-inducible promoter), 2) MX2 over-expression (with 100ng/ml doxycycline treatment resulting in 2-10 fold increase of MX2 levels). We identified differentially expressed genes in MX2 over-expression samples compared to MX2 control samples for pathway analysis at both 6hr and 72hr time points.


title: Transcriptome of subsets of human haematopoietic stem cells from non-mobilised peripheral blood of healthy donors

status: Public on May 01 2020

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

summary: Integration of index sorting and single cell functional assays identified two functionally distinct subsets of phenotypic haematopoietic stem cells and multipotent progenitors (HSC/MPPs) in the peripheral blood (PB) from healthy individuals. CD71- HSC/MPPs from PB are multipotent and can repopulate the NSG xenograft model. CD71+ HSC/MPPs are a subset of phenotypic HSC/MPPs that is uniquely restricted to give rise to erythroid and megakaryocytic lineages, and expands in conditions with chronic stimulation of platelet production (e.g. frequent platelet donation, idiopathic thrombocytopenic purpura, essential thrombocythaemia). Here, we report the bulk transcriptomes of pools of 20 cells from CD71- HSC/MPPs (CD19- CD38- CD45RA- CD34lo CD71-) and CD71+ HSC/MPPs (CD19- CD38- CD45RA- CD34lo CD71+). Altogether the data shows the transcriptional similarities and differences between both subsets. It shows, that the unique erythroid/megakaryocytic lineage-priming of CD71+ HSC/MPPs is already initiated at transcriptional level, and that CD71+ HSC/MPPs differ from CD71- HSC/MPPs with regards to their protein synthesis/metabolic pathways.

overall_design: Examination of the genome-wide transcriptome of bulk sorted (20 cells) CD71+ and CD71- HSC/MPPs from 4 different donors (donor1-4). Samples were sequenced as 3 technical replicates per subset and donor.

first: Nicole

last: Mende

first: Evangelia

last: Diamanti


title: Massively parallel reporter assays combined with cell-type specific eQTL identified a functional melanoma risk variant in HIV-1 restriction gene, MX2 [MPRA NGS]

overall_design: We tested allelic transcriptional activities of 840 melanoma-associated common variants using MPRA. 832 variants were selected based on their colocalization to open chromatin and active histone marks in melanoma-relevant cell types. The other 8 were selected as controls that do not overlap with these functional genomic signatures. Luciferase reporter libraries were constructed by taking 145bp genomic sequence encompassing the risk or protective allele of each variant. Each 145bp sequence was tested in both forward and reverse directions and was assigned 10 different unique 10bp barcode sequences. We also included a scrambled sequence for each variant, where 21 bases encompassing the variant were scrambled to serve as a pseudo-baseline. Resulting 50,400 unique oligo sequences were cloned into two separate MPRA libraries with or without the minimal promoter (TATA).  Libraries were then transfected into a melanoma cell line (UACC903) and the HEK293FT cell line. Resulting transcribed output as well as DNA input were then quantified by sequencing. A total of 22 samples were sequenced including 4 input DNA samples representing 2 libraries with (Enh) or without (Pro) TATA element, and 8 RNA output samples from the transfections into UACC903 representing 2 libraries with (Enh) or without (Pro) TATA in two transfection replicates each, and 10 RNA output samples from the transfections into HEK293FT representing 2 libraries with (Enh) or without (Pro) TATA in two transfection replicates each, except for four replicates for library 1 Enh constructs.


title: Gasdermin-D-dependent IL-1 alpha release from microglia promotes protective immunity during chronic Toxoplasma gondii infection

status: Public on Mar 10 2020

city: Charlottesville

first: Tajie

address: 409 Lane Rd

institute: University of Virginia

summary: RNA-seq experiment on FACS-sorted microglial and macrophage cell populations (infected with T. gondii type II strain Me49)

overall_design:
mRNA profiles of microglia and macrophages were generated using an Illumina MiSeq

Sequencing performed at UVa Genome Analysis & Technology Core,
Office of Research Core Administration.
University of Virginia Health System,
P.O. Box 800741,
Charlottesville, VA 22908-0741

first: Samantha

last: Batista

first: David

last: Johanson


title: Comprehensive Expression Analysis of mRNA and microRNA for Investigation of Compensatory Mechanisms in the Rat Kidney after Unilateral Nephrectomy (Male_miRNA)

first: Kohei

last: Matsushita

overall_design: Male rats (F344/NSlc, 10-weeks-olds) were performed to unilateral nephrectomy sham operation (n=4). After 2 days, residual kidney samples were supplied for microRNA microarray analysis.


title: Profiling of histone 3 lysine 27 acetylation reveals its role in the chronic DSS-induced colitis mouse model

status: Public on Jan 18 2020

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate whether the H3K27ac is involved in the development of inflammatory bowal disease. We established dextran sulfate sodium (DSS)-induced chronic colitis and performed RNA-sequencing and Chromatin Immunoprecipitation followed by NGS sequencing for H3K27ac in the mice colon tissues. We find that the global H3K27ac distribution in colon tissue had no significant difference, while on the typical-enhancers specific in the DSS group, H3K27ac signals were significantly enriched when compared with the control. Furthermore, we identified 89 candidate genes which represented the susceptible genes to H3K27ac change and predicted transcription factors (TFs) upon the DSS treatment. Collectively, our study revealed that H3K27ac increase on special typical-enhancers is possibly related to the development of intestinal inflammation by up-regulating adjacent gene expression and shifting TFs networks.

overall_design:
We established the dextran sulfate sodium (DSS)-induced chronic colitis and performed RNA-sequencing (RNA-seq) and Chromatin Immunoprecipitation followed by NGS sequencing (ChIP-seq) for H3K27ac in the mice colon tissues to investigate whether the H3K27ac is involved in the development of intestinal inflammation.
This submission consists of ChIP-Seq component of study.

first: Meng

last: Chen

last: Cao

first: Yanan

last: Deng

first: Lianyun

first: Qiu

last: Zhao

first: Min

last: Wu

first: Mei

last: Ye


title: Ibrutinib-mediated atrial fibrillation

city: Boston

last: Milan

address: 185 Cambridge St

institute: MGH

summary: The aim of this study is to perform transcriptome analysis on mouse left atrium tissue after long-term ibrutinib treatment or cardiac CSK knockout, in order to compared the enriched gene clusters.

overall_design: In total 10 samples were sequenced. These include 3 replicates for vehicle treated (CTL) and 3 replicates for ibrutnib treated (IBR); 2 replicates from wild-type untreated (WT) and 2 replicates from cardiac CSK KO (KO)extraction

first: Ling

last: Xiao


title: In vivo screen identifies LXR agonism potentiates sorafenib killing of hepatocellular carcinoma

city: Philadelphia

first: Julia

middle: Elise

last: Kieckhaefer

state: Pennsylvania

address: 421 Civic Center Blvd, BRB 927

department: Gastroenterology

institute: University of Pennsylvania

summary:
Background & Aims: Existing drug therapies for hepatocellular carcinoma (HCC), including sorafenib, extend patient survival by only three months. We sought to identify novel druggable targets for use in combination with sorafenib to increase its efficacy.
Methods: We implemented an in vivo genetic screening paradigm utilizing a library of 43 genes-of-interest expressed in the context of repopulation of the injured livers of Fumarylacetoacetate Hydrolase-deficient (Fah-/-) mice, which led to highly penetrant HCC. We treated mice with vehicle or sorafenib, then determined the genetic drivers of each tumor from the library. Liver X Receptor alpha (LXRalpha) emerged as a potential target. To examine LXRalpha agonism in combination with sorafenib treatment, we added varying concentrations of sorafenib and LXRalpha agonist drugs to HCC cell lines. To elucidate the mechanism of tumor death, we performed transcriptomic analysis.
Results: Fah-/- mice injected with the screening library developed HCC tumor clones containing Myc cDNA plus various other cDNAs. Treatment with sorafenib resulted in sorafenib-resistant HCCs that were significantly depleted in Nr1h3 cDNA, encoding LXRalpha, suggesting that LXRalpha activation is incompatible with tumor growth in the presence of sorafenib treatment in vivo. Combination treatment using sorafenib and LXR agonist drugs in multiple HCC cell lines led to enhanced cell death as compared to monotherapy, due to reduced expression of cell cycle regulators and increased expression of genes associated with apoptosis. Combination therapy also enhanced cell death in a sorafenib-resistant primary human HCC cell line.
Conclusions: We have completed a novel drug resistance screen in vivo, and identified that LXR agonism potentiates the efficacy of sorafenib in treating HCC.

overall_design: mRNA profiling of Huh7 and Hep3B cells treated with control, GW3965, sorafenib, or combination GW3965/sorafenib for 24 hours.

first: Kirk

last: Wangensteen

first: Morgan

last: Preziosi


title: Transcriptional signature of prion-induced neurotoxicity in a Drosophila model of transmissible mammalian prion disease

status: Public on Jan 31 2020

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

summary: Prion diseases are fatal transmissible neurodegenerative conditions of humans and animals that arise through neurotoxicity induced by PrP misfolding. The cellular and molecular mechanisms of prion-induced neurotoxicity remain undefined. Understanding these processes will underpin therapeutic and control strategies for human and animal prion diseases, respectively. Prion diseases are difficult to study in their natural hosts and require the use of tractable animal models. Here we used RNA-Seq-based transcriptome analysis of prion-exposed Drosophila to probe the mechanism of prion-induced neurotoxicity. Adult Drosophila transgenic for pan neuronal expression of ovine PrP targeted to the plasma membrane exhibit a neurotoxic phenotype evidenced by decreased locomotor activity after exposure to ovine prions at the larval stage. Pathway analysis and quantitative PCR of genes differentially expressed in prion-infected Drosophila revealed up-regulation of cell cycle activity and DNA damage response, followed by down-regulation of eIF2 and mTOR signalling. Mitochondrial dysfunction was identified as the principal toxicity pathway in prion-exposed PrP transgenic Drosophila. The transcriptomic changes we observed were specific to PrP targeted to the plasma membrane since these prion-induced gene expression changes were not evident in similarly-treated Drosophila transgenic for cytosolic pan neuronal PrP expression, or in non-transgenic control flies. Collectively, our data indicate that aberrant cell cycle activity, repression of protein synthesis and altered mitochondrial function are key events involved in prion-induced neurotoxicity, and correlate with those identified in mammalian hosts undergoing prion disease. These studies highlight the use of PrP transgenic Drosophila as a genetically well-defined tractable host to study mammalian prion biology.

overall_design: Whole head homogenates treated with scrapie or normal brain homogenate; 5, 30, 40 days of age

first: Alana

last: Thackray

first: Raymond

last: Bujdoso


title: Metabolic Alterations in JAK2 Mutant Hematopoietic Cells Represent Therapeutic Vulnerabilities for Myeloproliferative Neoplasms

status: Public on Nov 29 2019

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Increased energy requirement and metabolic reprograming is a hallmark of cancer cells. We found that mouse models of myeloproliferative neoplasms (MPN) expressing mutant JAK2 displayed systemic metabolic changes including hypoglycemia and adipose atrophy. Modulation of nutrient availability modified MPN manifestations and survival. Hypoglycemia in MPN mice correlated with hyperactive erythropoiesis and was due to a combination of elevated glycolysis and increased oxidative phosphorylation. Transcriptomic and metabolomic analyses together with functional assays in hematopoietic stem and progenitor cells identified vulnerable metabolic nodes for therapeutic targeting. Inhibition of Pfkfb3, a key regulatory enzyme of glycolysis, increased blood glucose levels, improved blood counts and reduced splenomegaly. We observed additive efficacy with ruxolitinib. Mechanistically, altered redox homeostasis promoted apoptosis of susceptible MPN cells.

overall_design: Triplicates for each genotype

first: Tata

last: Rao

first: Radek

middle: C

last: Skoda


title: Search for genes regulated by WIPK and SIPK in wounded tobacco leaves

status: Public on Dec 10 2019

city: Minamiminowa

first: Shinpei

last: Katou

state: Kamiina, Nagano

department: Faculty of Agriculture

institute: Shinshu University

summary: WIPK and SIPK, two tobacco MAPKs, are rapidly activated by wounding. Goal is to identify the genes regulated by WIPK and SIPK. For this purpose, we produced transgenic tobacco plants in which expression of WIPK and SIPK (WIPK/SIPK-suppressed plants) is suppressed by RNAi.

overall_design: Single experiment; transgenic tobacco plants in which expression of WIPK and SIPK (WIPK/SIPK-suppressed plants) is suppressed by RNAi, leaves were wounded for 9 hours.


title: Transcriptomic profiling of mesenchymal stem cells (MSC) differentiation into mesangial cells

status: Public on Nov 26 2019

city: Kajang

first: Chee-Yin

last: Wong

state: Selangor

address: Jalan Sungai Long, Bandar Sungai Long

department: Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

summary:
Purpose: To study the pattern of transcriptomic changes during MSC differentiation into mesangial cells and to identify biomarkers or key genes involved in this differentiation.
Methods: Differentiation of MSC into mesangial cells was induced by co-culturing with injured mesangial cells in trans-well dishes (n=3). Total RNA from co-cultured MSC at different time point were extracted before running RNA sequencing. Generated RNA-seq data was analysed.
Results and conclusions: A systematic analysis has identified several monotonic pattern key genes (either ascending or descending). These identified descending monotonic key genes are related to stemness or regulation of cell cycle while ascending monotonic key genes are associated with the functions of mesangial cells.

overall_design: A time ordered study of transcriptomic profiling during MSC-mesangial cells differentiation process generated using RNAseq.

first: I-Fang

last: Chung

first: Yang-Mooi

last: Lim


title: Evaluation of HSP90 inhibitor expsosure on Immune Cell Gene Expression

status: Public on Jan 01 2020

city: Tampa

first: Alex

last: Jaeger

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: Moffitt Cancer Center

summary: We report RNA-sequencing analysis of human peripheral blood mononuclear cells exposed to clinically recommended doses (500 nM) of the HSP90 inhibitor ganetispib. Global analysis of the expression profiles of treated cells revealed wide spread changes in gene expression, specifically, upregulation of protein folding and assembly pathways, with downregulation of antigen presentation through MHC Class I and Class I.

overall_design: Examination of PBMCs treated with vehicle or ganetispib for 24 hrs

first: Giorgio

last: Gaglia

first: Luke

last: Whitesell


title: Coronary arterial development is regulated by a Dll4-Jag1-EphrinB2 signaling cascade

status: Public on Dec 03 2019

city: Madrid

first: Jose Luis

last: de la Pompa

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).

summary: Coronaries are essential for myocardial growth and heart function. Notch is crucial for mouse embryonic angiogenesis, but its role in coronary development remains uncertain. We show Jag1, Dll4 and activated Notch1 receptor expression in sinus venosus (SV) endocardium. Endocardial Jag1 removal blocks SV capillary sprouting, while Dll4 inactivation stimulates excessive capillary growth, suggesting that ligand antagonism regulates coronary primary plexus formation. Later endothelial ligand removal, or forced expression of Dll4 or the glycosyltransferase MFng, blocks coronary plexus remodeling, arterial differentiation, and perivascular cell maturation. Endocardial deletion of Efnb2 phenocopies the coronary arterial defects of Notch mutants. Angiogenic rescue experiments in ventricular explants, or in primary human endothelial cells, indicate that EphrinB2 is a critical effector of antagonistic Dll4 and Jag1 functions in arterial morphogenesis. Thus, coronary arterial precursors are specified in the SV prior to primary coronary plexus formation and subsequent arterial differentiation depends on a Dll4-Jag1-EphrinB2 signaling cascade.

overall_design: RNA was isolated at E12.5, from whole hearts, for WT (4 replicate samples, pooling 4 embryos) and Jag1flox;Nfatc1-Cre embryos(4 replicate samples, pooling 4 embryos), and for WT (4 replicate samples, pooling 4 embryos) and Dll4flox;Nfatc1-Cre (4 replicate samples, pooling 4 embryos). It was isolated at E15.5, from heart ventricles, for WT (4 replicate samples, pooling 3 embryos) and Dll4flox; Cdh5(PAC)-CreERT (3 replicate samples, pooling 3 embryos) and for WT (4 replicate samples, pooling 3 embryos) and Dll4GOF;Tie2-Cre (3 replicate samples, pooling 3 embryos). Finally, it was isolated at E16.5, from heart ventricles, for WT (4 replicate samples, from one embryo) and Efnb2flox;Nfatc1-Cre (4 replicate samples, from one embryo).

first: S

middle: I

last: Travisano

first: D

last: MacGrogan

first: J

middle: L

last: Pompa


title: Target identification of hepatic fibrosis therapy using Pien Tze Huang based on mRNA and lncRNA

status: Public on Dec 18 2019

city: Shanghai

first: Jinhang

last: Zhu

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

summary: Pien Tze Huang (PZH) is a traditional Chinese medicine which was widely utilized in Asia for hepatic diseases. We construct two groups hepatic fibrosis mice model using CCl4, one group using PZH treatment and another group didn’t treatment. We found that the liver functional indices including ALB, ALT and AST were significantly increased in non-PZH treatment group. HE staining showed that inflammation was emerged surrounding the hepatic vein in the non-PZH treatment group, Masson staining revealed that there are blue collagenous fibre surrounding hepatic vein in the non-PZH treatment group, this result indicated that PZH cured the hepatic inflammation and fibrosis. We performed the mRNA and LncRNA sequencing aim to explore the drug target using PZH treatment on transcriptome level. 905 protein coding transcripts and 23 lncRNA transcripts were differentially expressed. Our research provided potential transcriptional therapeutic target for the clinical treatment using PZH.

first: Shengyin

last: Qin

first: Di

last: Zhang


title: 6mer seed toxicity in viral microRNAs

status: Public on Nov 13 2019

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: We provide evidence that viral miRNAs use 6mer seed toxicity to kill cells

overall_design: Samples of HeyA8 ovarian cancer cells transfected with different miRNAs or siRNAs

first: Andrea

last: Murmann


title: Massively parallel reporter assays combined with cell-type specific eQTL identified a functional melanoma risk variant in HIV-1 restriction gene, MX2

first: Tongwu

overall_design: Refer to individual Series


title: A functional link between nuclear RNA decay and transcritional control mediated by the Polycomb Repressive Complex 2

status: Public on Nov 12 2019

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Pluripotent embryonic stem (ES) cells constitute an essential cellular niche in animal development. It is well documented that ES cells are sustained by epigenetic and transcriptional regulation, but the role of post-transcriptional processes remains less explored. Here, we identify a link between nuclear RNA levels, regulated by the ‘polyA RNA exosome targeting’ (PAXT) connection, and transcriptional control, regulated by the Polycomb Repressive Complex 2 (PRC2). Knockout of the PAXT component ZFC3H1 in mouse ES cells impairs their differentiation. In addition to the upregulation of bona fide PAXT substrates, Zfc3h1-/- cells abnormally express developmental genes usually subjected to PRC2-mediated repression. Such de-repression is paralleled by decreased PRC2 binding to chromatin at target genes, and low PRC2-directed H3K27 methylation. PRC2 complex stability is compromised in Zfc3h1-/- cells with elevated levels of unspecific RNA bound to PRC2 components. We propose that excess RNA hampers PRC2 function through its sequestration from DNA and complex destabilisation. Our results highlight the importance of balancing nuclear RNA levels and demonstrate the capacity of bulk RNA to regulate chromatin-associated proteins.

overall_design: Refer to invidual series

first: Itys

last: Comet

first: Mengjun

last: Wu

first: Aliaksandra

last: Radzisheuskaya

first: Leonor

last: Rib

first: Kristoffer

last: Vitting-Seerup

first: Marta

last: Lloret-Llinares

first: Albin

last: Sandelin

first: Kristian

last: Helin

first: Torben

middle: H

last: Jensen


title: Genomewide Screen Reveals Potential Synergistic Partners for FLT3 Mutant Myeloid Leukemia

status: Public on Jan 09 2020

city: COLUMBUS

first: Lindsey

last: Brinton

state: Oh

address: 410 W 12TH AVE

department: Internal Medicine

institute: The Ohio State University

summary: CRISPR knockout screening on MOLM-13 cells with midostaurin or gilteritinib

overall_design: MOLM-13 cells were transduced with Brunello CRISPR knockout library (Addgene 73179) with 4 bioreplicates per condition: 1) baseline (7 days post library infection), 2) midostaurin-treated, 3) gilteritinib-treated, 4) DMSO control.

middle: T

first: Rosa

last: Lapalombella

first: James

middle: S

last: Blachly


title: CD164 and FCRL3 are highly expressed on CD4+CD26- T cells in Sezary syndrome; inverse correlation between CD164 and CD26 expression

status: Public on Nov 21 2019

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary: Sezary syndrome (SS) represents a leukemic variant of cutaneous T cell lymphoma (CTCL) with circulating malignant CD4 T cells trafficking to the skin. The cell surface molecules present on malignant cells are also expressed on normal CD4 T cells. Therefore, we attempted to find a specific marker for malignant cells that would distinguish them from normal cells. Comprehensive microarray analysis of gene expression in the malignant cells indicated significantly increased levels of mRNA for cell surface markers CD164, a sialomucin found on human CD34+ hematopoietic stem cells, as well as FCRL3, a molecule present on a subset of human natural T regulatory cells. Both markers were increased in CD4 T cells from the SS patients compared to those from Mycosis Fungoides patients and healthy volunteers. Subsequent studies utilizing QPCR and flow cytometry confirmed the increased expression of CD164 and FCRL3 mainly in CD4+CD26- T cells of SS patients. Our results suggest that CD164 can serve as a marker for diagnosis as well as disease monitoring of CTCL/SS, whereas the FCRL3 expression correlates with disease progression.

overall_design: Gene expression was analyzed in CD4 T cells from 6 SS patients and 3 healthy donors. Samples from patients included 3 clonal patients with a defined TCR Vbeta (85-99% of CD4 T cells) of Vbeta-7,Vbeta-13.2 and Vbeta-22. The remaining 3 samples were from non-clonal patients with medium to low circulating tumor cell burdens, as defined by 20%-50% of the patients lymphocytes identifiable as CD4+ CD26- cells and/or by one micron section analysis of fixed peripheral blood buffy coats. RNA was processed as previously described and hybridized on Illumina Human WG 8v2 microarray chips. All arrays were processed in the Wistar Institute Genomics Facility.

first: Maria

last: Wysocka

first: Andrew

middle: V

last: Kossenkov

first: Bernice

last: Benoit

first: Elisha

last: Singer

first: Andras

last: Schaffer

first: Tzvete

last: Dentchev

first: Satoshi

last: Nagata

first: Tomoko

last: Ise

first: Alain

last: Rook


title: CircRNAome diversity in human mature B-cells, T-cells and monocytes

status: Public on Dec 17 2019

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) were shown to be expressed in all human tissue but detailed insight in circRNA diversity among tissues and cellular differentiation stages is lagging behind. This study provides comprehensive data on circRNA expression in the three major mature blood cell populations of healthy subjects.  Over 36,000 circRNAs were identified in B-cells, T-cells and monocytes, 34% of which were novel. In addition, putative new genes producing circRNAs were uncovered. The definition of cell type specific circRNA expression signatures revealed that alternative circularization is a common phenomenon showing cell population specific patterns. Abundance of circRNAs resulted largely uncorrelated to host gene linear expression. Several circRNAs were validated, including circular isoforms expressed by leukemia-associated genes PAX5 and IKZF1.  These results and new data will help to further our understanding of molecular mechanisms underlying cell biology of blood cells, and are a reference to explore circRNA alterations in haematological diseases.

overall_design: Mononuclear cells were isolated from peripheral blood of healthy adult donors. CD45+ population was separated into B-cells, T-cells and monocytes, after labeling with anti CD19, CD3, CD14 antibodies. For each cell type, 4 biological replicates were obtained from different donors. Total RNA was extracted and used for RNA-seq.

first: Geertruy

last: te Kronnie

first: Enrico

last: Gaffo


title: Active fluctuations of the nuclear envelope shape the transcriptional dynamics in oocytes

status: Public on Sep 11 2019

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: Nucleus position in cells can act as a developmental cue. Mammalian oocytes position their nucleus centrally using an F-actin mediated pressure gradient. The biological significance of nucleus centring in mammalian oocytes being unknown, we sought to assess the F-actin pressure gradient effect on the nucleus. We addressed this using a dedicated computational 3D imaging approach, biophysical analyses, and a nucleus repositioning assay in mouse oocytes mutant for cytoplasmic F-actin. We found that the cytoplasmic activity, in charge of nucleus-centring, shaped the nucleus while promoting nuclear envelope fluctuations and chromatin motion. Off-centred nuclei in F-actin mutant oocytes were misshaped with immobile chromatin and modulated gene expression. Restoration of F-actin in mutant oocytes rescued nucleus architecture fully and gene expression partially. Thus, the F-actin mediated pressure gradient also modulates nucleus dynamics in oocytes. Moreover, this study supports a mechano-transduction model whereby cytoplasmic microfilaments could modulate oocyte transcriptome, essential for subsequent embryo development.

overall_design: 2 samples of Fmn2 +/- oocytes, 50 oocytes each and 2 samples of Fmn 2-/- oocytes, 50 oocytes each. For each biological sample, 3 technical replicates were done.

last: Almonacid

first: Adel

last: Al Jord

first: Stephany

last: El-Hayek

first: Alice

last: Othmani

first: Fanny

last: Coulpier

first: Sophie

last: Lemoine

first: Kei

last: Miyamoto

first: Robert

last: Grosse

first: Christophe

last: Klein

first: Tristan

last: Piolot

first: Philippe

last: Mailly

first: Raphaël

last: Voituriez

first: Auguste

last: Genovesio

first: Marie-Hélène

last: Verlhac


title: Sandwich cortical lamination and single-cell analysis decodes the developing spatial processing system

status: Public on Aug 08 2019

city: Copenhagen

first: Tobias

middle: Borgtoft

last: Bergmann

address: Strandboulevarden 32, 2.63

department: Veterinary and Animal Sciecnes

institute: University of Copenhagen

summary: We here capture the transciptome of all cells in the developing entorhincal cortex of procine brain, from ethe beginning of second trimester (E50) up untill the adult brain.

overall_design: Exploring the cellular heterogeneity at single cell level in the developing porcine entorhinal cortex

first: Vanessa

middle: J

last: Hall

middle: B

first: Yong

last: Lui


title: Longitudinal Blood Transcriptomic Changes Predict Lung Function Decline in Idiopathic Pulmonary Fibrosis

status: Public on Sep 30 2019

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary:
The Rationale: Molecular markers of disease activity that are predictive of forced vital capacity (FVC) progression in idiopathic pulmonary fibrosis are needed.
Objectives: Develop a predictor using longitudinal within-patient gene expression differences (ΔGE) in peripheral blood mononuclear cells (PBMC) to predict of FVC progression.
Methods: Patients in the training cohort (n=74) experiencing ≥10% relative reduction in FVC% of predicted over 12 months were categorized as progressors in contrast to the remaining stable patients. Baseline to 4-month within-patient ΔGE were correlated with FVC status. FVC-predictor genes were prioritized by two-group comparison with FDR<5%, logistic LASSO regression with p<0.05, and 10-Fold Cross-Validation with ≥50% support. Receiver operating characteristic with area under the curve (AUC) analyses were conducted in training subsets and independent validation cohorts from UChicago (n=27), UPMC (n=35), and Imperial (n=24) where different transcriptome assay platforms and varying transcriptome sampling times were used to derive ΔGE.
Results: Intra-subject Compared to cross-sectional analysis of baseline GE, our longitudinal ΔGE variation approach demonstratedlargely reduced within-group sample variation and increased statistic power fin progressor and stable groups for prediction model development. A 25-gene FVC-predictor separated “progressors” from “stable” by Principal Component Analysis in the training and subsets of the training cohort. The resulting FVC-predictor consistently demonstrated high discriminatory performance independent of transcriptome assay platforms and varying sampling times in validation cohorts (AUC= 0.77-0.80). TGF beta was the highest-ranking canonical pathway by Gene Set Enrichment Analysis.
Conclusions: Our novel short-term longitudinal within-patient ΔGE approach identified a FVC-predictor which may reflect disease activity and prove to be a reliable biomarker predictive of future FVC decline.

overall_design: Subjects included in this analysis were participants in COMET-IPF (Correlating Outcomes with biochemical Markers to Estimate Time-progression in Idiopathic Pulmonary Fibrosis), a prospective, observational study correlating biomarkers with disease progression (NCT01071707) (E1). This multicenter investigation recruited subjects at nine clinical centers in the US. Inclusion criteria required diagnosis of IPF was confirmed using a multidisciplinary diagnostic approach per international guidelines using expertise from clinicians, radiologists, and pathologists at the local, enrolling clinical center and age 35-80 years. Subjects were excluded if the diagnosis of IPF was >4 years prior to screening or if there was a diagnosis of collagen-vascular disorder, FEV1/FVC <0.60, evidence of active infection at screening, or comorbid conditions other than IPF likely to result in death within one year. Subjects underwent protocol-directed visits every 4 months after the baseline (0 visit) for a minimum of 1 year, establishing four transcriptome sampling timepoints. Registry patients with PBMC gene expression (GE) sampling and pulmonary function tests (PFT) over at least two time points were included in each cohort. Informed consent was obtained from all participants. The study protocol was reviewed by the institutional review board of each participating center.

first: Justin

middle: M

last: Oldham

first: Shwu-Fan

last: Ma

first: Fernando

last: Martinez

first: Imre

last: Noth


title: Gene expression analysis of Jurkat cells cultured with or without BCAA

status: Public on Jul 01 2019

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

institute: Kyushu University

summary: The branched-chain amino acid (BCAA) metabolism plays pleiotropic roles in homeostasis. Here we show that human acute leukemia-initiating cells (LICs), but not normal hematopoietic stem cells, are heavily addicted to the BCAA metabolism, irrespective of myeloid or lymphoid types. To clarify how BCAA metabolism affect the gene expression of human acute leukemia cells, we examined the gene expression alteration in human acute leukemia cell lines in control and BCAA-resrticted culture conditions.

overall_design: To clarify the global gene expression alteration in  ALL cells after BCAA metabolism inhibition, Jurkat cells were cultured with or without BCAA. After 8-10 days of culture, FACS-purified Jurkat cells were subjected to transcriptome analysis.

first: Koichi

last: Akashi


title: Gene expression analysis of Kasumi9 cells cultured with or without BCAA

overall_design: To clarify the global gene expression alteration in  ALL cells after BCAA metabolism inhibition, Kasumi9 cells were cultured with or without BCAA. After 8-10 days of culture, FACS-purified Kasumi9 cells were subjected to transcriptome analysis.


title: Gene expression analysis of human CD34+ AML cells cultured with or without gabapentin

status: Public on Jun 01 2019

summary: To clarify the global gene expression alteration in primary CD34+ AML cells after BCAA metabolism inhibition, CD34+ AML cells were treated with or without gabapentin in vitro. After 9-12 hours of culture with or without gabapentin, FACS-purified CD34+ AML cells were subjected to transcriptome analysis.

overall_design: To clarify how BCAA metabolism affect the gene expression of human CD34+ AML cells, CD34+ AML cells from 4 independent patients were treated with or without 40mM gabapentin, a specific BCAT1 inhibitor for 9-12 hours. After BCAA metabolism inhibition by gabapentin, CD34+ AML cells were purified and total RNA was extracted from control and treated samples.


title: RNA-seq mouse donor T-cells 7 days post HSCT

status: Public on Jul 27 2019

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: The overal goal was to characterize the differential expression of protein-coding genes and lncRNAs in donor T-cells 7 days after experimental HSCT.

overall_design: Independent biologic triplicate donor T-cells were harvested for RNA-seq from a pool of 2-4 mouse recipients detailed below 7 days after allogeneic or syngeneic HSCT or from healthy control, non-transplanted animals.

first: Pavan

last: Reddy

first: Daniel

last: Peltier

first: Yaping

last: Sun

first: Rebecca

last: Tagett


title: Gene expression analysis of THP-1 cells cultured with or without BCAA

overall_design: To clarify the global gene expression alteration in  AML cells after BCAA metabolism inhibition, THP-1 cells were cultured with or without BCAA. After 3-5 days of culture, FACS-purified THP-1 cells were subjected to transcriptome analysis.


title: Indole signaling at the host-microbiota-pathogen interface

status: Public on Jan 05 2019

city: Dallas

first: Aman

last: Kumar

state: Texas

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: UT Southwestern Medical Center

summary: RNA seq experiment was perfomed in the presence and absence of 500uM indole

overall_design: EHEC strain 86 24 was used for this study. WT and △tnaA EHEC were grown until late log phase in low gluocse DMEM in the presence and absence of 500µM indole. RNA was extracted from these samples. The experiment was conducted with three biological replicates.

last: Sperandio


title: Nucleotide resolution of RNA polymerase II transcription in human cytomegalovirus

status: Public on Jan 16 2019

city: Iowa City

first: David

last: Price

state: Iowa

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

summary: We performed paired-end PRO-Seq and/or PRO-Cap on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h (strain TB40/E) or 96 h (strain Towne varS). Each sample has matched uninfected controls. Towne experiments were also performed with adapters containing 4 nt of random sequence flanking both sides (8 total bases of randomness) to enable deduplication. Reads were first mapped to the human genome (hg38) (files available on GEO). Unmapped reads were then mapped to HCMV (Genbank FJ616285.1) (track hub available at https://github.com/P-TEFb/trackHub_HCMV).

overall_design: TB40/E: PRO-Seq on uninfected HFF treated with 0.1% DMSO 1 h, or 4 h infected HFF treated with 0.1% DMSO 1 h or 1 µM flavopiridol 1 h. Towne: PRO-Seq and PRO-Cap on uninfected or 96 h infected HFF treated with 0.1% DMSO 1 h or 1 µM flavopiridol 1 h.

first: Kyle

last: Nilson

first: Mrutyunjaya

last: Parida

first: Chris

last: Ball

first: Ming

last: Li

first: Jeffery

last: Meier


title: Genome-wide maps of H3K27me3 chromatin modification status regulated by branched chain amino acids (BCAA) metabolism in human acute leukemia

status: Public on Aug 01 2019

summary: The branched-chain amino acid (BCAA) metabolism plays pleiotropic roles in homeostasis. Here we show that human acute leukemia-initiating cells (LICs), but not normal hematopoietic stem cells, are heavily addicted to the BCAA metabolism, irrespective of myeloid or lymphoid types. Human acute leukemia cells had a high level of BCAAs, transporting free BCAAs into the cytoplasm. Functional inhibition of BCAA transaminase-1 (BCAT1), a catalytic enzyme for BCAAs, induced apoptosis of human LICs, and suppressed reconstitution of human leukemia in xenograft models. Furthermore, deprivation of BCAAs from daily diet in mice transplanted with human LICs strongly inhibited their expansion and self-renewal in vivo. The BCAT1 inhibition inactivates the PRC2 function for epigenetic maintenance of stem cell signatures via downregulation of EZH2 and EED, critical PRC2 components, and inhibited the mTORC1 signaling for leukemia propagation. Thus, targeting the BCAA metabolism should be a powerful approach to erase cancer stemness in human acute leukemias.

overall_design: We examined the alteration of H3K27me3 histone modification status in human acute leukemia cells in vitro and in vivo. Briefly, (acute myeloid leukemia (AML) cell line THP-1, primary CD34+ acut lymphoblastic leukemia (ALL) cells and primary CD34+ AML cells were treated with or without gabapentin (GABA) in vitro, and subsequently submitted to ChIP-Seq analysis. We also evaluated the alteration of H3K27me3 histone modification status of primary ALL cells in vivo. Briefly, primary CD34+ ALL cells were transplanted into the immunodeficient mice (NSG mice), and the recipients mice were fed with control diets or BCAA=free diets. After the dietary restriction of BCAAs, reconstituted human CD34+ ALL cells were harvested from the recipient mice, and then submitted to ChIP-Seq analysis.

first: Yuichiro

last: Semba


title: mRNA expression analysis of mice intestine profiles between PBS and free ubiquitin after irradiation

status: Public on Jun 27 2019

city: suzhou

first: zhang

middle: shu

last: yu

state: Jinagsu

address: 199 Ren'ai Rd

department: Radiation Medicine

institute: soochow University

summary: This study aims to compared mRNA expression between PBS- and free ubiquitin-treated intestines after 7 Gy radiation (total body radiation) by microarray analysis. Mice intestine tissues were collected 3.5 days after radiation.

overall_design: This study aims to compared mRNA expression between PBS- and free ubiquitin-treated intetines after radiation by microarray analysis.

first: Shuyu

last: Zhang

first: Jianping

last: Cao

first: Yang

last: Jiao


title: ZIKV-infected A549 cells SBC Human (4*180K) lncRNA Microarray(V6.0)

status: Public on Dec 20 2018

city: Guangzhou

first: Wang

last: Yi

address: Room1426, Yixue Keji Lou,74 Zhongshan 2nd Road

department: Department of Immunology

institute: Zhongshan School of Medicine, Sun Yat-sen University

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

summary: Viral infection has a great impact on cellular expression profile of non-coding RNAs and genes. By microarray screening, our study identified 79 long non-coding RNAs (lncRNAs) and 140 mRNAs that were differentially expressed in human lung epithelial A549 cells infected with Zika virus (ZIKV). The bioinformatics analysis indicated that many differentially expressed lncRNAs were located in same chromosome as the differentially expressed mRNAs; and these lncRNAs and mRNAs were involved in the host responses to viral infection, including the innate immune response.

overall_design:
The expression profiles of cellular lncRNAs and mRNAs in the mock-infected and ZIKV-infected A549 cells at 24 hp.i. were measured by microarray assay.
Total RNA samples isolated from three independent experiments were used for Arraystar Human LncRNA Microarray V6.0.

first: Zhang

last: Ping


title: Renal congestion (Rattus)

status: Public on Nov 14 2018

city: Sendai

first: Satoshi

last: Shimada

address: 2-1, Seiryo-machi

institute: Tohoku University

summary: We created a rat renal congestion model and investigated the effect of renal congestion on hemodynamics and molecular mechanisms. The inferior vena cava (IVC) between the renal veins was ligated by suture in male Sprague-Dawley rats to increase upstream IVC pressure and induce congestion in the left kidney only. Left kidney congestion reduced renal blood flow, glomerular filtration rate, and increased renal interstitial hydrostatic pressure. Tubulointerstitial and glomerular injury and medullary thick ascending limb hypoxia were observed only in the congestive kidneys. Molecules related to extracellular matrix expansion, tubular injury, and focal adhesion were upregulated in microarray analysis. Renal decapsulation ameliorated the tubulointerstitial injury. Electron microscopy captured pericyte detachment in the congestive kidneys. Transgelin and platelet-derived growth factor receptors, as indicators of pericyte-myofibroblast transition, were upregulated in the pericytes and the adjacent interstitium. With the compression of the peritubular capillaries and tubules, hypoxia and physical stress induce pericyte detachment, which could result in extracellular matrix expansion and tubular injury in renal congestion.

overall_design: Three rats were operated. Three days after surgery, congestive left kidney were compared to control right kidney. Cortex and outer medulla are separately analyzed.

first: Takefumi

last: Mori


title: microRNA expression profiles for DLD-1 cells with circLONP2 knockdown

status: Public on Oct 27 2018

first: han

last: kai

state: Guangdong

address: Dongfeng Road East

institute: Sun Yat-sen university cancer center

summary: We have employed microRNA microarray expression profiling as a discovery platform to identify the specific microRNAs that were regulated by circLONP2.

overall_design: Human colorectal carcinoma cell line DLD-1 were transfected with circLONP2-specific siRNA or negative control siRNA, and microRNA microarray were applied.

first: Han

last: Kai


title: CD95L mRNA is toxic to cells [SmallRNA_AGOpulldownCD95L_50hrs_HeyA8_CD95KO]

status: Public on Sep 20 2018

first: Marcus

last: Peter

summary: >80% of a large number of tested siRNAs and shRNAs targeting CD95 or CD95 ligand (CD95L) induce a form of cell death that is characterized by the simultaneous activation of multiple death pathways and preferentially affects transformed and cancer stem cells. We now show that these si/shRNAs kill cancer cells through canonical RNAi by targeting the 3’UTR of critical survival genes in a unique form of off-target effect.  We also provide evidence showing that the full length CD95L mRNA is also toxic and produces small Ago-associated RNAs.

overall_design: Examination of small RNAs (18-23bp) pulled-down with Ago proteins in cells infected with either pLenti or pLenti- CD95L.

first: William

last: Putzbach

middle: E

first: Elizabeth

last: Bartom


title: CD95L mRNA is toxic to cells [SmallRNA_CD95L.50hrs.Drosha_ko]

overall_design: Examination of differential gene mRNA expression in empty vector control cells versus cells over-expressing CD95L mRNA.


title: CD95/Fas ligand mRNA is toxic to cells

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

overall_design: Refer to individual Series


title: CD95L mRNA is toxic to cells [SmallRNA.CD95L.50hrs.HeyA8]


title: Single cell transcriptomes of cord blood derived subsets of human haematopoietic stem cells, LMPP and MLP myelo-lymphoid restricted progenitors [49f+ HSCs, 49f+ Subset1, 49f+ Subset2, Subset1, Subset2]

status: Public on Sep 14 2018

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

institute: University of Cambridge

summary: Integration of index sorting and single cell functional assays allowed identification of novel haematopoietic stem cell (HSC) and multiprogenitor subsets (MPP) that differ in their lineage differentiation potential in vitro and in vivo, cell cycle properties and long-term repopulation capacity in the NSG xenograft model. Here we report single cell transcriptomes of CD49f+ HSCs as well as those of CD49f+ Subset1 (CD19- CD38- CD45RA- CD90+ CD49f+ CD34lo CLEC9Ahi, Myelo-erythroid-skewed in vitro but Lymphoid-competent) and CD49f+ Subset2 cells (CD19- CD38- CD45RA- CD90+ CD49f+ CD34hi CLEC9Alo, Myelo-Lymphoid competent but Erythroid-deficient). We also report bulk transcriptomes of pools of 20 cells from HSC/MPP Subset1 (CD19- CD38- CD45RA- CD34lo CLEC9Ahi) and HSC/MPP Subset2 (CD19- CD38- CD45RA- CD34hi CLEC9Alo). Altogether these data show a diffuse transcriptional landscape of the CD49f+ HSC compartment, which is polarised along an axis that separates Myelo-Erythroid and Myelo-Lymphoid lineage-priming. Consistently with their differentiation capacity in vitro, CD49f+ Subset1 cells cluster at the Myelo-Erythroid end of the landscape, while CD49f+ Subset2 cells cluster at the Myelo-Lymphoid end. In addtion, these lineage-priming signatures were found to be more marked in HSC/MPP Subset1 and HSC/MPP Subset2, than in the equivalent CD49f+ subsets. In conclusion, 49f+ Subset1 and 49f+ Subset2 populations have activated distinct transcriptional lineage-priming programmes corresponding to the phenotypic lineage-skewing observed in vitro, that then become reinforced within the broader HSC/MPP pool. Altogether our data shows that lineage-priming and lineage-restriction programmes are initially established within the CD49f+ HSC subset in humans.

overall_design: Examination of the genome-wide transcriptome of 192 single CD49f+ HSCs and 192 single cells from two CD49f+ HSC subsets (CD49f+ Subset1 and CD49f+ Subset2), as well as replicates of 20 cells of HSC/MPP Subset1 and HSC/MPP Subset2

first: Serena

last: Belluschi

first: Evangelia

last: Diamanti


title: Genome-wide expression microarray data of MCSP- and ABCB5-enriched CTCs

status: Public on May 11 2018

city: perth

first: Carlos

middle: A

last: Aya-bonilla

state: WA

address: 32 kinship street

institute: Telethon Kids Institute

summary: Circulating Tumour Cells (CTCs) act as tumour seeds for haematogeneous melanoma spread of melanoma. Since CTCs have been reported to be heterogeneous in melanoma, the characterisation of the different melanoma CTC subpopulations harbours biological and clinical significance. For detection of melanoma CTCs, melanoma-associated markers (i.e. MCSP, melanoma-associated chondroitin sulphate proteoglycan) have been used; however, recent studies have found that melanoma CTCs commonly express ABCB5 (ATP-binding cassette sub-family B member 5) a melanoma-initiating marker. Here, we used a genome-wide expression microarray to interrogate the transcriptome of MCSP-enriched and ABCB5-enriched CTC fraction in order to provide a better understanding of their biology and role in melanoma metastasis.  Findings from this study highlited the distinct transcriptional programming of both CTC subpopulations.

overall_design: Blood samples from healthy donors (n=6) and metastatic melanoma patients (n=6) were incubated with magnetic beads coated with antibodies against MCSP or ABCB5 for immunomagnetic enrichment of either MCSP or ABCB5 CTCs. Total RNA was extracted from the total of 24 samples and microarray gene expression profiling was performed uisng the Affymetrix® GeneChip® genome 2.0 ST array protocol (Affymetrix, US). Gene  expression data from MCSP or ABCB5 enriched CTCs of  healthy donors and melanoma patient blood samples were compared.

last: Aya-Bonilla

first: Elin

last: Gray

first: Mel

last: Ziman


title: 6mer seed toxicity in tumour suppressive microRNAs

status: Public on Sep 11 2018

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

overall_design:
Samples of human ovaries were generated by deep sequencing, using Illumina HiSeq4000.  HeyA8 cells treated with Doxorubicin, Carboplatinum, Etoposide.

We provide evidence that miR-34a is toxic to cancer cells mostly through its toxic 6mer seed sequence. RNA isolated from HeyA8 cells 48 hrs after transfection with either a nontargeting siRNA (siNT2), miR-34a Seed, pre-miR-NC, or pre-miR-34a was subjected to deep sequencing, using Illumina HiSeq4000.

first: Quan

last: Gao


title: Bmp2 and Notch cooperate to pattern the embryonic endocardium

status: Public on Jun 14 2018

city: Madrid

first: Jose Luis

last: de la Pompa

address: Melchor Fernández Almagro 3

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).

summary: Our study describes in detail the role of Bmp2 during cardiac valve developmnent and its implication in Notch pathway activation.

overall_design: Hearts were isolated from WT and Bmp2GOF;Nkx2.5-Cre mouse embryos at stage E9.5 and their expression profile characterized by RNA-seq

first: Tania

last: Papoutsi

first: Luis

last: Luna-Zurita

first: Belén

last: Prados

first: Stéphane

last: Zaffran

first: José Luis


title: Identification of transcriptional targets of FGF20.

status: Public on Aug 01 2018

city: Helsinki

first: Marja

last: Mikkola

address: P.O.B 56 (Viikinkaari 5)

country: Finland

institute: University of Helsinki

summary: Fgf20 is expressed from the hair follicle placode and is required for development of the dermal condensate. Here we used RNAseq to identify the immediate transcriptional targets of FGF20 in Fgf20-/- dermis at E13.5, a timepoint immediately prior to dermal condensate initiation.

overall_design: 5 dermises from E13.5 Fgf20-/- embryos were divided in half and cultured with either rFGF20 (1 µg/ml) or BSA vehicle control for 3 hours. Each FGF20-treated half was compared with its BSA control.

first: L

last: Biggs

first: O

last: Mäkelä

first: R

last: Das Roy

first: M


title: Direct effects of Methamphetamine and HIV-1 Tat in the recruitment of RNA Polymerase to innate immune cell gene promoters

status: Public on Aug 25 2018

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

state: CA

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

summary:
Genome-wide maps of RNA polymerase II binding to chromatin in THP1 monocytic cell lines following Meth and HIV Tat exposure
We report the most immediate effects of exposure to Methamphetamine and HIV Tat peptide, and their interactions, revealed by the recruitment of RNA Polymerase to gene promoters, in innate immune THP1 cells.

overall_design: Examination of RNA Polymerase binding to chromatin in 1 cell line 15 minutes after the exposure to Methamphetamine or HIV Tat, or both.

middle: G

first: Liana

last: Basova


title: Myocardial Bmp2 overexpression leads to ectopic cardiac EMT and promotes chamber cardiomyocyte proliferation and immaturity

status: Public on Apr 11 2018

summary: Defective valve and septa formation constitute a substantial part of congenital heart defects affecting the neonate or the adult. During cardiac development, restricted myocardial Bmp2 expression is a key signal for the specification and patterning of the valve-forming field in the atrio-ventricular canal (AVC) region and the initiation of the epithelial-mesenchyme transition (EMT) that gives rise to the valve primordia. We have generated a mouse transgenic line conditionally expressing Bmp2. Nkx2.5Cre-driven Bmp2 overexpression in the myocardium leads to foetal lethality, due to valve and chamber dysmorphogenesis, and rescue of the AVC specification defect of Bmp2-null embryos. Nkx2.5Cre/+;Bmp2tg/+ transgenic embryos show ventricular septal defect, thickened valves, enlarged trabeculae and dilated ventricles, whose endocardium is able to undergo EMT when explanted onto collagen gels. Gene profile and marker analysis indicates that cellular proliferation is increased and chamber differentiation and patterning is impaired in Nkx2.5Cre/+;Bmp2tg/+ embryos, but the ventricular-specific gene expression program is not abolished. We obtained similar results using a second myocardial driver (cTnTCre) to activate Bmp2 expression, but not with an endothelial-specific one (Tie2Cre), as Tie2Cre/+;Bmp2tg/+ mice are normal and survive to adulthood, indicating that Bmp2 must emanate from the myocardium to exert its EMT-driving and cardiomyocyte maturation blocking effect. Forced Bmp2 expression in vitro stimulates EBs proliferation and blocks their progression into cardiomyogenesis, an effect partially rescued by Noggin. These data show that widespread myocardial Bmp2 expression directs ectopic valve primordium formation and maintains chamber myocardium and early cardiac progenitors in a primitive, proliferative state, identifying Bmp2 as a potential factor for the expansion of immature cardiomyocytes.

overall_design: RNA was isolated from ventricles and valves of WT and  Nkx2.5-Cre;Bmp2 mouse embryos at stage E14.5 (12 hearts per genotype), pooled into three replicates of each genotype RNA was prepared using the standard Illumina TrueSeq RNASeq library preparation kit. Libraries were sequenced in a GAIIx Illumina sequencer using a 75bp single end elongation protocol.

first: Paula

last: Gómez-Apiñaniz

first: Stephan

first: José

last: María Pérez-Pomares

last: Luis de la Pompa


title: Genome-wide RNA-seq and Epigenetic analysis of human monocyte derived macrophage responses to Zika virus infection

status: Public on Sep 10 2018

city: La Jolla

first: Aaron

middle: F

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

summary: Interpretation of genome-wide investigations of host-pathogen interactions are often obscured by analyses of mixed populations of infected and uninfected cells. Thus, we developed a system whereby we simultaneously characterize and compare genome-wide transcriptional and epigenetic changes in pure populations of virally-infected and neighboring uninfected cells to identify viral-regulated host-responses. Using patient-derived unmodified Zika viruses (ZIKV) infecting primary human macrophages, we reveal that ZIKV suppresses host transcription by multiple mechanisms. ZIKV infection causes both targeted suppression of type I interferon responses and general suppression by reducing RNA polymerase II protein levels and DNA occupancy. Simultaneous evaluation of transcriptomic and epigenetic features of infected and uninfected cells provide a powerful method for identifying coincident evolution of dominant pro-viral or anti-viral mechanisms.

overall_design: Analysis of transcriptional and epigenetic response of human monocyte derived macrophages to Zika virus infection

first: Sujan

last: Shresta

first: Christopher

middle: K

last: Glass


title: Single cell transcriptomes of cord blood derived subsets of human haematopoietic stem cells, LMPP and MLP myelo-lymphoid restricted progenitors

first: Elisa

last: Laurenti


title: Gene expression profiling study by RNA-seq for identifying genes associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors

status: Public on May 28 2018

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: Treatment with ALK tyrosine kinase inhibitors often elicits profound initial antitumor responses in ALK fusion-positive patients with lung adenocarcinoma. However, patients invariably develop acquired resistance to ALK inhibitors. In this study, we aimed to identify molecular events that limit the response to ALK inhibition using genetic and epigenetic approaches. To identify novel mechanisms of acquired resistance to ALK inhibitors, we established in vitro models of acquired resistance to ceritinib using H3122 cell. For in vitro model, H3122 parental cells, ceritinib-treated resistant cells, and non-resistant cells that combinely treated with certinib and panobinostat were used for RNA-seq based gene expression profiling.

overall_design: RNA-seq data of 6 samples, two H3122 parental cells, two ceritinib-treated resistant cells, and two non-resistant cells that combinely treated with certinib and panobinostat, were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using NextSeq 500 platform (Illumina).

first: Jeong-Hwan

first: Mirang

first: Mi-Ran

last: Yun

first: Sun-Min

last: Lim

first: Byoung-Chul

last: Cho


title: Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors

type: Methylation profiling by high throughput sequencing


title: A Upf3b-mutant mouse model with behavioral and neurogenesis defects

status: Public on Apr 09 2018

first: Heidi

last: Cook-Andersen

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

summary: Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA degradation pathway that acts on RNAs terminating their reading frames in specific contexts. NMD is regulated in a tissue-specific and developmentally controlled manner, raising the possibility that it influences developmental events. Indeed, loss or depletion of NMD factors have been shown to disrupt developmental events in organisms spanning the phylogenetic scale. In humans, mutations in the NMD factor gene, UPF3B, causes intellectual disability (ID) and are strongly associated with autism spectrum (ASD), attention deficit hyperactivity disorder (ADHD), and schizophrenia (SCZ). Here, we report the generation and characterization of mice harboring a null Upf3b allele. These Upf3b-null mice exhibit deficits in fear-conditioned learning, but not spatial learning. Upf3b-null mice also have a profound defect in prepulse inhibition (PPI), a measure of sensorimotor gating commonly deficient in individuals with SCZ and other brain disorders. Consistent with both their PPI and learning defects, cortical pyramidal neurons from Upf3b-null mice display deficient dendritic spine maturation in vivo. In addition, neural stem cells from Upf3b-null mice have impaired ability to undergo differentiation and they require prolonged culture to give rise to functional neurons with electrical activity. RNA sequencing (RNAseq) analysis of the frontal cortex identified UPF3B- regulated RNAs, including direct NMD target transcripts encoding proteins with known functions in neural differentiation, maturation, and disease. We suggest that Upf3b-null mice serves as a novel model system to decipher cellular and molecular defects underlying ID and neuro-developmental disorders.

overall_design: Analyzing differential gene expression in frontal cortex of wild type versus Upf3b-null mice

first: Jennifer

last: Chousal

first: Samantha

last: Jones


title: Triplet nucleotide repeat-based siRNAs are highly toxic to cancer cells

status: Public on Jan 12 2018

city: Chicago

first: Marcus

last: Peter

summary: Triplet repeat siRNAs as found amplified in diseases such as Huntingtons disease can be used to kill cancer cells

overall_design: RNA isolated from HeyA8 cells 48 hrs after transfection with either a nontargeting siRNA (siScr), siCAG/CUG or siCGA/UCG were subjected to deep sequencing, using Illumina HiSeq4000.

first: Andrea

last: Murmann

first: Elizabeth

last: Bartom


title: Transcriptome of cord blood derived subsets of human haematopoietic stem cells, LMPP and MLP myelo-lymphoid restricted progenitors [49f+ Subset2, Subset2, LMPPs, MLPs]

overall_design: Examination of the genome-wide transcriptome of  143 49f+ HSC Subset2, 142 LMPPs, 143 MLPs, 142 HSC/MPP Subset2

first: Serena

last: Belluschi

first: Evangelia

last: Diamanti


title: RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls

status: Public on Jun 22 2018

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

institute: Wellcome Trust Centre for Human Genetics

summary: SF3B1, SRSF2 and U2AF1 are the most frequently mutated splicing factor genes in MDS. We have performed a comprehensive analysis to determine the impact of these commonly mutated splicing factors on pre-mRNA splicing in the stem/progenitor cells and in the erythroid and myeloid precursors in splicing factor mutant MDS. Using RNA-seq, we determined the aberrantly spliced genes and dysregulated pathways in bone marrow CD34+ cells of a large group of 82 MDS patients. Splicing factor mutations in MDS result in different mechanistic alterations in splicing and largely affect different genes, but these converged in common dysregulated pathways and cellular processes, including RNA splicing, translation and mitochondrial dysfunction, indicating that these mutations operate through common mechanisms in MDS. Many of these dysregulated pathways and cellular processes can be linked to the known disease pathophysiology and to the phenotypes associated with splicing factor mutations in MDS, whilst several others have not been previously associated with MDS, such as sirtuin signalling.

overall_design:
RNA-sequencing was performed on bone marrow CD34+ hematopoeitic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls to identify differential splicing between samples with mutations in the splicing factor SF3B1, SRSF2 or U2AF1 comparative to samples from myelodysplactic syndrome patients without mutations in these splicing factors and healthy controls.

Processed data for the CD34+ hematopoeitic stem and progenitor cells are available in the files: CPM_table.txt.gz, Count_table.txt.gz and TPM_table.txt.gz.

RNA-sequencing was also performed on monocytic, granulocytic and erythroid precursors from the bone marrow of patients with myelodysplastic syndrome and healthy controls to identify aberrant splicing in samples with mutations in splicing factors SF3B1 and SRSF2 comparative from healthy controls.

Processed data for the monocytic, granulocytic and erythroid precursors are available in the files: CPM_table_fractions.txt, Count_table_fractions.txt and TPM_table_fractions.txt.

first: Violetta

last: Steeples


title: Global hepatic gene expression data from PPARa liver-specific KO and PPARa liver wild-type male mice fed ad libitum

status: Public on Dec 16 2017

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

summary: To identify genes whose expression is under the strict dependence of hepatocyte PPARa activity, we used a mouse strain of PPARa-specific deletion in hepatocyte (albumin-Cre+/- Pparaflox/flox or LKO) and we compared them to their liver WT littermates (albumin-Cre-/- Pparaflox/flox or LWT) fed ad libitum or fasted for 24 hours.

overall_design: There are 24 liver samples, each from an individual mouse. The samples are from Ppara liver KO (LKO) and liver WT (LWT) male mice of 8 week-old from the same genetic background (C57Bl/6J) fed ad libitum or fasted for 24 hours (n=6 mice/genotype/group). All mice were sacrified at ZT16.

first: Marion

last: Régnier

first: Arnaud

last: Polizzi

first: Yannick

last: Lippi

first: Edwin

last: Fouché

first: Claire

last: Naylies

first: Walter

last: Wahli

first: Alexandra

last: Montagner


title: Sequential ligand-dependent Notch signaling activation regulates valve primordium formation and morphogenesis

status: Public on Jan 31 2018

first: Jose Luis

last: de la Pompa

summary: Our studies identify a mechanism of signaling crosstalk during valve morphogenesis that sheds light on the origin of congenital heart defects associated with reduced Notch function.

overall_design: Aortic and pulmonary cardiac valves were isolated by laser microdissection from WT and Jag1flox;Nkx2.5-Cre mouse embryos at stage E14.5, and their expression profile characterized by RNA-Seq.

first: D

last: MacGrogan

first: J

last: Pompa


title: Astrocyte mRNA expression - comparison of wild type animals to CETP transgenic animals

status: Public on Mar 01 2018

city: Montreal

first: Lisa

middle: Marie

last: Munter

state: Quebec

address: 3649 Prom. Sir-William-Osler

department: Pharmacology

country: Canada

institute: McGill University

summary:
CETP transfers lipids and cholesteryl esters between lipoproteins. This leads to elevated LDL-cholesterol levels. We found elevated cholesterol levels in the brains CETP transgenic animals. We wanted to test whether this is due to increased cholesterol synthesis by astrocytes
2 animals that were genotyped as wild type showed CETP transcription in our RT-qPCR (WT_1 & WT_5) and were excluded

overall_design: purified astrocytes from wild type animals on a standard mouse diet are compared to astrocytes from CETP tansgenic animals on a 1% cholesterol diet (dietary cholesterol induced CETP expression)

first: Felix

last: Oestereich


title: CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [shL3.shR6.RNAseq.lg]

status: Public on Sep 16 2017

first: Marcus

last: Peter

summary: The death receptor CD95/Fas can be activated by immune cells to kill cancer cells. However, most siRNAs or shRNAs targeting either CD95 or CD95L induce DICE (Death Induced by CD95/CD95L Elimination), a form of cell death in which a combination of different cell death pathways are activated, that is selective for transformed cells, and that preferentially affects cancer stem cells. We now provide evidence that both CD95 and CD95L are part of a network of genes that contain sequences that when expressed as either siRNAs or shRNAs are toxic to cancer cells. They act through canonical RNAi by targeting the 3'UTRs of critical survival genes. We propose that these embedded toxic sequences are part of a conserved mechanism that regulates cell death, and we predict the existence of endogenous siRNAs, that when produced, induce cell death to regulate genome fidelity. Our data have implications for cancer therapy and the use of RNAi.

overall_design: 293T (shL3 site deleted) cells were infected with either pTIP-shScr or pTIP-shL3 and following puromycin selection large RNAs were analyzed by deep sequencing 50 or 100hrs after addition of doxycycline/HeyA8 (shR6 site deleted) cells were infected with either pLKO-shScr or pLKO-shR6 and following puromycin selection large RNAs were analyzed by deep sequencing 50 or 100hrs after addition of selection.

first: William

last: Putzbach

first: Elizabeth

last: Bartom


title: CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [shL3.shR6.RNAseq.sm]

overall_design: 293T (shL3 site deleted) cells were infected with either pTIP-shScr or pTIP-shL3 and following puromycin selection small RNAs were analyzed by deep sequencing 50 or 100hrs after addition of doxycycline/HeyA8 (shR6 site deleted) cells were infected with either pLKO-shScr or pLKO-shR6 and following puromycin selection small RNAs were analyzed by deep sequencing 50 or 100hrs after addition of selection.


title: Genome-wide association analysis identifies 13 novel susceptibility loci for Carpal Tunnel Syndrome

status: Public on Dec 14 2017

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

institute: Oxford University

summary: Carpal tunnel syndrome (CTS) is a common and disabling condition of the hand caused by entrapment of the median nerve at the level of the wrist. It is the commonest entrapment neuropathy, with estimates of prevalence ranging between 5-10%1–3. We undertook the first GWAS to date of an entrapment neuropathy, using 12,106 CTS cases identified in UK Biobank and 387,347 controls. We discovered 13 novel susceptibility loci for CTS with p≤5x10-8. We identified likely causal genes in the pathogenesis of CTS, including ADAMTS17, ADAMTS10 and EFEMP1, and demonstrated expression of these genes in surgically resected tenosynovium from CTS patients. We suggest that variants within genes implicated in growth and extracellular matrix architecture contribute to the genetic predisposition to CTS.

overall_design: RNA-seq Illumina HiSeq4000

first: Akira

last: Wiberg

first: Annina

last: Schmid

first: David

last: Bennett

first: Dominic

last: Furniss


title: CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [shL1.RNAseq.lg]

summary: We provide evidence that shRNAs and siRNAs derived from CD95 and CD95L preferentially target the 3' UTRs of survival genes culminating in a very robust mode of cell death we call DISE (Death Induced by Survival gene Elimination)

overall_design: 293T cells were infected with either pTIP-shScr or pTIP-shL1 and following puromycin selection RNA was analyzed by deep sequencing 100hrs after addition of doxycycline


title: CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [FasLRNAseq.lg]

summary: >80% of a large number of tested siRNAs and shRNAs targeting CD95 or CD95 ligand (CD95L) induce a form of cell death that is characterized by the simultaneous activation of multiple death pathways and preferentially affects transformed and cancer stem cells. We now show that these si/shRNAs kill cancer cells through canonical RNAi by targeting the 3’UTR of critical survival genes in a unique form of off-target effect.  We also provide evidence showing that the full length CD95L mRNA is also toxic and produces small Ago-associated RNAs.

overall_design: Examination of differential gene mRNA expression in empty vector control cells versus cells over-expressing CD95L mRNA.


title: CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [AGOpulldownRNAseq.sm]

overall_design: Examination of small RNAs (18-23bp) pulled-down with Ago proteins in cells infected with either pLenti or overexpressing CD95L.


title: CD95L derived si- and shRNAs and the CD95L mRNA kill cancer cells through an RNAi mechanism by targeting survival genes [siL3.RNAseq.lg]

overall_design: RNA isolated from HeyA8 cells 48 hrs after transfection with either a nontargeting siRNA (siScr) or a CD95L derived siRNAs (siL3) were subjected to deep sequencing, using Illumina HiSeq4000.


title: Single-cell RNA sequencing of Zfp36l2 knock-out and floxed GV mouse oocytes.

status: Public on Sep 25 2017

first: Heidi

last: Cook-Andersen

summary: Global transcriptional silencing is a highly conserved evolutionary event central to the transition from the fully differentiated oocyte to the totipotent embryo. Despite its importance in the development of all animals, this pivotal genome-wide event remains poorly understood. Here, we report the unexpected finding that oocyte global transcriptional silencing depends on an mRNA decay activator. Oocyte-specific loss of ZFP36L2—an RNA-binding protein critical for AU-rich element-mediated mRNA decay—prevents oocytes from undergoing global transcriptional silencing. ZFP36L2- deficient oocytes are developmentally incompetent, with defects in maturation and fertilization leading to complete female infertility. Single cell RNA-seq analysis revealed that ZFP36L2 regulates scores of transcription regulators with central roles in chromatin modification and transcription initiation and elongation. This dysregulation resulted in failure to accumulate histone methylation marks associated with the silent, competent state. Our results define a critical role for an oocyte mRNA decay activator in the downregulation of transcription activators, leading to histone methylation, global transcriptional silencing and competence to transition from oocyte to embryo.

overall_design: Examination of differential gene expression in mouse oocytes upon loss of Zfp36l2.

first: Jennifer

last: Chousal


title: Endothelial Jag1-RBPJK signaling promotes inflammatory leukocyte recruitment and  atherosclerosis

status: Public on Jun 30 2017

summary:
Aim: To determine the role of NOTCH during the response-to-injury and subsequent chronic inflammatory process of the arterial wall underlying atherosclerosis.
Methods and results: We have generated an endothelial-specific RBPJK depleted mice using the Cdh5 cadherin promoter (ApoE-/-;RBPJflox/flox;Cdh5- CreERT). Endothelial-specific deletion of the Notch effector RBPJK or systemic deletion of the Notch1 receptor in athero-susceptible ApoE-/- mice fed a HC diet for 6 weeks resulted in reduced atherosclerosis in the aortic arch and sinus. Intravital microscopy revealed decreased leukocyte rolling on the endothelium of ApoE-/-;RBPJflox/flox;Cdh5- CreERT, that correlated with the lesser presence of leukocyts and macrophages in the vascular wall. Consistent with this, transcriptome analysis revealed that proinflammatory and endothelial activation pathways were downregulated in atherosclerotic tissue of RBPJk-mutant mice.. Jagged1 signaling upregulation in endothelial cells  promotes the physical interaction and nuclear translocation of the intracellular domain of the Notch1 receptor (N1ICD) with NF-kB,. This N1ICD and NF-kB interaction is required for reciprocal transactivation of target genes including vascular cell adhesion molecule-1 (Vcam1).
Conclusions: Notch signaling pathway inactivation decreases leukocyte rolling, thereby preventing endothelial dysfunction and vascular inflammation. Thus attenuating Notch signaling may constitute  a useful therapeutic strategy for atherosclerosis.
Key words: atherosclerosis, endothelium, signaling pathways, Notch, NF-kB, transcriptional regulation

overall_design: RNA was isolated from the aortic arches of three ApoE-/-;RBPJflox/flox and three ApoE-/-; RBPJflox/flox;Cdh5-CreERTmice

first: Meritxell

last: Nus

first: Beatriz

last: Martínez-Poveda

first: Donal

first: Rafael

last: Chevre

first: Gaetano

last: D`Amato

first: Mauro

last: Sbroggio

first: Cristina

last: Rodríguez

first: José

last: Martínez-González

first: Vicente

last: Andrés

first: Andrés

last: Hidalgo

middle: L


title: Transcriptomic analysis of control and Myzocytiopsis humicola-infected C. elegans

status: Public on Jul 26 2017

city: London

first: Michalis

last: Barkoulas

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

summary: We used RNA-seq to identify gene expression changes in C. elegans after 12 hrs and 24 hrs of exposure to pathogen Myzocytiopsis humicola

overall_design: Total RNA was extracted from whole C. elegans adults after exposure to Myzocytiopsis humicola

first: Guled

last: Osman

first: Sneha

last: Koneru

first: Peter

last: Sarkies


title: CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes

first: Marcus

last: Peter

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

overall_design: Refer to individual Series


title: Gas-fermenting acetogens regulate their metabolism to maintain ATP homeostasis

status: Public on May 22 2017

city: Tartu

first: Kaspar

last: Valgepea

state: Tartumaa

address: Nooruse 1

department: Institute of Technology

country: Estonia

institute: University of Tartu

summary: Acetogens are promising cell factories for producing fuels and chemicals from waste feedstocks via gas fermentation, but quantitative characterization of carbon, energy, and redox metabolism is required to guide their rational metabolic engineering. Here, we explore acetogen gas fermentation using physiological, metabolomics, and transcriptomics data for Clostridium autoethanogenum steady-state chemostat cultures grown on syngas at various gas-liquid mass transfer rates. We observe that C. autoethanogenum shifts from acetate to ethanol production to maintain ATP homeostasis at higher biomass concentrations but reaches a limit at a molar acetate/ethanol ratio of ∼1. This regulatory mechanism eventually leads to depletion of the intracellular acetyl-CoA pool and collapse of metabolism. We accurately predict growth phenotypes using a genome-scale metabolic model. Modeling revealed that the methylene-THF reductase reaction was ferredoxin reducing. This work provides a reference dataset to advance the understanding and engineering of arguably the first carbon fixation pathway on Earth.

overall_design: RNA sequencing of syngas-grown Clostridium autoethanogenum at four steady-state biomass concentrations; 12 samples in total with various number of biological replicate samples

first: Renato

middle: D

last: Lemgruber

first: Kieran

last: Maeghan

first: Robin

middle: W

last: Palfreyman

first: James

last: Behrendorff

first: Tanus

last: Abdalla

first: Björn

last: Heijstra

first: Ryan

last: Tappel

first: Michael

last: Köpke

first: Lars

last: Nielsen

first: Esteban

last: Marcellin


title: CD95/Fas increases stemness in cancer cells by inducing a STAT1 dependent Type I interferon response [ChIP-seq]

status: Public on Feb 16 2017

summary: CD95 was found to be important for both the formation of CSCs and their maintenance.  Using a stable isotope labeling by amino acids in cell culture (SILAC) analysis  we have now identified STAT1 as a critical gene that mediates the CSC-driving activity of CD95.  We report that chronic stimulation of CD95 by either agonist antibodies, soluble CD95L or stably  expressed membrane CD95L causes both serine and tyrosine phosphorylation of STAT1 and activation  of STAT1 regulated genes. The genes most significantly induced were part of an interferon (IFN)-related  DNA damage resistance signature (IRDS) recently identified in a radiation resistant squamous cell  carcinoma cell line Nu61 when compared to parental SCC61 cells. The IRDS was found to strongly correlate with therapy resistance (chemotherapy and radiation) in multiple cancer cells as well as in 5 human  primary cancers. We now report that CD95 stimulation of breast cancer cell lines or the SCC61 cells induces  the upregulation of Type I IFNs that bind to both Type I receptors IFNAR1 and IFNR2 resulting in activation  of JAK kinases, activation of STAT1 and induction of a number of STAT1-regulated genes. This process can be  inhibited by active caspases. Consequently, we identified Type I IFNs as drivers of cancer stemness.  Knockdown of STAT1 using either siRNAs or shRNAs, or deleting two independent sites in the STAT1 gene in MCF-7  cells using the CRIPSR/Cas9 gene editing system resulted in a loss of the ability of CD95 to increase stemness.  This identifies STAT1 as a critical mediator of the CSCs-inducing activity of CD95. androgen receptor (AR) activation independently of androgen. We have previously reported that AR can directly repress the expression of many target genes, one of which is NOV/CCN3. Here we show that NOV, primarily localized in the cytoplasm, physically interacts with AR at its Nterminus and sequesters AR and AR variants in the cytoplasm, thereby reducing AR chromatintargeting. This negative feedback loop, however, is disrupted in CRPC due to epigenetic silencing of NOV by the  Polycomb group protein EZH2, rendering AR transcriptional activities and drug-resistant prostate cancer  progression. Our findings thus suggest a working model wherein AR-repressed genes critically prevent  CRPC through negative feedback loops inhibiting AR signaling.

overall_design: One samples per condition

first: Abdul

middle: S

last: Qadir

first: Paolo

last: Ceppi