title: Local inhibition of PRC2 activity by histone H3.3K27M drives replication defects through misregulation of the JNK pathway [ChIP-seq]

summary: Substitution of lysine 27 with methionine in histone H3.3 is a recently discovered driver mutation of pediatric high-grade gliomas. Tumor cells carrying the mutation show a dramatic decrease in H3K27me3 levels due to physical inhibition of PRC2 methyltransferase activity. Here we use a C. elegans model to quantify the antagonistic effects of the H3.3K27M oncohistone on H3K27 trimethylation genome wide. We demonstrate that PRC2 is locally both simulated by H3K27me3 and inhibited by the oncohistone in a concentration-dependent manner.

overall_design: Examination of relevant histone modifications and K27M incorporation in gonads of several C. elegans strains by ChIP-seq.

first: Kamila

last: Delaney


title: CD8+ T Cells Promote Maturation of Liver-Resident NK Cells via the CD70-CD27 axis

status: Public on Apr 22 2019

city: Hefei

first: Xiaolei

last: Hao

state: Anhui

address: huangshan Road 443

country: China

institute: Institute of Immunology, USTC

type: Expression profiling by high throughput sequencing

summary: We discovered that LrNK cells exhibit a relatively immature phenotype and impaired cytotoxic capacity in the absence of CD8+ T cells. The provision of CD8+ T cells to Cd8-/- or Rag1-/- mice led to the restoration of LrNK cell maturation

overall_design: LrNK  and cNK mRNA profiles of  wild type (WT) and CD8-/- mice were generated by deep sequencing, in triplicate, using Illumina

first: Lu

last: Bai

first: Zhigang

last: Tian


title: Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

summary: A-to-I RNA editing is widespread in eukaryotic transcriptomes and plays an essential role in the creation of proteomic and phenotypic diversity. Loss of ADARs, the proteins responsible for A-to-I editing, results in lethality in mammals. In C. elegans, knocking out both ADARs, ADR-1 and ADR-2, results in aberrant behavior and abnormal development. Studies have shown that ADR-2 can actively deaminate dsRNA while ADR-1 cannot. However, as most studies of C. elegans ADARs were performed on worms mutated in both ADAR genes, the effects observed cannot be attributed to a single ADAR or to the interactions between ADAR genes. Therefore, we set to study the effects of each C. elegans ADAR on RNA editing, gene expression, protein levels and the contribution of each of ADAR to the phenotypes observed in worms mutated in both genes, in order to elucidate their distinct functions. We found significant differences in the phenotypes observed in worms mutated in a single ADAR gene. Worms harboring adr-1 mutations have a significant reduction in their lifespan, while worms harboring adr-2 mutations have extended lifespan. We also observed severe abnormalities in vulva formation mainly in adr-1 mutants, and we suggest that these phenotypes are a result of an RNA editing independent function of ADR-1. Mutations in each ADAR resulted in expressional changes in hundreds of genes, and a significant downregulation of edited genes. However, very few changes in the protein levels were observed. In addition, we found that ADR-1 binds many edited genes. Our results suggest that ADR-1 has a significant function in the RNA editing process and by altering editing levels it causes the severe phenotypes that we observed. In contrast, a complete lack of RNA editing is less harmful to the worms. Furthermore, our results indicate that the effect of RNA editing on the protein content in the cell is minor and probably the main purpose of these modifications is to antagonize or enhance other gene regulatory mechanisms that act on RNA.

overall_design: RNA was extracted from wildtype C. elegans synchronized to embryo or L4 larval stage. For each stage, 3 independent biological replica RNA samples were used for construction of mRNA libraries.

middle: T


title: Expression data from RAB3C overexpression in CX-1 Colon cancer cell line.

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary:
We demonstrate that RAB3C up-regulation significantly promoted cell migration and invasion in lower invasive colon cancer cell lines in vitro, as well as in distal metastases in vivo
We used microarrays to analyze the RAB3C regulated gene expression underlying invasion-metastasis cascade.

overall_design: CX-1 colon adenocarcinoma cells with RAB3C overexpression were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yu-Chan

last: Chang


title: Intracerebral Hemorrhage Induces Inflammatory Gene Expression in Peripheral Blood: Global Transcriptional Profiling in ICH Patients

status: Public on Apr 21 2019

city: Cincinnati

first: Xiaoting

last: Zhu

state: OH

address: 3333 burnet avenue,MLC7024

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary: Intracerebral hemorrhage (ICH) is a severe neurological disorder with no proven treatment. While there is substantial interest in post-ICH neuroinflammation and associated pathophysiological mechanisms, these processes remain poorly understood. To further advance our understanding, we performed RNA-seq in the peripheral blood of ICH patients to test the hypothesis that ICH would induce inflammatory biological pathways.  16,640 genes were identified and 216 were significant DEGs after ICH (FDR<0.1). IPA identified three canonical pathways as the most statistically significantly activated by ICH:  colorectal cancer metastasis signaling (Z-score 3.00, P=1.71E-5), interleukin-8 (IL-8) signaling (3.00, 8.44E-5), and nuclear factor-kappa B (NF-kB) activation by viruses (2.55, 1.78E-4). Inflammatory mediators of particular relevance included IL-8, NF-kB, ERK 1/2, and the integrins β3, α2b, and β5.  Conclusion:  ICH induced peripheral blood gene expression at 72 to 96 hours compared with 0 to 24 hours from symptom onset. DEGs that were highly expressed in the significant biological pathways included those related to inflammation and activation of the immune response. Further research is needed to determine if these changes affect outcomes and may represent new therapeutic targets.

overall_design: In 11 patients with ICH, the first peripheral blood sample was collected within 24 hours of symptom onset or last known well, and a second blood draw occurred 72 hours (+ 6) following the first. RNA-seq was conducted to identify differentially expressed genes (DEGs) between the first and second samples. Biological pathway enrichment analysis was performed with Ingenuity® Pathway Analysis (IPA).

first: Kyle

middle: B

last: Walsh

first: Xiang

last: Zhang

first: Eric

last: Wohleb

first: Daniel

last: Woo

first: Long

last: Lu

first: Opeolu

last: Adeoye


title: Transcriptome of human coronory endothelial cells in response to nitro-conjugated linoleic acid

status: Public on Apr 25 2019

city: Ann Arbor

first: Haocheng

state: Michigan

address: 2800 plymouth road

department: Internal Medicine

institute: University of Michigan

summary: In the present study, a distinct transcriptome regulated by NO2-CLA was revealed in primary human coronary artery endothelial cells (HCAECs) through RNA sequencing. Differential gene expression and pathway enrichment analysis identified numerous regulatory networks of cell cycle regulation, inflammation and redox responses, nitric oxide biosynthesis, hypoxia and chaperones in response to NO2-CLA, suggesting potent and diverse effects of NO2-CLA on cellular processes.

overall_design: For RNA-seq experiment, HCAECs at 90% confluence were treated with DMSO, CLA (10µM) or NO2-CLA (10µM) for 1 hour, followed by adding with either ethanol (Control) or PA (200 µM) (Cayman Chemical) for the subsequent 6 hours. There are 6 groups for RNA seq: DMSO + control (ethanol), CLA (10µM) + control, NO2-CLA (10µM) + control, DMSO + PA, CLA (10µM) + PA, NO2-CLA (10µM) + PA. Each group has 4 biological replicates.

first: Jinjian

last: Sun

first: Yanbo

last: Fan


title: BCL6 corepressor contributes to Th17 cell formation by inhibiting Th17 fate suppressors

status: Public on Apr 26 2019

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CD4+ T helper 17 (Th17) cells protect vertebrate hosts from extracellular pathogens at mucosal surfaces. Th17 cells form from naïve precursors when signals from the T cell antigen receptor (TCR) and certain cytokine receptors induce the expression of the RORγt transcription factor, which activates a set of Th17-specific genes. Using T cell-specific loss-of-function experiments we find that two components of the Polycomb Repressive Complex 1.1 (PRC1.1), BCL6 corepressor (BCOR) and KDM2B, which helps target the complex to unmethylated CpG DNA islands, are required for optimal Th17 cell formation in mice after Streptococcus pyogenes infection. Genome-wide expression and BCOR chromatin immunoprecipitation studies revealed that BCOR directly represses Lef1, Runx2, and Dusp4, whose products inhibit Th17 differentiation. Together, the results suggest that PRC1.1 components, BCOR and KDM2B, work together to enhance Th17 cell formation by repressing Th17 fate suppressors.

overall_design: ChIP-Seq (Input and BCOR-Specific ChIP) and RNA-Seq (WT vs BCOR-deficient cells for each of the 4 CD4+ T cell subsets)

first: Jessica

middle: A

last: Kotov

middle: D

first: Marc

middle: K

last: Jenkins


title: Simultaneous quantifications of protein-DNA contacts and transcriptomics in single cells (mESC data)

city: Utrecht

first: Koos

last: Rooijers

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Here we present a new version of the DamID method that allows efficient capturing of protein-DNA interactions and mRNA output from the same single cell. With this protocol, we have measured the direct impact of spatial genome positioning and chromatin accessibility on mRNA output in mouse embryonic stem cells

overall_design: (i) 7 libraries with a total of 336 single-cell mESC samples expressing Dam-LMNB1, in two separate clonal lines (ii) 5 libraries with a total of 288 single-cell mESC samples expressing Dam (untethered) in serum, 2i and differentiated conditions, (iii) 2 libraries with a total of 192 single-cell mESC samples expressing Dam-RING1B in serum and differentiated conditions and (iv) 2 libraries with a total of 96 single-cell mESC samples (clone expressing untethered Dam), where AluI digestion is performed, instead of DpnI digestion

first: Corina

last: Markodimitraki

first: Franka

last: Rang

first: Siddharth

last: Dey

first: Jop

last: Kind


title: miRNA expression in EBC

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

summary: Cystic Fibrosis (CF) is the most common life limiting genetic disorder, characterized by chronic respiratory failure secondary to inflammation and chronic bacterial lung infection. Pseudomonas aeruginosa lung infection is associated with more severe lung disease and rapid progression of respiratory failure when compared to Staphylococcus aureus infection.  We hypothesized that a specific signature of epigenetic factors targeting specific gene transcripts contributes to the increased morbidity seen in CF patients with chronic Pseudomonas infection. We collected exhaled breath condensate (EBC) from 27 subjects and evaluated miRNA signatures in these samples using commercial PCR array. We identified predicted mRNA targets and associated signaling pathways using Ingenuity Pathway Analysis.  We found 11 differentially expressed miRNAs in EBC of patients infected with Pseudomonas aeruginosa compared to EBC from CF patients who were not chronically infected with Pseudomonas aeruginosa.

overall_design:
We extracted RNA  from 0.5 mL of EBC from control and CF patients (Pseudomonas infection positive or negative) using the Plasma/Serum RNA Purification Kit. The expression of 1,066 human miRNAs was quantified using the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z). Results (Ct values) were normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.

variable control: Sample C01, Sample C02, Sample C04, Sample C05, Sample C06, Sample C07, Sample C08, Sample C09, Sample C10

variable CF Pseudomonas (+):  Sample CF03, Sample CF07, Sample CF08, Sample CF11, Sample CF13, Sample CF14, Sample CF15, Sample CF17, Sample CF18, Sample CF19

variable CF Pseudomonas  (-):Sample CF01, Sample CF02, Sample CF04, Sample CF05, Sample CF06, Sample CF09, Sample CF10, Sample CF12, Sample CF16

first: Roopa

last: Siddaiah


title: Simultaneous quantifications of protein-DNA contacts and transcriptomics in single cells (KBM7 data)

summary: Here we present a new version of the DamID method that allows efficient capturing of protein-DNA interactions and mRNA output from the same single cell. With this protocol, we have measured the direct impact of spatial genome positioning and chromatin accessibility on mRNA output in human haploid cells

overall_design: (i) 5 libraries with a total of 240 single-cell samples of KBM7 clone 14, expressing Dam-LMNB1, generated with 2 different DamID adapter concentrations, (ii) 3 libraries with a total of 144 single-cell samples of KBM7 clone 5.5, also expressing Dam-LMNB1, (iii) 2 libraries with a total of 96 single-cell samples of KBM7 clone 5.8, expressing Dam (untethered) and (iv) a single library with 24 single-cell samples of wild-type KBM7, digested with the AluI restriction enzyme, processed without combined transcriptomic measurements


title: Simultaneous quantifications of protein-DNA contacts and transcriptomics in single cells

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

country: Austria

institute: Medical University of Vienna

summary: E2F transcription factors are central regulators of cell division and cell fate decisions. E2F4 often represents the predominant E2F activity in cells. E2F4 is a transcriptional repressor implicated in cell cycle arrest and whose repressive activity depends on its interaction with members of the RB family. Here we show that E2F4 is important for the proliferation and the survival of mouse embryonic stem cells. In these cells, E2F4 acts in part as a transcriptional activator that promotes the expression of cell cycle genes. This role for E2F4 is independent of the RB family. Accordingly, E2F4 functionally interacts with chromatin regulators associated with gene activation and we observed decreased histone acetylation at the promoters of cell cycle genes and E2F targets upon loss of E2F4 in RB family-mutant cells. Taken together, our findings uncover a non-canonical role for E2F4 that provide insights into the biology of rapidly dividing cells.

overall_design:
RNA-seq analysis of mESCs representing WT, E2F4KO, Rb TKO, Rb + E2F4 QKO

ChIP-seq analysis of H3K4me3 and H3K9ac in Rb TKO and Rb + E2F4 QKO mESCs.

first: Jenny

last: Hsu

first: Julien

last: Sage


title: Identification of a pro-angiogenic functional role for FSP1 positive fibroblast subtype in wound healing

status: Public on Apr 20 2019

city: Nashville

first: Sarika

last: Saraswati

state: TN

address: 1161 21st Avenue South, MCN C2217

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

summary:
RNA sequencing was performed on uninjured, and injured (FSP1, and aSMA expressing) fibroblasts from mice hearts.
Fibrosis accompanying wound healing can drive the failure of many different organs. Activated fibroblasts are the principal determinants of post-injury pathological fibrosis as well as physiological repair, making them a difficult therapeutic target. Fibroblasts are a heterogeneous cell population lacking unique functional classification. We demonstrated that FSP1 and αSMA expressing cells are distinct, post-injury fibroblasts in the heart, kidney, and skin and exhibit unique temporal expression patterns. Using mice that express GFP under the FSP1 or αSMA promoters, we isolated these fibroblasts from mouse hearts after myocardial infarction. Protein and transcript arrays, cellular assays as well as in vivo granulation tissue formation were used to determine their functional role(s) in healing and fibrosis. Whereas αSMA+ fibroblasts predominated in producing matrix proteins, FSP1+ fibroblasts significantly promoted angiogenesis. These studies have the potential to shift our focus towards viewing fibroblasts not only molecularly but also as functionally heterogeneous and provide a new paradigm with which to approach treatment for organ fibrosis.

overall_design: Fibroblasts were isolated from uninjured BL6 mice for control. FSP1 and aSMA expressing fibroblasts were isolated from transgenic mice that express GFP under FSP1 or aSMA promoter. GFP positive cells were freshly sorted 10 days following myocardial infarction from mice ventricles. RNA was prepared using Ambion RNAqueous kit and submitted for RNA sequencing.

first: Pampee

last: Young


title: Time point studies of bPGN treated HCT-116 cell line

city: Frederick

first: Barry

middle: Richard

last: O'Keefe

state: Maryland

address: Bldg. 562, Rm. 201, NCI at Frederick

department: Center for Cancer Research

institute: National Cancer Institute

summary:
HCT-116 cell lines were treated with bPGN and treated cells were harvested at time-point 0, 1hour and 24hours.
Identification of RNA-interacting pharmacophores could provide new chemical probes and potentially novel RNA-based therapeutics. Herein, using a high-throughput differential scanning fluorimetry assay, we identified small molecule natural products with the capacity to bind the discrete stem-looped structure of pre-miR-21. The most potent compound identified was a prodiginine-type compound, butylcylcoheptyl prodiginine (bPGN), with the ability to inhibit Dicer-mediated processing of pre-miRNA-21 in vitro and in cells. Time dependent RT-qPCR, western blot, and transcriptomic analyses showed modulation of miR-21 expression and its target genes such as PDCD4 and PTEN upon treatment with bPGN, supporting on-target inhibition. Consequently, inhibition of cellular proliferation in HCT-116 colorectal cancer cells was also observed when treated with bPGN. The discovery that bPGN can bind and modulate the expression of regulatory RNAs such as miR-21 helps set the stage for further development of this class of natural product as a molecular probe or therapeutic agents against miRNA-dependent diseases.

overall_design:
Cells were treated with bPGN and cells were harvested for nanostring analysis at time-points 0, 1, and 24 hours.

Contributor: NCI Genomics Center

first: Joe

last: Matarlo


title: Long non-coding and protein-coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy

status: Public on Apr 19 2019

city: Beijing

first: Zhou

last: Zhou

address: Beilishi Street 167, Xi Cheng District

institute: Fuwai Hospital, the Chinese Academy of Medical Sciences

summary: Hypertrophic cardiomyopathy (HCM) represents one of the most common heritable heart diseases. However, the signalling pathways and regulatory networks underlying the pathogenesis of HCM remain largely unknown. Here, we present a strand-specific RNA-seq dataset for both coding and lncRNA profiling in myocardial tissues from 28 HCM patients and 9 healthy donors. This dataset constitutes a valuable resource for the community to examine the dysregulated coding and lncRNA genes in HCM versus normal conditions.

overall_design: SRA Study accession:SRP186138; BioProject accession:PRJNA522931; Strand-specific RNA-seq of myocardial tissues from 28 HCM patients and 9 healthy donors using illumina Hiseq X Ten

first: Xuanyu

last: Liu


title: Genome-wide miRNA expression analysis of Caenorhabditis elegans AXIN mutant

city: boston

first: Ayush

middle: Vasant

last: Ranawade

state: MA

address: 360 Huntington Ave

department: Bioengineering

institute: Northeastern University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goal of this study is to identify differentially expressed microRNAs in pry-1/Axin mutant compare to N2 wild-type (WT).
Our study represents the first microRNA analysis of Axin transcriptome in C. elegans and facilitates investigations of axin mediated processes.

overall_design: Whole animal total RNA was extracted from L1 synchronized worms and total small RNA profiles of WT and pry-1(mu38) animals were generated by single end deep sequencing, using Illumina HISeq 2000. The sequence reads that passed quality filters were analyzed using mirbase cel.gff3 with mirDeep2 star to estimate transcript abundances and differentially-expressed microRNAs at a false discovery rate (FDR) of 0.05%.

first: Bhagwati

last: Gupta

first: Avijit

last: Mallick


title: Single-Cell RNA Sequencing Reveals Regional Reprogramming during Adaptation to Massive Small Bowel Resection in Mice

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

summary: Single-cell RNA sequencing reveals interactions between the retinoid metabolism pathway and molecular “proximalization”, or regional reprogramming, of distal small intestine epithelium following proximal small bowel resection. This provides novel insight into physiological adaptation to short gut syndrome.

overall_design: Single-cell RNA sequencing was performed on epithelial cells isolated from distal SI (ileum) of mice following small bowel resection vs. sham surgery.

first: Sarah

middle: E

last: Waye


title: Transcriptional characterization of adipose progenitors

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: Adipose stem and progenitor cells, defined as live CD45- CD31- Ter119- CD140a+ Sca1+ PDPN+, were sorted from the epididymal adipose tissue of three wild type 12 week old male mice for transcriptional analysis.

overall_design: Epididymal adipose tissue of excised from three naïve wild type 12 week old male mice. Tissue was digested in Collagenase II and the stromal vascular fraction cells stained with antibodies for cell sorting. Live CD45- CD31- Ter119- CD140a+ Sca1+ PDPN+ cells were sorted to high purity into lysis buffer. RNAseq library was prepared and sequence using the Illumina platform.

first: Tanel

last: Mahlakõiv

first: David

last: Artis


title: Total tRNA level and tRNA charged fraction in DLD-1 cells treated with 4-hydroxytamoxefen and compared to untreated cells

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

summary: Comparison of overall tRNA level and fraction of charged tRNAs upon treatment with 4-hydroxytamoxefen and compared to untreated cells

overall_design: Control cells used for tRNA charging and abundance - 5 replicates; treatment with 4-hydroxytamoxifen for 2h - 2 replicates; teratment with 4-hydroxytamoxifen for 4h - 5 replicates; treatment with 4-hydroxytamoxifen for 8h - 4 replicates for charging and 3 for total tRNA abundance; control without Leu - 3 replicates

first: Christine

last: Polte

first: Zoya

last: Ignatova


title: Opposite microglial activation stages upon loss of PGRN result in reduced cerebral glucose metabolism

status: Public on Apr 18 2019

city: Munich

first: Anja

last: Capell

state: Bavaria

address: Feodor-Lynen Str 17

department: Biomedical Center (BMC)

country: Germany

institute: Ludwig-Maximilians-University

summary: Microglia adopt numerous fates with homeostatic microglia (HM) and a microglial neurodegenerative phenotype (MGnD) representing two opposite ends.  A number of variants in genes selectively expressed in microglia are associated with an increased risk for neurodegenerative diseases such as Alzheimer's disease (AD) and Frontotemporal lobar degeneration (FTLD).  Among these genes are progranulin (GRN) and the triggering receptor expressed on myeloid cells 2 (TREM2).  Both cause neurodegeneration by mechanisms involving loss-of-function.   We have now isolated microglia from Grn–/– mice and compared their transcriptomes to those of Trem2–/– mice.  Surprisingly, while loss of Trem2 enhances the expression of genes associated with a homeostatic state, microglia derived from Grn–/– mice showed a reciprocal activation of the MGnD molecular signature and suppression of genes characteristic for HM.  The opposite mRNA expression profiles are associated with divergent functional phenotypes. Although loss of TREM2 and progranulin resulted in opposite activation states and functional phenotypes of microglia, FDG (fluoro-2-deoxy-D-glucose)-µPET of brain revealed reduced glucose metabolism in both conditions, suggesting that opposite microglial phenotypes result in similar wide spread brain dysfunction.

overall_design: In this study we analyzed microglial gene expression in total RNA from acutely isolated microglia of brain from adult mice. We compared the expression profile of Grn knockout mice (n=5, 5.5 months, male) to wildtype mice (n=5, 5.5 months, male).

first: Julia

last: Götzl


title: Genome wide screening for binding of TCF4 (E2-2) transcription factor in SU-DHL-2 ABC like diffuse large B-cell lymphoma lines.

city: HOUSTON

first: Michael

last: Green

state: TEXAS

address: 7455 fannin street, SCR2.2026, Department of Lymphoma/Myeloma

institute: MD Anderson Cancer Center

summary: We identified potential TCF4 targeted genes by performing CHIP-Seq using TCF4 antibody in ABC like DLBCL cell lines. We have identified strong binding of TCF4 to enhancer elements of B-cell receptor signaling components which drives B-cell receptor signaling.

overall_design: SU-DHL-2 ABC-DLBCL cell lines with no TCF4 copy number gain was used to overexpress tetracyclin based TCF4 expression exogeneously. ChIP-Seq was performed 24 hours after tetracyclin treatment.


title: Targetable genetic alterations of TCF4 (E2-2) drive immunoglobulin expression in the activated B-cell subtype of diffuse large B-cell lymphoma.


title: PD-1/PD-L1 checkpoint blockade harnesses monocyte-derived macrophages to combat cognitive impairment in a tauopathy mouse model

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: Alzheimer’s disease (AD) is a heterogeneous disorder with multiple etiologies. Harnessing the immune system by blocking the programmed cell death receptor (PD)-1 pathway in an amyloid beta mouse model was shown to evoke a sequence of immune responses that lead to disease modification. Here, blocking PD-L1, a PD-1 ligand, was found to have similar efficacy to that of PD-1 blocking in disease modification, in both animal models of AD and of tauopathy. Targeting PD-L1 in a tau-driven disease model resulted in increased immunomodulatory monocyte-derived macrophages within the brain parenchyma. Single cell RNA-seq revealed that the homing macrophages expressed unique scavenger molecules including macrophage scavenger receptor 1 (MSR1), which was shown here to be required for the effect of PD-L1 blockade in disease modification. Overall, our results demonstrate that immune checkpoint blockade targeting the PD-1/PD-L1 pathway leads to modification of common factors that go awry in AD and dementia, and thus can potentially provide an immunotherapy to help combat these diseases.

overall_design: Cell populations were sorted with FACSAriaIII (BD Biosciences, San Jose, CA). Prior to sorting, all samples were filtered through a 40-μm nylon mesh. For the isolation of monocytes-derived macrophages, samples were gated for CD45high and CD11bhigh (Brilliant-violet-421, 1:150, 30-F11, Biolegend Inc. San Diego, CA; APC CD11b, 1:100, M1/70, eBioscience), while excluding doublets. Isolated cells were single cell sorted into 384-well cell capture plates containing 2 μL of lysis solution and barcoded poly(T) reverse-transcription (RT) primers for single-cell RNA-seq84. Four empty wells were designated in each 384-well plate as a no-cell control during data analysis. Immediately after sorting, each plate was spun down to ensure cell immersion into the lysis solution, snap frozen on dry ice, and stored at −80 °C until processing. Single-cell libraries were prepared as previously described73. In brief, mRNA from cells sorted into cell capture plates was barcoded, converted into cDNA, and pooled using an automated pipeline. The pooled sample was then linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pooled barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality, and concentration was assessed, as described73.

first: Neta

last: Rosenzweig

first: Raz

last: Dvir-Szternfeld

first: Afroditi

last: Tsitsou-Kampeli

first: Hadas

last: Keren-Shaul

first: Assaf

last: Weiner

first: Michal

last: Schwartz


title: Functional robustness of spermatogonial stem cells after induction of hyperactive Hras

first: Marco

last: Seandel

department: Surgery

institute: Weill Cornell Medical College

summary: We report on gene expression in stem cell-enriched, undifferentiated spermatogonia isolated from the adult mouse testis, in which one group are wild type and the other group contain a heterozygous Hras G12V mutation.

overall_design: Comparison of two different genotypes

first: Makiko

last: Yamada


title: Next Generation Sequencing Facilitates Quantitative Analysis of PSKγ1ox and control Transcriptomes

city: Shanghai

first: Liangliang

last: Yu

address: 381 Nanchen Road, Baoshan District

institute: Shanghai University

summary: Phytosulfokine-α (PSK-α), a sulfated pentapeptide hormone with the sequence YIYTQ, plays important roles in many aspects of plant growth and development. In this study, we identified a pair of putative precursor genes in soybean, GmPSKγ1 and -2, encoding a PSK-like peptide: PSK-γ. Similar to PSK-α in amino acid composition, the sequence of PSK-γ is YVYTQ, and the tyrosines undergo sulfonylation. Treatment of Arabidopsis seedlings with synthetic sulfated PSK-γ significantly enhanced root elongation, indicating that PSK-γ might be a functional analog of PSK-α. Expression pattern analysis revealed that the two GmPSKγ genes, especially GmPSKγ1, are primarily expressed in developing soybean seeds. Heterologous expression of GmPSKγ1 under the control of a seed-specific promoter markedly increased seed size and weight in Arabidopsis, and this promoting effect of PSK-γ on seed growth was further confirmed in transgenic tobacco constitutively expressing GmPSKγ1. Cytological analysis of transgenic Arabidopsis seeds revealed that PSK-γ promotes seed growth by inducing embryo cell expansion. In addition, transcriptome analysis of GmPSKγ1-expressing Arabidopsis seeds suggested that PSK-γ signaling may regulate cell wall loosening to promote cell expansion. Overall, our results shed light on the mechanism by which PSK-γ promotes seed growth, paving the way for the use of this new peptide for biotechnological improvement of crop seed/grain size and yield.

overall_design: Seed (10 DAP) transcriptomes of  OLEOp:GmPSKγ1 and OLEOp:GmPSKγ1tc (control) were generated by deep sequencing using Illumina Hiseq 2500. RNA isolated from three individual lines of each genotype were pooled together for sequencing.

first: Li

last: Luo


title: Differential gene expression analysis in BRD4-PROTAC treated diffuse large B-cell lymphoma cell lines

summary: We identified differential gene expression after treatment with BRD4-PROTAC ARV771 in two ABC-like diffuse large B-cella lymphoma cell lines. We have identified cluster of gene expression regulated after BRD4 inhibition which are criticaly important for DLBCL malignancy.

overall_design: Two ABC-DLBCL cell lines were used to identify the changes in gene expression profile after BRD4-PROTAC (ARV771) treatment.


title: Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma [RNA-seq]

status: Public on Apr 17 2019

city: Strasbourg

first: Irwin

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

summary: We have used a mouse model where melanoma can be induced by Tamoxifen treatment that induces expression of oncogenic Braf and deletion of Pten in the melanocyte lineage using a Tyr::Cre-ER-T2 transgene to mediate recombination. Cells from these melanoma tumours were cultured in vitro and the effects of siRNA mediated silencing of transcription factors Mitf and Sox10 was performed and analysed by RNA-seq. We then crossed these mice with mice bearing floxed alleles of the genes encoding the chromatin remodelling factors Bptf and Brg1 (Smarca4). Tumour cells were grown in culture and Bptf or Brg1 inactivated by 4-OHT treatment. The effects on gene expression were assessed by RNA-seq.

overall_design: Triplicate RNA-seq data for: Control siRNA, siMitf and siSox10. Triplicate RNA-seq data for 4-OHT control cells, 4OHT floxed Brg1 (Smarca4), 4-OHT floxed Bptf.

first: Patrick

last: Laurette

first: Sebastien

last: Coassolo

first: Guillaume

first: Isabelle

last: Michel

first: Wenjin

last: Yao

first: Pierre

last: Sohier

first: Mei

last: Li

first: Lionel

last: Larue

first: Gabrielle

last: Mengus

first: Giovanni

last: Gambi


title: Genome wide screening for binding of TCF4 (E2-2) transcription factor in ABC like diffuse large B-cell lymphoma line TMD8.

first: Michael

last: Green

overall_design: TMD8 ABC-DLBCL cell lines with no TCF4 copy number gain was used to overexpress tetracyclin based TCF4 expression exogeneously. ChIP-Seq was performed 24 hours after tetracyclin treatment.


title: Daedalus and Gasz recruit Armitage to mitochondria, bringing piRNA precursors to the biogenesis machinery

city: Cambridge

first: Marzia

last: Munafo

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

institute: University of Cambridge

summary: The piRNA pathway is a small RNA-based immune system that silences mobile genetic elements in animal germlines. piRNA biogenesis requires a specialised machinery that converts long single-stranded precursors into small RNAs of ~25-nucleotides in length. This process involves factors that operate in two different subcellular compartments: the nuage/Yb-body and mitochondria. How these two sites communicate to achieve accurate substrate selection and efficient processing remains unclear. Here, we investigate a previously uncharacterized piRNA biogenesis factor, Daedalus (Daed), that is located on the outer mitochondrial membrane. Daed is essential for Zucchini-mediated piRNA production and for the correct localisation of the indispensable piRNA biogenesis factor Armitage (Armi). We find that Gasz and Daed interact with each other and likely provide a mitochondrial “anchoring platform” to ensure that Armi is held in place, proximal to Zucchini, during piRNA precursor processing. Our data suggest that Armi initially identifies piRNA precursors in nuage/Yb-body in a manner that depends upon Piwi and then moves to mitochondria to present them to the biogenesis machinery. These results represent a significant step in understanding a critical aspect of transposon silencing, namely how RNAs are chosen to instruct the piRNA machinery in the nature of its silencing targets.

overall_design:
Characterization of newly discovered Drosophila melanogaster gene CG10880 (Daedalus) involvement in piRNA biogenesis
smallRNA seq: OSCs were treated with indicated siRNA
CLIPseq: OSCs were treated with siRNA and transfected with indicated plasmids

last: Munafò

first: Vera

last: Manelli

first: Federica

last: Falconio

first: Ashley

last: Sawle

first: Emma

last: Kneuss

first: Evelyn

middle: L

last: Eastwood

first: Jun

middle: W

last: Seah

first: Benjamin

last: Czech

first: Gregory

middle: J

last: Hannon


title: Interleukin-17 receptor D constitutes an alternative receptor for interleukin-17A important in psoriasis-like skin inflammation

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: To understand the overall function of IL-17RD and IL-17RC in IL-17A signaling, RNAseq was performed with WT, Il17rc KO, and Il17rd KO primary mouse keratinocytes following IL-17A treatment along with untreated WT control. Keratinocyte from neonatal WT, Il17rd KO, and Il17rc KO mice were cultured and stimulated with IL-17A (100 ng/mL, PeproTech) for 8h.

overall_design: Keratinocyte from neonatal WT, Il17rd KO, and Il17rc KO mice were cultured in 154CF medium plus HKGS kit. Cells were stimulated with IL-17A (100 ng/mL) for 8hm and then harvest for RNA-seq.

first: Yang

last: Su

first: Xiaohong

last: Zhao


title: Long-term intranasal insulin aspart: a profile of gene expression, memory, and insulin receptors in aged F344 rats

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Intranasal insulin is a safe and effective method for ameliorating memory deficits associated with pathological brain aging. However, the impact of different formulations and the duration of treatment on insulin’s efficacy and the cellular processes targeted by the treatment remain unclear. Here, we tested whether intranasal insulin aspart, a short-acting insulin formulation, could alleviate memory decline associated with aging and whether long-term treatment affected regulation of insulin receptors and other potential targets. Outcome variables included measures of spatial learning and memory, autoradiography and immunohistochemistry of the insulin receptor, and hippocampal microarray analyses. Aged Fischer 344 rats receiving long-term (3 months) intranasal insulin did not show significant memory enhancement on the Morris water maze task. Autoradiography results showed that long-term treatment reduced insulin binding in the thalamus but not the hippocampus. Results from hippocampal immunofluorescence revealed age-related decreases in insulin immunoreactivity that were partially offset by intranasal administration. Microarray analyses highlighted numerous insulin-sensitive genes, suggesting insulin aspart was able to enter the brain and alter hippocampal RNA expression patterns including those associated with tumor suppression. Our work provides insights into potential mechanisms of intranasal insulin and insulin resistance, and highlights the importance of treatment duration and the brain regions targeted.

overall_design: All subjects were male F344 rats. Subjects were young (2 months old) or aged (18 months old) at arrival, and were treated daily for 12 weeks with intranasal insulin aspart or saline (control). On the last week of treatment, all animals underwent Morris water maze protocol. Right hippocampi were dissected from N = 26 animals (young saline n = 6, young aspart n = 5, aged saline n = 8, aged aspart n = 7) were isolated over ice and placed in a -80 °C freezer until processed for RNA extraction. To extract RNA, hippocampi were thawed on ice and homogenized in RiboZol™ Extraction Reagent (#97064-948; VWR®, Radnor, PA). RNA was precipitated with chloroform and isopropanol, then resuspended in a 75% ethanol solution. Following extraction, RNA integrity numbers (RIN) were obtained for each sample using standard protocols (University of Kentucky Genomics Core, Lexington, KY). Mean values for each group were as follows: young saline = 7.32 ± 0.14, young aspart = 7.34 ± 0.15, aged saline = 7.33 ± 0.12, aged aspart = 7.29 ± 0.13. No significant difference in RIN was noted between the groups (2-way ANOVA; p > 0.5). Samples were stored in a -80 °C freezer until thawed for microarray analysis (Affymetrix™ rat Clariom™ S Assay; Thermo Fisher Scientific, Waltham, MA). Gene signal intensities were calculated using the Robust Multiarray Average algorithm at the transcript level and data were associated with vendor-provided annotation information.

first: Hilaree

middle: N

last: Frazier

first: Adam

middle: O

last: Ghoweri

first: Emily

last: Sudkamp

first: Eleanor

middle: S

last: Johnson

first: Katie

last: Anderson

first: Grant

last: Fox

first: Keomany

last: Vatthanaphone

first: Kia

last: Megfan

first: Lin

last: Ruei-Long

first: Kendra

last: Hargis-Staggs

first: Nada

last: Porter

first: James

middle: R

last: Pauly

first: Olivier

last: Thibault


title: Zfp217 orchestrates m6A mRNA methylation and gene expression to promote adipogenic differentiation

city: wuhan

first: yang

last: yang

address: 1 Shizishan Road

institute: Huazhong Agricultural Universit

type: Methylation profiling by high throughput sequencing

summary:
We performed RNA sequencing (RNA-seq) and m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in control and Zfp217 knockout 3T3L1 cells with MDI treatment for 0d and 2d
Loss-of-function study demonstrates that Zfp217 deficiency impaired adipogenesis together with a global increase of m6A modification in 3T3L1cells. To gain an overview of the global role of Zfp217 in adipogenesis, we performed RNA sequencing (RNA-seq) in control and Zfp217 knockout 3T3L1 cells with MDI treatment for 0d and 2d and identified 12,188 and 11,566 different expressed genes (DEG) for 0d and 2d, respectively. Next, to elucidate the mechanism by which Zfp217 regulates m6A restriction, m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to analyze the m6A mRNA methylation in control and Zfp217 knockout 3T3L1 cells with MDI treatment for 0d and 2d, and identified 3149 and 294 of m6A peaks experienced an increase in m6A RNA modification after Zfp217 depletion, respectively.

overall_design: Examination of gene expressive levels, m6A enrichment levels, in control and Zfp217 knockout 3T3L1 cells with MDI treatment for 0d and 2d

first: tongxing

last: song


title: XX sex chromosome complement promotes hyperlipidemia and atherosclerosis in mice

summary: It is well recognized that men and women differ in circulating lipid profiles and consequently coronary artery disease (CAD). While sex hormones like estrogens are thought to protect women from CAD risk by promoting protective lipid profiles, hormone replacement therapy in women paradoxically increases CAD risk. Biological sex is determined by both sex chromosomes and sex hormones. We used mouse models to separate effects of sex chromosomes and hormones on atherosclerosis, circulating lipids and intestinal fat metabolism. We found that an XX sex chromosome complement increases food intake, body weight, fat absorption, serum lipid concentrations and atherosclerosis in gonadal male and female mice, indicating a primary effect of sex chromosome complement. Small intestine expression of enzymes involved in lipid absorption and chylomicron assembly were increased in XX male and female mice with elevated intestinal lipids. These results reveal that an XX sex chromosome complement promotes the absorption and bioavailability of dietary fat to accelerate the development of atherosclerosis.

overall_design: Liver tissue was harvested from 24-28 week old Ldlr-/- male and female mice with an XX or XY chromosomal complement that had been surgically gonadectomized at 8-12 weeks of age and then fed a Western high fat diet for 16 weeks (n = 5 female XX, n = 5 female XY, n = 4 male XX, n = 5 male XY; no technical replicates were performed). Harvested liver RNA samples were of sufficient quality and did not differ significantly among treatment groups (Agilent Bioanalyzer RNA Integrity Number [RIN]: 9.55 ± 0.05 – p > 0.29; two-way ANOVA main effect of Sex p = 0.25; main effect of chromosome p = 0.13; interaction p = 0.42). Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0; one array per subject). Signal intensities were calculated using the Robust Multi-array Average (RMA) algorithm at the transcript level in Genomics Suite (Partek, St Louis). Data were transferred to flat files in Excel and associated with Gene Expression Omnibus annotations for this microarray platform (GPL20775). Pre-statistical filtering retained unique, annotated probe sets with signal intensity ≥ 4.2 on at least 2 arrays in the study. Filtered signal intensities were analyzed by two-way ANOVA to identify significant main effects of genotype (XX versus XY), phenotypic sex (Male vs Female), as well as Interaction.  The False Discovery Rate (FDR) procedure, as modified by Storey was used to control for the error of multiple testing (q ≤ 0.01).

first: Yasir

last: AlSiraj

first: Sean

last: Thatcher

first: Ryan

last: Temel

first: Lei

last: Cai

first: Wendy

last: Katz

first: Heba

last: Ali

first: Michael

last: Petriello

first: Andrew

last: Morris

first: Arthur

middle: P

last: Arnold

first: Karen

last: Reue

first: Patrick

last: Tso

first: Lisa

last: Cassis


title: A comprehensive map of intron branchpoints and lariat RNAs in plants

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: Lariat is formed by excised intron, in which the 5' splice site joints with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by DBR1 (RNA debranching enzyme 1), recent findings in animals showed that many lariat RNAs were widely detected under physiological conditions. In contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing datasets to document plant BPs and lariat RNAs on a genome-wide scale. In total, we identified 13872, 5199, 29582, and 13478 BPs in Arabidopsis, tomato, rice, and maize, respectively. Features of plant BPs are highly similar to those in yeast and human, in that BPs are adenine-preferred and flanked by uracil-enriched sequences. Intriguingly, ~20% of introns harbor multiple BPs, and BP usage is tissue-specific. Furthermore, 10580 lariat RNAs accumulate in wild type Arabidopsis plants, and most of these lariat RNAs originate from longer or retroelement-depleted introns, and the expression of these lariat RNAs significantly correlated with the incidence of back-splicing of parent exons. Collectively, our results provide the first comprehensive map of intron BPs and lariat RNAs in plants, and uncover a novel link between lariat turnover and splicing.

overall_design: 8 samples for two geneotypes (Col-0 and dbr1-2) are used for analysis, which includes 4 samples of Rnase R-minus and 4 samples for Rnase R-plus samples. Both Col-0 and dbr1-2 has two replicates for Rnase R-minus and Rnase R-plus, respectively

first: Binglian


title: Genome wide binding of Top2 (in WT and uls1 delta cells) and Uls1 (in WT cells) both in the presence and absence of the Top2 poison acriflavine (ACF)

city: St Andrews

first: Helder

last: Ferreira

address: North Haugh

institute: University of St Andrews

summary: Topoisomerase II (Top2) is an essential enzyme that decatenates DNA via a transient Top2-DNA covalent intermediate. This intermediate can be stabilised by a class of drugs termed Top2 poisons, resulting in massive DNA damage. Thus, Top2 activity is a double-edged sword that needs to be carefully controlled to maintain genome stability. We show that Uls1, an ATP-dependent chromatin remodelling (Snf2) enzyme, can alter Top2 chromatin binding and prevent Top2 poisoning in yeast. Deletion mutants of ULS1 are hypersensitive to the Top2 poison acriflavine (ACF), activating the DNA damage checkpoint. We map Uls1’s Top2 interaction domain and show that this, together with its ATPase activity, is essential for Uls1 function. By performing ChIP-seq, we show that ACF leads to a general increase in Top2 binding across the genome. We map Uls1 binding sites and identify tRNA genes as key regions where Uls1 associates after ACF treatment. Importantly, the presence of Uls1 at these sites prevents ACF-dependent Top2 accumulation. Our data reveal the effect of Top2 poisons on the global Top2 binding landscape and highlights the role of Uls1 in antagonising Top2 function. Remodelling Top2 binding is thus an important new means by which Snf2 enzymes promote genome stability.

overall_design: Four independent ChIP replicates of each condition were pooled to form two DNA sequencing replicates. 2 x 75bp paired-end Illumina sequencing


title: Global Gene Changes in Hearts from CardioMRKO Mice

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Heart failure is one of the leading causes of death in the Western world, and stress is increasingly associated with adverse cardiac outcomes. Glucocorticoids are primary stress hormones that regulate homeostasis through two closely related nuclear receptors, the glucocorticoid receptor (GR) and mineralocorticoid receptor (MR). Cardiomyocytes express both receptors but little is known concerning their coordinated actions in heart physiology and pathology. To examine the in vivo function of glucocorticoid signaling in the heart, we generated mice with cardiomyocyte-specific deletion of GR (cardioGRKO), MR (cardioMRKO), or both GR and MR (cardioGRMRdKO). The cardioMRKO mice exhibited normal heart function whereas the cardioGRKO mice spontaneously developed cardiac hypertrophy and left ventricular systolic dysfunction. Surprisingly, the cardioGRMRdKO mice were protected from cardiac disease. Genome-wide microarrays were performed on isolated hearts from each mouse model to 1) identify genes subject to regulation by GR alone, MR alone, or both GR and MR and 2) identify the genes responsible for the cardiac pathology in the cardioGRKO mice and for the cardioprotection in the cardioGRMRdKO mice.

overall_design: Mice harboring a floxed MR allele (MRflox) were crossed with cardiomyocyte-specific αMHC-Cre mice to generate the cardioMRKO mice.  Total RNA for microarray analysis was harvested from whole hearts isolated from 4 male 1-month old cardioMRKO mice, 4 male 1-month old littermate controls, 4 male 2-month old cardioMRKO mice, and 4 male 2-month old littermate controls.  Littermate controls were Cre negative MRflox mice.

first: Robert

middle: H

last: Oakley

first: John

last: Cidlowski


title: Global Gene Changes in Hearts from CardioGRMRdKO Mice

overall_design: Mice harboring a floxed GR allele and floxed MR allele (dflox) were crossed with cardiomyocyte-specific αMHC-Cre mice to generate double knockout mice lacking both GR and MR in the heart (cardioGRMRdKO mice).  Total RNA for microarray analysis was harvested from whole hearts isolated from 3 male 1-month old cardioGRMRdKO mice, 3 male 1-month old littermate controls, 3 male 2-month old cardioGRMRdKO mice, and 3 male 2-month old littermate controls.  Littermate controls were Cre negative dflox mice.


title: Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

summary: Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. To gain insights into the genome-wide transcriptional regulation in lentil root and leaf under short- and long-term drought conditions, we performed RNA-seq on a drought-sensitive lentil cultivar (Lens culinaris Medik. cv. Sultan). After establishing drought conditions, lentil samples were subjected to de novo RNA-seq-based transcriptome analysis. The 207,076 gene transcripts were successfully constructed by de novo assembly from the sequences obtained from root, leaf, and stems. Differentially expressed gene (DEG) analysis on these transcripts indicated that period of drought stress had a greater impact on the transcriptional regulation in lentil root. The numbers of DEGs were 2915 under short-term drought stress while the numbers of DEGs were increased to 18,327 under long-term drought stress condition in the root. Further, Gene Ontology analysis revealed that the following biological processes were differentially regulated in response to long-term drought stress: protein phosphorylation, embryo development seed dormancy, DNA replication, and maintenance of root meristem identity. Additionally, DEGs, which play a role in circadian rhythm and photoreception, were downregulated suggesting that drought stress has a negative effect on the internal oscillators which may have detrimental consequences on plant growth and survival. Collectively, this study provides a detailed comparative transcriptome response of drought-sensitive lentil strain under short- and long-term drought conditions in root and leaf. Our finding suggests that not only the regulation of genes in leaves is important but also genes regulated in roots are important and need to be considered for improving drought tolerance in lentil.

overall_design: mRNA profiles of Lens culinaris Medik. cv. Sultan cells were obtained under short- (24 hours) and long-term (96 hours) drought conditions with no-stress controls by deep sequencing, in two biological replicates, using Illumina HiSeq platform.

first: Mehmet

last: Tardu

first: Hande

last: Morgil

first: Gul

last: Cevahir

first: Ibrahim

last: Kavakli


title: Global Gene Changes in Hearts from CardioGRKO Mice

overall_design: Mice harboring a floxed GR allele (GRflox) were crossed with cardiomyocyte-specific αMHC-Cre mice to generate the cardioGRKO mice.  Total RNA for microarray analysis was harvested from whole hearts isolated from 3 male 1-month old cardioGRKO mice, 3 male 1-month old littermate controls, 3 male 2-month old cardioGRKO mice, and 3 male 2-month old littermate controls.  Littermate controls were Cre negative GRflox mice.


title: Transcriptomics analysis of cells treated with Schizocommunin and its analogue

status: Public on Apr 16 2019

city: Ottawa

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

summary:
Schizocommunin is a natural alkaloid produced from the Schizophyllum commune fungus. In 1994, the first case of allergic bronchopulmonary mycosis caused by the fungus was described.
We sought to determine the effects of Schizocommunin treatment on the human transcriptome to identify mechanisms through which the pathogen may be causing the allergic response.

overall_design: Human liver heptoma cells were treated with Schizocommuinin and a synthetic analogue. RNA was extracted and analyzed using a Affymetrix Human Gene ST.2.0 array.

first: Roxana

last: Filip

first: Tyler

last: Shaw

first: Atsushi

last: Nishida


title: Global Gene Changes in Hearts from Mice with Conditional Knockout of GR, MR, or both GR and MR in Cardiomyocytes

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

overall_design: Refer to individual Series


title: LKB1 orchestrates dendritic cell metabolic quiescence and  anti-tumor immunity [HT_MG-430_PM]

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary:
Loss of LKB1 leads to aberrant DC maturation and production of cytokines and immunoregulatory molecules.
DCs (n = 7 per genotype) were isolated from the spleen, and CD25+CD4+ Tregs (n = 4 for WT, n = 3 for LKB1ΔDC mice) were isolated from the spleen and peripheral lymph nodes of WT and LKB1ΔDC mice.

overall_design: This series includes 6 samples of splenic DCs (3 WT and 3 LKB1 KO DCs)

first: Yanyan

last: Wang

first: Yogesh

last: Dhungana


title: Regulation of the Hsf1-dependent transcriptome via conserved bipartite contacts with Hsp70 promotes survival in yeast

city: Houston

first: Kevin

middle: A

last: Morano

state: TX

address: 6431 Fannin St, MSB 1.300

department: Microbiology and Molecular Genetics

institute: UT Medical School at Houston

summary: Protein homeostasis and cellular fitness in the presence of proteotoxic stress is promoted by heat shock factor 1 (HSF1), which controls basal and stress-induced expression of molecular chaperones and other targets. The major heat shock proteins Hsp70 and Hsp90 in turn participate in a negative feedback loop that ensures appropriate coordination of the heat shock response with environmental conditions. Features of this regulatory circuit in the budding yeast Saccharomyces cerevisiae have been recently defined, most notably regarding direct interaction between Hsf1 and the constitutively expressed Hsp70 Ssa1. We sought to further explore the complex nature of Ssa1/Hsf1 regulation. Ssa1 is found to interact independently with both the previously defined CE2 site in the Hsf1 carboxyl-terminal transcriptional activation domain as well as a novel site that we identify within the amino-terminal activation domain. Consistent with both sites bearing a recognition signature for Hsp70, we demonstrate that Ssa1 contacts Hsf1 using its substrate binding domain and abolishing either regulatory site results in loss of Ssa1 association. Removing Hsp70 regulation of Hsf1 results in global dysregulation of Hsf1 transcriptional activity, with synergistic effects when both sites are disrupted together on both gene expression and cellular fitness. Finally, we find that Hsp70 interacts with both transcriptional activation domains of Hsf1 in the related yeast Lachancea kluyveri, implying a conserved mechanism of regulation to promote cellular proteostasis.

overall_design: Three biological replicates were analyzed for four different yeast strains at 30˚C, and one strain (wild type) at 37˚C for 15 min

first: Sara

last: Peffer

first: Davi

last: Gonclaves


title: Single-Cell Transcriptomics Identifies TOX as a Key Transcriptional Regulator of Progenitor-Like CD8 T Cells in Chronic Infection [RNA-seq]

city: Bethesda

first: Tuoqi

last: Wu

state: MD

address: 49 Convent Dr.

institute: National Institute of Allergy and Infectious Diseases

summary: Stem-like CD8 T cells maintain long-term antiviral CD8 immunity during chronic infection, and share regulatory pathways with memory precursor effector cells generated after acute infection. However, it is unclear whether stem-like CD8 T cells require distinct transcriptional and epigenetic regulation for their longevity and adaptation to the immunosuppressive environment in chronic infection. Here, our comparison of single-cell transcriptomes and epigenetic profiles of CD8 T cells responding to acute and chronic viral infections revealed that stem-like CD8 T cells became distinct from memory precursors before clonal expansion ended. We found that a coexpression gene module containing Tox exhibited higher transcriptional activities and active histone marks in stem-like T cells than memory precursors. Moreover, TOX promoted persistence of antiviral CD8 T cells, and was required for stem-like CD8 differentiation. Our results indicate that stem-like CD8 T cells require unique transcriptional and epigenetic programs for their differentiation and persistence during chronic viral infection.

overall_design: Single-cell tcranscriptomic and epigentic analysis of antigen specific CD8 T cells after acute and chronic viral infection. Transcriptome analysis of TOX over expression in antigen specific CD8 T cells after chronic viral infection.

first: C

last: Yao

first: H

last: Sun

first: J

last: O'Shea

first: P

last: Schwartzberg

first: T

middle: Q


title: LKB1 orchestrates dendritic cell metabolic quiescence and anti-tumor immunity [MoGene-2_0-st]

overall_design: This series includes: splenic DCs (4 WT and 4 LKB1 KO DCs) and Tregs (4 WT and 3 Lkb1 KO Tregs).


title: Single-Cell Transcriptomics Identifies TOX as a Key Transcriptional Regulator of Progenitor-Like CD8 T Cells in Chronic Infection [ChIP-seq]

overall_design: Single-cell tcranscriptomic and epigentic analysis of antigen specific CD8 T cells after acute and chronic viral infeciton. Transcrptome analysis of TOX over expression in antigen specific CD8 T cells after chornic viral infection.


title: Single-Cell Transcriptomics Identifies TOX as a Key Transcriptional Regulator of Progenitor-Like CD8 T Cells in Chronic Infection


title: Transcriptome profiling of brown adipocytes treated with BML-260, DMSO or ISO for revealing the BML-260 mechanism

first: Zhuanghui

last: Feng

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: To explore BML-260 how to increase thermogenesis, we treated brown adipocytes with BML-260 and DMSO for 1 day or 3 days after seven days' differenciation. Meanwhile, we also set ISO (isoproterenol)-treated brown adipocytes as positive control. We found that BML-260 treatment led to very significant upregulation of genes involved in oxidative phosphorylation, fatty acid beta-oxidation, and mitochondrial function.When compared to cells treated with ISO, although both showed significant upregulation of UCP1, BML-260-treated cells showed a rather distinct gene profile when compared to ISO-treated cells. This work provides evidences that BML-260 can also exert a JSP-1-independent effect in activating UCP1 and thermogenesis in adipocytes, and be potentially applied to treat obesity.

overall_design: Five groups of compound-treated brown adipocytes, including one-day and three-day BML-260 or DMSO treatment as well as ISO treatment. Each group has two samples.

first: Qiurong

last: Ding

first: Yuda

last: Wei

first: Yongxian

last: Zhang

first: Yan

last: Qiu

first: Xiaojian

last: Liu

first: Hua


title: Single-Cell Transcriptomics Identifies TOX as a Key Transcriptional Regulator of Progenitor-Like CD8 T Cells in Chronic Infection [single-cell RNA-seq]

summary: Stem-like CD8 T cells maintain long-term antiviral CD8 immunity during chronic infection, and share regulatory pathways with memory precursor effector cells generated after acute infection. However, it is unclear whether stem-like CD8 T cells require dist

overall_design: Single-cell tcranscriptomic and epigentic analysis of antigen specific CD8 T cells after acute and chronic viral infeciton. Transcrptome analysis of TOX over expression in antigen specific CD8 T cells after chronic viral infection.


title: Next Generation Sequencing analysis of Hes1+/+ Cre-ERT2 and Hes1fl/fl Cre-ERT2 bone marrow derived macrophages transcriptomes.

city: Beijing

first: Fei

last: Ning

address: Tsinghua Yuan Street

institute: Institute for Immunology

summary: To evaluate the potential role of Hes1 in regulation of type I IFNs and the downstream ISGs expression, we generated the bone marrow-derived macrophages (BMDMs) from Hes1+/+ Cre-ERT2 and Hes1fl/fl Cre-ERT2 mice. RNA-sequencing analysis of Poly(I:C) [(polyinosinic: polycytidylic acid), a mimic of viral double-stranded RNA]-treated BMDMs revealed that 49 genes were induced more than two-fold by Poly(I:C) for 3 hrs in Hes1-deficient BMDMs relative to their expression in Hes1+/+Cre-ERT2 cells. Notably, 67.3% of these upregulated genes were ISGs by screening the Interferome database, suggesting that Hes1 inhibits expression of TLR-mediated ISGs,these results indicated that Hes1 negatively regulates TLR3-mediated induction of ISGs in macrophages.

overall_design: mRNA profiles of BMDMs from Hes1+/+ Cre-ERT2 and Hes1fl/fl Cre-ERT2  mice with or without Poly(I:C) treatment for 1 or 3 hours.

first: Bin


title: Expansion of an FCRL5+ B cell subset resembling atypical memory B cells in an animal model of malaria

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary:
Background: In human malaria, parasites of the genus Plasmodium elicit expansion of atypical memory B cells (atMBCs), which lack the classical markers CD21 and CD27. We have identified a putative population of analogous B cells in a murine model of infection with P. chabaudi, delineated by the marker FCRL5. We performed RNA-Seq on FCRL5+ and FCRL5- B cells sorted from infected mice, so as to characterize the transcriptional profile of these cells and permit comparison to atMBCs in humans.
Results: FCRL5+ B cells were found to have distinct transcriptional profiles from FCRL5- B cells, with approximately 400 genes exhibiting significant differences between the two groups. Additionally, about 25% of these differentially expressed genes were also differentially expressed in human atMBCs versus classical MBCs, as previously described by Sullivan et al (PLoS Pathogens 2015).
Conclusions: FCRL5+ class-switched B cells are a transcriptionally distinct subset arising in P. chabaudi infection, with transcriptional similarities to human atMBCs that develop in chronic malaria settings.

overall_design: Class-switched B cells (IgM- IgD- CD19+) were isolated into FCRL5+ and FCRL5- populations by double-sorting from the blood of C57BL/6 adult female mice 21 days post-infection with Plasmodium chabaudi.   Pools of ~1000 cells were isolated and processed for RNA sequencing. 5 biological replicates were analyzed for each sample type.

first: Charles

middle: C

first: Mary

middle: F

last: Fontana

first: Alyssa

last: Baccarella


title: Intergenerational transmission of the positive effects of physical exercise on brain and cognition

city: Madrid

first: José Luis

last: Trejo

state: Madrid

address: Avenida Doctor Arce 37

country: Spain

institute: Instituto Cajal

summary: Parental moderate exercise induces positive effects on sedentary litter’s behavior, and on hippocampal gene expression, adult neurogenesis and mitochondrial activation

overall_design: A first set of animals was assigned to 2 groups: 'Sedentary fathers' or 'Exercised fathers'. Animals from this second group were put into a physical activity program (40 mins of treadmill activity every day for 6 weeks) while the sedentary group was kept without access to treadmill or any physical activity. After 6 weeks, the performance of both groups was tested in different hippocampal-dependent tasks to collect behavioural data. Then they were all put into breed to obtain a second generation. The fathers were killed at 7 months and their hippocampus collected for RNA Sequencing. Then we tested the offspring of this first set of animals. We had two groups in this second generation: 'litters from sedentary fathers' and 'litters from exercised fathers'. We tested the litters in the same hippocampal-dependant tasks than fathers to collect behavioural data. Then were killed at 5.5 months and their hippocampus collected for RNA Sequencing. The two main goals of RNA Sequencing were: 1) to compare the levels of gene expression in hippocampus of exercised fathers with respect to sedentary ones; 2) to compare the levels of gene expression in hippocampus of litters from exercised fathers with respect to litters from sedentary ones.

first: Kerry

last: McGreevy

first: Patricia

last: Tezanos

first: Iria

last: Ferreiro-Villar

first: Anna

last: Pallé

first: Marta

last: Moreno

last: Esteve-Codina

first: Ismael

last: Lamas-Toranzo

first: Pablo

last: Bermejo-Álvarez

first: Julia

last: Fernández-Punzano

first: Alejandro

last: Martín-Montalvo

first: Raquel

last: Montalbán

first: Sacri

last: Ferrón

first: Elizabeth

last: Radford

first: Ángela

last: Fontán-Lozano


title: The effect of doxycycline-induced expression of host-cell-factor 2 (HCF-2) proteins on the global gene expression in HEK-293 cells

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

summary: Here we study the effect of doxycycline induced expression of HCF-2 (the host-cell-factor 2) proteins - HCF-2WT and its mutant HCF-2Fn3nc* on the global gene expression in HEK-293 cells. We identified 7175 genes that were differentially expressed after day 1 in any of the HCF-2WT or HCF-2Fn3nc* samples (log2 (fold change) > 0.5 or < -0.5 and FDR < 0.05). The maximal gene-expression changes over time were on day 6 in each case, with more genes up-regulated (2199 vs. 1241) in the HCF-2WT samples and more genes down-regulated (2513 vs. 1555) in the HCF-2Fn3nc* samples after six days compared to day 1. Notably, there was little overlap between the genes affected by the induced synthesis of HCF-2WT or HCF-2Fn3nc* indicating that the HCF-2Fn3nc* mutation seriously disrupts HCF-2 function. In total, we found that up-regulated genes in HCF-2WT were associated with developmental and morphogenesis programs induction, whereas down-regulated genes were linked to the inhibition of cellular metabolism and proliferation.

overall_design: Flag-Cherry-HCF-2-encoding Flp-In T-Rex-HEK-293 cells were induced in duplicates with doxycycline (1ul/ml) and samples were collected 1, 2, 4, and 6 days post induction (16 samples in total).

first: Daria

last: Gudkova

first: Oleksandr

last: Dergai

first: Viviane

last: Praz

first: Winship

last: Herr


title: Transcriptomic analysis of the role of the integrin a6b4 in detached cells

city: Worcester

first: Marcus

last: Ruscetti

address: 364 Plantation Street, LRB-613, LRB-613

department: MCCB

institute: Umass Chan Medical School

summary: Analysis of gene expression profiles of matrix-detached cells with and without expression of ITGB4, in clustering and non-clustering conditions. The experiment tested the hypothesis that the integrin beta 4 (ITGB4) mediates a significant amount of pro-survival signaling in matrix-detached conditions. Expression of ITGB4 in cancer is correlated with poor patient survival and is impliated in increased metastatic spread. Survival in matrix-deprived conditions is essential to metastasis and targeting signaling downstream of the integrin beta 4 may help curtail metasasis.

overall_design: Examination of gene expression profile following 3 hours of incubation in matrix-deprived conditions in duplicate

first: Caitlin

last: Brown

first: Art

last: Mercurio


title: Zika virus infection induces RNAi-mediated antiviral immunity in human neural progenitors and brain organoids

status: Public on Apr 15 2019

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

institute: Wuhan University

summary:
The re-emergence of Zika virus (ZIKV) in the Western Hemisphere has resulted in global public health crisis since 2015. ZIKV
preferentially infects and targets human neural progenitor cells (hNPCs) and causes fetal microcephaly upon maternal infection.
hNPCs not only play critical roles during fetal brain development, but also persist in adult brain throughout life. Yet the mechanism
of innate antiviral immunity in hNPCs remains largely unknown. Here, we show that ZIKV infection triggers the abundant
production of virus-derived small interfering RNAs in hNPCs, but not in the more differentiated progenies or somatic cells. Ablation
of key RNAi machinery components significantly enhances ZIKV replication in hNPCs. Furthermore, enoxacin, a broad-spectrum
antibiotic that is known as an RNAi enhancer, exerts potent anti-ZIKV activity in hNPCs and other RNAi-competent cells. Strikingly,
enoxacin treatment completely prevents ZIKV infection and circumvents ZIKV-induced microcephalic phenotypes in brain organoid
models that recapitulate human fetal brain development. Our findings highlight the physiological importance of RNAi-mediated
antiviral immunity during the early stage of human brain development, uncovering a novel strategy to combat human congenital
viral infections through enhancing RNAi.

sample_organism:
Aedes aegypti
Homo sapiens

platform_organism:
Aedes aegypti
Homo sapiens

overall_design: Small RNA profile of virus-infected cells

first: Yan-Peng

last: Xu

first: Yang

last: Qiu

first: Boya

last: Zhang

first: Guilai

last: Chen

first: Qi

first: Miao

last: Wang

first: Fan

last: Mo

first: Jiuyue

first: Jin

last: Wu

first: Rong-Rong

first: Meng-Li

last: Cheng

first: Na-Na

first: Bao

last: Lyu

first: Wen-Liang

last: Zhu

first: Meng-Hua

first: Qing

last: Ye

first: Da

first: Jiang-Hong

last: Man

first: Xiao-Feng

last: Li

first: Jie

last: Cui

first: Zhiheng

first: Baoyang

last: Hu

first: Xi

last: Zhou

first: Cheng-Feng

last: Qin


title: p38 SAPK and SKIIP induced changes in alternative splicing patterns upon osmostress

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

institute: Cell Signaling Group, IRB Barcelona

summary: Alternative splicing is a crucial mechanism for gene regulation that is modulated in response to a wide range of extracellular stimuli. Stress-activated protein kinases (SAPKs) play a key role in controlling several steps of mRNA biogenesis. Here, we show that osmostress has a major impact on the regulation of alternative splicing (AS), which is partly mediated through the action of the p38 SAPK. Remarkably, a splicing network analysis revealed a functional connection between p38 and the spliceosome component SKIIP. Depletion of SKIIP abolished a significant part of the p38-mediated alternative splicing.

overall_design:
Alternative Splicing analysis of non-treated, stressed, and stressed cells pre-treated with the p38 SAPK inhibitor under control or SKIIP knock down conditions.

Sequencing Core Facility: CRG

first: Caterina

last: Carbonell

first: Claudia

last: Vivori

first: Arnau

last: Ulsalmer

first: Panagiotis

last: Papasaikas

first: René

last: Böttcher

first: Mane

last: l Joaquin

first: Belén

last: Miñana

first: Juan

last: Tejedor

first: Eulàlia

last: de Nadal

last: Valcárcel


title: Transcriptome profiling of mouse subcutaneous white adipose tissue treated with BML-260

status: Public on Apr 14 2019

city: Shanghai

first: Zhuanghui

last: Feng

summary: To explore BML-260 how to increase thermogenesis, we examined the effect of BML-260 by direct in situ injection into the subcutaneous white adipose depot. Three days after a single injection, mice were dissected and subcutaneous adipose tissues were obtained for RNA extraction. we noticed that BML-260 treatment resulted in a very significant upregulation of genes involved in thermogenesis. And gene signatures of muscle cell differentiation, muscle structure development, regulation of muscle system process were among the most enriched GO terms. Our work provides evidences that BML-260 can also exert a JSP-1-independent effect in activating UCP1 and thermogenesis in adipocytes, and be potentially applied to treat obesity.

overall_design: Four mice subcutaneous white adipose tissues from 8 mice: 4 mice were treated with BML-260, 4 mice were treated with vehicle.

first: Qiurong

last: Ding

first: Yuda

last: Wei

first: Yongxian

last: Zhang

first: Yan

last: Qiu

first: Xiaojian

last: Liu


title: Lamin B1 loss promotes lung cancer development and metastasis  by epigenetic derepression of RET [ChIP-Seq]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Although abnormal nuclear structure is an important criterion for cancer diagnostics, remarkably little is known about its relationship to tumor development. Here we report that loss of lamin B1, a determinant of nuclear architecture, plays a key role in lung cancer.  We found that lamin B1 levels were reduced in lung cancer patients. Lamin B1 silencing in lung epithelial cells promoted epithelial-mesenchymal transition, cell migration, tumor growth and metastasis. Mechanistically, we show that lamin B1 recruits the polycomb repressive complex 2 (PRC2) to alter the H3K27me3 landscape and repress genes involved in cell migration and signaling. In particular, epigenetic derepression of the RET proto-oncogene by loss of PRC2 recruitment, and activation of the RET/p38 signaling axis, play a crucial role in mediating the malignant phenotype upon lamin B1 disruption. Importantly, loss of a single lamin B1 allele induced spontaneous lung tumor formation and RET activation. Thus, lamin B1 acts as a tumor suppressor in lung cancer, linking aberrant nuclear structure and epigenetic patterning with malignancy.

overall_design: ChIP-seq for H3K27me3 of control (n=2; H3K27me3_Lmnb1_ctrl_MLE12_ChIP_seq_rep1 and H3K27me3_Lmnb1_ctrl_MLE12_ChIP_seq_rep2) and lamin B1 knockdown (n=2; H3K27me3_Lmnb1_KD_MLE12_ChIP_seq_rep1 and H3K27me3_Lmnb1_KD_MLE12_ChIP_seq_rep2) MLE12 cells along with respective input samples.

first: Yanhan

last: Jia

first: Julio

last: Cordero


title: Overexpression of HDAC8 establishes a unique gene signature in BRAF-mutant melanoma cells

city: TAMPA

first: Marco

last: Davila

state: Florida

address: 12902 USF MAGNOLIA DRIVE, MRC2

institute: Moffitt Cancer Center

summary: Systems level analyses using mass spectrometry-based phosphoproteomics and RNA-Seq implicated HDAC8 in the regulation of MAPK and AP-1 signaling pathways. Introduction of HDAC8 into drug-naïve melanoma cells conveyed resistance both in vitro and in in vivo xenograft models. HDAC8-mediated BRAF inhibitor resistance was mediated via receptor tyrosine kinase (RTK) activation leading to Ras/CRAF/MEK/ERK signaling. Although HDACs primarily function at the histone level, they also regulate signaling through the modulation of non-histone substrates. In line with this, HDAC8 introduction decreased the acetylation of c-Jun, increasing its transcriptional activity and enriching for an AP-1 gene signature. Mutation of the putative c-Jun acetylation site at lysine residue 273 reduced the transcriptional activation of c-Jun in melanoma cells and conveyed resistance to BRAF inhibition through increased RTK expression and enhanced MAPK pathway activity.

overall_design: There are 4 separate cell lines sequenced once. HDAC8 overexpression was compared to empty vector cell lines in 2 separate cell lines.

first: Smalley

last: Keiran

first: Michael

last: Emmons

first: Tania

last: Mesa


title: Lamin B1 loss promotes lung cancer development and metastasis  by epigenetic derepression of RET

overall_design: Refer to individual Series


title: ChIP-seq assay for RocS binding to the Streptococcus pneumoniae genome

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

summary: We performed ChIP-seq, comparing immunoprecipitation of FLAG-labelled RocS with whole-cell extract. We did not detect any significant peaks in any of the samples. This might be due to data quality, but, additionally, other data showed that RocS binds DNA aspecifically and therefore no specific peaks are expected.

overall_design: Comparison of pulldown DNA with whole-cell extract of a pneumococcal strain carrying FLAG-labelled RocS

first: C

last: Mercy

first: A

last: Ducret

first: J

first: S

last: Nagarajan

last: Lavergne

last: Freton

first: P

last: Garcia

first: M

last: Noirot-Gros

first: N

last: Dubarry

last: Nourikyan

last: Veening

last: Grangeasse


title: Studies of a rice sterile mutant sstl

city: Taipei

first: Yue-ie

middle: Caroline

last: Hsing

address: Sinica  Address：128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

institute: Academia Sinica,Taiwan

summary: We report a mutant that has defective pollens and abnormal anthers from its semi-sterile mutant (sstl) progeny segregates. Comparative transcriptomics analysis illustrates the mechanism of male sterility.

overall_design: Examination of 2 different anther developmental stages in fertile rice and sterile mutant.

first: Chia-Ling

last: Chang


title: Gene expression-based, whole genome-wide expression profile differences for CUL4B-depleted LNCaP cells compared with control

status: Public on Apr 13 2019

city: Jinan

first: meng

last: jiao

address: No.247, beiyuan street

institute: 2nd Hospital of Shandong University

summary: Cancer stem-like traits contribute to prostate cancer (PCa) progression and metastasis. Discovering and clarifying the underlying molecular mechanisms associated with PCa stem-like traits would be great beneficial to clinical treatment of advanced PCa. Cullin 4B (CUL4B) is a scaffold protein overexpressed in several solid malignancies. It is known to silence tumor suppressor through post-transcriptional manner. In this study, through gain- and loss-of-function experiments, we showed that CUL4B promotes PCa pluripotency-associated markers expression, sphere formation and anchorage-independent growth ability in virto. Mechanically, we identified BMI1 as a target of CUL4B. CUL4B unregulates BMI1 expression via epigenetically repressing microRNA-200b (miR200b) and microRNA-200c (miR200c). In addition, miR200b and miR200c (miR200b/c) could partially reverse CUL4B-induced BMI1 and pluripotency-associated marker expression. Finally, our study revealed a CUL4B-miR200b/c-BMI1 oncoprotein axis in PCa, which might give novel insight into how CUL4B promotes PCa progression through regulating cancer stem-like traits.

overall_design: We carried out gene expression profiling in PCa using LNCaP cells with siRNA transfection vs. Negative control. The interference efficiency was verified by Real-Time PCR (qPCR) and western blot. Differentially expressed genes were identified based on standard and advanced quality control metrics (Fold change >2.0 and P-values <0.05). We found that there were 525 downregulated genes and 619 upregulated in CUL4B siRNA-transfected LNCaP cells.

first: Meng

last: Jiao

first: Qi

last: Mei

first: Jing

last: Hu

first: Bo

last: Han


title: Multi-walled carbon nanotube-induced gene expression in vitro

status: Public on Apr 12 2019

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

summary: There is a current interest in reducing the in vivo toxicity testing of nanomaterials in animals by increasing toxicity testing using in vitro cellular assays; however, toxicological results are seldom concordant between in vivo and in vitro models. This study compared global multi-walled carbon nanotube (MWCNT)-induced gene expression from human lung epithelial and microvascular endothelial cells in monoculture and coculture with gene expression from mouse lungs exposed to MWCNT. Using a cutoff of 10% false discovery rate and 1.5 fold change, we determined that there were more concordant genes (gene expression both up- or downregulated in vivo and in vitro) expressed in both cell types in coculture than in monoculture. When reduced to only those genes involved in inflammation and fibrosis, known outcomes of in vivo MWCNT exposure, there were more disease-related concordant genes expressed in coculture than monoculture. Additionally, different cellular signaling pathways are activated in response to MWCNT dependent upon culturing conditions. As coculture gene expression better correlated with in vivo gene expression, we suggest that cellular cocultures may offer enhanced in vitro models for nanoparticle risk assessment and the reduction of in vivo toxicological testing.

overall_design: SAEC and HMVEC coculture and mono-culture at 6 hr and 24 hr, correlated with in vivo animal studies


city: Miami

first: Shamroop

middle: kumar

last: Mallela

address: 1580 NW 10th Ave

institute: University of Miami

summary: Sphingomyelin phosphodiesterase acid-like 3b (SMPDL3b) is a lipid raft enzyme that regulates plasma membrane (PM) fluidity. Here we report that SMPDL3b excess, as observed in podocytes in diabetic kidney disease (DKD), impairs insulin receptor isoform B-dependent pro-survival insulin signaling by interfering with insulin receptor isoforms binding to caveolin-1 in PM. SMPDL3b excess affects the production of active sphingolipids resulting in decreased ceramide-1-phosphate (C1P) content as observed in human podocytes in vitro and in kidney cortexes of diabetic db/db mice in vivo.  Podocyte-specific Smpdl3b deficiency in db/db mice is sufficient to restore kidney cortex C1P content and to protect from DKD. Exogenous administration of C1P restores IR signaling in vitro and prevents established DKD progression in vivo. Taken together, we identified SMPDL3b as a modulator of insulin signaling and demonstrated that supplementation with exogenous C1P may represent a lipid therapeutic strategy to treat diabetic complications such as DKD.

overall_design:
RNA sequence data in whole cell extracts of differentiated human podocytes
RNA from Ctrl and SMPDL3b OE podocytes was isolated and analyzed for differences in the mRNA expression profile
RNA extraction, Preparation and sequencing RNA libraries, Illumina Sequencing RNA Data Analysis

middle: K

first: Alla

last: Mitrofanova


title: MicroRNA expression in CUL4B-depleted LNCaP cells and control

summary: We examined a global miRNA expression in CUL4B-depleted LNCaP cells to identify miRNA(s) regulated by CUL4B.

overall_design: We carried out miRNA expression profiling in LNCaP cells with siRNA transfection vs. Negative control. The interference efficiency was verified by Real-Time PCR (qPCR) and western blot. Differentially expressed genes were identified based on standard and advanced quality control metrics (Fold change >2.0 and P-values <0.05).


title: Disease modelling of core pre-mRNA splicing factor haploinsufficiency

city: Manchester

first: Huw

middle: Batten

last: Thomas

state: Greater Manchester

address: Dover Street

department: Biological Sciences

institute: University of Manchester

summary: We generated a human EFTUD2 knockdown cell line using a CRISPR cas9 nickase strategy to investigate the effects of decreased expression of core spliceosome components on cell characteristics and global transcriptome expression/splicing patterns

overall_design: 6 biological replicates of WT or CRISPR knock-down cells were generated and analysed by RNA-Seq

first: Katherine

last: Wood

first: Charlie

last: Rowlands

middle: B

first: Weronkia

last: Buczek

first: Tracy

last: Briggs

first: Simon

middle: J

last: Hubbard

first: Willam

middle: G

last: Newman

first: Raymond

middle: T

last: O'Keefe


title: Genomic and bioinformatic characterization of mouse mast cells (P815) upon different influenza A virus (H1N1, H5N1, and H7N2) infections

first: Yanxin

state: Beijing

address: no. 2 Yuanmingyuan west road

institute: China Agricultural University

summary: Background: Influenza A virus (IAV) is a segmented negative-stranded RNA virus that brings a potentially serious threat to public health and animal husbandry. Mast cells play an important role in both the inherent and adaptive immune response. Previous studies have indicated that mast cells support the productive replication of H1N1, H5N1, and H7N2. To date, the distinct molecular mechanism behind the pathogenesis in mast cells among the three different viruses has been poorly understood.  Methods: We investigated the genomic profiles in detail and the dynamic change of genomes regulated by different subtypes of IAV in mouse mast cells using microassays in order to the distinct molecular mechanism behind the pathogenesis in mast cells among the three different viruses. Mouse mast cells (P815) were infected at a multiplicity of infection of 1 (infectious viruses/cell) and incubated for 12 hr before collection of total RNA and microarray anlaysis using the Affymetrix platforms. Any two of the three IAV-infected groups were compared to detect genomic distinct. Based on the results of microassays, the further verification was performed by real-time PCR and western blotting. Here, the mRNA levels of 5-HT, PKG and HIF-1 in P815 cells following H1N1, H5N1 and H7N2 infection were determined by real-time PCR. The protein levels of exosomes in P815 cells following H1N1, H5N1 and H7N2 infection were detected by western blotting.  Results: Compared with any two of the three IAV-infected groups, much more diﬀerentially expressed genes (DEGs), cellular functions and signaling pathways were confirmd in H1N1 or H7N2 group, and H7N2 group showed the highest levels. However, few DEGs were detected as well as various cellular functions and signaling pathways were dramatically suppressed in H5N1 group. With an in-depth study on H1N1 and H7N2 group, we demonstrated the 5-HT signaling pathway and cGMP/PKG signaling pathway terms were enriched in P815 cells infected by H1N1 while HIF-1 signaling pathway terms were enriched in P815 cells infected by H7N2 virus. Furthermore, RT-qPCR results also showed significantly increased mRNA of 5-HT and PKG in H1N1-infected P815 cells as well as HIF-1 in H7N2-infected P815 cells. Besides, exosomes were highly secreted from H1N1-infected or H7N2-infected P815 cells.  Conclusions: H1N1 and H7N2 viruses could result in a variety of DEGs in mast cells and activate various cellular functions and signaling pathways while H5N1 virus cause the few DEGs in mast cells as well as suppression of cellular functions and signaling pathways. Furthermore, 5-HT signaling pathway and cGMP/PKG signaling pathway were preferentially activated in P815 cells infected by H1N1 while HIF-1 signaling pathway were preferentially activated in P815 cells infected by H7N2 virus. In addition, exosomes were also preferentially secreted from H1N1-infected or H7N2-infected P815 cells that are potentially pivotal in innate immunity to fight IAV infection. The study provides novel information and insight into the distinct of molecular mechanism of H1N1, H5N1 and H7N2 viruses in mast cells from the perspective of genomic profiles.

overall_design: Cells were infected with IAVs at a multiplicty of infection of 1 and cells were incubated for 12 hr at 37 C before RNA extraction and analysis of genomic and bioinformatic characterization.

first: Caiyun

last: Huo

first: Hongping

last: Wu

first: Jin

last: Xiao

first: Di

last: Meng

first: Shumei

last: Zou

first: Ming

last: Wang

first: Peng

last: Qi

first: Haiyan

last: Tian


title: Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cell [RRBS]

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: Totipotency is defined as the ability of a cell to generate all the cell types of an organism, including those of the extraembryonic tissues. Unlike pluripotency, the molecular features and the establishment of totipotency are poorly understood. In mouse embryonic stem cell (ESC) culture, a small percentage of cells transits into a totipotent state by expressing a group of genes that are only expressed in 2-cell-stage embryos. To understand how this transition takes place, we performed single cell RNA-seq analysis which revealed a two-step transcriptional reprogramming process characterized by downregulation of pluripotent genes in the first step and upregulation of the 2-cell embryo-specific genes in the second step. To identify factors controlling the transition process, we performed a CRISPR/Cas9-mediated genetic screen which revealed Myc and Dnmt1 as two factors preventing the transition. Mechanistic studies demonstrate that Myc prevents down-regulation of the genes in the first step, while Dnmt1 impedes gene activation in the second step. Collectively, our study reveals insights into the mechanism underlying establishment and regulation of totipotent state in ESCs.

overall_design: Here we performed bulk RNA-seq on ESC, D1 2C-negative, and D1 2C-positive cells. And performed single cell RNA-seq on Dux-induced ESC at 0h, 12h, 24h, and 36h. In addition, we performed bulk RNA-seq on sgGFP, sgDnmt1, sgMyc ESCs before and after Dux induction. Last, we performed RRBS on sgGFP and sgDnmt1 ESCs before and after Dux induction.

first: Xudong

last: Fu

first: Xiaoji

first: Mohamed

middle: N

first: Yi

last: Zhang


title: Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cell [CRISPR-Cas9 screen]

overall_design: We performed a genome-wide CRISPR screen by transducing the ES cells containing LTR-tdTomato and inducible Dux transgene with a mouse CRISPR library expressing 79,632 gRNAs targeting 19,674 genes. After 24h of Dux induction, 2C+ and 2C- cell populations were purified for sequencing to determine the relative abundance of sgRNAs.


title: A subset of type I conventional dendritic cells control cutaneous bacterial infections through VEGFa-mediated recruitment of neutrophils

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

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


title: Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cell [RNA-Seq]


title: Tissue-Specific Differences in Metabolites and Transcripts Contribute to the Heterogeneity of Ricinoleic Acid Accumulation in Ricinus communis L. (castor) Seeds

status: Public on Apr 11 2019

city: Denton

first: Drew

last: Sturtevant

state: TEXAS

address: 155 Union Circle #305220

department: BioDiscovery Institute

institute: University of North Texas

summary: To examine the differential gene expression of genes invovled in hydroxy fatty acid accumulation within the endosperm and embryo tissues of castor seeds

overall_design: Sequencing of mRNA of each endosperm and embryo tissues of mature castor seeds

first: Kent

middle: D

last: Chapman


title: Alterations in GRHL2-OVOL2-ZEB1 Axis and Aberrant Activation of Wnt Signaling Lead to Altered Gene Transcription in Posterior Polymorphous Corneal Dystrophy

city: Los Angeles

first: Anthony

middle: John

last: Aldave

state: California

address: 200 Stein Plaza, DS 3-143

department: Ophthalmology

institute: University of California, Los Angeles

summary: To investigate the molecular basis of posterior polymorphous corneal dystrophy (PPCD) by examining the transcriptome in an affected individuals with an OVOL2 promoter mutation c.307T>C (PPCD1).

overall_design: Cornea endothelial tissue from a patient (P7), age 67,  with PPCD were obtained when the patient underwent keratoplasty . The Descemet membrane and endothelium were placed onto a piece of filter paper and submerged in TRI Reagent (Thermo Fisher, Waltham, MA) for RNA isolation. Human cornea tissue from an age-matched donor (C7), age 63, was obtained from an commercial eye bank. Descemet’s membrane and corneal endothelium were stripped from the donor cornea using a published technique and placed into TRI Reagent for RNA isolation.

first: Doug

last: Chung


title: Single cell transcriptome profiling of the bone marrow niche at steady state and under stress conditions (validation experiment)

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Single-cell RNA-seq analysis of bone marrow niche populations.

overall_design: Single-cell RNA-sequencing libraries of  BM niche.

first: Anastasia

last: Tikhonova

first: Aristotelis

last: Tsirigos

first: Iannis

last: Aifantis


title: Single cell transcriptome profiling of LSKs in the absence of vascular Dll4.

summary: Single-cell RNA-seq analysis of LSK populations.

overall_design: Single-cell RNA-sequencing libraries of LSK cells.


title: Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cell [Drop-seq]

last: Wu


title: Down-regulated expression of OsDCL3b affects small RNA biogenesis and panicle development in rice

city: Nanchang

first: Dong

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

summary: Two types of small (18-24 nt) non-coding RNAs (ncRNAs), microRNAs (miRNAs) and small interfering RNAs (siRNAs) have been found to exist widely in higher plants. OsDCL3b has just been reported to process the 24-nt phased small RNAs in rice, which are preferentially expressed in panicle. In this study, we find that down-regulated expression of OsDCL3b leads to lower pollen sterility and seed setting rate, which results in decreased grain yield per plant in rice. Next, small RNA and mRNA sequencing were performed to study the decrease of pollen fertility and seed setting rate. 942 differentially expressed genes were identified, and some of them have already been known to be involved in rice panicle development. Our results indicate that there is a close correlation between small RNA and rice yield.

overall_design: RNA-seq and small RNA-seq from wild-type and dcl3b knockdown mutant rice.

first: Shaobo

last: Li

first: Lan

last: Yang


title: Targeting the CBM signalosome induces Treg to prime the tumor environment for effective immune checkpoint therapy

status: Public on Apr 09 2019

city: Charlestown

first: Alexandra-Chloe

last: Villani

institute: MGH

summary: We report here the transcriptome analysis on resting and activated mature Treg cells from mice with conditional deletion of CARMA1

overall_design: RNA-Sequencing on CARMA1fl/fl, CARMA1fl/+ and CARMA1 ++ activated (eTreg) and resting (cTreg) done in triplicates

first: Thorsten

last: Mempel