title: Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error

city: Milwaukee

first: Ross

middle: F

last: Collery

state: Wisconsin

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: We compare dissected ocular tissues from wild-type and lrp2-/- mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2, a transmembrane receptor, cause ocular enlargement and high-myopia. LRP2 is expressed by the RPE and eye ciliary epithelia, binding many extracellular ligands, including Bmp4 and Shh. Signaling mediated by LRP2 is very context-dependent, and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled, sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia (proper refraction). Using human iPSC-derived RPE, and zebrafish, we demonstrate that BACE sheddase-dependent LRP2 cleavage produces a soluble domain that binds BMP4, inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand-binding receptor forms available: a soluble BMP trap, and a membrane-bound RPE signaling facilitator. By modulating LRP2 cleavage, cells can fine-tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth.

overall_design: Examination of whole eyes, sclera/choroid, RPE and retina in wild-type and lrp2-/- mutant zebrafish at 1 month post-fertilization.

first: Brian

last: Link


title: Trim27 confers myeloid hematopoiesis competitiveness by upregulating myeloid master genes

status: Public on Jun 01 2018

city: Guangzhou

first: Tongjie

last: Wang

address: No.190 Kaiyuan Road

country: China

institute: Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: RNAseq were performed to analyze the transcriptomic differences between Trim27-overexpressing MP and empty vector control MP

overall_design: RNAseq: four Trim27-overexpressing MP samples, four empty vector control MP

first: Yong

last: Dong

first: Jinyong


title: The allelic  difference of histone modifications at Pvt1 locus during the differentiation from mESC to mNPC

status: Public on May 31 2018

city: Stanford

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

country: USA

institute: Stanford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq data of H3K9me3 and K3K4me3  in  mouse embryonic stem cells and neural progenitor cells

overall_design: Chromatin immunoprecipitation has been done for two histone markers in two cell lines with two replicates.

first: S

middle: W

last: Cho

first: H

middle: Y


title: Allele specific expression showing the cis-regulation of  Pvt1 and Myc  in mouse

summary: RNAseq of neural progenitor cell lines from hybrid  F1  mouse.

overall_design: RNAseq has been done for 4 neural progenitor cell clones with two replicates.


title: Integrative Analysis of Tamoxifen-resistant Cell Line Models Based on Sequencing Genomes, Transcriptomes and Epigenomes

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

type: Non-coding RNA profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of  allele specific transcription of PVT1 and MYC in mouse nueronal progenitor clonal cells

summary: PVT1 and MYC transcription is inversely correlated

overall_design: MYC and PVT1 transcripts are converted to cDNA by qRT-PCR reaction, and then targeted region was amplified and sequenced


title: Integrative Analysis of Tamoxifen-resistant Cell Line Models Based on Sequencing Genomes, Transcriptomes and Epigenomes [seq]

summary:
Purpose: Tamoxifen is the most commonly used antiestrogen drug for breast cancer treatment, however, acquired resistance is a considerable challenge in clinic. Complexity and redundancy in biological system implies tamoxifen resistance is associated with complex biological processes. The aim of this study is to attempt to reveal the mechanism of tamoxifen resistance using high-throughput sequencing technique.
Methods: We applied digital gene expression (DGE), RNA-seq, Small RNA-seq, bisulifte-seq (reduced representation bisuflite sequencing (RRBS)) with Illumina sequencing platforms, and Array CGH to analyze two well-established tamoxifen resistant cell line models: one is the LCC cell line model that was derived from MCF-7 breast cancer cell line and developed tamoxifen resistance following a step-wise strategy. This cell line model includes LCC0 (estrogen-dependent and tamoxifen sensitive), LCC1 (estrogen-independent and tamoxifen sensitive), LCC2 (derived from LCC1 with increased small-dosage tamoxifen treatment, estrogen-independent, and tamoxifen-resistant), and LCC9 (derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to both fluvestrant and tamoxifen). The other is the TAMR cell line model that was derived from MCF-7 breast cancer cell line and developed four tamoxifen-resistant sublines following the strategy of high-dosage of tamoxifen treatment. Each subline was developed from the survived single cell after the tamoxifen treatment.
Results: The DGE and RNA-seq results showed characteristic expression features for the both cell line models, for instance, high expression of SOX2 and alterations of other SOX gene family members, decreased expression of PGR, PTEN, TP53, EZH2, SMAD3, TGF-β1, DNMT1, APOBEC3B, FOXO3 and FOXO4, and increased expression of CDH1, APOBEC3H, FOXA1, TET2, TET3, TDG, MBD4, DNMT3a and DNMT3b between the tamoxifen-resistant cell lines with their matched parental cell lines. Small RNA seq showed the decreased expressions of miR-1, miR-196-3p, miR-18a-5p, miR-125b-5p, and the increased expression of miR-23a-3p, miR-26b-5p, miR-320d, miR-141-3p, miR-23a-3p, miR-30a-5p, miR-9-5p, miR-200c, miR-129-5p, miR-125b-5p, miR-1285-3p and miR-30b-5p between the tamoxifen-resistant cell lines and their matched parental cell lines. Additionally, let-7a and let-7c have been found to present high expression levels in the tamoxifen resistant cells in the both cell line models, even it showed significantly decreased in some TAMR cells compared with their parental cell line. The RRBS showed similar DNA methylation levels between the LCC cell lines. Array CGH showed a small number of copy number variants between the LCC cell lines.
Conclusion:  Our present study suggests the development of tamoxifen resistance is associated with a dynamic process of cell fate changing. Therefore, new therapeutic method that targets whole cell system and cell fate dynamics, will be a promising strategy.

overall_design: Integrative analysis of genomic, transcriptomic and epigenomic profiles of the two well-established tamoxifen-resistant cell line models.

first: Xue

last: Lin

first: Shida

last: Zhu

first: Fei

last: Teng

last: Huang

first: Ning

first: Jihua

last: Sun

first: Boxin

last: Wu

first: Anne

middle: E

last: Lykkesfeldt

first: Jun

first: Henrik

middle: J

last: Ditzel

first: Nils

last: Brünner

first: Huanming

last: Yang

first: Lars

last: Bolund


title: Next Generation Sequencing for Chromatin accessbility by ATAC-seq for HeLa cell line

summary: CCAT1 enhancer is accessible specifically in HeLa, not in MCF7 or MDA-MB-231.

overall_design: 50,000 HeLa cells were treated by Tn5 to generate sequencing library


title: Comparative transcriptome analysis of murine macrophages infected with Brucella suis vaccine strain S2 and the virulent Brucella suis strain 1330

city: Beijing

first: Hui

last: Jiang

address: NO.8 Zhonguancun South Street

institute: China Insititute of Veterinary Drug Control

summary: Brucellosis is one of the most common zoonotic epidemics worldwide. Vaccination against Brucellosis is an important control strategy to prevent the disease in many high-prevalence regions. At present, Brucella vaccine strain S2 is the most widely used vaccine in China. In this study, to uncover the related mechanisms underlie virulence attenuation of S2, we characterized the transcriptional profile of S2 and 1330 infected macrophages by transcriptome analysis. The results revealed that expressions of 440 genes were significantly different between macrophages infected by 1330 and S2. Data analysis showed that in the gene ontology term, the different expressed genes involved in innate immune response, phagoctyosis, recognition, and inflammatory response were significantly enriched. Pathway enrichment analysis indicated that the genes involved in transcriptional misregulation in cancer, staphylococcus aureus infection pathways and NF-kappa B signaling pathway were significantly affected. To reveal the molecular mechanisms related to different expression profiles of infected macrophages, the transcription levels of the different genes between the two bacterial genomes were also detected. In total, the transcription of 29 different genes was significantly changed in either culture medium or infected microphages. The results of current study can be conducive to the promotion of better understanding of the related mechanisms underlie virulence attenuation of S2 and interactions between host cells and brucella strains.

overall_design: Two groups were analyzed, and each group contained 3  replicates.

first: Hao

first: Liangquan

first: Xiaowei

last: Peng

first: Yu

last: Feng

first: Yong

first: Jiabo

last: Ding

first: Hongjie

last: Fan


title: RNAseq analysis of the effects of light and the carS mutation in Fusarium fujikuroi and Fusarium oxysporum

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

department: Genetics

country: Spain

institute: University of Seville

summary: In the fungi Fusarium fujikuroi and Fusarium oxysporum, the induction of carotenogenesis by light and its deregulation in carS mutants, affected in a protein of the RING-finger family, are achieved on transcription of the structural genes of the pathway, some of them organized in a cluster. We have carried out global RNAseq transcriptomics analyses to investigate the relationship between the regulatory effects of light and the carS mutation. Either illumination or the absence of a functional carS gene exert wide effects on the transcriptome of F. fujikuroi, with a predominance of activated over repressed genes, and a greater functional diversity in the case of genes induced by light. The number of the latter decreases drastically in the carS mutant, indicating that the deregulation produced by the carS mutation affects the light response of many genes. In addition, light and CarS strongly influence the expression of some genes associated with stress responses. The effects of light and carS mutation on the F. oxysporum transcriptome were partially coincident with those in F. fujikuroi, indicating conservation of the objectives of their regulatory mechanisms. In conclusion, the CarS RING finger protein down-regulates many genes whose expression is up-regulated by light in the wild-type strains of the two Fusarium species investigated, indicating regulatory connections between the control by light and by the CarS protein.

sample_organism:
Fusarium fujikuroi
Fusarium oxysporum f. sp. lycopersici

overall_design: To check the effect of light in the F. fujikuroi and F. oxysporum transcriptomes we compared dark-grown cultures with parallel cultures exposed for one hour to light. To examine the effect of the carS mutation, in F. fujikuroi we used a formerly investigated carS mutant (SG39), and as an additional control, we used SG256, a stable carS complementing strain (SG256) obtained from SG39 by replacement of the carS mutant allele by a wild type allele. In F. oxysporum, the effect of the carS mutation was inferred from the analysis of two independent carS mutants, SX2 and SX3. Each strain and condition has two independent experimental replicates.

first: M

middle: C

last: Limón


title: In situ Hi-C profiles of mouse CD4+ T cells, CD8+ T cells and B cells

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Over recent decades, it has been proposed that DNA interactions between mammalian chromosomes play an important role in the regulation of gene expression and cell fate determination. To study how DNA interactions change between cell types, high throughput chromosome confirmation capture (Hi-C) profiles were collected from CD4+ T cells, CD8+ T cells and B cells from mice.

overall_design: In situ HiC was performed separately on three cell types (CD4+ T cells, CD8+ T cells and B cells) extracted from two mice. This lead to six samples in total with the two mice providing biological replicates for each cell type.

first: Timothy

middle: M

last: Johanson

first: Hannah

middle: D

last: Coughlan

first: Rhys

last: Allan


title: Next Generation Sequencing Facilitates Quantitative Analysis of chromatin conformational interaction between MYC and PVT1 in MCF7

first: Howard

last: Chang

summary: MYC-PVT1 interaction is cell line specific

overall_design: Interactions were measured with UMI-4C by two technical replicates for two biological replicates (with 2 different anchor point, two primers for each anchor).

first: S

last: Cho

first: H


title: Next Generation Sequencing Facilitates Quantitative Analysis of PVT1 mutant alleles have distinct growth advantage which was introduced by CRISPR in MDA-MB-231 human breast cancer cell line

summary: PVT1 deletion alleles have growth advantage over 30 passages

overall_design: Compare allele frequency between passage 0,10,20,30 in competitive growth by two independent Cas9-sgRNA RNP transfections


title: mRNA sequence data of three powdery mildew fungi - GcM3, OnM2 and GcC1 (mycelia and haustoria containing infected plant leaves)

city: Rockville

first: Shunyuan

last: Xiao

state: MD

address: 9600 Gudelsky Drive

department: Institute of Bioscience and Biotechnology Research

institute: University of Maryland

summary: Powdery mildew (PM) is one of the most important and widespread plant diseases caused by obligate biotrophic Ascomycete fungi in the order of Erysiphales. Monocot PM fungi such as Blumeria graminis f.sp. hordei (Bgh) infectious on barley and B. graminis f.sp. tritici (Bgt) infectious on wheat exhibit high-level of host-specialization. By contrast, many dicot PM fungi display rather broad host ranges. To understand why different PM fungi adopt distinct modes of host-adaption, we sequenced the genomes of four dicot PM strains belonging to Golovinomyces cichoracearum (GcC1, GcM1, GcM3) or Oidium neolycopersici (OnM2) and conducted comparative sequence analyses. PM fungi have highly repetitive genomes that are difficult to perform gene prediction. By combing RNA-seq expression evidence with ab initio gene prediction, we successfully improved the number of predicted genes from 4000 to 6000. By comparing the transcriptional profiling from haustoria with mycelia in OnM2 and GcM3, we found that 86%-96% of the predicted genes are expressed in mycelia and/or haustoria, indicating an efficient expression system of PM fungi. Besides, our results showed that gene regulation mechanisms in haustorial cells maybe under gone a much higher level of diversification between OnM2 and GcM3, since they share only a small proportion (21%) of genes up-regulated in huastoria cells. Notably, a higher proportion of candidate effector genes are selectively up-regulated in haustorial cells, agreeing with their function in suppressing host defense and facilitating nutrient uptake.

sample_organism:
Golovinomyces cichoracearum
Erysiphe neolycopersici

overall_design: This RNA-seq data set contains the transcriptional profiling from mycelia of two powdery mildew biotypes, as well as transcriptional profiling of haustoria containing plant leaves at 6 dpi. Haustoria containing samples were collected in three replicates, whereas only one replicate was collected for mycelia sample. Pair-end 101bp RNA-seq was performed on all samples. Libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit v2. Fragments were selected for sequencing on Illumina HiSeq1500 at the UM-IBBR Sequencing Core at the University of Maryland.

first: Xianfeng

last: Ma

first: Ying

last: Wu


title: The FlbA-regulated predicted transcription factor rpnR of Aspergillus niger is involved in protein secretion and stress resistance

city: Utrecht

first: Wieke

middle: R

last: Teertstra

address: Padualaan 8

department: Science, Biology

country: Netherlands

institute: Utrecht University

summary: Proteins are secreted throughout the mycelium of Aspergillus niger except for the sporulating zone. Inactivation of flbA results in colonies that do not reproduce asexually and secrete proteins throughout the colony. Moreover, ΔflbA hyphae lyse and have thinner cell walls. This pleiotropic phenotype is associated with differential expression of 38 transcription factor genes, of which rpnR was inactivated in this study. Biomass formation and sporulation was not affected in strain ΔrpnR but protein secretion was severely reduced. Moreover, ΔrpnR showed decreased resistance to H2O2 and the unfolded protein response inducing agent dithiothreitol. The secretomes of ΔrpnR and wild type consisted of 342 and 367 proteins, respectively. Secretion of several CAZymes and proteins involved in cell wall remodeling was more strongly reduced when compared to other proteins within the secretome of ΔrpnR. Whole genome expression analysis of xylose-grown colonies showed that RpnR activates expression of ribosomal subunits as well as small secreted proteins. On the other hand, it inhibited expression of the genes encoding the arabinofuranosidases AbfA, AbfB and AbfE, as well as genes related to amino acid metabolism, xenobiotics biodegradation and metabolism, lipid metabolism, and metabolism of cofactors and vitamins. Taken together, RpnR is involved in protein synthesis and may also be involved in cell wall architecture. Both functions could explain the reduced protein secretion and proteotoxic stress resistance in the deletion strain.

overall_design: mRNA profiles from ΔrpnR and the control strain MA234.1 were generated by Illumina Hiseq using duplicate samples from liquid shaken cultures.

first: David

last: Aerts

first: Stijn

middle: G

last: van den Bergh

first: Robin

middle: A

last: Ohm

first: Han

middle: B

last: Wösten


title: Quantitative proteomic characterization and comparison of T helper 17 and iTreg cells

city: Turku

first: Imran

middle: Ahammad

last: Mohammad

state: Finland

address: Tykistokatu 6

department: Lymphocytes and Inflammation

country: Finland

institute: Turku center for Biotechnology

summary: Using mass spectrometry-based label-free quantitative (LFQ) proteomics analysis of in vitro differentiated murine Th17 and induced T regulatory (iTreg) cells. More than 4000 proteins covering almost all subcellular compartments were detected. Quantitative comparison of the protein expression profiles resulted in the identification of proteins specifically expressed in the Th17 and iTreg cells. Importantly, our combined analysis of proteome and gene expression data revealed protein expression changes that were not associated with changes at the transcriptional level.

overall_design: Naïve CD4+ T cells were isolated from 8–10-week-old C57BL/6 mice spleens.  Cells were polarized to Th0, Th17 and iTreg conditions for three days. Four biological replicates  were prepared for RNA-seq.

first: Chen

last: Zhi

first: Lähdesmäki

last: Harri

first: Mohammad

last: Imran

first: Nousiainen

last: Kari

first: Starskaia

last: Inna

first: Rokka

last: Anne

first: Goodlett

last: David

first: Bhosale

last: Santosh D

first: Moulder

last: Robert


title: mRNA sequencing  of WT and dpl2∆ cells in conjugation 3, 4, 5, 6 and 7 (C3, C4, C5, C6 and C7) hours of Tetrahymena thermophila

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

summary: The goals of this study are to investigate the function of Dpl2 of Tetrahymena thermophila.

overall_design: Compare the expression of genes amnong WT and dpl∆ cells in C3, C4, C5, C6 and C7.


title: Genome wide transcriptome analysis of Jak2 KD persistent murine Eμ-Crlf2/Jak2R683G B-ALL cells

city: MELBOURNE

first: SANGKYU

last: KIM

state: VICTORIA

address: 305 GRATTAN ST

department: RESEARCH

institute: PETER MACCALLUM CANCER CENTRE

summary: RNA-seq was performed to  compare the transcriptional programmes of murine Eµ-Crlf2/Jak2R683G-expressing B-ALL cells subjected to short-term (2 days) versus long-term (21 days) shRNA-mediated Jak2 knockdown in vivo.

overall_design: NSG recipient mice of Eµ-Crlf2/Jak2R683G-pREBIR-shRenilla.713  or Eµ-Crlf2/Jak2R683G–pREBIR-shJak2.3323 cells were sacrificed at either 48 hr (acute knockdown) or 21 days (chronic knockdown) post shRNA induction and RNA-Seq was performed using total RNA isolated from dsRed+/eBFP2+ splenocytes. Experiment was performed in triplicate (three independent mice).

first: SangKyu

last: Kim

first: Ricky

last: Johnstone


title: Comparative gene expression profiling of MHH-CALL4 cells subject to pharmacological JAK2 inhibitor treatment (ruxolitinib or CHZ868) or shRNA-mediated JAK2 depletion in vitro

summary: Gene expression profiling was performed to characterise transcriptional programs associated with response to type I JAK2 inhibitor ruxolitinib, type II JAK2 inhibitor CHZ868 or shRNA-mediated JAK2 knockdown in MHH-CALL4 cells.

overall_design: CRLF2-rearranged/JAK2I682F-expressing MHH-CALL4 cells were treated with vehicle (DMSO), CHZ868 (300 nM) or ruxolitinib (1000 nM) for 24 hours in duplicate and total RNA was freshly extracted for 3'-RNA-Seq. MHH-CALL4 cells were transduced with constitutive (pLMS-GFP) retroviral vectors harbouring shRNAs targeting JAK2 (shJAK2.209 or shJAK2.2826) or scrambled (shSCR) in duplicate and GFP+ cells were harvested at day 5 post-transduction for 3'-RNA-Seq.


title: APOE4 Causes Widespread Molecular and Cellular Alterations Associated with Alzheimer's Disease Phenotypes in Human iPSC-Derived Brain Cell Types

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: The apolipoprotein E4 (APOE4) variant is the single greatest genetic risk factor for sporadic Alzheimer's disease (sAD). However, the cell-type-specific functions of APOE4 in relation to AD pathology remain understudied. Here, we utilize CRISPR/Cas9 and induced pluripotent stem cells (iPSCs) to examine APOE4 effects on human brain cell types. Transcriptional profiling identified hundreds of differentially expressed genes in each cell type, with the most affected involving synaptic function (neurons), lipid metabolism (astrocytes), and immune response (microglia-like cells). APOE4 neurons exhibited increased synapse number and elevated Ab42 secretion relative to isogenic APOE3 cells while APOE4 astrocytes displayed impaired Ab uptake and cholesterol accumulation. Notably, APOE4 microglia-like cells exhibited altered morphologies, which correlated with reduced Ab phagocytosis. Consistently, converting APOE4 to APOE3 in brain cell types from sAD iPSCs was sufficient to attenuate multiple AD-related pathologies. Our study establishes a reference for human cell-type-specific changes associated with the APOE4 variant.

overall_design: We used CRISPR/Cas9 to create isogenic APOE3 and APOE4 human iPSC lines that enable us to carry out comprehensive analysis of biochemical, cellular, and transcriptional changes by APOE variants in multiple iPSC-derived brain cell types

first: Yuan-Ta

last: Lin

first: Jinsoo

last: Seo

first: Fan

last: Gao


title: Transcriptome sequencing of human coronary artery smooth muscle cell under treatment of nitrated fatty acid

city: Shanghai

first: Shengdi

last: Li

address: 320 Yueyang Road

institute: SIBS

summary: RNA-seq profiling of human coronary artery smooth muscle cells under treatment of nitrated conjugated linoleic acids (NO2-CLA)

overall_design: We sequenced the cDNA from 4 NO2-CLA treated, 4 CLA treated and 4 untreated hCASMC samples

first: Jifeng

last: Zhang

first: Yixue

first: Yuqing

last: Chen


title: SET-9 and SET-26, the C. elegans homologs of human MLL5, are critical for germline development and longevity

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 520 Campus road

institute: Cornell University

summary: SET-9 and SET-26 are highly homologous paralogs that share redundant function in germline development, but SET-26 alone plays a key role in longevity and heat stress response. SET-26 is broadly expressed, but SET-9 is only detectable in the germline, which likely account for their different biological roles. SET-9 and SET-26 bind to H3K4me3 in vitro and in vivo, and their loss results in broadening of H3K4me3 domains. SET-9 and SET-26 also regulate the RNA expression of a subset of their target genes, irrespective of their H3K4me3 status. We propose that SET-9 and SET-26 function to organize local chromatin environment and to regulate the expression of specific target genes, and these activities together contribute to their critical roles in germline development, stress response, and longevity. SET-9 and SET-26 are highly homologous to human MLL5, a factor implicated in leukemia and glioblastoma, and our findings help to provide new insights into MLL5.

overall_design: H3K4me3 in N2 and set-9 set-26; and SET-9/26 ChIP; RNA-seq for N2, set-9, set-26 and set-9 set-26

first: Wenke

last: Wang


title: CARM1/PRMT4 is essential for myeloid leukemogenesis but dispensable for normal hematopoiesis

status: Public on Jun 10 2018

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary:
We investigated the role of PRMT4 in normal and malignant hematopoiesis.
We found that knockdown of PRMT4 impairs cell cycle progression, induces apoptosis, and downgretulateds E2F target genes in leukemia cell lines, identifying several mechanisms for the leukemia-specific dependence on PRMT4.

overall_design:
Three AML cell lines (SKNO1, MV411, and MOLM-13) were subjected to high-throughput RNA sequencing three days after shRNA inhibition of PRMT4 or scramble control.   All cell lines sequencing experiments were repeated in triplicate.
Differential expression of each cell line was performed independently comparing to controls.   Additionally, differential analysis was performed by combining all cell line PRMT4 inhibited cells and comparing to all controls.

first: Greenblatt

last: Sarah

first: Karl

last: Daniel


title: Impaired locomotor behavior of C. elegans neuroligin mutants is dependent of the catechol-O-methyltransferase COMT-4

city: Cordoba

first: Manuel

last: Ruiz-Rubio

address: Campus Rabanales s/n

institute: University of Cordoba

summary: Neuroligins are neuronal membrane adhesion molecules that have been involved in neuro-psychiatric and neuro-developmental disorders. They interact with neurexins and other specific proteins in the synaptic cleft. The nlg-1 gene of Caenorhabditis elegans encodes NLG-1, an ortholog of human neuroligins. NLG-1 is involved in dopaminergic and serotoninergic signaling that controls the locomotory rate of the nematode. When well fed animals are transferred to a plate with food (bacterial lawn) they reduce the locomotory rate. This behavior, which depends on dopamine, is known as basal slowing response (BSR). Alternatively, food deprived animals when moved to a plate with a bacterial lawn, further decrease their locomotory rate. This behavior, known as enhanced slowing response (ESR) is serotonin dependent. C. elegans nlg-1- deficient mutants are impaired in BSR, ESR and other locomotory behaviors such as gentle touch response. Here we report that nlg-1 mutants upregulate the expression of comt-4 which encodes an enzyme that presumably has catechol-O-methyltransferase activity involved in dopamine degradation. Our study also shows that comt-4(RNAi) in nlg-1-deficient mutants recovers wild type phenotypes of BSR, ESR and gentle touch responses. Based on these results we propose a model for the neuroligin function in modulating the dopamine-dependent locomotory behavior in the nematode.

overall_design: Examination of differentially expressed RNAs between Caenorhabditis elegans N2 wild type strain and the nrx-1 (tm1961), nlg-1 (ok259)  and nrx-1; nlg-1 (tm1961; ok259) double mutants.

first: Angel

last: Rodríguez-Ramos

first: María-Mar

last: Gámez-del-Estal

first: Montserrat

last: Porta-de-la-Riva

first: Julián

last: Cerón


title: The effect of Tmem135 overexpression on the mouse heart

city: Madison

first: Akihiro

last: Ikeda

address: 5322 Genetics Biotechnology Center, 425 Henry Mall

department: Medical Genetics

institute: University of Wisconsin-Madison

summary: Transgenic mice overexpressing a novel regulator of mitochondrial dynamics, transmembrane protein 135 (Tmem135) have age-related heart phenotypes. Here we report the gene expression profiles of 6 mo old WT and Tg whole hearts. RNAseq was conducted on Illumina HiSeq 2000 platform.

overall_design: Generated mRNA expression profiles of 6 mo WT and Tmem135 Tg whole hearts.

first: Sarah

last: Lewis

first: Tetsuya

last: Takimoto

first: Anna-Lisa

last: Doebley


title: Next Generation Sequencing Facilitates Quantitative Analysis of chromatin conformational interaction between MYC and PVT1 in MDA-MB-231, MCF7, HCT116 cancer cell line

first: Howard

last: Chang

overall_design: interactions were measeured UMI-4C by two technical replicates for two biological replicates (with 3 different anchor point, two primers for each anchor).

first: S

last: Cho

first: H


title: A data mining paradigm for identifying key factors in biological processes using gene expression data

city: Bethesda

first: Maria

middle: I.

last: Morasso

address: Building 50, Room 1525 10 Center Drive

department: National Institute for Arthritis and Musculoskeletal and Skin Diseases

institute: National Institutes of Health

summary: RNA-Seq was performed on the mouse keratinocyte cultures with Sbsn knockeddown to study the role of Sbsn in the regulation of epidermis devleopment.

overall_design: The RNA-Seq was performed on mouse keratinocyte cultures with three treatments (no siRNA treated, siControl treated and siSbsn treated) of high calcium concentration. Two batches of replicates were generated for each condition. batch 1 has two replicates for each of the three conditions, and batch2 has three replicates for two conditions (siControl and siSbsn). The comparison between siSbsn vs siControl was performed to identify the differentially expressed genes.

first: Jin

last: Li

first: Le

last: Zheng

first: Akihiko

last: Uchiyama

first: Lianghua

last: Bin

first: Theodora

last: Mauro

first: Peter

last: Elias

first: Tadeusz

last: Pawelczyk

first: Monika

last: Sakowicz-Burkiewicz

first: Magdalena

last: Trzeciak

first: Donald

last: Leung

middle: I

first: Peng

last: Yu


title: Next Generation Sequencing Facilitates Quantitative Analysis for H3K27ac mediated chromatin conformation capture of Wild Type and PVT1 Knockdown by CRISPRi in MDA-MB-231 human breast cancer cell line

middle: Y.

institute: Stanford

summary: CRISPRi targeting PVT1 specifically decrease PVT1-MYC interaction

overall_design: HiChIP performed with biological replicates for CRISPRi-PVT1 with H3K27ac


title: JAK2 is dispensable for maintenance of JAK2 mutant B-cell acute lymphoblastic leukemias

first: SANGKYU

last: KIM

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: Next Generation Sequencing for Chromatin accessbility by ATAC-seq for MDA-MB-231, MCF7 or HCT116 cell line

summary: CRISPRi on PVT1 did not induce drastic changes on chromatin accessbility in MDA-MB-231 cell line. CCAT1 enhancer is accessble specifically in HCT116, not in MCF7 or MDA-MB-231.

overall_design: MDA-MB-231 cell line was treated non-targeting control sgRNA or PVT1 targeting sgRNA. All cell lines express dCas9-BFP-KRAB integrated via lentivirus.

middle: W


title: Next Generation Sequencing Facilitates Quantitative Analysis of PVT1 mutant alleles have distinct growth advatage which was introduced by CRISPR in MDA-MB-231 human breast cancer cell line

summary: PVT1 deletion alleles have growth adavatage after 10 passages

overall_design: Comapare allele frequency between passage 0 and 10 in competitive growth by two independent Cas9-sgRNA RNP transfection

middle: Y


title: circRNA-sequencing

city: Taiyuan

first: Ruifeng

last: Liu

state: Shanxi

address: No. 1 Dong San Dao Xiang

department: Institute of Dermatology

institute: Taiyuan City Centre Hospital

summary: circRNA sequencing for 6 samples

overall_design: Examing 2 conditions, each with 3 replicates


title: A non-catalytic role of TET3 promotes open chromatin and enhances global transcription

first: Christel

last: Krueger

state: -- None --

address: Babraham Research Campus

country: United Kingdom

institute: Babraham Institute

summary: The methylcytosine dioxygenase Tet3 is highly expressed as a specific isoform in oocytes and zygotes but essentially absent from later stages of mouse preimplantation development. Here, we show that Tet3 expression promotes transdifferentiation of embryonic stem cells to trophoblast-like stem cells. By genome-wide analyses we demonstrate that TET3 associates with and co-occupies chromatin with RNA Polymerase II. Tet3 expression induces a global increase of transcription and total RNA levels, and its presence further enhances chromatin accessibility in regions open for transcription. This novel function of TET3 is not specific to the oocyte isoform, independent of its catalytic activity, the CXXC domain, or its interaction with OGT, and is localised in its highly conserved exon 4. We propose a more general role for TET3 promoting open chromatin and enhancing global transcription during changes of cellular identity, separate from its catalytic function.

overall_design: Transcriptome, ChIP and chromatin accessibility profiling  for ESC overexpressing TET3

first: Julian

last: Peat

first: Melanie

last: Eckersley-Maslin

first: Tim

last: Hore

first: Hisham

last: Mohammed

first: Simon

last: Andrews

first: Wendy

last: Dean

first: Wolf

last: Reik


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and PVT1 Knockdown by CRISPRi in MDA-MB-231 human breast cancer cell line

city: Stanford

first: Howard

last: Chang

address: 269 Campus Drive, CCSR 2130

summary: Induced MYC expression by CRISPRi targeting PVT1 was validated by RNA-seq

overall_design: total RNA profiles were sequenced by two independent viral infection

first: S

last: Cho

first: H


title: Promoter of lncRNA gene *PVT1* is a tumor suppressor DNA element


title: The arginine methyltransferase CARM1 represses p300•ACT•CREMt axis and is required for spermiogenesis

status: Public on May 30 2018

city: Smithville

first: Jianqiang

last: Bao

state: Texas

address: 1808 Park Road 1C (P.O. Box 389), Smithville  TX 78957

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: DEGs in the round and elongating spermatids between the WT and Carm1-null testis.

overall_design: DEGs upon Carm1 KO in the round and elongating spermatids.

first: Mark

last: Bedford


title: Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii.

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

country: France

institute: CNRS

type: Genome binding/occupancy profiling by genome tiling array

platform_organism:
Toxoplasma gondii
Toxoplasma gondii ME49


title: Transcript changes in rsc mutants compared to wild type by RNA sequencing

city: Berkeley

first: Tina

middle: Lynn

last: Sing

state: California

address: Barker Hall, Rm 616, University of California, Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Mutations in non-essential RSC genes was shown to cause spontaneous diploidization due to defective spindle pole body (SPB) duplication. RNA sequencing was performed to assess whether these effects were due to altered transcript profiles in rsc mutants

overall_design: Strains containing the indicated rsc mutation were grown to logarithmic phase and mRNA was sent for sequencing

middle: L

first: Grant

last: Brown


title: Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii. [RNA-seq]

summary: Toxoplasma gondii is a unicellular eukaryote belonging to the Apicomplexa phylum. It is an obligate intracellular parasite of critical importance to primarily infected pregnant women and immunosuppressed patient. ApiAP2 are a family of conserved transcription factors (TF) that play an important role in regulating gene expression in apicomplexan parasites. Previous studies had revealed the ability of one of these TFs, TgAP2XI-5, to bind to transcriptionally active promoters of genes expressed during the S/M phase such as rhoptry and micronemes genes. However, expression of TgAP2XI-5 is constitutive during the tachyzoite cell cycle. To better understand how its function is regulated, we identified proteins interacting with TgAP2XI-5 including a cell cycle regulated ApiAP2 TFs, TgAP2X-5. The purpose of the study is to determine the impact of the absence of a TF (TgAP2X-5) on the wide expression profile of a Toxoplasma gondii strain.

overall_design: mRNA profiles of wild type (WT) and iKD TgAP2X-5 parasites generated by high throughput sequencing using HiSeq 2500 system (Illumina)

first: Kevin

last: Lesage


title: Next Generation Sequencing Facilitates Quantitative Analysis for Chromatin Immunoprecipitation of Wild Type and PVT1 Knockdown by CRISPRi in MDA-MB-231 human breast cancer cell line

summary: CRISPRi targeting PVT1 specifically increased H3K9me3 at PVT1

overall_design: ChIP performed with biological replicates for CRISPRi-PVT1 with H3K9me3, H3K27ac, HA-dCas9-KRAB


title: Twin-miRs and their many weak targets

city: Cold Spring Harbor

first: Yixin

last: Zhao

state: NEW YORK

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: MicroRNAs (miRNA) are small, endogenous RNAs that regulate the expression of mRNAs posttranscriptionally. To identify miRNAs that produce twin products, we sequenced these five small RNA libraries and collected other published datasets to represent a systematic coverage of the major tissue types (head, body and sexual organs) in D. melanogaster. To survey the repression effects of twin miRs on the their targets, we dissected testes from adult flies that lacked Dm310s due to a knock-out mutation (Tang, et al. 2010) and performed an RNA-seq analysis.

overall_design:
Five small RNA samples mainly from reproductive organs, and four RNA-seq samples from testes, were analyzed in D. melanogaster.

Please note that the 'CanS testes' raw data fastq file is unavailable and only fasta file containing clean reads and read counts was generated as following; the sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and collapsed to the fasta format, on which the further analysis was carried out.

The Gene_Expression_log2(RPKM).txt contains two additional data columns - miR-313-3p_target and  miR-313-5p_target - showing  whether it is a TargetScan predicted target of dme-miR-313-3p or -5p, respectively.

Both 'Dm310s mutant' and 'Control' flies are generated from the stock EP(2)2587 [P(3)l(2)05510EP2587; Szeged Stock Center)]. The detailed construction method is described in Tang, T., et al. (2010; PMID 20615957)

first: Pei

last: Lin

first: Zhongqi

last: Liufu

first: Hao

last: Yang

first: Yang

last: Lyu

first: Xu

last: Shen

first: Chung-I

last: Wu

first: Tian

last: Tang


title: Transcriptome analysis of adult Klinefelter testis tissue samples compared to controls

city: Copenhagen

first: Kristian

last: Almstrup

address: Blegdamsvej 9, Section GR-5064

department: Dept. of Growth and Reproduction

institute: Rigshospitalet, Copenhagen University Hospital

summary: In humans, the most common sex chromosomal disorder is Klinefelter syndrome (KS), caused by the presence of one or more extra X-chromosomes. The KS patients display a diverse adult phenotype with increased height, gynaecomastia, and hypergonadotropic hypogonadism as the most common symptoms. Men with KS are almost always infertile due to testicular degeneration, which accelerates during puberty. Very few studies investigated the global gene expression analysis of adult KS testes and, more importantly, which cell types the differentially expressed transcripts originate from. Transcriptome analysis by RNA sequencing of fixed and paraffin embedded testes originating from 3 adult KS samples and 3 adult cellularity-matched controls revealed 236 differentially expressed transcripts in the adult KS testis. To examine the cellular origin of the differentially expressed transcripts, transcriptome profiling was also carried out on 4 testes with Sertoli Cell-Only and 4 testes with full spermatogenesis. Also, pre-pubertal KS and controls were RNA-sequenced.

overall_design: Includes a total of 22 testis samples. 3 adult Klinefelter, 3 Klinefelter-like, 4 Sertoli Cell-Only, 4 with full spermatogenesi, 4 pre-pubertal Klinefelter and 4 pre-pubertal controls

first: Sofia

last: Boeg Winge

first: Marlene

last: Danner Dalgaard

first: Kirstine

last: Belling

first: Jacob

last: Malte Jensen

first: John

middle: E

last: Nielsen

first: Lise

last: Aksglaede

first: Mikkel

last: Heide Schierup

first: Søren

last: Brunak

first: Niels

last: Skakkebaek

first: Anders

last: Juul

first: Ewa

last: Rajpert-De Meyts


title: The Polycomb Group Gene EMF2B modulates protein coding and non-coding RNAs in developing rice panicles.

city: Davis

first: Venkatesan

last: Sundaresan

state: CA

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

summary: The Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of Lysine 27 of Histone H3. The functions of the plant PRC2 have been chiefly described in Arabidopsis but specific PRC2 functions in other plant species, especially the cereals, are still largely unknown. Here we utilize ChIP-seq data in the analysis of protein coding and non-coding RNAs in early WT panicles of rice.

overall_design: Genomic profiling of trimethylated H3K27 histone density in WT rice panicles was assessed via ChIP-seq.

first: Cameron

last: Johnson

first: Ravi

last: K Patel

first: Liza

middle: J

last: Conrad

first: Sarah

last: Anderson

first: Chenxin

last: Li


title: The transition from proliferation to quiescence in glioblastoma stem-like cells requires Ca2+ signaling and mitochondria remodeling

city: illkirch

first: jacques

last: h

address: 74, route du rhin

department: esbs

institute: strasbourg university

summary: Quiescence is a reversible cell-cycle arrest used by Cancer Stem Cells (CSCs) to evade killing following conventional therapies. Quiescent CSCs are therefore one of the main cause of cancer recurrence. In glioblastoma, the most common and aggressive primary brain tumors, the quiescent glioblastoma stem-like cells (GSCs) are localized in hypoxic and acidic microenvironments and microenvironmental changes can control cell cycle re-entering of the GSCs. Here, we show that proliferating GSCs isolated from patients can be induced and maintained in a quiescent state by lowering the extracellular pH. Through RNA-seq analysis we characterized the RNA signatures of quiescent versus proliferating GSCs. We identified genes involved in the control of Ca2+ signaling and differentially expressed between the two states. Using the bioluminescent Ca2+ reporter EGFP-aequorin targeted to the mitochondria or the cytosol we explored the changes in Ca2+ homeostasis occurring during the switch from proliferation to quiescence. This remodeling is controlled through store-operated channels (SOCs). SOCs play a causal role since the inhibition of the Ca2+ influx through SOC drives proliferating GSCs to quiescence. We showed that the switch to quiescence is characterized by both an increased capacity of GSCs’ mitochondria to capture Ca2+ and a dramatic and reversible change of mitochondrial morphology from a tubular to a donut shape. Our data suggest that the remodeling of the Ca2+ homeostasis and the reshaping of mitochondria during the transition from proliferation to quiescence constitute a protective mechanism that favors cancer stem-like cells’ survival and their aggressiveness in glioblastoma.

overall_design: To establish RNA signatures of proliferative and quiescent GSLCs we have adopted the following strategy. Several experiments were performed in order to take into account different type of variabilities (Table S1); (1) Variability due to laboratories environments; experiments have been done in two laboratories ( Strasbourg and Toulouse) following identical protocols. The cells were obtained from the same master cell bank and the composition of the growing media was identical. (2) Cellular variability: two cell lines TG1 and OB1 were used. (3) Variability in inducing quiescence; the switch to quiescent state was obtained by either the non replacement of the medium during 9 days, acidification of the medium to pH 6.5 or 6.2 for 5 days or treatment of the cell by 10 µM SKF-96365 in the growing medium (pH 7.4) at day 1 and 3 and analysis at day 5. In normal medium at pH 7.4, the cells are in a proliferative state. Total RNA was extracted as described above and RNA quality was controlled with AATI Fragment Analyser (Advanced Analytical Technologies, Inc). RNA-seq was obtained from the IGBMC platform and the short reads were aligned using the reference genome hg38 (http://genomeast.igbmc.fr). The Qlucore software (http://www.qlucore.org) was used for the analysis.

first: Jacques

last: Haiech

first: Jihu

last: Dong


title: Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre-neoplastic melanocytes

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

summary: A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour, cancer cells have escaped the initial immune response mechanisms. To date, no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone-inducible binary system allowing for temporal control of different Ras-oncogene (NRasK61Q, HRasG12V, KRasG12V) expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma, revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1, fgf6, cathepsin H, cathepsin L, galectin 1 and galectin 3.

overall_design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA-seq analysis of the active transcriptome.

first: Amy

last: Kenyon

first: Daria

last: Gavriouchkina

first: Giorgio

last: Napolitani

first: Vincenzo

last: Cerundolo


title: Genome-wide gene-expression profile of mouse intestinal stem cells

city: Cambridge

first: Maria

middle: M

last: Mihaylova

state: MA

address: 9 Cambridge Center

institute: Whitehead Institue

summary: The goal of this project is to generate transcriptome profiling of intestinal stem cells for a systemic analysis of cellular pathways involved in responses to fasting.

overall_design: Examination of one cell type in two conditions.

first: Omer

middle: H

last: Yilmaz

first: David

last: Sabatini


title: Genome-wide mapping of the Arabidopsis thaliana heat shock transcription factor A1b binding sites under non-stress and heat stress conditions

city: Colchester

first: Philip

last: Mullineaux

state: Essex

address: Wivenhoe Park

department: Environmental and Plant Bioscience Research Group

institute: University of Essex


title: Genome-wide mapping of the Arabidopsis thaliana heat shock transcription factor A1b binding sites under non-stress and heat stress conditions [RNA-seq]

summary: We used Illumina-based RNA-seq to identify differentially expressed genes in wild-type Arbaidopsis or in transgenic plants over-expressing HSFA1b-RFP. These data were interescted with ChIP-seq experiments conducted under the same conditions. The aim of the combined analyses was to identify HSFA1b-regulated genes involved in growth to stress transitions.

overall_design: RNA-seq in the Arabidopsis genome (wild type and 35S::HSF1b-RFP) under non-stress and heat stress conditions

first: Waleed

middle: S

last: Albihlal


title: Gene expression in Blumeria graminis f. sp. hordeii (Bgh) isolate DH14 during plant pathogenesis

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

summary: We performed RNA-sequencing of Bgh-infected barley leaves at two different time-points after infection to examine gene expression in the barley powdery mildew isolate DH14 during plant pathogenesis.

overall_design: Detached leaves of the barley cultivar Pallas were infected with Bgh isolate DH14. Epidermal peels were used to enrich fungal RNA. The samples were collected at 16 and 48 hours post inoculation (hpi).

first: Saskia

last: Bauer

first: Takaki

last: Maekawa

first: Paul

last: Schulze-Lefert


title: Genome-wide mapping of the Arabidopsis thaliana heat shock transcription factor A1b binding sites under non-stress and heat stress conditions [ChIP-seq]

summary: We used illumina-based next generation sequencing technology to to identify the regions bound by HSFA1b in the Arabidopsis genome. We sequenced HSFA1b chromatin immunoprecipitated genomic sequences under non-stress and heat stress conditions to understand the changes in the HSFA1b binding map when the growth conditions are switched from favorable to heat stress. We show that the binding map of HSFA1b in the Arabidopsis genome is subject to reconfiguration when the growth conditions are switched from non-stress to heat stress response. We also show that HSFA1b is targeting genes involved in developmental processes beside genes involved in stress response under both conditions indicating that HSFA1b possibly regulates the expression of both developmental and stress genes under non-stress and under heat stress, possibly for a limited duration prior heat acclimation.

overall_design: Mapping the binding sites if HSFA1b in the Arabidopsis genome under non-stress and heat stress conditions


title: Transcriptome responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes)

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

summary: Domestication leads to a spectrum of striking behavioral changes whose genetic basis remains largely unknown. Silver foxes have been selectively bred for tame and aggressive behaviors for over 50 years at the Institute for Cytology and Genetics in Novosibirsk, Russia. To further understand the genetic basis and molecular mechanisms underlying tame and aggressive behavioral phenotypes segregating in selected strains of the silver fox, we quantified genome-wide gene expression levels using RNA-seq in two selected brain tissues, right prefrontal cortex and basal forebrain, from 12 aggressive and 12 tame individuals. Expression analysis reveals 146 differentially expressed genes in prefrontal cortex between tame and aggressive individuals at a 5% FDR, and 33 hits were found in basal forebrain. These candidates include genes in key pathways known to be critical to neurological processing, such as serotonin and glutamate receptor pathways.  The data relate in interesting ways to neurological and pharmacological effects that are actively being studied to understand human aggression. In addition, we identified 31,000 high quality exonic SNPs, 295 of which show significant allele frequency differences between tame and aggressive individuals at an adjust P-value < 0.05 level from gene dropping simulation based on the entire pedigrees. A non-synonymous change in a glutamate receptor, GRM3, is among these significant SNPs, indicating that expression and allele-frequency changes are hitting the same pathways. These changes in expression level and allele frequency might be the direct response to the artificial selection and will help understand the genetic basis of mammalian domestication process.

overall_design: Profile of transcriptome-wide gene expression levels in 1.5-year old tame and aggressive fox brain

first: Xu

last: Wang

first: Anna

middle: V

last: Kukekova

middle: G


title: Comparative gene expression profiling of mouse pXEN, XEN, ES, and rat XENP cells

status: Public on May 29 2018

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

summary: We derived and describe a novel mouse cell type that we name primitive XEN (pXEN) cells, and compare their gene expression profiles with other stem cell types previously derived from rodent blastocysts.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Each cell type was cultured in its respective maintenance condition. Samples were collected after 2 days of culture.  Each sample corresponds to an independently derived cell line: Mouse pXEN cells, 3 samples; mouse XEN cells, 3 samples; rat XENP cells, 4 samples; mouse ES cells, 2 samples.

first: Yixiang

last: Zhong

first: Kyoung

last: Jung

first: Young


title: Loss of c-Jun NH2-Terminal Kinase in Mammary Epithelial Cells is Sufficient for Adenosquamous Tumor Formation

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: The JNK pathway has been implicated in breast cancer, both from human tumor sequencing studies and from mouse models. To see if JNK deletion is able to form tumors in mice, we crossed Mapk8 and Mapk9 conditional animals with the WAP-Cre expressing mouse to specifically delete JNK in luminal epithelial cells of the breast. We found that JNK suppresses tumors and that the loss of JNK leads to adenosquamous carcinoma formation. To understand the role of JNK in the mammary epithelium, we performed RNA sequencing and analyzed gene expression from tumor-derived cell lines. Several pathways were perturbed in the carcinoma cell lines. Our results demonstrate that loss of JNK alone is sufficient to cause tumor formation and they reveal a gene signature of adenosquamous tumors that can help in better understanding and treating the disease.

overall_design: Mammary epithelial cell (control) and adenosquamous tumor cell line expression was analyzed using three independent libraries of each

first: Nomeda

last: Girnius

first: Roger

last: Davis


title: Timeseries of small RNA and mRNA expression during zebrafish heart regeneration

city: Orono

first: Benjamin

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

summary: Adult zebrafish are capable of regenerating cardiac tissue following ventricular resection within 30 days. We profiled both small RNA and mRNA expression in uninjured (0dpa), 1, 3, 7, 14, 21 and 30 days post amputation to study biological processes orchestrate each stage of regeneration.

overall_design: Small and mRNA gene expression profiling during 0, 1, 3, 7, 14, 21 and 30 days post ventricular resection.

first: B

first: V

middle: P

last: Yin


title: IMP3 regulated gene expression in breast cancer cells

first: Julie

last: Zhu

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

summary: IMP3 (IGF2-mRNA binding protein 3) is a member of a family of IGF2-mRNA binding proteins that function in RNA stabilization, trafficking and localization.  It exhibits the properties of an oncofetal protein and its expression correlates with the aggressive behavior of many tumors.  In breast cancer, IMP3 is associated with the highly aggressive triple-negative subtype (TNBC) The challenge is to identify specific proteins and functions that are regulated by IMP3. As an approach to this problem, we compared the mRNA expression profile of SUM-1315 cells, a TNBC cell line, to the same cells that had been depleted of IMP3.

overall_design: SUM-1315 breast cancer cells were were infected with lentivirus for control shRNA and two different IMP3 shRNAs and processed for RNA-sequencing

first: Sanjoy

last: Samanta

first: Arthur

last: Mercurio


title: Loss of JNK in Breast Epithelium Accelerates Tumor Formation

summary: Members of the JNK pathway have been found to be mutated in human breast cancer. Mouse studies examining JNK loss in different tissues have demonstrated that the JNK pathway can play a role in cancer. Using and autochthonous mouse model, we found that JNK deficiency on a p53-null background resulted in more rapid tumor onset. To learn more about these tumors we generated cells lines and performed various in vitro assays, as well as RNAseq in hope of finding differentially expressed genes that may explain the differences we observed in vivo.

overall_design: Tumors were harvested from mice and cells lines were established from them. RNA was isolated from established tumor cell lines.


title: Pioneer transcription factor FoxA maintains an open nucleosome configuration for tissue-specific gene activation [MNase-Seq]

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin.  Yet the nucleosomal status of such open chromatin, e.g., at active enhancers, is not clear.  Here we develop a combination of low and high levels of MNase digestion along with core histone ChIP-seq to assess the presence of nucleosomes at enhancers and promoters in mouse liver. We find that liver-specific enhancers retain preferentially MNase-accessible nucleosomes, with factors bound, substantially more than ubiquitous enhancers.  Furthermore, the pioneer factor FoxA2 is required to keep enhancer nucleosomes accessible in chromatin at active liver genes.  Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.

overall_design: This experiment includes two technical replicates (F1, F2) of two biological replicates each, examining high and low concentration MNase-seq digestions of adult mouse liver chromatin, either in WT mice or in mice with a deletion of FoxA1 and FoxA2, size-selecting libraries with full nucleosomes or at the sub-nucleosomal size distribution. It does not include sub-nucleosomal sequencing runs for high MNase-seq digestion.

first: Makiko

last: Iwafuchi-Doi

first: Greg

first: Akshay

last: Kakumanu

first: Jason

middle: A

last: Watts

first: Shaun

last: Mahony

middle: F

last: Pugh

first: Dolim

last: Lee

first: Klaus

last: Kaestner

first: Kenneth

last: Zaret


title: Genome-wide maps of chromatin state in epiblast stem cells and nodal inhibited ebiblast stem cells

city: Shanghai

first: Naihe

last: Jing

address: Yue Yang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: We reported H3K4me3, H3K27ac and H3K27me3 histone modification in EpiSCs and Nodal inhibited EpiSCs(EpiSCS/F).  Using ChIP sequencing,  we demonstrate that the active modification of H3K4me3 and H3K27ac level are higher in  EpiSCS/F, suggesting EpiSCsS/F were in an active  chromatin state. Interestingly, H3K27me3, the supressive modification enriched more in EpiSCS/F down regulated genes, suggesting H3K27me3 plays pivital roles in regulating gene expression.

overall_design: Examination of 3 different histone modifications in 2 cell types

first: Chang

last: Liu

first: Xianfa

last: Yang

first: Zhisong

last: He


title: RNA sequencing of Epiblast stem cells, nodal inhibited epiblast stem cells and embryonic samples

summary: To characterize the molecular properties of the EpiSCsS/F, we compared the transcriptome of EpiSCsS/F with that of EpiSCs and that of the epiblast cells sampled from embryos (and different parts of the embryo) at the cavity stage (E5.5) to early bud stage (E7.5)

overall_design: Examination of the gene expression profiles of two type of stem cells and 10 embryonic tissue samples

first: Rang

last: Wang


title: DERARE RNA-seq

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: We analyzed the transcriptome of LT-HSCs sorted from wildtype and DERARE knockout mice. We aim at identifying differentially expressed genes and downstream signaling pathways associated with HSC defects in DERARE KO mice, and determining whether Wnt5a treatment could rescue the HSC defects in DERARE KO mice.

overall_design: RNA-seq of LT-HSCs (Lineage-Sca-1+c-Kit+CD34-Flk2-CD49blo) from wildtype and DERARE knockout mice.

first: Pengxu

last: Qian

first: Linheng

last: Li

first: Shiyuan

last: Chen


title: WGBS assessment of global methylation alterations in hematopoietic stem and progenitor cells [methyl-seq]

summary: We generated global DNA methylation maps of 4 types of adult hematopoietic stem and progenitor cells sorted from wildtype C57BL/6 mice.

overall_design: Whole genome bisulfite sequencing of cells using Illumina HiSeq 2500


title: Enhancer chromatin mark H3K27ac in hematopoietic stem and progenitor cells [ChIP-seq]

summary: We mapped H3K27ac chromatin mark of 4 types of adult hematopoietic stem and progenitor cells sorted from wildtype C57BL/6 mice.

overall_design: Maps of enhancer chromatin mark H3K27ac in hematopoietic stem and progenitor cells were obtained by sequencing on Illumina HiSeq 2500


title: Translation cooperation of FGF and WNT signaling

city: HOUSTON

first: Jeffrey

last: Rosen

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Cooperation between FGF and WNT signaling is well documented in normal development, stem cell biology and cancer progression. However, the molecular mechanisms underlying this cooperativity remain poorly understood. In this study, we employed an inducible FGFR1 to interrogate the dynamics of RNA, ribosome occupancy and protein expression as a function of FGFR signaling in the mouse mammary gland with constitutive WNT hyperactivation. We demonstrate that FGFR signaling increases the translation efficiency of WNT signaling components with structured 5’ UTRs harboring a (CGG)4 motif that can potentially form G-quadruplex structures, and that tumorigenesis driven by this mechanism is vulnerable to inhibition of eIF4A, a RNA helicase important in translation initiation. This study also provides novel insights into the contribution of RNA levels and translational regulation to protein expression in pre-malignant mammary epithelial cells dynamically responding to FGFR signaling.

overall_design: RNA and ribosome footprint profiles of WNT-hyperactive mammary epithelial cells from 4-week old mice with and without FGFR1 signaling overactivation in the mammary glands were generated by deep sequencing, in triplicate, using the HiSeq 2500 platform

first: Tuan

last: Nguyen

first: Elena

middle: B

last: Kabotyanski

first: Yongchao

last: Dou

first: Lucas

middle: C

last: Reineke

first: Peng

last: Zhang

first: Xiang

first: Anna

last: Malovannaya

first: Sung

last: Jung

first: Qianxing

last: Mo

first: Kevin

last: Roarty

first: Yiwen

first: Bing

first: Joel

last: Neilson

first: Richard

last: Lloyd

first: Charles

last: Perou

first: Matthew

last: Ellis


title: A retinoid-dependent and methylation-sensitive enhancer in Hoxb cluster maintains haematopoietic stem cells and prevents leukaemogenesis

first: Madelaine

last: Gogol

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

overall_design: Refer to individual Series


title: Comparison of CD4+ and CD8+ T cells from spleen of mice raised in standard or in enriched environment.

status: Public on May 28 2018

city: Valbonne - Sophia-Antipolis

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: C57BL6/J female mice were raised either in standard environment (SE) for 8 weeks after birth or were put in enriched environment (EE) at postnatal 4 weeks up to 8 weeks old. Mice were sacrificed at 8 weeks and spleen were harvested. CD4+ and CD8+ T cells were sorted by FACS and CD4+ or CD8+ T were profiled using a low-input protocol adapted from single-cell RNAseq.

overall_design: 21 samples were profiled: for CD8+ T Cells, n=6 in EE and n=4 in SE. For CD4+ T Cells, N=6 in EE and N=5 in SE.

first: Alice

last: Guyon

first: Hadi

last: Zarif

first: Marie-Jeanne

last: Arguel

first: Agnes

last: Paquet

first: Pascal

last: Barbry


title: Comparison of CD4+ and CD8+ T cells from choroid plexus of mice raised in standard or in enriched environment.

summary: C57BL6/J female mice were raised either in standard environment (SE) for 8 weeks after birth or were put in enriched environment (EE) at postnatal 4 weeks up to 8 weeks old. Mice were sacrificed at 8 weeks and choroid plexus in the brain were harvested. CD4+ and CD8+ T cells were sorted by FACS and 5-20 CD4+ or CD8+ T were profiled using a low-input protocol adapted from single-cell RNAseq.

overall_design: 31 samples were profiled: for CD8+ T Cells, n=7 in EE and n=7 in SE. For CD4+ T Cells, N=9 in EE and N=8 in SE.


title: Changes in mRNA in the dorsal root ganglion after CNS injury and intramuscular neurotrophin-3 treatment

city: Geneva

first: Claudia

last: Kathe

address: Chemin des MInes 9

department: Center for Neuroprosthetics

country: Switzerland

institute: EPFL

summary: Brain and spinal injury often impair sensorimotor processing in the spinal cord and reduce mobility. We established that complete transection of corticospinal pathways in the pyramids leads to increased spasms, excessive mono- and polysynaptic spinal reflexes and impaired locomotion in rats. Intramuscular neurotrophin-3 treatment at a clinically-feasible time-point after injury reduced these signs of spasticity. We found Neurotrophin-3 reduced spastic movements and improved neurophysiological sensorimotor control. Furthermore, the balance of inhibitory and excitatory synapses in the cord and the level of an ion transporter in motor neuron membranes required for normal reflexes were normalized. We discovered that Neurotrophin-3 is transported in sensory afferents from muscles to the dorsal root ganglia. Using genome-wide RNA sequencing of the whole cervical level 6-8 dorsal root ganglia, we explored mRNA changes in afferent neurons that were present 10 weeks after bilateral pyramidotomy. Many of the dysregulated genes are involved in axon guidance and plasticity. Intramuscular neurotrophin-3 treatment normalized many of those gene changes and may be one of the mechanisms how reflexes, functional recovery and molecular markers in the spinal cord are restored. This identifies neurotrophin-3 as a therapy that treats the underlying causes of spasticity and not only its symptoms.

overall_design: RNA-Seq was performed on whole C6-8 dorsal root ganglia of six rats from three different groups: naïve rats, rats 10 weeks after bilateral pyramidotomy lesions and AAV1-GFP treatment into the muscle, rats 10 weeks after bilateral pyramidotomy lesions and AAV1-prepro-neurotrophin-3 treatment into the muscle. Differential expression was analyzed between each of the groups.

first: Lawrence

last: Moon


title: Changes in miRNAs in the dorsal root ganglion after CNS injury and intramuscular neurotrophin-3 treatment

summary: Brain and spinal injury often impair sensorimotor processing in the spinal cord and reduce mobility. We established that complete transection of corticospinal pathways in the pyramids leads to increased spasms, excessive mono- and polysynaptic spinal reflexes and impaired locomotion in rats. Intramuscular neurotrophin-3 treatment at a clinically-feasible time-point after injury reduced these signs of spasticity. We found Neurotrophin-3 reduced spastic movements and improved neurophysiological sensorimotor control. Furthermore, the balance of inhibitory and excitatory synapses in the cord and the level of an ion transporter in motor neuron membranes required for normal reflexes were normalized. We discovered that Neurotrophin-3 is transported in sensory afferents from muscles to the dorsal root ganglia. Using genome-wide small RNA sequencing of the whole cervical level 6-8 dorsal root ganglia, we explored miRNA changes in afferent neurons that were present 10 weeks after bilateral pyramidotomy. Many of the dysregulated genes are involved in axon guidance and plasticity. Intramuscular neurotrophin-3 treatment normalized many of those gene changes and may be one of the mechanisms how reflexes, functional recovery and molecular markers in the spinal cord are restored. This identifies neurotrophin-3 as a therapy that treats the underlying causes of spasticity and not only its symptoms.


title: Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells

first: Naihe

last: Jing


title: Expression profiling by small RNA-seq for identifying miRNA associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors

city: Daejeon

first: Seon-Kyu

last: Kim

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

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

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

overall_design: miRNA-seq data of 6 samples, two H3122 parental cells, two ceritinib-treated resistant cells, and two non-resistant cells that combinely treated with certinib and panobinostat, were generated. Total RNA was isolated using the mirVana miRNA isolation kit (Ambion). Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified. Sequencing was performed in single end reads (75 bp) using NextSeq 500 platform (Illumina).

first: Jeong-Hwan

first: Mirang

first: Mi-Ran

last: Yun

first: Sun-Min

last: Lim

first: Byoung-Chul

last: Cho


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

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

overall_design: MBD-seq data of 6 samples, two H3122 parental cells, two ceritinib-treated resistant cells, and two non-resistant cells that combinely treated with certinib and panobinostat, were generated. Methylated DNA was precipitated using the MethylMiner methylated DNA enrichment kit (Invitrogen). The purified methylated DNA fragments were ligated to a pair of adaptors. Sequencing was performed in single end reads (75 bp) using NextSeq 500 platform (Illumina).


title: ChIP-seq for identifying molecules associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors

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

overall_design: ChIP-sequencing was performed in each cell group. Cells were fixed using 1% formaldehyde, lysed and sonicated using a Bioruptor (Diagenode Inc.). Immunoprecipitation was performed with anti-H3K27ac(Millipore, 06-599) or anti-H3K4me1(Abcam, ab8895). 250-400 bp genomic libraries were generated from the input and immunoprecipitated DNA and sequenced using Illumina NextSeq500 to generate 75 bp single-end reads.


title: Changes in mRNA and small RNA in the dorsal root ganglion after CNS injury and intramuscular neurotrophin-3 treatment


title: Circulating microRNA and 5’ tRNA halves signatures of genotype-by-age interactions in the longlived Ames dwarf mouse.

status: Public on May 27 2018

city: Elk Grove

first: joseph

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

summary: Recent evidence demonstrates that serum levels of specific small noncoding RNAs (sncRNAs) including miRNAs and 5’ tRNA halves significantly change with age. The ability of circulating sncRNAs to act as signaling molecules and regulate a broad spectrum of cellular functions implicates them as key players in the aging process. To discover circulating sncRNAs that impact aging in the long-lived Ames dwarf mice, we conducted deep sequencing of small RNAs extracted from serum of young and old mice. Our analysis showed genotype-specific changes in the circulating levels of 43 miRNAs and 19 5’ tRNA halves during aging [Genotype-by-Age interaction (GbA)]. GbA miRNAs showed four distinct expression patterns and significant over-targeting of transcripts involved in age-related processes.  Functional enrichment analysis of putative miRNA targets highlighted cellular processes such as tumor suppression, anti-inflammatory response, and modulation of Wnt, insulin, mTOR, and MAPK signaling pathways, among others. The comparative analysis of circulating GbA miRNAs in Ames mice with circulating miRNAs modulated by calorie restriction (CR) in another long-lived mouse suggests CR-like and CR-independent mechanisms contributing to longevity in the Ames mouse. In conclusion, we showed for the first time a signature of circulating miRNAs and 5’-tRNA halves modulated by age in the long-lived Ames mouse.

overall_design: Comprehensive survey of miRNAs from young and old dwarf and normal mice.

first: J

last: Dhahbi


title: A global transcriptome analysis of human epidermal keratinocytes upon inhibition of lncRNA WAKMAR1

status: Public on May 26 2018

city: Stockholm

first: Ning

last: Xu

state: Stockholm

address: CMM L8:02, Karolinska Institutet

department: Medicine

country: Sweden

institute: Karolinska Institutet

summary:
Recent study has revealed that long non-coding RNAs (lncRNAs) perform as important regulators of cellular physiology and pathology, which makes them promising therapeutic and diagnostic entities. We found lncRNA WAKMAR1 is significantly down-regulated in wound-edge keratinocytes from venous ulcer and diabetic foot ulcer compared to the normal wounds. To study the genes regulated by WAKMAR1, we transfected lncRNA GapmeRs into human primary epidermal keratinocytes to inhibit its expression.  We performed a global transcriptome analysis of keratinocytes upon inhibition of WAKMAR1 using Affymetrix arrays.
We performed a global transcriptome analysis of keratinocytes upon inhibition of WAKMAR1 using Affymetrix arrays.

overall_design: Expression profiling of primary human epidermal keratinocytes transfected with 20nM WAKMAR1 GapmeRs (GapmeR-WAKMAR1) 20nM control oligos (GapmeR-Ctrl) for 24 hours (biological triplicates in each group) was performed using Affymetrix GeneTitan system.

first: Dongqing

last: Li


title: 5-hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder

city: Atlanta

first: Ying

last: Cheng

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary: Autism spectrum disorders (ASD) comprise a group of disorders characterized by impaired language, social, and communication skills, in addition to restrictive behaviors or stereotypies. However, with a prevalence of 1.5% in developed countries and relatively high comorbidity rates, no clear underlying mechanism that unifies the heterogeneous phenotypes of ASD is known. 5-hydroxymethylcytosine (5hmC) has been reported highly enriched in brain, and is now recognized as an important epigenetic mark in developmental and neurological disorders. To explore the role of 5hmC in ASD, we utilized the genomic DNA isolated from the postmortem cerebellum of both ASD patients and age-matched controls to profile genome-wide distribution of 5hmC. We identified 797 age-dependent differential hydroxymethylated regions (DhMRs) (q-value < 0.05, FDR adjusted) in young group (age ≤ 18), while no significant DhMR was identified in the groups over 18-year-old. Pathway and disease association analyses indicated that the intragenic DhMRs were located in the genes that involved in cell-cell communication and neurological disorders. By comparing the 5hmC counts (ASD vs. Control) in each psychiatric gene (±10kb), we observed significant 5hmC changes in larger fraction of psychiatric genes than in reference genes. Interestingly, we found that the predicted cis functions of non-coding intergenic DhMRs strikingly associated with ASD and intellectual disorders. A significant fraction of intergenic DhMRs were overlapped with topologically associating domains (TAD). These results together suggest that 5hmC dynamic alteration is associated with ASD, particularly in the early development stage, and could contribute to the pathogenesis of ASD.

overall_design: To explore the role of 5hmC in ASD, we isolated genomic DNA from the postmortem cerebellum of 17 ASD patients and 19 age-matched controls, and profiled the genome-wide 5hmC distribution by employing a previously established chemical labeling and affinity purification method, coupled with high-throughput sequencing technology.  Age groups are defined as: young (< 18) , middle (18< age < 35), old (>35).

first: Peng

last: Jin


title: Expression profiling of Dicer loss-of-function macrophages

status: Public on May 25 2018

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

summary: The role of microRNAs in the inflammatory response of macrophages to LPS was adressed by expression analysis in DicerKO (LysMcre/+;Dicerfl/fl;ApoE-/-) vs wildtype (LysMcre/+;Dicer+/+ApoE-/-) macrophages when challenged either with vehicle (PBS) or LPS.

overall_design: Bone marrow-derived macrophages of male LysMcre/+;Dicerfl/fl;ApoE-/- and there litter mate control mice (LysMcre/+;Dicer+/+;ApoE-/-) were isolated and differentiated in vitro. After 6h treatment with either vehicle (PBS) or 100 ng/ul LPS, macrophages were harvested. The RNA was isolated and sequenced. 3 replicates per genotype and treatment were analyzed.

first: Nina

last: Uhlenhaut

first: Yuanyuan

last: Wei

first: Andreas

last: Schober


title: Analysis of the DNA accessibility upon multiple histone H1 variants by ATAC-seq

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

summary:
Combined depletion of H1.2 and H1.4 has a strong deleterious effect in the cancer cells examined, and induces a strong interferon (IFN) response with up-regulation of many IFN-stimulated genes (ISGs), which is not seen in individual H1 knock-downs.
Although H1 participates to repress ISG promoters, its activation upon H1 KD is mainly generated by the activation of the IFN response through cytosolic nucleic acids receptors, IFN synthesis and JAK-STAT pathway activation.
The IFN response may be triggered by the expression of noncoding dsRNAs generated from heterochromatic repeats or endogenous retroviruses upon H1 KD.
H1 KD promotes the appearance of accessibility sites genome wide and, particularly, at satellites and other repeats.

overall_design: 4 samples

last: Jordan Vallés

first: Andrea

last: Izquierdo-Bouldstridge


title: Expression data from purified hepatoblasts and differentiated hepatocytes and cholangiocytes

status: Public on May 24 2018

city: Chiba

first: Tetsuhiro

last: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology and Nephrology

country: Japan

institute: Graduate School of Medicine, Chiba University

summary: To identify differentially expressed genes involved in differentiation process of Dlk+ cells, we have conducted whole genome microarray expression profiling. Subsequently, genes exhibiting a change greater than 2.0-fold were selected.

overall_design: Purified Dlk-positive hepatoblasts and differentiation-induced hepatoblasts were subjected to RNA extraction and hybridization on Agilent microarrays.

first: Atsushi

last: Iwama

first: Naoya

last: Kato


title: Strand-specific Dual RNA-seq of Bronchial Epithelial cells Infected with Influenza A/H3N2 Viruses Reveals Splicing of Gene Segment 6 and Novel Host-Virus Interactions

city: Bethesda

first: Andrew

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

summary: Host-influenza virus interplay at the transcript level has been extensively characterized in epithelial cells. Yet, there are no studies that simultaneously characterize human host and influenza A virus (IAV) genomes. We infected human bronchial epithelial BEAS-2B cells with two seasonal IAV/H3N2 strains, Brisbane/10/07 and Perth/16/09 (reference strains for past vaccine seasons) and the well-characterized laboratory strain Udorn/307/72. Strand-specific RNA-seq of the infected BEAS-2B cells allowed for simultaneous analysis of host and viral transcriptomes, in addition to pathogen genomes, to reveal changes in mRNA expression and alternative splicing (AS). In general, patterns of global and immune gene expression induced by the three IAVs were mostly shared. However, AS of host transcripts and small nuclear RNAs differed between the seasonal and laboratory strains. Analysis of viral transcriptomes showed deletions of the polymerase components (defective interfering (DI)-like RNAs) within the genome. Surprisingly, we found that the neuraminidase gene undergoes AS, and that the splicing event differs between seasonal and laboratory strains. Our findings reveal novel elements of the host-virus interaction and highlight the importance of RNA-seq in identifying molecular changes at the genome level that may contribute to shaping RNA-based innate immunity.

sample_organism: Influenza A virus (A/Udorn/307/1972(H3N2))

sample_organism: Influenza A virus (A/Brisbane/10/2007(H3N2))

sample_organism: Influenza A virus (A/Perth/16/2009(H3N2))

overall_design: Examination of RNA from three different H3N2 viruses (and mock infection) at three timepoints with 3 biological replicates each.

first: Giulia

last: Fabozzi

first: Jun

last: Zhu

first: Kanta

last: Subbarao

first: Ronald

last: Rabin


title: Novel and Conserved microRNAs in soybean floral whorls

city: Porto Alegre

first: Guilherme

last: Cordenonsi da Fonseca

state: RS

address: Av. Bento Gonçalves, 9500

department: Centro de Biotecnologia

country: Brazil

institute: UFRGS

summary: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (19–24 nt) that regulates de gene expression, mainly through mRNA targets cleavage and translation inhibition. In plants, miRNAs have been shown to play pivotal roles in a wide variety of metabolic and biological processes like plant growth, development, and response to biotic and abiotic stress. Soybean is one of the most important crops worldwide, due to the production of oil and its high protein content. The reproductive phase is considered the most important for the yield of soybean, which is mainly intended to produce the grains. The identification of miRNAs is not yet saturated in soybeans, and there are no studies linking them to the different floral organs. In this study, three different soybean floral whorls were used in the construction of sRNA libraries. The sequencing of petal, carpel and stamen libraries by the Solexa platform generated a total of 10,165,661 sequences. Subsequently analyses detected 200 miRNAs sequences, from those 41 were novel miRNAs never detected before, 80 were conserved soybean miRNAs, 31 were new antisense conserved soybean miRNAs and 46 soybean miRNAs isoforms. We also found a new miRNA conserved in other plant species, and finally one miRNA-sibling of a soybean conserved miRNA. Conserved and novel miRNAs were evaluated by RT-qPCR. We observed a differential expression across the three whorls for six miRNAs analyzed. A computational prediction of targets for miRNAs analyzed by RT-qPCR was performed. Many of the predicted targets have described functions related to the reproductive process in plants. In summary, the increased accumulation of specific and novel miRNAs in different whorls indicates that miRNAs are an important part of the regulatory network in soybean flower.

overall_design: microRNA profiles in 4 different libraries (stamens, petals, carpels and whole flower) of Glycine max by deep sequencing (Illumina HiSeq2000).

first: Franceli

middle: R

last: Kulcheski

first: Lorrayne

last: Molina

last: da Fonseca

last: de Morais

first: Luiz

last: de Oliveira

first: Rogério

last: Margis


title: Global maps of ProQ binding in vivo reveal target recognition via RNA structure and stability control at mRNA 3' ends

city: Würzburg

first: Thorsten

last: Bischler

address: Josef-Schneider-Straße 2 / D15

department: Core Unit SysMed

institute: University of Wuerzburg

summary: In this study binding sites for the RNA-binding protein ProQ was determined in Salmonella and Escherichia coli

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: To detect the binding sites for Salmonella or E. coli ProQ we collected three biological replicates of Salmonella strain SL1344 and two biological replicates of E. coli strain MG1655 where the proQ gene was fused to a 3xFLAG tag. Half of each replicate culture was irradiated with UV light (254 nm, 800 mJ/cm2) (+CL), while the other half was left untreated (-CL). Bacteria were lysed and the FLAG-tagged protein was immunoprecipitated using a monoclonal anti-FLAG antibody. The samples were treated with benzonase nuclease, calf intestine phophorylase, and polynucleotide kinase in the presence of radioactive gamma-ATP. Samples were separated with SDS-PAGE followed by transfer to nitrocellulose membranes. Radioactively labelled RNA-protein complexes were eluted from membranes and treated with Proteinase K. Purified RNA was used as input for library preparation using the NEB Next Small RNA Library kit.

first: Erik

last: Holmqvist

first: Lei

last: Li

first: Lars

last: Barquist

first: Jörg

last: Vogel


title: Tobacco pollen sequestrome dynamics

city: Prague 6

first: David

last: Honys

state: CZ

address: Rozvojova 263

country: Czech Republic

institute: IEB ASCR

summary: Transcriptome profiling of four RNA fractions in six developmental stages of  tobacco (Nicotiana tabacum) male gametophyte

overall_design: Total RNA and RNA isolated from polysomes, RNPs and EPP complexes isolated from six tobacco pollen developmental stages was hybridised on Agilent Tobacco Gene Expression Microarray 4x44K in two biological replicates per sample


title: Increased expression of immune regulatory mediators independently detects tuberculosis in advanced HIV

status: Public on May 23 2018

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 south orange ave

institute: Rutgers University

summary: Tuberculosis (TB) is the major cause of death in HIV-infected individuals. However, diagnosis of TB in HIV remains challenging. The aim of this study was to determine the performance of published gene signatures in distinguishing active TB in advanced HIV. We concluded that gene expression of FcGR1A and BATF2, and plasma protein levels of IFNγ and CXCL10 can singly classify active TB in HIV-infected with advanced HIV.

overall_design: Case-control study of whole blood RNA-Seq and plasma cytokine/chemokine analysis of HIV-infected individuals with CD4+ T cell count of <100 cells/µl (advanced HIV), with and without active TB.

first: Peicheng

last: Du

first: Sheetal

last: Verma


title: In vivo analysis of function of pulmonary pericytes

city: Muenster

first: Katsuhiro

last: Kato

address: Roentgenstrasse 20

department: Department of Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

summary: RNA-seq libraries generated from pulmonary pericytes expressing PdgfrbCreERT2 control or Yap1;Wwtr1 double floxed allele using the Ribotag allele to understand the function and identity of pericytes.

overall_design: Lungs were extraced from 3 mice (P8) PdgfrbCreERT2;Yap1+/-;Wwtr1+/-;Ribotag or PdgfrbCreERT2;Yap1-/-;Wwtr1/-;Ribotag mice. After homogenization, RNA was purified from pericyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag.

first: Rodrigo

last: Diéguez-Hurtado

first: Ralf

last: Adams


title: Beta cell-targeted glucokinase overexpression

city: Rochester

first: Yasuhiro

last: Ikeda

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: RNA sequecing of isolated mouse islets from C57BL/6J mice fed high fat diet following control or AAV-mIP2-GCK injection.

overall_design: Differential expression and pathway analysis of isolated mouse islets following in vivo transduction with AAV-mIP2-GCK

first: Brian

last: Lu


title: Gene expression data from the HCT-116 colon cancer cell line in the presence or absence of siRNA targeting APC

city: Columbus

first: Joanna

last: Groden

state: OH

address: 986 BRT 460 West 12th Ave.

department: Department of Cancer Biology and Genetics

institute: The Ohio State University, College of Medicine

summary: Gene expression data were collected by RNA-seq from HCT-116 cells in the presence or absence of siRNA targeting APC and 1,376 transcripts changed in expression following APC silencing were identified relative to scrambled siRNA-transfected and untreated controls.

overall_design: Examination of gene expression under 3 different transfection conditions

first: William

last: Hankey

first: Xun

last: Lan

first: Victor

middle: X

last: Jin


title: Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: Uracil in DNA can be generated as a result of cytosine deamination or dUMP misincorporation. However, its distribution in the human genome is poorly understood, due to the lack of a sensitive detection method. Here we present “dU-seq”, a selective labeling and pull-down technology, to profile uracil in the human genome. dU-seq specifically labels uracil-containing DNA via an in vitro base excision repair reaction and identifies thousands of uracil peaks in the human genome.

overall_design: dU-seq performed on three wild-type cell lines, one KO cell line and two 5-fluorodeoxyuridine treated cells; sample Titles with "biotin-dCTP" means in the dU-seq library preparation, the DNA labeling step utilized biotin-dCTP while other samples utilized biotin-dUTP; sample Titles with "5F" means 5-fluorodeoxyuridine treated cells.

first: Xiaoting

last: Shu

first: Zhike

first: Chengqi

last: Yi


title: Transcriptomic Differences Associated with TSC2 Gene Expression Loss in Lymphangioleiomyomatosis

city: Philadelphia

first: Blanca

last: Himes

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Heterogeneity in early lymphoid compartments [CLP and LP]

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC


title: B-cell activating factor (BAFF) stimulation of Burkitt Lymphoma cell line [RNA-Seq]

city: Goettingen

first: Alexander

last: Wolff

state: Lower Saxony

address: Humboldtallee 32

department: Medical Statistics

institute: UMG

summary:
RNA-Seq profiling of Burkitt Lymphoma cell line (BL2) with B-cell activating factor (BAFF) for 24 hrs .
The Burkitt Lymphoma cell line were either only cultured in cell culture medium supplemented with 10 mM HEPES at 1 × 106 cells/ml  or additionally incubated with B-cell activating factor (BAFF) for 24 hrs

overall_design: Two conditions of  BL2 cells each in 3 replicates:  1. non-stimulated control (BL2),  2. Baff stimulated (BL2Baff)

first: Michaela

last: Bayerlová

first: Dieter

last: Kube

first: Jochen

last: Gaedcke

first: Tim

last: Beißbarth