title: Spermidine synthase regulates extracellular vesicle secretion in castration resistant prostate cancer.

status: Public on Jun 21 2020

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

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

institute: National cancer center research institute

summary: Extracellular vesciles (EVs) have an important role in the tumor progression. However, the precise regulatrory mechanisms of EV secretion has not been clarified yet. We performed quantitive high-throughput screening to eluciade the key miRNAs for EV biogenesis in castration resistant prostate cancer (CRPC) using 22RV1 cells, and miR-1908 was selected as the miRNA regulating EV biogenesis in CRPC. To identify the genes that could be targeted by miR-1908, we performed mRNA micorarray analysis in 22RV1 after transfected of miR-1908 mimic or control miRNA.

overall_design: 22RV1 cells were seeded into 6-well plates, and 48 hours later, the transfection of miR-1908 mimic or controls was accomplished with the DharmaFECT Transfection Reagent 1 (Dharmacon) according to the manufacturer’s protocol. After 24 hours, the CM was changed to Advanced DMEM medium containing 2 mM L-glutamine without an antibiotic-antimycotic. Total mRNAs were extracted from the 22RV1 cells 48 hours after the medium change.  We used Agilent microarray chip (SurePrint G3 Human GE v3).

first: Fumihiko

last: Urabe

first: Nobuyoshi

last: Kosaka

first: Yurika

last: Sawa

first: Kagenori

last: Ito

first: Takahiro

last: Kimura

first: Shin

last: Egawa

last: Ochiya


title: The circadian PRRs quintet orchestrates photoperiodic responsive hypocotyl growth by transcriptionally repressing PIF4/PIF5 in Arabidopsis

city: Beijing

first: Lei

last: Wang

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

country: China

institute: insitute of botany, chinese academy of sciences

type: Expression profiling by high throughput sequencing

summary: Functional analysis of TOC1 and PRR5 in Arabidopsis

overall_design: We analyzed the transcriptomic profile of Col-0 and toc1-21 prr5-1 double mutant using 10-day-old seedlings. Three biological replicates were performed with the tissues harvesting at ZT15.

last: Li

first: Yuanyuan

last: Zhang


title: RNA aptamers specific for  IL4-treated MSC2 cell line

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: We performed an unsupervised, high-throughput (HT) sequencing-cell SELEX (systematic evolution of ligands by exponential enrichment) using the MDSC-derived cell line MSC2. Specifically untreated MSC2 and IL4 treated MSC2 were used as negative and positive selector respectively. Selection was started from a 5 ug of 40bp variable region linked to two constant region.

overall_design: HT-SELEX across 11 cycles for the selection of RNA aptamers

first: Jimmy

last: Caroli

first: Paolo

last: Serafini


title: Polycomb proteins, Ezh1 and Ezh2, co-regulate chromatin accessibility and nephron progenitor cell lifespan

status: Public on Jun 22 2020

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: Louisiana

address: 1430 Tulane Avenue

department: Pediatric Nephrology

country: USA

institute: Tulane University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Bulk ATAC_seq on GFP expressing FACS-isolated cells from E16.5 and P0  Six2TGC and compound Ezh1 and Ezh2 mutant kidneys( Six2TGC_Ezh2-/- , Ezh1+/-; Six2TGC_Ezh2-/-; and Ezh1-/- ;
scRNA-seq analysis of NPCs (Six2/GFP+ cells) from E16.5 as well as P2 kidneys. Genotypes analyzed:  Six2TGC (E16.5&P2),  Six2TGCEzh2-/- (E16.5),   Ezh1+/-;Six2TGCEzh2-/- (E16.5),  and Ezh2-/-;Six2TGCEzh2-/- (E16.5)
Six2/GFP+ nephron progenitor cells (NPCs) give rise to all epithelial cell types of the nephron, the filtering unit of the kidney.  NPCs have a limited lifespan and are consumed near the time of birth.   Pre-term birth or prenatal stress further shorten the lifespan of NPCs and result in nephron deficit and chronic kidney disease.  Accordingly, there is a pressing need to better understand the factors that regulate NPC lifespan in order to develop novel regenerative strategies.  Epigenetic factors are implicated in maintenance of organ-restricted progenitors such as NPCs, but the chromatin-based mechanisms are not well understood. In this study, we examined the role of the H3K27 methyltransferases, Enhancer of zeste (Ezh1 and Ezh2), in NPC maintenance using a combination of gene targeting, chromatin profiling, and single-cell RNA analysis.  We find that Ezh2 expression correlates with NPC growth potential, and that Ezh2 is the dominant H3K27 methyltransferase in NPCs and epithelial descendants. Surprisingly, NPCs lacking H3K27me3 maintain their progenitor state albeit cycle slowly leading to formation of fewer nephrons.  Unlike Ezh2 loss-of-function, dual inactivation of Ezh1 and Ezh2 triggers overexpression of the transcriptional repressor Hey1 and downregulation of Six2 and result in unscheduled activation of Wnt4-driven differentiation, early termination of nephrogenesis and severe renal dysgenesis.  Double-mutant NPCs also overexpress the Six family member, Six1. However, in this context, Six1 is unable to access the closed Six2 enhancer and fails to maintain NPC stemness.  At the chromatin level, Ezh1 and Ezh2 act by restricting accessibility of AP1 factors to their genomic binding motifs and their absence provokes a regulatory landscape akin of differentiated and non-lineage cells.  We conclude that Ezh2 is required for NPC renewal potential, while maintenance of NPC lifespan and tempering the differentiation program require cooperation of both Ezh1 and Ezh2.

overall_design: Chromatin accessibility and transcriptomic profiling of Ezh1 and Ezh2 mutant Six2-positive cap mesenchyme cells at E16.5 and P0.

first: S


title: RNA-Seq and ChIP-Seq profiling of ELF3, an prion-like domain-containig in ELF3 that functions as a thermosensor in Arabidopsis.

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

country: United Kingdom

institute: Cambridge University

summary: Temperature is a major environmental variable governing plant growth and development. ELF3 contains a polyglutamine (polyQ) repeat 8–10, embedded within a predicted prion domain (PrD). We find the length of the polyQ repeat correlates with thermal responsiveness. Plants from hotter climates appear to have lost the PrD domain, and these versions of ELF3 are stable at high temperature and lack thermal responsiveness. ELF3 temperature sensitivity is also modulated by the levels of ELF4, indicating that ELF4 can stabilise ELF3 function. This RNA-Seq dataset provides evidence for the hypothetical ELF3 function of temperature sensing .

overall_design: Single samples were taken at each time point. RNA-Seqs and ChIP-Seqs were performed for different genotypes at different temperature and objective time.

first: Jaehoon

last: Jung

first: Katja

last: Jaeger

first: Feng

last: Geng


title: Transcriptomic profiling of 62 breast cancer cell lines and PDX models

city: Boston

first: Kartik

last: Subramanian

address: 200 Longwood Avenue

institute: Harvard Medical School

summary: 62 breast cell lines composed of 27 Triple negative breast cancers (TNBC), 5 Non malignant (NM) lines, 14 Hormone receptor positive (HR+) and 16 Her2 amplified lines (Her2amp) were profiled

overall_design: mRNA levels of 62 breast cancer cell lines were profiled at baseline i.e in the absence of perturbation. 6 cell lines were profiled in biological duplicate and 2 cell lines were profiled in triplicate for a total of 72 samples

first: Caitlin

first: Sarah

last: Boswell

first: Marc

last: Hafner

first: Maulik

first: Chris

last: Chen

first: Peter

middle: K

last: Sorger


title: In-vivo inhibition of Fgfr2b signalling in embryonic whole mouse lungs at E14.5

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: In this experiment we inhibited FGF signalling in E14.5 mouse lungs by using a dominant negative mouse model. We are interested in assessing the genetic regulation by FGF signalling at this stage of lung development.  Specifically, we used a tetracycline controlled transcriptional activation model (Tet(o)) to manipulate FGF signalling. Genetically modified male mice that expressed a reverse tetracycline-controlled trans activator (rtTA) on the Rosa26 locus and a soluble FGFR2b on the Tet(o) promoter (Tet(o)sFgfr2b) (B6.Cg-Gt(ROSA)26Sortm1.1(rtTA,EGFP)NagyTg(tetO-Fgfr2b/Igh)1.3Jaw/sbel), were crossed with females lacking the Tet(o)sFgfr2b allele. Pregnant females were injected with doxycycline intraperitonally at E14.5. Doxycycline then induced the transcription soluble FGFR2b in the embryos, which inhibited FGF signalling by sequestering FGF ligands, preventing them from binding to the native FGFR2b receptor. We harvested embryonic lungs after 9 hrs of inhibition. We took the left lobe of each sample for RNA isolation. We set-up our matings so that 50% of the embryos in a litter were expected to contain the soluble FGFR2b. The remaining littermates will serve as the control group. We will compare the gene expression profiles of the experimental embryonic lungs with those of littermate controls.

overall_design: 2 groups, each with 4 biological replicates

first: Cho-Ming

last: Chao


title: The major pre- and post-menopausal estrogens play opposing roles in obesity driven mammary inflammation and breast cancer development

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

summary: Purpose: The goals of this study : Estrone(E1) vs Estradial (E2) in breast cancer inflammatory signaling and breast cancer progression.  Is HSD17B14 that convert E2 to E1 the oncogene.

overall_design: RNA seq : 1)CFBS,E1 Vs E2 at 10nM treatment to MCF7.2)cFBS,T, T+E1 Vs T+E2. 3)Control Vs HSD17B14. 4) E1,HSD17B14 +E2, HSD17B14 +E1 Vs E2

first: Joyce

middle: M

last: Slingerland

first: Rehana

last: Qureshi


title: Expression data from spleen-derived and tumor-induced CD11b+ MDSC

first: Silvio

last: Bicciato

summary:
CD11b+ myeloid-derived suppressor cells (MDSCs) have been shown to become activated at the tumor site and acquired a more suppressive phenotype compared to the splenic counterpart. This activated status promotes cancer progression by creating an immune suppressive niche around the tumor, by providing nourishment to the neoplastic cells, and by promoting metastases. To start understanding the differences between splenic and tumor infiltrating CD11b, genome-wide transcriptome analysis was performed.
We used gene expression analysis to identify those factors, secreted by tumor-infiltrating MDSC, which could drive emathopoiesis. Moreover, we compare gene expression profile of tumor-induced MDSC, obtained from either the spleen or the tumor infiltrate of tumor-bearing mice.

overall_design: CD11b+ cells were immunomagnetically enriched from various murine tissues and experimental conditions. cRNA samples were prepared according to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004, and hybridized to the Affymetrix GeneChip MOE430 2.0 array which contains more than 45,000 probe sets, representing more than 34,000 genes. CD11b+ cells obtained from the spleen of healthy BALB/c mice were used as reference sample for tumor induced CD11b+ MDSC, enriched from either the spleen or the tumor infiltrate of tumor-bearing mice.

first: Paolo


title: Expression data from myeloid-derived suppressor cells (MDSCs)

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

overall_design: Refer to individual Series


title: Transcriptome Sequencing Revealed that Knockdown of FOXL2 Affects Cell Proliferation, Cycle, and DNA Replication in Chicken pre-ovulatory Follicles Cells

status: Public on Jun 20 2020

city: Wuhan

first: Wei

last: Luo

state: Hubei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province

institute: Huazhong Agricutural University

summary: Forkhead box L2 (FOXL2) is a single-exon gene encoding a forkhead transcription factor, which is mainly expressed in the ovary, eyelids and pituitary gland. FOXL2 plays an essential role in ovarian development. To reveal the effects of FOXL2 on biological process and gene expression of ovarian granulosa cells (GCs), we established stable FOXL2-knockdown GCs and then analyzed using transcriptome sequencing. It is observed that knockdown the FOXL2 affects the biological processes of cell proliferation, DNA replication, apoptosis and cell cycle. In which, the FOXL2 knockdown promoted cell proliferation and DNA replication, decreased cell apoptosis, and promoted mitosis. In addition, by comparing the transcriptome by FOXL2 knockdown, we found a serious of DEGs and their related pathways. These results indicated that, through mediating these genes and pathways, the FOXL2 might induce the cell proliferation, cycle, and DNA replication, and play a key role during ovarian development and maintenance.

overall_design: Sixteen mRNA profiles of primary granulosa cells which were transfected with FOXL2-specific siRNA (FOXL2-siRNA) or NC nonsense siRNA (NC-siRNA) respectively.were generated by deep sequencing, in triplicate, using Illumina Hiseq X-ten platform.Illumina Hiseq X-ten platform.

first: Yanzhang

last: Gong


title: Clark RNA-Seq Sample from Immature Seed Coats

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: 1 RNA-Seq sample from Clark (PI548532) from seed coats of 100-200mg immature seeds

overall_design: 1 sample total, no replicates

middle: O

first: Young

middle: B

last: Cho

middle: I

last: Jones


title: Gfi1 knockout in Raw264.7 macrophages

city: Xinxiang

first: Qianqian

last: Zheng

address: 601 Jinsui Road

institute: Xinxiang Medical University

summary:
Gfi1 is a transcription factor broadly participate in differentiation of immune cells and loss of Gfi1 could result in severe neutrophil deficiency.
To gain insight into the consequences of lack of Gfi1 on a genome-wide level, we conducted genome-wide transcriptome profiling in Wide-type (WT) and Gfi1–/– Raw264.7 macrophage cells using Affymetrix Mouse 3’ IVT microarrays

overall_design: 7 samples are analyzed. Sample1-3 are Wildtype Raw264.7 cells as control group.Sample1-3 are Gfi1 Knockout cells.

first: Yinming

last: Liang


title: Identification of GLYMA.04G093300 binding sites in soybean early maturation embryos

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.04G093300  in early maturation embryos using ChIP-seq.

overall_design: Identification of GLYMA.04G093300 binding sites in soybean embryos at the early maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates, using two different antibodies.  A total of 6 samples were sequenced using the Illumina HiSeq2500 platform.

first: Julie

last: Pelletier

first: Leonardo

last: Jo

first: Rie

last: Uzawa

first: Min

first: Robert

last: Golberg

middle: J


title: Identification of GLYMA.07G038400 binding sites in soybean early maturation embryos

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.07G038400  in early maturation embryos using ChIP-seq.

overall_design: Identification of GLYMA.07G038400 binding sites in soybean embryos at the early maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 4 samples were sequenced using the Illumina HiSeq2500 platform.

last: Chen


title: Single cell sequencing of Tomato+ cells in hindlimb muscles from Prrx1-CreERT;Tomato mice with the treatment of Tamoxifen for 3 days

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: We report single-cell RNA-seq reveals gene signatures associated with hindlimb muscles from adult Prrx1-CreERT.

overall_design: Tomato+ cells' mRNA profiles of hindlimb muscles from adult Prrx1-CreERT;Tomato mice with the treatment of Tamoxifen for 3 days were generated by single cell  sequencing

first: Baojie

last: Li


title: Growth hormone resistance exacerbates cholestasis-induced murine liver fibrosis

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary:
Growth hormone (GH) resistance has been associated with liver cirrhosis in humans but its contribution to the disease remains controversial. In order to elucidate whether GH resistance plays a causal role in the establishment and development of liver fibrosis, or rather represents a major consequence thereof, we challenged mice lacking the Growth hormone receptor gene (Ghr-/-, a model for GH resistance) by crossing them with Mdr2 knockout mice (Mdr2-/-), a mouse model of inflammatory cholestasis and liver fibrosis.  Ghr-/-;Mdr2-/- mice showed elevated serum markers associated with liver damage and cholestasis, extensive bile duct proliferation and increased collagen deposition relative to Mdr2 -/- mice, thus suggesting a more severe liver fibrosis phenotype. Additionally, Ghr-/-;Mdr2-/- mice had a pronounced down-regulation of hepato-protective genes Hnf6, Egfr and Igf-1, and significantly increased levels of ROS and apoptosis in hepatocytes, compared to control mice.
Moreover, single knockout mice (Ghr-/-) fed with a diet containing 1% cholic acid displayed an increase in hepatocyte ROS production, hepatocyte apoptosis and bile infarcts compared to their wildtype littermates, indicating that loss of Ghr renders hepatocytes more susceptible to toxic bile acid accumulation. Surprisingly, and despite their severe fibrotic phenotype, Ghr-/-;Mdr2-/- mice displayed a significant decrease in tumour incidence compared to Mdr2-/- mice, indicating that loss of Ghr signaling may slow the progression from fibrosis/cirrhosis to cancer in the liver.

overall_design: Control: Liver WT; MDR2-/-: Liver MDR2 knock-out. GHR-/-: Liver GHR knock-out. GHR-/-MDR2-/-: Liver GHR/MDR2 double knockout. Livers were collected at 8 weeks of age. Three liver were pool per genotype

first: Patricia

last: Stiedl

first: Emilio

last: Casanova


title: A Comprehensive Transcriptional Profiling of Pepper Responses to Root Knot Nematode

city: Gainesville

first: Weiming

last: Hu

address: 1881 Natural Area Dr.

department: Entomology and Nematology

institute: University of Florida

summary: We sequenced the transcriptomes of resistant and susceptible cultivar roots uninoculated and with RKN M. incognita, over three time points; 1-, 4-, and 7-days post inoculation. Over 300 million high quality reads from 36 samples were mapped to the pepper reference genome. Comparing inoculation and resistance profiles revealed generic biotic stress responses and specific nematode resistance responses. Comparisons along the time course revealed resistance responses are often induced early in the infection process and a large portion of these are restricted to chromosome P9, encoding the known nematode resistance loci

overall_design: There are 35 samples included, each treatment has three replicates, negative control samples were also included into each treatment

first: Vincent

last: Colantonio

first: Krista

last: Kingsbury

first: Peter

last: DiGennaro


title: RNA-seq analysis of mTOR{delta}APC and WT lung and spleen APC subsets

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Purified CD11b+, Alveolar macrophage and HDM induced inflammatory DCs from WT and mTOR{delta} APC mice were profiled by RNA-seq to understand mTOR-dependent gene expression

overall_design: FACS purified CD11b+, Alveolar macrophage and HDM induced inflammatory DCs were profiled by RNA-seq

first: Charles

last: Sinclair

first: Gayathri

last: Bommakanti

first: Steven

last: Bosinger

first: Bali

last: Pulendran

first: Nirav

last: Patel

first: Greg


title: Expression data from MSC2 cells treated with IL4

first: Silvio

last: Bicciato

summary:
The immortalized myeloid-derived suppressor cells MSC2 (Apolloni et al. JI 2000) are a useful tool to explore the mechanisms by which MDSCs suppress tumor immunity. This immortalized MDSC cell line acquired the capacity to suppress T cell proliferation and CTL activity only after incubation with Interleukin 4.
We used microarrays to detail the global program of gene expression that differentiate the non-suppressive untreated MSC-2 from the suppressive IL-4 treated MSC2.

overall_design: CD11b+Gr1+ cells isolated from the spleens of immunosuppressed mice were immortalized using a retrovirus encoding for v-myc and v-raf. The MSC2 cell line was selected from the empirical screening of immortalized clones because of its characteristic of becoming immune suppressive only after treatment with IL-4.

first: Paolo

last: Serafini

first: Vincenzo

last: Bronte


title: Development of gene expression signatures for WT (Hif1afl/fl) mice and VSMC-specific HIF1α disruption (Hif1a△SMC) mice VSMCs treated with 150μM CoCl2 for 24hours

city: beijing

first: Dan

last: Qi

state: Please Select

address: No.10 Xitoutiao Road, YouAnmen

institute: Capital Medical University

summary:
HIF1α is a key regulator of hypoxia, however, the changes of its target genes in VSMCs under hypoxia  were unknown.  CoCl2 is a chemical hypoxia agent which leads to the stabilization of HIF1-α and the expression of hypoxia responsive genes, Therefore Hif1afl/fl and Hif1a△SMC VSMCs were treated with CoCl2 and performed microarray analysis.
We used microarray to detail the gene expression of WT (Hif1afl/fl) mice and VSMC-specific HIF1α disruption (Hif1a△SMC)  mice VSMCs treated with 150μM CoCl2 for 24hours.

overall_design: RNA extraction from WT (Hif1afl/fl) mice and VSMC-specific HIF1α disruption (Hif1a△SMC) mice VSMCs treated with 150μM CoCl2 or an equal volume of  PBS for 24 hours and hybridization on Agilent microarrays. The VSMCs were devided into four groups: 1. Hif1afl/fl VSMCs treated with PBS for 24 hours, 2. Hif1a△SMC VSMCs treated with PBS for 24 hours, 3. Hif1afl/fl VSMCs treated with CoCl2 for 24 hours, 4.Hif1a△SMC VSMCs treated with CoCl2 for 24 hours.

first: Aijuan

last: Qu


title: Rates of acquisition of de novo mutations in human pluripotent stem cells under different culture conditions

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary:
The presence of mutations in human pluripotent stem cells (PSC), whether embryonic stem (ESC) cells, or induced pluripotent stem (iPSC) cells, is a concern for their safe use in therapeutic applications.  Indeed, in one case, a potential trial of retinal pigment cells from an autologous iPS cell line was abandoned because the cells carried a mutation of unknown significance (Mandai et al. 2017).  Certainly some such variants are likely to have been present in the embryos or somatic cells from which particular PSC were derived and can be classed as ‘variants of origin’ (Amps et al. 2011).  However, the propensity of PSC to acquire genetic variants on prolonged passage poses additional concerns, not only because of the difficulty for their early detection (Baker et al. 2016), but also their selective growth advantages might presage malignant potential (Andrews et al. 2017).
In this study, to determine the rate and types of mutation that occur during culture of human PSC, we have used a cloning strategy coupled with whole genome- and RNA-sequencing to compare two well characterized, clinical grade human ES cell lines, as well as the effects of culture in the presence of a Rho kinase inhibitor, now commonly used in routine culture of human PSC, and of culture under low oxygen (5% O2) conditions.  We have tested whether the mutations are randomly distributed throughout the genome or clustered in regions related to chromatin structure and gene expression.  Our results indicate that the mutation rate is low compared to estimates in somatic or cancer cells, and can be further reduced by culture under low oxygen conditions. Furthermore, the mutational signature of human PSC is similar to that of other cultured human cells, but low oxygen culture does alter the frequency of some types of base pair change associated with oxidative damage.

overall_design:
For these experiments, we chose two male human ES cell lines, MShef4 and MShef11 that we derived under GMP-like conditions suitable for their potential clinical use in regenerative medicine.  During their initial derivation, banking, and characterisation, no karyotypic variants of MShef4 had been observed, and it was designated, a priori, as a genetically stable line.  By contrast, several cultures of MShef11, though not those used to produce master and working banks, were found to contain chromosomal aberrations and so this line was designated, a priori, as genetically less stable.  To assess the mutation rates in these cells, the strategy we adopted was to produce a clonal subline that was karyotypically diploid, grow that clone for a defined period, and then produce a series of subclones that were subjected to whole genome genetic, epigenetic and transcriptional analysis.
In the case of MShef4, we initially isolated clones by single cell deposition.  Following cytogenetic and SNP array assessment for the absence of any gross genetic or karyotypic changes at the earliest possible time during their expansion, one clone was selected for further analysis.  This was grown under our standard growth-conditions (see Methods for details) for a total of 109 days following initiation, after which 20 subclones were isolated and expanded to provide DNA and RNA for sequencing.
In the case of MShef11 we compared mutation rates of cells grown under the standard conditions used for MShef4, with mutation rates of cells grown in either the presence of the Rho Kinase inhibitor, Y27632, or under low oxygen (5% O2) conditions.  To achieve this, we produced an initial MShef11 clone that was screened by SNP array and karyotyping to exclude gross genetic variants, and then re-cloned as soon as possible, with single cells being deposited directly for growth under one of the three conditions (Figure 1).  These clones were again screened by SNP array and karyotyping as early as possible to exclude gross variants, and genetically normal clones carried forward for further analysis.  Two such clones were grown under standard conditions, and two were grown in the presence of the Rho Kinase inhibitor at each passage, for 111 days and 115 days respectively. We then produced 10 subclones from each parent clone for sequence analysis – i.e. 20 subclones for each culture condition but in two cohorts.  In the case of low oxygen, two clones were grown for 111 days but we were only able to produce nine viable subclones from one of these. Therefore, a further cohort of 12 subclones was derived from a continuation culture of the first low oxygen clone, but only after it had been removed from low oxygen at 111 days and maintained under standard conditions for a further 28 days
Bulk samples are defined as cultures of MShef4 and MShef11 that have been expanded from the same cell bank as was used to create the clones and subclones, but are not themselves clonal cultures, and have been expanded under 'standard' conditions as described in the methods.

first: Oliver

last: Thompson

first: Ferdinand

last: von Meyenn

first: Zoe

last: Hewitt

first: John

last: Alexander

first: Andrew

last: Wood

first: Richard

last: Weightman

first: Sian

last: Gregory

first: Simon

last: Andrews

first: Ivana

last: Barbaric

first: Harry

middle: D

last: Moore

first: Wolf

last: Reik

first: Marta

last: Milo

first: Serena

last: Nik-Zainal

first: Kosuke

last: Yusa

middle: W


title: Effect of dioxin on maternal rats at postpartum day 7

city: Hadano

first: Tomoki

last: Takeda

address: Hirasawa 2445

country: Japan

institute: Japan Bioassay Research center


title: Androgens Regulate Ovarian Gene Expression through Modulation of H3K27me3 in Granulosa Cells

status: Public on Jun 19 2020

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

institute: Michigan State University


title: RNA-seq of the brain of Nothobranchius furzeri at different time points and strains (smallRNA)

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

type: Non-coding RNA profiling by high throughput sequencing

summary: Comparison of temporal gene expression profiles. The RNA-seq data comprises  different strains (GRZ and MZM-0410) and different ages

overall_design: 16 samples in 4 groups: GRZ 5 wph (4 samples), MZM-0410 5wp (4 samples), MZM-0410 12 wph (4 samples), MZM-0410 39 wph (4 samples)

first: Alessandro

last: Cellerino

last: Ori

first: Erika

last: Kelmer-Sacramento

first: Mario

last: Baumgart

first: Mariateresa

last: Mazzetto

first: Cinzia

last: Caterino


title: Androgens Regulate Ovarian Gene Expression through Modulation of H3K27me3 in Granulosa Cells [RNA-Seq]

summary: This study reports androgen-induced gene expression in granulosa cells of the ovary and provides a molecular insight of how androgens regulate granulosa cell gene expression through modulating the epigenetic mark H3K27me3.

overall_design: RNA-Seq of androgen-induced modifications of granulosa cells in mice.

first: Sambit

last: Roy


title: Extensive proteomic and transcriptomic changes quench the TCR/CD3 activation signal of latently HIV-1 infected T cells

city: Birmingham

first: Olaf

last: Kutsch

state: AL

department: Medicine

institute: University of Alabama at Birmingham

summary: HIV-1 latency is a critical hurdle to a cure for HIV-1 infection, but our understanding of the molecular biology of latency control is still incomplete. We provide experimental evidence that HIV-1 infection of primary T cells and T cell lines generates a substantial amount of TCR/CD3 activation-inert latently infected T cells. Proteomic and genome-wide RNA-level analysis comparing CD3-responsive and CD3-inert latently HIV-1 infected T cells, followed by software-based data integration suggested two phenomena to govern CD3-inertness: (i) the presence of extensive transcriptomic noise that affected the efficacy of CD3 signaling and (ii) defined changes to specific signaling pathways. Validation experiments demonstrated that compounds known to increase transcriptomic noise further diminished the ability of TCR/CD3 stimulation to trigger HIV-1 reactivation. Conversely, targeting specific central nodes in the generated PINs such as STAT3 improved the ability of TCR/CD3 activation to trigger HIV-1 reactivation in T cell lines and primary T cells. The data emphasize that latent HIV-1 infection is largely the result of extensive, stable biomolecular changes to the signaling network of the host T cells harboring latent HIV-1 infection events. We discuss the implications of these findings for the idea of using single drug therapies to trigger HIV-1 reactivation in the latent T cell reservoir in patients.

overall_design: Gene expression profiling of two replicates each: uninfected Jurkat cells, latently HIV-1 infected CD3 responsive JWEAU-A10 cells, and latently HIV-1 infected CD3 unresponsive JWEAU-C6 cells.

first: Eric

last: Carlin

first: Braxton

last: Greer

first: Alexandra

last: Duverger

first: Frederic

last: Wagner

first: David

last: Moylan

first: Alexander

last: Dalecki

first: Shekwonya

last: Samuel

first: Mildred

last: Perez

first: Kelsey

last: Lowman

first: Steffanie

last: Sabbaj


title: Effect of dioxin on hypothalamic mRNAs in maternal rats at postpartum day 7

first: Tomoki

last: Takeda

summary: We found that oral administration of TCDD (1 µg/kg) to pregnant rats on gestational day 15 suppressed maternal production of prolactin, a pituitary hormone essential for nursing including milk production, during the lactational stage. To comprehensively investigate genes linked to the lower prolactin expression, we performed a DNA microarray analysis in the hypothalamus, which regulates the pituitary prolactin synthesis, of lactating dam rats.

overall_design: Total RNAs were extracted from the hypothalami of the control and TCDD-exposed dam rats  at postpartum day 7 (each N=4), and their cDNAs were applied to the analysis using Agilent Whole Rat Genome Microarray 4×44K version 3

first: Misaki

last: Fujii

first: Hideyuki

last: Yamada


title: Androgens Regulate Ovarian Gene Expression through Modulation of H3K27me3 in Granulosa Cells [ChIP-seq]

first: Aritro

last: Sen

overall_design: ChIP-seq studies with H3K27me3 antibodies to identify the ovarian genes and their enhancer regions that are regulated by androgen-induced regulation of H3K27me3 mark.


title: bulk mRNA sequencing of splenic Red Pulp Fibroblasts (RPF) and lymph node Fibroblastic Reticular Cells (FRC)

city: Marseille Cedex 9

first: Marc

last: Bajenoff

address: Parc Scientifique et Technologique de Luminy 163 avenue de Luminy Case 906

country: France

institute: CIML – Centre d’Immunologie Marseille-Luminy

summary: bulk mRNA sequencing was used to compare the fibroblastic nature of RPF and FRC transcriptomes, and the transcriptionnal response induced  in RPF by Red Pulp Macrophages depletion

overall_design: In total, 45,000 FRC were isolated from 78 lymph nodes from 6 untreated Wt1CreERT2 RosatdTomato CD64DTR mice, 45,000 RPF were isolated from 6 spleens from 6 untreated Wt1CreERT2 RosatdTomato CD64DTR mice and 45,000 RPF were isolated from 6 spleens from 6 diphteria-toxin-treated Wt1CreERT2 RosatdTomato CD64DTR mice. Each sample represents data from two mice.

first: Alicia

last: Bellomo

first: Lionel

last: Spinelli


title: Gene expression profiles of FoxO4 overexpressing TH1 cells.

city: Beijing

first: Chen

last: Dong

state: Beijing

address: 30 Shuangqing Rd

institute: Tsinghua University

summary: To assess the function of FoxO4 in processes of TH1 differentiation, we have performed a whole genome microarray assay to discover the significant changed genes in normal and FoxO4 overexpressing TH1 cells.

overall_design: Isolated naive CD4+CD25−CD62LhiCD44lo T cells from 8-week-old C57BL/6 mice were activated with anti-CD3 and anti-CD28. 20 hours later, cells were infected with RV or RV-FoxO4, and cultured in TH1 polarizing condition for 72 hours. Next, total RNA was extracted from sorted GFP positive cells, and Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray were used to probe global gene expression changes.

first: Hui

last: Wang

first: Yunfei


title: Effect of dioxin on pituitary mRNAs in maternal rats at postpartum day 7

summary: We found that oral administration of TCDD (1 µg/kg) to pregnant rats on gestational day 15 suppressed maternal production of prolactin, a pituitary hormone essential for nursing including milk production, during the lactational stage. To comprehensively investigate genes linked to the lower prolactin expression, we performed a DNA microarray analysis in the pituitary of lactating dam rats.

overall_design: Total RNAs were extracted from the pituitaries of the control and TCDD-exposed dam rats  at postpartum day 7 (each N=4), and their cDNAs were applied to the analysis using Agilent Whole Rat Genome Microarray 4×44K version 3


title: FoxO4 ChIP-Seq profiles of WT differentiated TH1 cells

summary: This study is to analyze genome-wide occupancy of FoxO4 in WT TH1 cells.

overall_design: Naive CD4+ T cells from spleens and lymph nodes were isolated from 8-week-old C57BL/6 mice using a BD FACSAria sorter and cultured in TH1 polarizing condition for 60 hours. ChIPed DNAs were prepared with Active Motif’s ChIP assay kit and subjected to library preparation using NEXTflexTM ChIP-Seq DNA Sequencing Kit. Finally, the DNA libraries were sequenced on an Illumina HiSeq2500 Sequencer.

first: Xiang

last: Chen


title: Foxo4 transcriptional factor represses TH1 cell differentiation and effector function by regulating Dickkopf-3 production

summary: Forkhead box O transcriptional factors, especially FoxO1 and FoxO3a, play critical roles in physiologic and pathologic immune responses. Here, in studies to explore the function of FoxO4 in lymphocyte biology, we showed that loss of FoxO4 in T cells promotes TH1 cell differentiation and augments the production of interferon-γ (IFN-γ) in vitro. Correspondingly, conditional deletion of FoxO4 in CD4+ T cells enhances T cell-specific responses to Listeria monocytogenes infection in vivo. Genome-wide occupancy and transcriptomic analyses identified DKK3 (encoding Dickkopf-3 protein) as a direct transcriptional target gene of FoxO4. Consistent with the FoxO-DKK3 relationship, recombinant DKK3 protein restored normal levels of IFN-γ production in FoxO4-deficient TH1 cells, through downregulation of Lef1 expression. Together, our data identify and validate a novel FoxO4-DKK3-LEF-1 axis in TH1 cell differentiation, providing an important insight and supplement for FoxO family proteins in T lymphocyte biology, and revealing a promising target for treatment of immune-related diseases.

overall_design: ChIP-Seq (input and FoxO4-specific ChIP) and Microarray (RV vs RV-FoxO4 infected TH1 cells)。


title: RNA-seq of the brain of Nothobranchius furzeri at different time points and strains

first: Marco

last: Groth

summary: Comparison of temporal gene expression profiles. The RNA-seq data comprises different strains (GRZ and MZM-0410) and different ages.

overall_design: 16 samples in 4 groups: GRZ 5 wph (4 samples), MZM-0410 5 wph (4 samples), MZM-0410 12 wph (4 samples), MZM-0410 39 wph (4 samples).

first: Alessandro

last: Cellerino

first: Erika

last: Kelmer-Sacramento

first: Mario

last: Baumgart

first: Mariateresa

last: Mazzetto


title: Acrylonitrile-mediated nascent RNA sequencing for transcriptome-wide profiling of RNA dynamics

first: Zonggui

address: No.5 Yiheyuan Road Haidian District

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

summary: RNA sequencing has greatly facilitated gene expression studies but are weak in studying temporal RNA dynamics. This issue can be addressed by profiling nascent RNAs. Here, we presented a NGS-compatible method for nascent RNA analysis in single-base resolution based on s4U cyanoethylation reaction. Our strategy can high-efficiently recover nascent RNA information from total RNAs. We validated our method by measuring RNA stabilities transcriptome wide in human cells. By capturing immediate gene expression changes, we successfully determined the direct gene targets of a G-quadruplex stabilizer, which has been regarded as potential antitumor drug. We also identified the influence of G-quadruplex stabilization to mRNA maturation. Furthermore, we found G-quadruplex stabilizer positively regulated the transcriptional activity of upstream antisense RNAs, uncovering its novel potential gene regulation pathway in vivo.

overall_design: total mRNA profiles of 4sU-labeled HEK293T cells (PDP-treated or PDP-untreated) were generated by deep sequencing, in duplicate, using HiSeq X Ten.

last: Zhou

first: Yuqi

first: Fan

last: Wu

first: Zhiyong

last: He


title: Myeloid ALX/FPR2 promotes revascularization during limb ischemia

city: Debrecen

first: Nikolaos

last: Giannakis

address: Egyetem ter 1

department: Department of Biochemistry and Molecular  Biology

country: Hungary

institute: University of Debrecen

summary: RNA-seq analysis of bone marrow derived macrophages stimulated with resolvin D1(RvD1)

overall_design: Total RNA was isolated with TRIZOL reagent according to the manufacturer’s recommendation. 20ug glycogen (Ambion) was added as carrier for RNA ethanol precipitation.

first: Brian

middle: E

last: Sansbury

first: Nikolas

first: Andreas

last: Patsalos

first: Matthew

last: Spite

first: Laszlo

last: Nagy


title: Lysine acetyltransferase Tip60 is required for hematopoietic stem cells maintenance

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: Hematopoietic stem cells (HSC) have the potential to replenish the blood system for the lifetime of the organism. Their two defining properties, self-renewal and differentiation, are tightly regulated by the epigenetic machineries. Here, using conditional gene knockout models, we demonstrate a critical requirement of lysine acetyltransferase 5 (also known as Tip60) for murine HSC maintenance both in the embryonic and adult stages, which depends on its acetyltransferase activity. Genome-wide chromatin and transcriptome profiling revealed that Tip60 co-localizes with c-Myc and that Tip60 deletion suppress the expression of Myc target genes, which are associated with critical biological processes for HSC maintenance, cell-cycle and DNA repair. Notably, acetylated H2A.Z (acH2A.Z) was enriched at the Tip60-bound active chromatin and Tip60 deletion induced a robust reduction in the acH2A.Z / H2A.Z ratio. These results uncover a critical epigenetic regulatory layer for HSC maintenance through Tip60 dependent H2A.Z acetylation to activate Myc target genes.

overall_design: Tip60 KO RNA-Seq and ChIP-Seq

first: Akihiko

last: Numata

first: Hui

last: Kwok

first: Qi-Ling

first: Vladimir

last: Angarcia

first: Rebecca

last: Hannah

first: Jihye

last: Park

first: Vaidehi

last: Krishnan

first: Touati

last: Benoukraf

first: Yanzhou

last: Zhang

first: Siqin

first: Robert

last: Welner

first: Motomi

last: Osato

first: Sudhakar

last: Jha

first: Berthold

last: Göttgens

first: Henry

last: Yang

first: Stefan

last: Bohlander

first: John

last: Lough

first: Deepak

last: Bararia

first: Daniel

middle: G

last: Tenen


title: Total RNA sequencing of pre- and post-heat shocked wild type, mpk1 knockout, rrp6 knockout and mpk1rrp6 double knockout strains

status: Public on Jun 18 2020

city: Los Angeles

first: Guillaume

middle: Francois

last: Chanfreau

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

summary: RNA-seq was performed to determine if Rrp6p plays a role with the cell wall integrity pathway to regulate the proper expression of genes during stress

overall_design: Analysis of gene expression of 4 different strains during heat shock. Each strain has 3 biological replicates. 2 Different heat shock times are tested for each sample as well as a non heat-shock control.

first: Charles

last: Wang

first: Igor

last: Mandric

first: Samuel

last: DeMario

middle: F


title: Transcriptomic Characterization of LIPA+/+ and LIPA-/- iPSC-derived Macrophages

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

summary: Using RNA-Seq, we examined the transcriptome profiles of human iPSC-derived macrophage (IPSDM) with knockout of the LIPA gene by CRISPR/Cas9 gene editing technologies.

overall_design: LIPA+/+ and LIPA-/- IPSDM were sequenced by Illumina HiSeq 2500 with poly-A selection

first: Hanrui


title: Expression data from Tg(Pcp2-L10a-Egfp) TRAP mice over postnatal mouse development. [Affymetrix 1]

first: Tom

middle: Samuel

last: Carroll

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: To model human cerebellar disease, we developed a novel, reproducible method to generate cerebellar Purkinje cells (PCs) from human pluripotent stem cells (hPSCs) that formed synapses when cultured with mouse granule cells and fired large calcium currents, measured with the genetically encoded calcium indicator jRGECO1a. Using translating ribosomal affinity purification (TRAP) to compare gene expression of differentiating hPSC-PCs to developing mouse PCs, we found hPSC-PCs to be most similar to late juvenile (P21) mouse PCs. Analysis of mouse PCs defined novel developmental expression patterns for mitochondria and autophagy associated genes, recapitulated in hPSC-PCs. We further identified species differences in gene expression and confirmed protein expression of CD40LG in native human, but not mouse PCs. This study provides a robust method for generating relatively mature hPSC-PCs with human specific gene expression and defines novel genetic features in comparison to the first comprehensive analysis of global gene expression patterns of postnatal mouse PC development.

overall_design: 15 samples of 5 postnatal mouse time points in triplicate.

first: David

last: Buchholz

first: Thomas

first: Arif

last: Kocabas

first: Xiaodong

last: Zhu

first: Hourinaz

last: Behesti

first: Phyllis

middle: L

last: Faust

first: Lauren

last: Stalbow

first: Yin

last: Fang

first: Mary

last: Hatten


title: Glycyrrhizic acid improves cognitive levels of aging mice by regulating T/B cell proliferation

first: Hailiang

last: Liu

institute: Tongji university

summary: We implemented transcriptomic analyses of blood of 12M mice; These mice with the treatment of Glycyrrhizic acid for 6 weeks.


title: Membrane potential limits growth and substrate utilization in C. bescii, alleviation dramatically improves productivity

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: Caldicellulosiruptor bescii is an anaerobic hyper thermophile that can utilize a wide range of substrates. However, inhibitors released from biomass can result in unfavorable growth conditions and limit bioconversion to products. Medium as well as intracellular pH are conditions critical for growth and prone to change in effect of fermentation end or by products such as, CO2, organic acids etc. Growth pH for C. bescii as currently reported is a narrow range of 6.8-7.3. In this study, we examined the physiological and systems level responses of C. bescii to growth at acidic pH. Samples collected from bottles, controlled batch, fed-batch and chemostat systems were subjected to growth, product and integrated omics profiling.  It was discovered that in batch reactors, lowering pH from 7.2 to 6.0 at the mid-log phase, led to a significant increase in growth and product yields. Time course transcriptomics data collected from these batch reactors was analyzed to try and get a better understanding of the underlying mechanisms for improved growth.

overall_design: Wild type strain DSM6725 was grown under batch fermentation conditions in two setups namely, control and treated fermenters in triplicates. In the control fermenter setup, cells were grown at pH 7.2 throughout the growth curve monitored whereas, in the treated fermenter setup, cells were grown at pH 7.2 until mid-log phase and pH was then lowered to 6.0 by acid addition. RNA-seq samples were collected at 5, 10, 30, 60 and 90 min time points post-acid addition from both control and treated fermenters.

first: Punita

last: Manga

first: Steven

last: Brown


title: Hsp70 affects memory formation and behaviourally relevant gene expression in Drosophila melanogaster.

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

summary: Heat shock proteins (Hsps), in particular Hsp70, play a central role in proteostasis in eukaryotic cells. Due to its chaperone properties, Hsp70 is involved in various processes both after stress and under normal physiological conditions. In contrast to mammals and many Diptera species, members of the Hsp70 family in Drosophila are constitutively synthesized at a low level and undergo dramatic induction after temperature elevation or other forms of stress. In the courtship suppression paradigm used in this study, Drosophila males that have been repeatedly rejected by mated females during courtship are less likely than naive males to court other females. Although numerous genes with known function were identified to play important roles in long-term memory, there is, to the best of our knowledge, no direct evidence implicating Hsp70 in this process. To eliminate this gap, we used D. melanogaster strains containing different hsp70 copy numbers, including strains carrying a deletion of all six hsp70 genes. Our investigations exploring the memory of courtship rejection paradigm demonstrated that a low constitutive level of Hsp70 is required for learning and the formation of short and long-term memories in males. The performed transcriptomic studies demonstrate that males with different hsp70 copy numbers differ significantly in the expression of a few definite groups of genes involved in mating and reproduction, as well as methionine metabolism and immune genes in response to rejection. Specifically, our analysis reveals several major pathways that depend on the presence of hsp70 copies in the genome and apparently participate in memory formation and consolidation, including the cAMP signalling cascade.

overall_design: Deep RNA sequencing of Drosophila melanogaster heads

first: A

middle: P

first: O

last: Zatsepina

first: S

middle: Y

last: Funikov

first: M

last: Evgenev


title: Expression data from Tg(Pcp2-L10a-Egfp) TRAP mice over postnatal mouse development.

first: Tom

last: Carroll

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

overall_design: Refer to individual Series


title: Expression data from Tg(Pcp2-L10a-Egfp) TRAP mice over postnatal mouse development. [Affymetrix 2]

overall_design: 2 samples of P7 mouse cerebellum, TRAP purified and unbound

first: David

last: Buchholz

first: Thomas

middle: S

first: Arif


title: Cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency

last: Goldstein

department: Institute for Genomic Medicine

institute: Columbia University Med Center

summary: We obtained cell-type-specific transcriptomic profiles from the neocortex and hippocampal brain regions of a mouse model of HNRNPU haploinsufficiency.

overall_design: Single cell profiles derived from 4 neocortical and hippocampal samples each: 2 heterozygous mutants and 2 wildtype littermates, one of each sex.

first: Sarah

middle: A

last: Dugger

first: Ryan

last: Dhindsa


title: Identification of ventricle-specific methylation patterns in cell-free DNA and correlation with myocardial apoptosis and acute cellular rejection after heart transplantation

city: Calgary

last: Greenway

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

summary: Increased levels of donor-derived cell-free DNA (dd-cfDNA) in recipient plasma have been associated with acute cellular rejection (ACR) after heart transplantation. DNA sequence differences have been used to distinguish between donor and recipient cfDNA but epigenetic differences could also potentially identify dd-cfDNA. This study aimed to assess the feasibility of using ventricle-specific methylation patterns in human cfDNA as an alternative biomarker for ACR in cardiac transplantation.

overall_design: Serial samples of plasma (n=24) were collected from adult heart transplant recipients undergoing routine endomyocardial biopsy (EMB) for post- transplant rejection surveillance. Publicly available methylomes and genomic DNA from various human tissues were leveraged to identify ventricle-specific differentially methylated regions of DNA (DMRs) detectable in isolated plasma cfDNA. Correlation of these novel DMRs with pathology-graded ACR was then validated in serial plasma samples.

first: Sabrina

last: Pattar

first: Mohammad

last: Aleinati

first: Fatima

last: Iqbal

first: Aiswarya

last: Madhu

first: Samuel

last: Blais

first: Xuemei

last: Wang

first: Frederic

last: Dallaire

first: Yinong

first: Debra

last: Isaac

first: Nowell

last: Fine

middle: C


title: Bacteriostatic effects of benzyl isothiocyanate on Vibrio parahaemolyticus: Transcriptomic analysis and morphological verification

city: Dalian

first: Ke

last: Zhang

address: NO.1 Light-Industry Garden, Ganjingzi Borough, Dalian 116034, China

institute: Dalian polytechnic university

summary: We investigated antibacterial activities of benzyl isothiocyanate (BITC) against V. parahaemolyticus by transcriptomic analysis and morphological verification. Treatment with 1/8MIC BITC resulted in 234 up-regulated genes and 273 down-regulated genes. In V. parahaemolyticus, we selected six genes that were significantly down-regulated from the transcriptome results and verified them using quantitative Real-time Polymerase Chain Reaction (qRT-PCR). The verification experiments indicated that the relative expressions of the six virulence genes VP0820, VP0548, VP2233, VPA2362, fliA and fliG were only 31.0%, 31.1%, 55.8%, 57.0%, 75.3%, and 79.9% of the control group, respectively. Among them, VP2233, fliA and fliG are related to flagella, and VP2362 can regulate a protein related to biofilm formation. From the morphological aspect, we verified that under the action of 1/8 MIC BITC, the swimming diffusion diameter of V. parahaemolyticus was significantly reduced by 14.9%, and biofilm formation was significantly inhibited. These results indicate that 1/8 MIC BITC can reduce the pathogenicity of V. parahaemolyticus by inhibiting virulence gene expression related to flagella and biofilm, which is helpful for further understanding of bacteriostatic mechanism of BITC on V. parahaemolyticus and other food-borne pathogens.

overall_design: Analysis of genetic changes in Vibrio parahaemolyticus after BITC addition

first: Jie

last: Song

first: Hongyan

last: Wu

first: Gongliang


title: Pacific white shrimp (Litopenaeus vannamei) hepatopancreas response to Vibrio parahaemolyticus inoculation

city: Taian

first: Huicui

state: Shandong

address: No. 61 Daizong Street

department: College of Animal Science and Technology

institute: Shandong Agricultural University


title: RNA sequencing analysis of Purkinje cells differentiating from human pluripotent stem cells

first: Tom

last: Carroll

overall_design: Examination of translating (TRAP) RNA by RNA sequencing of differentiated Purkinje cells from human plutipotent stem cells at two time points, day 24 and day +95 after co-culture with mouse glia and granule cells. Triplicate samples from each time point were analyzed.

first: David

last: Buchholz

first: Thomas

first: Arif

last: Kocabas

first: Xiaodong

last: Zhu

first: Hourinaz

last: Behesti

first: Phyllis

last: Faust

first: Lauren

last: Stalbow

first: Yin

last: Fang

first: Mary

last: Hatten


title: Transcriptome analysis of pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Vibrio parahaemolyticus inoculation

summary: In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a transcriptome analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.

overall_design: Healthy shrimps were randomly divided into 2 groups; shrimps in treatment group (T) were injected with Vibrio parahaemolyticus, and shrimps in control group (C) were injected with sterile PBS.A total of six libraries, in the control group (C1, C2, C3) and those in the treatment group (T1, T2, T3) were constructed and sequenced by Illumina HiSeq 2500 platform,three biological replicates in each group.

first: Hui


title: Identification of differentially expressed host microRNAs that respond to Vibrio parahaemolyticus infection in the pacific white shrimp Litopenaeus vannamei.

summary: In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a miRNA-seq analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.

overall_design: Healthy shrimps were randomly divided into 2 groups; shrimps in treatment group (T) were injected with Vibrio parahaemolyticus, and shrimps in control group (C) were injected with sterile PBS. A total of six libraries, in the control group (C1, C2, C3) and those in the treatment group (T1, T2, T3) were constructed and sequenced by Illumina HiSeq 2500 platform,three biological replicates in each group.


title: Global transcriptom of  3 Atlantic cod larval stages in response to increased pCO2 compared to ambient pCO2

city: Kiel

first: Felix

middle: Hans

last: Mittermayer

address: Düsternbrooker Weg 20

department: Evolutionary Ecology of Marine Fishes

institute: GEOMAR Helmholtz Centre for Ocean Research

summary: We report on differences in the transcriptome of larvea of Gadus morhua at age 6,13 and 36 days post hatch after exposure to predicted end-of-centrury pCO2 levels during embryonic and larval stage. Number of DE genes increases with age. At 6 and 13 dph, 3 and 16 genes are DE, while 1314 are DE at 36dph, most likely caused by divergent development in response to increased pCO2

overall_design: 8 biological replicates for each of the 2 pCO2 treatments (ambient and high) and sampling point (6,13 and 36 dph)

middle: H

first: Martina

last: Stiasny

first: Catriona

last: Clemmesen

first: Sissel

last: Jenthoft

first: Till

last: Bayer

first: Velmurugu

last: Puvanendran

first: Thorsten

middle: B

last: Reusch


title: Expression data from Lin- ckit+ FLT3+ hematopoietic stem and progenitor cells isolated from Cebpa wildtype and Cebpa knockout mice after FLT3L stimulation

status: Public on Jun 17 2020

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

institute: Medical University Graz

summary:
Cebpa is a gene known for its role in hematopoetic development. Though it is proven to be indispensible in myelopoesis, the details of the role played by Cebpa in dendritic cell development is fairly unknown.  Steady state DC development can be modelled in vitro by treating Lin- HSPC with FLT3L.
We used microarrays to analyse the genetic landscape of lin- cKit+ FLT3+ HSPC isolated from both Cebpa wildtype and Cebpa knockout mice before and after stimulation with FLT3L for 4 hours.

overall_design: We isolated bone marrow cells from the Cebpa WT and KO mice, subjected them to lineage depletion followed by enrichment using FACS double sorting for cKit+ FLT3+ populations. The lin- cKit+ FLT3+ HSPCs were then immediately analysed or set in culture for 4 hours with  FLT3L . The RNA was isolated from these cells and hybridised on  Affymetrix Chips.

first: Albert

last: Wölfler

first: Angelika

last: Rosenberger

first: Subramanian

last: Anirudh


title: A divergent cyclin/cyclin-dependent kinase complex controls progression through the atypical replicative cycles during Plasmodium berghei gametogony

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Cell-cycle transitions are generally triggered by variations in the activity of cyclin-dependent kinases (CDKs) bound to cyclins. Malaria-causing parasites have evolved unique cell-cycles with a repertoire of ancestral CDKs and cyclins whose functions and interdependency remain elusive. Here, we show that the divergent Plasmodium berghei CDK-related kinase 5 (CRK5), is a critical cell-cycle regulator of gametogony required for transmission to the mosquito. It phosphorylates canonical CDK motifs on components of the pre-replicative complex and is essential for DNA replication. We also provide evidence for indirect regulation of the concomitant progression through M-phase. Over a replicative cycle, CRK5 stably interacts with a single Plasmodium-specific cyclin (SOC2) with no evidence of SOC2 cycling through transcription, translation nor degradation. Our results present evidence that during Plasmodium gametogony, a unique and divergent cyclin/CDK pair evolved to fulfil the functional space of multiple eukaryotic cell-cycle kinases controlling S-phase entry and progression through M-phase.

overall_design: Gametocytes (non-activated -0 min- and activated -15 min-) were collected from CRK5-KO and WT lines. Total RNA was isolated from purified parasites using an RNeasy purification kit (Qiagen). RNA was vacuum concentrated (SpeedVac) and transported using RNA stable tubes (Biomatrica). Strand-specific mRNA sequencing was performed from total RNA using TruSeq Stranded mRNA Sample Prep Kit LT (Illumina) according to the manufacturer's instructions. Briefly, polyA+ mRNA was purified from total RNA using oligo-dT dynabead selection. First strand cDNA was synthesised primed with random oligos followed by second strand synthesis where dUTPs were incorporated to achieve strand-specificity. The cDNA was adapter-ligated and the libraries amplified by PCR. Libraries were sequenced in an Illumina Hiseq machine with paired-end 100bp read chemistry.  RNA-seq read alignments were mapped onto the P. berghei ANKA genome (May 2015 release in GeneDB—http://www.genedb.org/) using Tophat2 (version 2.0.13) with parameters “-library-type fr-firststrand–no-novel-juncs–r 60”. Transcript abundances were extracted as raw read counts using the Python script ‘HTseq-count’ (model type – union, http://www-huber.embl.de/users/anders/HTSeq/). Counts per million (cpm) values were obtained from count data and gene were filtered if they failed to achieve a cpm value of 1 in at least 30% of samples per condition. Library sizes were normalized by the TMM method using EdgeR software and further subjected to linear model analysis using the voom function in the limma package43. Differential expression analysis was performed using DESeq2 in R version 3.2.1. Genes with fold change greater than 2 and p-value less than 0.05 were considered as significantly differentially expressed. P. berghei GO terms (Gene Ontology) were downloaded from GeneDB (http://www.genedb.org/; May 2015 release) and gene ontology enrichment analysis was performed for the DEG lists using GOstats R package. All analyses and visualizations were done with R packages- cummeRbund and ggplot2.

first: Aurelia

last: Balestra

first: Mohammad

last: Zeeshan

first: Amit

last: Subudhi  Kumar

first: Arnab

last: Pain

first: Rita

last: Tewari

first: Mathieu

last: Brochet


title: Fibrosis and atrial fibrillation in Scn1b null mice

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Scn1b-/- mice are a model of Early Infantile Developmental Epileptic Encephalopathy (EIDEE). These mice exhibit characteristic seen in patients such as spontaneous siezures, ataxia, growth abnormalites, and a high incidence of premature mortality.  The goal of this study was to identify changes in gene expression between Scn1b wild-type and Scn1b-/- mice in the atria

overall_design: RNA-Seq in cardiac atrial tissue from 16-day old wild type (WT) and Scn1b-/- mice

first: Nnamdi

last: Edokobi

first: Alexandra

last: Bouza

first: Lori

last: Isom


title: Comprehensive analysis of transcripts and proteins relative abundance during Plasmodium falciparum blood stages

city: Paris

first: Gwladys

last: Bertin

address: rue de l'observatoire

institute: Institut de Recherche pour le Développement

summary: Plasmodium falciparum is the main causative agent of human malaria. During the intraerythrocytic development cycle, P. falciparum morphology changes dramatically from circulating young rings to sequestered mature trophozoites and schizonts. Sequestered forms contribute to the pathophysiology of severe malaria as the infected erythrocytes obstruct the microvascular flow in deep organs and induce local inflammation. However, the sequestration mechanism limits the access to the corresponding parasitic form in clinical samples from patients infected with P. falciparum. To complement this deficiency, we aimed to evaluate the relevance of mRNA study as a proxy of protein expression in sequestered parasites. To do so, we conducted a proteotranscriptomic analysis using five independent P. falciparum laboratory strains samples. RNA sequencing was performed on circulating ring stage parasites and LC-MS/MS on the corresponding sequestered mature forms. All analyzes were performed within the same development cycle for direct individual correlation. mRNA expression level was assessed at the circulating ring stage and the corresponding protein expression level was measured after 18h-24h of maturation to reach the mature trophozoite stage. Overall, our results showed a strong transcriptome/transcriptome and proteome/proteome correlation between samples. Moreover, strong correlations of mRNA and proteins expressions levels were found between ring stage transcriptomes and mature forms proteomes.  However, twice more transcripts were identified at ring stage than proteins at mature trophozoite stage. A high level of transcript expression did not guarantee the detection of the corresponding protein. Finally, we pointed out discrepancies at the individual gene level. Taken together, our results show that transcripts and proteins expression are overall correlated. However, mRNA abundance is not a perfect proxy of protein expression at the individual level. Importantly, our study shows limitations of the “blind” use of RNA-seq and the importance of multi-omics approaches for P. falciparum blood stage study in clinical samples.

overall_design: We used 3D7, HB3 and ITG laboratory strains, with specific binding background phenotypes (ICAM-1, Hbec-5i and CD36) for a total of five samples.

first: Claire

last: Kamaliddin

first: Emilie

last: Guillochon

first: Virginie

last: Salnot

first: David

last: Rombaut

first: Stéphanie

last: Huguet

first: François

last: Guillonneau

first: Sandrine

last: Houze

first: Michel

last: Cot

first: Philippe

last: Deloron

first: Nicolas

last: Argy

middle: I


title: Selective therapeutic targeting of the first and second bromodomains of the BET proteins in cancer and immuno-inflammation [SLAM-seq]

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: The evolutionarily conserved BET bromodomain family contain a distinctive tandem bromodomain structure that enables their chromatin binding to facilitate transcription. Whilst first-in-class drugsthat equally inhibit both bromodomains have shown pre-clinicaland clinical efficacy in a range of malignant and inflammatory pathologies, the functional contribution of the first (BD1) and second (BD2) bromodomains to these pathologies remains largely unknown. Here we haveexploited detailedstructuralinsights and our extensivemedicinal chemistry capabilities to develop novel compounds that are exquisitely selectivefor either BD1 or BD2 of the BET proteins. Using thesewell characterised domain-specific inhibitors we show that BD1 is required by all BET proteins to associate with chromatin and maintain established malignant transcriptional programs.Therefore, targeting BD1 alone phenocopies the therapeutic effects of current non-selective BET inhibitorsin models of cancer. Whilst steady state gene expression primarily requires BD1,we find that the rapid increase of gene expression effectedby a wide range of inflammatory stimuli requiresboth BD1 and BD2. Moreover, although BRD4 is the principal member required for the maintenance of established gene expression, efficient gene induction also requires BRD2 and BRD3. Selective inhibition of BD2 is effective in perturbing the recruitment of all the BET proteins for stimulated gene expression and consequently small molecule inhibitors of BD2 amelioratethe immunoinflammatory end organ damage seen in models of inflammatory arthritis, psoriasis and hepatitis. Together,these data provide novel biological and functional insights into this family of key transcriptional regulators. Importantly, they also help refine the future therapeutic approach when targeting the BET proteinsin distinct pathologies such as cancer and immuno-inflammation.

overall_design: SLAM-seq on three leukaemia cell lines treated with BET inhibitors

first: Omer

last: Gilan

first: Inmaculada

last: Rioja

first: Rab

middle: K

last: Prinjha


title: Global changes in nitration levels and DNA binding profile of Trypanosoma cruzi histones induced by incubation with host extracellular matrix

city: Ribeirão Preto

first: Rubens

middle: Daniel Miserani

last: Magalhães

state: SP

address: Av. Bandeirantes 3900

department: Department of Cellular and Molecular Biology and Pathogenic Bioagents

country: Brazil

institute: Ribeirão Preto Medical School

summary: Adhesion of T. cruzi trypomastigotes to components of the extracellular matrix (ECM) is an important step in mammalian host cell invasion. We have recently described a significant increase in the tyrosine nitration levels of histones H2A and H4 when trypomastigotes are incubated with components of the ECM. In this work, we used chromatin immunoprecipitation (ChIP) with an anti-nitro-tyrosine antibody followed by mass spectrometry to identify nitrated DNA binding proteins in T. cruzi and to detect alterations in nitration levels induced upon parasite incubation with the ECM.  Histone H1, H2B, H2A and H3 were detected among the 9 most abundant nitrated DNA binding proteins using this proteomic approach. One nitrated tyrosine residue (Y29) was identified in Histone H2B in the MS/MS spectrum. In addition, we observed a significant increase in the nitration levels of histones H1, H2B, H2A and H4 upon parasite incubation with ECM. Finally, we used ChIP-Seq to map global changes in the DNA binding profile of nitrated proteins. We observed a significant change in the binding pattern of nitrated proteins to DNA after parasite incubation with ECM. This work provides the first global profile of nitrated DNA binding proteins in T. cruzi and additional evidence for modification in the nitration profile of histones upon parasite incubation with ECM. Our data also indicate that the interaction of the parasite with the ECM induces alterations in chromatin structure, possibly affecting nuclear functions.

overall_design: Examination of the changes of nitrated proteins interactions with chromatin in T.cruzi after incubation with host extracelular matrix (ECM). Two samples of the parasite incubated or not with ECM (TyM and Ty) were prepared  in replicates (Rep1 and Rep2) to be submitted to ChIP-Seq technique. Paired-end experiments  generate files R1 and R2.

middle: D

first: Eliciane

last: Mattos

first: Andrei

last: Rozanski

first: Pedro

last: Galante

first: Giuseppe

last: Palmisano

first: Angela

last: Cruz

first: Walter

last: Colli

first: Anamaria

last: Camargo

first: Maria

middle: J

last: Alves


title: bioadapt2011_cytopheno-CYTOPHENO: Nucleo-cytoplasmic co-adaptation and adaptive plant phenotypes

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary:
The cytopheno project studies cytoplasmic-nucleus interactions by characterizing cytolines (same nucleus but different cytoplasm, and conversely) at several levels (growth, germination, transcriptomic, proteomic, metabolomic) notably in response to nitrogen deficiency. For this project, there are 48 hybridizations performed as following, on leaf samples from hydroponically grown plants.

bioadapt2011_cytopheno - bioadapt2011_cytopheno - Evaluation of the impact of nucleo-cytoplasmic co-adaptation disruptions on nuclear genome expression in Arabidopsis - Obtaining samples by hydroponic culture.

overall_design:
48 dye-swap hybridizations.
Nuclear and cytoplasm strain IDs have been included in the sample characteristics. These data are also available in the file Genotype_and_Treatment_strain_Cytopheno_project.xlsx located at the foot of this record.

first: Francoise

last: Budar

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [IGF2BP1 KD in PANC-1 (total RNA)]

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: The IGF2 mRNA-binding protein 1 (IGF2BP1) is a post-transcriptional enhancer of tumor growth. However, conserved effector pathway(s) and the feasibility of targeting IGF2BP1 in cancer cells remained elusive.   We demonstrate that IGF2BP1 is a conserved regulator of E2F-driven gene expression and cancer cell cycle progression. IGF2BP1 promotes positive regulators of G1/S transition by stabilizing the respective mRNAs. This regulation is 3’UTR-, miRNA- and m6A-dependent, suggesting a conserved role of m6A-enhanced cell cycle progression across cancers. IGF2BP1 stabilizes E2F-encoding mRNAs and some of their target transcripts revealing a post-transcriptional super-enhancer role of the protein in E2F-driven gene expression. The small molecule BTYNB disrupts this super-enhancer function by impairing IGF2BP1-RNA association and consequently interferes with tumor cell proliferation and tumor growth.

overall_design: total RNA-Seq of PANC-1 cells transfected with either control siRNAs (siC) or siRNAs directed against IGF2BP1. Three replicates per condition.

first: Simon

last: Müller

first: Nadine

last: Bley

first: Bianca

last: Busch

first: Marcell

last: Lederer

first: Claudia

last: Misiak

first: Tommy

last: Fuchs

first: Alice

last: Wedler

first: Jacob

last: Haase

first: Jean

last: Borges Bertoldo

first: Patrick

last: Michl

first: Stefan

last: Hüttelmaier


title: Selective therapeutic targeting of the first and second bromodomains of the BET proteins in cancer and immuno-inflammation

first: Mark

last: Dawson

overall_design: Refer to individual Series


title: Selective therapeutic targeting of the first and second bromodomains of the BET proteins in cancer and immuno-inflammation [RNA-seq]

overall_design: RNA-seq on Tcells treated with BET inhibitors

first: Omer

last: Gilan

first: Inmaculada

last: Rioja

first: Rab

last: Prinjha


title: Selective therapeutic targeting of the first and second bromodomains of the BET proteins in cancer and immuno-inflammation [ChIP-seq]

overall_design: ChIP-seq on two leukaemia cell lines and Tcells treated with BET inhibitors


title: Expression profiles of Rb-deficient islet cells in mouse

city: Kyoto city

first: YUKI

last: YAMAUCHI

state: Kyoto

department: Gastroenterology and Hepatology

institute: Kyoto university

summary: Pancreatic neuroendocrine tumors (PanNET) were classified into grades (G) 1-3 by the World Health Organization in 2017, but the precise mechanisms of PanNET initiation and progression have remained unclear. In this study, we used a genetically engineered mouse model to investigate the mechanisms of PanNET formation. Although pancreas-specific deletion of the Rb gene (Pdx1-Cre;Rbf/f) in mice did not affect pancreatic exocrine cells, the α-cell/β-cell ratio of islet cells was decreased at 8 months of age. During long-term observation (18-20 months), mice formed well-differentiated PanNET with a Ki67-labeling index of 2.7%. In contrast, pancreas-specific induction of a p53 mutation (Pdx1-Cre;Trp53R172H) had no effect on pancreatic exocrine and endocrine tissues, but simultaneous induction of a p53 mutation with Rb gene deletion (Pdx1-Cre;Trp53R172H;Rb f/f) resulted in the formation of aggressive PanNET with a Ki67-labeling index of 24.7% over the short-term (4 months). In Pdx1-Cre;Trp53R172H;Rb f/f mice, mRNA expression of Pten and Tsc2, negative regulators of the mTOR pathway, significantly decreased in the islet cells, and activation of the mTOR pathway was confirmed in subsequently formed PanNET. Thus, by manipulating Rb and p53 genes, we established a multistep progression model from dysplastic islet to indolent PanNET and aggressive metastatic PanNET in mice. These observations suggest that Rb and p53 have distinct roles in the development of PanNET.

overall_design: Total RNA of isolated pancreatic islet cells from two individual Pdx1-Cre and Pdx1-Cre:Rbf/f mice were used

last: Yamauchi

first: YUZO

last: Kodama


title: Gene expression profiling of human prostate spheres and organoids exposed to inorganic arsenic (iAs)

city: Chicago

first: Lishi

last: Xie

state: IL

address: 909S Wolcott CMRB 5120

department: Department of Urology

institute: University of Illinois at Chicago

summary: Gene expression analysis of prostate spheres and orgnoids in response to the inorganic arsenic exposure, to provide insight into the molecular mechenisms invovled in arsenic-induced homeostasis dysregulation of prostate stem-progenitor cells.

overall_design: Triplicates of prostate spheres/organoids treated with iAs were compared with groups treated with vehicle control

first: Gail

last: Prins


title: mRNA profiling after knockdown of lncRNA Cyrano

city: Hannover

first: Christian

last: Bär

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hannover Medical School

summary: Pluripotency is tightly regulated via versatile pathways and is crucial for the maintenance of stem cells and their implementation for regenerative medicine. Cyrano, a well conserved lncRNA, is highly expressed in stem cells suggesting an important role of Cyrano in pluripotency. Cyrano was previously described to be essential for the maintenance of mouse ESC pluripotency. In contrast, using different genetic models, we here found Cyrano to be dispensable in murine and human iPSCs and in human ESCs. RNAseq in human iPSC revealed only a moderate influence of Cyrano on the global transcriptome, pluripotency-related pathways remaining unaffected.

overall_design: Human iPSCs (monoclonal population with a guide RNA for Cyrano) were treated with 2µM doxycycline to induce the knockdown. The treatment for three days resulted in 98% knockdown of Cyrano. Total RNA was harvested, sequencing was performed in triplicates.

first: Hannah

last: Hunkler

first: Thomas

last: Thum


city: Chengdu

first: Xu

last: Zhongxian

address: NO. 211, Huiming Road, Wenjiang District

institute: Sichuan Agricultural University

summary: Developmental dynamics of miRNAs across chicken pectoral muscle and effect of gga-miRNA-454 on the differentiation of myoblasts inhibits myoblast differentiation by targeting SBF2

overall_design: miRNA-seq of pectoral muscle from embryonic day 5 through age of 12 years and brain, liver, ovary, spleen and kidney RNA-seq at age 300 days.

first: Min

last: Chen

first: Shaolan

last: Zhang

first: Zhongxian

last: Xu

first: Jian

last: Gao

first: Shailendra

last: Kumar Mishra

first: Qing

last: Zhu

first: Xiaoling

last: Zhao

first: Yan

last: Wang

first: Huadong

last: Yin

first: Yaodong

last: Hu

first: Xiaolan

last: Fan

first: Bo

last: Zen

first: Mingyao

last: Yang

first: Deying

first: Qingyong

last: Ni

last: Li

first: Mingwang

first: Diyan


title: Effects of Streptococcus oralis biofilm on peri-implant soft-tissue cells

first: Alexandra

last: Ingendoh-Tsakmakidis

address: Stadtfelddamm 34

department: Prosthetic Dentistry and Biomedical Materials Science

summary: Human gingival epithelial cells (HGEp) and fibroblasts (HGF) are the main cell types of the peri-implant soft-tissue, with HGEp constantly being exposed to bacteria and HGF residing protected in the connective tissue as long as an intact mucosa-implant seal is preserved. Streptococcus oralis belongs to the commensal bacteria, is highly abundant at healthy implant sites, and might exert host modulatory effects on soft-tissue cells as described for other streptococci. Thus, we aimed to investigate the effects of S. oralis biofilm on HGEp as well as HGF. HGEp or HGF were grown on titanium separately and responded to S. oralis biofilm challenge. The cell condition of HGF was dramatically impaired after 4 hours showing a transcriptional inflammatory and stress response. In contrast, S. oralis challenge induced only transcriptional inflammatory response in HGEp with their cell condition remaining unaffected. Subsequently, HGF were susceptible compared to HGEp. The proinflammatory IL-6 was attenuated in HGF and CXCL8 in HGEp indicating a general tissue-protective role of S. oralis, forasmuch as the HGF are not exposed. In conclusion, an intact implant-mucosa interface is a prerequisite so that commensal biofilms can promote homeostasis for tissue protection.

overall_design: S. oralis induced gene expression was HGF as well as HGEp was measured after 2 hours of co-culture. Three idenpendent experimental runs were performed for each cell type.

first: Andreas

last: Winkel

first: Meike

last: Stiesch


title: Knockdown studies of TAPIR lncRNAs in LNCaP cells

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: To unravel the molecular function of TAPIR-1 and -2, four different specific siRNAs were used to knockdown the TAPIR-transcripts in LNCaP-cells. Gene expression changes upon knockdown of TAPIR was assessed by Agilent SurePrint G3 Human Gene Expression Arrays at 24h and 48h after treatment.

overall_design: Total RNA was isolated from cells with TRIzol (ambion), following the manufacturers protocol. For each siRNA type four biological replicates were prepared for two conditions: 24h and 48h after treatment.

first: Maik

last: Friedrich

first: Karolin

last: Wiedemann

first: Markus

last: Kreuz

first: Gabi

last: Pfeifer

first: Ivonne

last: Zipfel

first: Stefanie

last: Binder

first: Sven-Holger

last: Puppel

first: Ulrike

last: Koehl

first: Gerd

last: Mueller

first: Kurt

last: Engeland

first: Achim

last: Aigner

first: Susanne

last: Fuessel

first: Stephan

last: Schreiber

first: Sabina

last: Christ

first: Joerg

last: Hackermueller

first: Ulrich

last: Sommer

first: Pia

last: Hoenscheid

first: Gustavo

last: Baretton

first: Manfred

last: Wirth

first: Friedemann

last: Horn


title: Downregulation of the Ubiquitin-E3 Ligase KPC1 promotes glioblastoma progression through upregulation of SerpinE1

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

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


title: Downregulation of the Ubiquitin-E3 Ligase KPC1 promotes glioblastoma progression through upregulation of SerpinE1 [RNA-seq]

summary:
We identified RNF123 (KPC1) ubiquitin E3 ligase is involved in glioblastoma progression through NF-kB-target SerpinE1. The goal of the RNA-Seq analysis is to determine the gene expression profile in LN18 cells overexpressing RNF123 compare to control empty vector (EV) cells.
By integration of reverse-phase protein array (RPPA) and RNA-Seq data in glioblastoma cells, we determined NF-kB1-target genes that significantly changed by RNF123 overexpression.

overall_design: mRNA profiles of LN18 cells overexpressing KPC1 (KPC1) or control vector (Ctrl) generated by deep sequencing using Illumina HiSeq 2500, in duplicate.

first: Xiaowen

last: Wang

first: Matias

last: Bustos

first: Ying

last: Mao


title: Co-repressors Mtg8 and Mtg16 regulate niche exit and early fate decision of crypt stem cells

city: London

first: Vivian

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute


title: Co-repressors Mtg8 and Mtg16 regulate niche exit and early fate decision of crypt stem cells (ChIP-seq)

summary: In this experiment we analyse Mtg16 binding to chromatin in isolated mouse intestinal crypts from VillinCreER, Rbpjfl/fl mice 4 days following TM induction (Notch inhibition).

overall_design: We have used intestinal crypts isolated from 2 Villin-CreERT2 RBPJfl/fl (biological test replicates) 4days after TM treatment. For each sample we have the input and the Mtg16 antibody pull down.

first: Anna

last: Baulies

first: Nikolaos

last: Angelis

first: Valentina

last: Foglizzo

first: Thomas

last: Danielson

first: Harshil

last: Patel

first: Laura

last: Novellasdemunt

last: Kucharska

first: Paolo

last: De Coppi


title: Transcriptional profile Lactobacillus plantarum WCFS1 : Hydroxytyrosol treated cells

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

summary: Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with hydroxytyrosol. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with hydroxytyrosol. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals the induction of genes related to defense mechanisms against oxidative challenge. This response include genes related to inactivation of toxic oxygen radicals, probably derived from the autooxidation of hydroxytyrosol and genes involved in repairing the damage of oxygen radicals on proteins, including those involved in the metabolism of sulphur amino acids. Genes involved in peptidoglycan turnover, strenghthening of the cell wall and genes coding for osmoprotectants transporters, were downregulated. In addition, genes coding for elements typically involved in the stringent response, including ribosomal proteins, enzymes involved in the metabolism of the ppGpp alarmone, nitrogen metabolism, cell division and general stress proteins, were differentially regulated by hydroxytyrosol.

overall_design: Biological triplicates: untreated cells: Control vs. Hydroxytyrosol treated cells: Experimental

first: Inés

last: Reverón

last: Plaza

first: Blanca

last: de las Rivas

first: Rosario

last: Muñoz

first: Félix

last: López de Felipe


title: Early cleavage of porcine preimplantation embryos is regulated by tRNAGln-TTG-derived small RNAs present in mature spermatozoa

city: Yangling

first: Xiaoxu

last: Chen

address: Litai street

institute: Northwest A&F University

summary: Purpose: To elucidate the expression pattern of tsRNAs in porcine spermatogenesis, sperm maturation. To gain insight the roles of tsRNAs in porcine embryo development.

overall_design: In the present study, by using pigs as a research model, we probed tsRNA dynamics during spermatogenesis and sperm maturation, and found that tRNAGln-TTG-derived small RNAs (Gln-TTGs) were highly enriched in ejaculated sperm. Later, by microinjection of the antisense sequence into in vitro fertilized (IVF) oocytes and and subsequent single-cell RNA-seq of blastomeres, we demonstrated that Gln-TTGs are involved in the first cleavage of porcine preimplantation embryos via modulating cell cycle-related genes and retrotransposons.

first: Wenxian

last: Zeng


title: Cohesion is established during DNA replication utilising chromosome associated cohesin rings as well as those loaded de novo onto nascent DNAs

status: Public on Jun 16 2020

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: Cohesin is established by two parallel pathways during DNA replication. Chromosome associated cohesin is converted to cohesive structures and this depends on four protein associated with the replisome; Tof1/Csm3, Ctf4 and Chl1 (TCCC). In TCCC mutants, chromosome associated cohesin is evicted from the DNA during S phase.

overall_design: Characterisation of the effect of WT and mutant cohesin complexes and associated factors on loading onto chromosomes in S. cerevisiae, assessed by calibrated ChIP-seq on an Ion Torrent Proton (Life Technologies)

first: Naomi

last: Petela


title: BMP4 Resets Primed to Naive Pluripotency by Reprogramming Chromatin Accessibility [ChIP-Seq]

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

summary: BMP4 regulates a plethora of developmental processes including dorsal-ventral axis and neural patterning. Here we report that BMP4 reconfigures nuclear archi-tecture during primed to naive transition (PNT). We first established a robust BMP4 driven PNT and shown by ATAC- and RNA-seq that it orchestrates the chromatin accessibility dynamics during PNT. Among the loci opened early by BMP4, we identified Zbtb7a/b as new targets that contribute to drive PNT. Mechanically, BMP first activates Zbtb7a/b in both chromatin and gene expression level, which in turn facilitate the opening of naïve pluripotent chromatin loci and allow the activation of naïve pluripotent genes. Surprisingly, Zbtb7a not only binds to chromatin loci near the genes to be activated, but also strategically occupies those to be silenced, thus resolving the conflicting role of BMP4 in both activating and suppressing gene ex-pression during PNT at the chromatin level. Our results reveal a previously un-known function of BMP4 in regulating nuclear architecture and link its targets Zbtb7a/b to chromatin remodeling and pluripotent fate control.

overall_design: We analyzed the chromatin remodeling during BMP4 induced PNT


title: RNA-seq data of endometrium from Yorkshire pigs

city: Jinan

first: Tao

last: Su

address: 440 Jiyan Rd

institute: Shandong Cancer Hospital and Institute

overall_design: Transcriptome sequencing of the endometrium from Yorkshire pigs

first: Bin

last: Hou

first: Dequan

last: Xu


title: The basic-helix-loop-helix transcription factor ngn-1/neurogenin activates transcription of multiple terminal selector transcription factors in the Caenorhabditis elegans nervous system

city: Kennesaw

first: Martin

middle: Lyn

last: Hudson

state: GA

address: 370 Paulding Avenue, Suite SC507, MD1201

department: Molecular and Cellular Biology

institute: Kennesaw State University

summary: Proper nervous system development is required for an organism’s survival and function. Defects in neurogenesis have been linked to neurodevelopmental disorders such as schizophrenia and autism spectrum disorders.  Understanding the gene regulatory networks that orchestrate neural development, specifically cascades of proneural transcription factors, can better elucidate which genes are most essential in governing early neurogenesis. Neurogenins are a family of such factors that are both sufficient and necessary for the development of neural sub-types in mice, primarily through the regulation of other factors, particularly neurod.  The objective of this study was to evaluate previously established regulatory targets of neurogenin (ngn-1) and to identify unknown downstream targets, using the nematode Caenorhabditis elegans as a model for these studies. We find that in C. elegans, neurogenin is required for axon outgrowth, cell fate specification, and epithelial integrity during embryonic development. Using RNA sequencing and comparative transcriptome analysis we found that ngn-1 acts primarily to repress transcription, facilitating proper embryogenesis.  We also identified specific candidates for activation by ngn-1, including hlh-34(npas1) and unc-42(prop1), which we further validated using genetic methods.  Our results identify novel pathways connecting ngn-1 to known terminal regulators, which maintain cell fate of terminally differentiated neural subtypes, and align neurogenins within the larger context of proneural transcription factors.

overall_design: RNAseq analysis of Caenorhabditis elegans embryogenesis in N2 wild type (n = 4) and ngn-1(ok2200) mutants (n = 4)

middle: L

first: Elyse

last: Christensen


title: TET1 is a tumour suppressor that inhibits bladder cancer progression

city: Shanghai

first: Yilin

last: Yan

address: 100 Haining Road

institute: Shanghai General Hospital

summary: Ten-Eleven Translocation 1 (TET1) is a member of methylcytosine dioxygenase, which catalyse 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) that promote the demethylation process. The diminished expression of TET1 protein and 5-hmC in many tumors indicate a critical role for the maintenance of cell stability. However, role of TET1 in bladder cancer development remains unclear. Here we found that TET1 expression was downregulated in bladder cancer tissues compared with normal urothelium and was inversely related to patient overall survival. TET1 silencing in bladder cancer cells increase proliferation and inhibited cell migration and invasion while its re-expression inhibits their proliferation and the growth of tumor xenografts.  Furthermore, we found that TET1 binds to the promoter of the TSG  to maintain its hypomethylated which interacts with β-catenin and suppress its nuclear translocation, thus inhibiting β-catenin transcriptional activity and downstream genes. In conclusion, TET1 acts as a tumor suppressor gene in bladder cancer cells by suppressing β-catenin signaling. This study may facilitate efforts to therapeutic strategy for patients with bladder cancer.

overall_design: Transcriptome analysis of T24 cell line expressing TET1-CD protein.

first: Jun


title: Robustness testing and optimization of an adverse outcome pathway on cholestatic liver injury

city: Jette

first: Eva

middle: Anne D

last: Gijbels

state: Brussels

address: Laarbeeklaan 103, Building G, 2th floor, Department IVTD

country: Belgium

institute: VUB

summary:
We used microarrays to provide a transcriptomic signature of different types of cholestasis evoked by 3 different drugs and obstructive surgery
Adverse outcome pathways (AOPs) have been recently introduced as tools to map the mechanisms underlying toxic events relevant for chemical risk assessment. AOPs particularly depict the linkage between a molecular initiating event and an adverse outcome through a number of intermediate key events. An AOP has been previously introduced for cholestatic liver injury. The objective of this study was to test the robustness of this AOP for different types of cholestatic insult and the in vitro to in vivo extrapolation. For this purpose, in vitro samples from human hepatoma HepaRG cell cultures were exposed to cholestatic drugs (i.e. intrahepatic cholestasis), while in vivo samples were obtained from livers of cholestatic mice (i.e. extrahepatic cholestasis). The occurrence of cholestasis in vitro was confirmed through analysis of bile transporter functionality and bile acid analysis. Transcriptomic analysis revealed inflammation and oxidative stress as key events in both types of cholestatic liver injury. Major transcriptional differences between intrahepatic and extrahepatic cholestatic liver insults were observed at the level of cell death and metabolism. Novel key events identified by pathway analysis included endoplasmic reticulum stress in intrahepatic cholestasis, and autophagy and necroptosis in both intrahepatic as extrahepatic cholestasis. This study demonstrates that AOPs constitute dynamic tools that should be frequently updated with new input information.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Sv129 mice underwent common bile duct ligation, as described by Van Camenhout et al. 2019 ('CBDL'; n=6). Control mice were sham operated, in which the common bile duct was isolated but not ligated ('Sham', n=6). HepaRG cells were exposed for 72 hours to atazanavir (ATA), cyclosporin A (CsA) and nefazodone (NEFA)  in the absence or presence of a 50 times concentrated bile acid mixture (BA). All in vitro experiments were conducted in 3 different HepaRG batches ('CTL; BA; ATA 60 µM; CsA 20µM; NEFA 30µM; ATA 60µM + BA; CsA 20 µM + BA; NEFA 30 µM + BA'; n=3).

first: Lindsey

last: Devisscher

first: Mathieu

last: Vinken