title: Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre

city: Santa Cruz

middle: David

last: Magasin

address: 1156 High Street

department: Ocean Sciences

institute: UC Santa Cruz

summary: Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities.

overall_design:
Transcription by surface water and deep water microbial communities was assessed for samples collected during the BioLINCS cruise from 6-21 September 2011 in the North Pacific Subtropical Gyre (NPSG).  In situ surface samples (24 m) were collected with an Environmental Sample Processer (ESP) each morning (5:00-6:00) and evening (17:00). As the ESP drifted along the boundary of two anticyclonic eddies from 14-16 September, large increases in nutrient concentrations were observed at the surface, possibly indicating vertical advection of deep, nutrient-rich water.  To study the surface community transcriptional response to this hypothesized advection event, morning and evening ESP samples from 14, 15, and 16 September (six ESP samples in total) were assayed with the MicroTOOLs microarray v2.0 (GPL24371).  Additionally, the surface community response to nutrient increases was assesed with MicroTOOLs in a mixing experiment (simulated advection). The mixing experiment used surface (25 m) and, by comparison, deep (130 m) water that was collected on 12 September and observed to have, respectively, low and high nutrient concentrations (typical of the NPSG in the late summer).  In order to distinguish the effects of nutrient changes versus biological interactions between surface and deep communities, the mixing experiment used both filtered and unfiltered water as follows (see Fig. 2 in our publication): Surf_FDW = unfiltered surface water (16 L) mixed with filtered deep water (4 L), to assess effects of nutrients alone on the surface community (by comparison to control Surf_Cnt); Deep_FSW = unfiltered deep water (4 L) mixed with filtered surface water (16 L), to assess effects of surface conditions on the deep community (by comparison to control Deep_Cnt); Surf_UDW = unfiltered surface and unfiltered deep water (16 L and 4 L, respectively), to assess biological effects (by comparison to Surf_FDW). Control samples mixed filtered and unfiltered water from the same depth: Surf_Cnt = unfiltered (16 L) and filtered (4 L) surface water; Deep_Cnt = unfiltered (4 L) and filtered (16 L) deep water.  Ten mixing experiment samples (5 types x 2 replicates) were assayed with MicroTOOLs.
[variable] other: in situ sample: ESP_Sep14_500_id_2012, ESP_Sep15_1700_id_2041, ESP_Sep14_1700_id_2061, ESP_Sep15_500_id_3045, ESP_Sep16_500_id_3052, ESP_Sep16_1700_id_3053
[variable] other: mixing experiment sample: Surf_FDW_id_52602, Surf_FDW_id_52603, Surf_Cnt_id_52604, Surf_Cnt_id_52605, Deep_FSW_id_52606, Deep_FSW_id_52607, Deep_Cnt_id_52608, Deep_Cnt_id_52609, Surf_UDW_id_52610, Surf_UDW_id_52611

first: Julie

last: Robidart

middle: D

first: Irina

last: Shilova

first: Kendra

last: Turk-Kubo

first: Sam

middle: T

last: Wilson

last: Karl

first: Christopher

last: Scholin

middle: P

last: Zehr


title: Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs

status: Public on Sep 04 2018

city: Chengdu

first: Mingzhou

last: Li

state: Sichuan

address: Huimin Road 211, Gongping Street

country: China

institute: Sichuan Agricultural University

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Lung tissue plays an important role in the respiratory system of mammals after birth. Early lung development includes six key stages, of which the saccular stage spans the pre- and neonatal periods and prepares the distal lung for alveolarization and gas-exchange. However, little is known about the changes in gene expression between fetal and neonatal lungs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in the lung tissue of fetal and neonatal piglets. A total of 19,310 lncRNAs and 14,579 mRNAs were identified and substantially expressed. Furthermore, 3248 mRNAs were significantly (FDR-adjusted p value ≤ 0.05, FDR: False Discovery Rate) differentially expressed and were mainly enriched in categories related to cell proliferation, immune response, hypoxia response, and mitochondrial activation. For example, CCNA2, an important gene involved in the cell cycle and DNA replication, was upregulated in neonatal lungs. We also identified 452 significantly (FDR-adjusted p value ≤ 0.05) differentially expressed lncRNAs, which might function in cell proliferation, mitochondrial activation, and immune response, similar to the differentially expressed mRNAs. These results suggest that differentially expressed mRNAs and lncRNAs might co-regulate lung development in early postnatal pigs. Notably, the TU64359 lncRNA might promote distal lung development by up-regulating the heparin-binding epidermal growth factor-like (HB-EGF) expression. Our research provides basic lung development datasets and will accelerate clinical researches of newborn lung diseases with pig models.

overall_design: Six female Tibetan-Meishan  (Patriarchal: Tibetan pig; Matriarchal: Meishan pig) hybrid piglets were used to simulate the adaptation of newborns. The pregnancy period was considered to be 113 days. The fetal group consisted of three piglets obtained from three pregnant sows of similar weights on the last day before birth. The neonatal group consisted of three piglets of similar weight obtained two days after birth from another three pregnant sows. All parents were of a similar-weight and were raised under the same feeding and rearing conditions until caesarean and parturition. Piglet lung tissues were rapidly sampled from each carcass and selectively separated into two parts. One part was fixed with 10% formalin for morphometric analysis, and the other part frozen immediately in liquid nitrogen and stored at −80 °C until required for RNA extraction, sequencing and transcriptome analysis.

first: Long

last: Jin

first: Silu

last: Hu

first: Teng

last: Tu

first: Surong

last: Shuai


title: Brr6 Plays a Role in Gene Recruitment and Transcriptional Regulation at the Nuclear envelope

status: Public on Sep 01 2018

city: San Francisco

first: Anne

last: de Bruyn Kops

state: California

address: UCSF Mission Bay, Genentech Hall N376, Guthrie Lab, 600 16th St

department: Biochemistry and Biophysics

country: USA

institute: UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Correlation between transcriptional regulation and positioning of genes at the nuclear envelope is well established in eukaryotes but the mechanisms involved are not well understood.  We provide evidence that Brr6 interacts with chromatin, helping to maintain normal chromatin architecture and transcriptional regulation of certain loci at the nuclear envelope. Specifically, our results showed that brr6-1 impairs PAB1 transcript levels and disrupts PAB1 and GAL1-10 locus positioning. In addition, RNAseq analysis revealed misregulation of both coding and non-coding transcription across the FUR4-GAL1,10,7 region as well as changes at numerous other genes. The discovery that brr6-1 is disomic for CHIII raised the possibility that some of these effects stemmed from increased copy number of CHIII genes.  However, disomy was not present in wild type cells where the NLS-Brr6N fragment was expressed, therefore we were able to use the Brr6N fragment to link many of the brr6-1 effects at the PAB1 and FUR4-GAL1,10,7 loci to Brr6 function, including: 1) decreased PAB1 expression, 2) defective PAB1 locus positioning, and 3) misregulation across the FUR4-GAL1-10 region. Together with our ChIPseq results showing zinc finger-dependent association of the Brr6N fragment with the FUR4 gene, these results strongly argue for a role for Brr6 in gene recruitment and regulation at the nuclear envelope.

overall_design: For RNAseq analysis: RNA was analyzed from 2 biological replicates of wild type or brr6-1 mutant (arg to lys point mutation in putative zinc finger domain of Brr6) samples grown in 2% glucose or in 2% raffinose/0.04% sucrose followed by 2hr induction in 2% galactose. RNA levels are compared between wild type and mutant for each condition. For ChIPseq analysis: extracts were prepared from wild type cells carrying empty vector, or non-membrane FLAG-tagged Brr6N and Brr6∆C4N fragment constructs (+/- putative zinc finger domain). r ChIP was done with FLAG antibody beads. IP'd DNA was normalized against DNA in total extract. The vector sample served as a control for non-specific background in the IP. The ∆C4N samples showed whether interaction was dependent on the zinc finger domain.

first: Jordan

middle: E

last: Burke

first: Christine

last: Guthrie


title: Genome-wide analysis of human prostate cancer cells

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

summary: human prostate epithelial cell line  of 10 cases having different metastatics were examined, such as  up- or down-regulated specific  cellular functions.

overall_design: Total RNA obtained from human prostate epithelial cell line, Human Genome U133A 2.0 Array being used


title: Notch3-dependent beta-catenin signaling mediates EGFR TKI drug persistence in EGFR mutant NSCLC

status: Public on Aug 31 2018

city: Columbus

first: Rajeswara

last: Arasada

state: OH

address: 420 W 12th Ave

institute: Ohio State University

summary: EGFR tyrosine kinase inhibitors cause dramatic responses in EGFR-mutant lung cancer, but resistance universally develops. The involvement of β-catenin in EGFR TKI resistance has been previously reported however the precise mechanism by which β-catenin activation contributes to EGFR TKI resistance is not clear. Here, we show that EGFR inhibition results in the activation of β-catenin signaling in a Notch3-dependent manner, which facilitates the survival of a subset of cells that we call “adaptive persisters”. We previously reported that EGFR-TKI treatment rapidly activates Notch3, and here describe the physical association of Notch3 with β-catenin, leading to increased stability and activation of β-catenin. We demonstrate that the combination of EGFR-TKI and a β-catenin inhibitor inhibits the development of these adaptive persisters, decreases tumor burden, improves recurrence free survival, and overall survival in xenograft models. These results supports combined EGFR-TKI and β-catenin inhibition in patients with EGFR mutant lung cancer.

overall_design: HCC4006 cells were transfected with NTC, Notch1 or Notch3 siRNAs. Cells split into two groups, one was treated with DMSO and the other was treated with erlotinib for 5 days. Total RNA was collected and subjected to transcriptome analysis.

middle: R

first: Jianying

last: Zhang


title: FoxO1 is a regulator of MHC-II expression and anti-tumor effect of tumor associated macrophages

city: Hefei

first: Jingbo

last: Yang

state: Anhui

address: Huangshan Road 443, Western Campus of USTC

department: School of Life Sciences and Institution of Immunology

institute: University of Science and Technology of China

summary:
Bone marrow derived macrophages from C57BL/6 mice were stimulated into M1 and M2 polarization state. Analysis of BMDMs from LysMcre;FoxO1Fl/FL mice and control littermates. Results provide insight into the regulatory role of FoxO1 during macrophage polarization.
BMDMs were stimulated with 100ng/ml LPS plus 20ng/ml IFN-γ into M1 polarization, and stimulated with 10ng/ml IL-4 plus 10ng/ml IL-13 into M2 polarization. Both for 24 hours. Unstimulated cells as M0 state.

overall_design: Six samples, including 3 polarization state from FoxO1 deficient BMDMs and WT BMDMs, separately.

first: Zhexiong

last: Lian


title: Gene expression during equine chorionic girdle development

city: North Mymms

first: Amanda

middle: M

last: de Mestre

state: Hertfordshire

address: Hawkshead Lane

department: Comparative Biomedical Sciences

country: United Kingdom

institute: Royal Veterinary College

summary: We obtained placental issue between days 27 and 34 of pregnancy from matched mare and stallion pairs. We used whole transcriptome profiling in order to measure and compare gene expression in chorionic girdle trophoblast and adjacent regressing chorion at pregnancy day 27 (initiation of proliferation and prior to differentiation), day 30 (initiation of differentiation), day 31 (consolidation of differentiation and movement of cells) and day 34 (when the majority of the trophoblast cells have terminally differentiated into binucleate eCG-secreting trophoblast and have started to obtain invasive qualities and immunomodulatory capacities). Differentially expressed genes were then identified to determine functions and signalling pathways whose activity was modulated over this critical period of trophoblast development. A selection of genes and pathways were subsequently validated.

overall_design: Using agilient horse one colour array, gene expression in equine placental chorionic girdle tissue and matched chorion (as a control) at gestation days 27, 30, 31 and 34. 5 replicates of each time pont and each tissue for a total of 40 RNA samples. Two samples were excluded as significant outliers on a PCA visualization.

last: Read


title: Gene Expression profile of brain in SCI rat by MSC intravenous transplantation.

city: Sapporo

first: Tsutomu

last: Oshigiri

state: Hokkaido

address: 1,minami 1jou nisi 17choume, chuoku

department: Orthopaedic Surgery

country: Japan

institute: Sapporo Medical University

summary:
We had analysed gene expression profile of brain in SCI rat by MSC. Compared with MSC intravenous and vehicle injection at SCI day3.
We used Clariom D / Gene Chip®  Rat Transcriptome Array (RTA 1.0., Affymetrix, Santa Clara, CA, USA).

overall_design: We permormed MSC or vehicle intravenous transplantation at 24 hours after SCI, and extracted motor cortex at day3 after transplantation, and RNA was purified.

first: Masanori

last: Sasaki

first: Kazue

last: Hashimoto-Torii

first: Tstutomu


title: Loss of neural crest-associated gene FOXD1 impairs melanoma invasion and migration via RAC1B downregulation

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

country: Germany

institute: DKFZ

summary: Recent studies suggest that malignant melanoma heterogeneity includes subpopulations of cells with features of multipotent neural crest (NC) cells. Zebrafish and mouse models have shown that reactivation of neural crest-specific pathways determines the invasiveness of melanoma cells. In this study, we show that the neural crest-associated transcription factor FOXD1 plays a key role in invasion and migration capacity of metastatic melanomas both in vivo and in vitro. Gene expression profiling analysis identified on one hand, an upregulation of FOXD1 in NC and melanoma cells, and on the other hand, a downregulation of several genes related to cell invasion in FOXD1 knockdown cells, including MMP9 and RAC1B. Furthermore, we demonstrate that knockdown of RAC1B a tumor-specific isoform of RAC1, significantly impaired cell migration and invasion in melanoma and could abrogate enhanced invasiveness induced by FOXD1 overexpression. We conclude that FOXD1 may influence invasion and migration via indirect regulation of MMP9 and RAC1B alternative splicing in melanoma cells.

overall_design:
mRNA isolated from NHM, D1, D1NC, HT144, MZ7, A375, MeWo, SK-NL-SETDB1, SKmel103
[GSM3039499-GSM3039504] Matrix 1: gene expression comparison between neural crest and hiPSC (related to Figure 1D).
[GSM3039505-GSM3039513] Matrix 2: gene expression comparison between melanoma lines and NHM (related to Figure 1D).
[GSM3039514-GSM3039528] Matrix 3: gene expression comparison between FOXD1 silenced cell lines and Control cell lines (related to Figure S4).

last: Larribère


title: Genome-wide maps of chromatin state in Medicago truncatula nodule and non nitrogen-starved root systems

city: Castanet Tolosan

first: Erika

last: Sallet

address: 24 Chemin de Borde Rouge, CS 52627

department: Plant Health and the Environment

country: France

institute: INRA/CNRS

summary: Study of repressive marks (two heterochromatic: H3K9me2 and H3K27me1; one euchromatic: H3K27me3) and one active mark (H3K9ac) by whole-genome ChIPseq

first: Moussa

last: Benhamed

first: David

last: Latrasse

first: Pascal

last: Gamas

first: Sandra

last: Moreau


title: The genome of oocytes can be edited in vivo in the zebrafish ovary

city: Beijing

first: Xiaotong

last: Wu

address: No. 1 Shuangqing Road, Haidian District

institute: Tsinghua University

summary: Oocytes, the irreplaceable gametes for generating a new organism, are matured in the ovary of living female animals. It is unknown whether any genetic manipulations can be applied to oocytes inside the living ovaries. As a proof-of-concept, we here demonstrate genetic amendments of zebrafish immature oocytes within the ovary. Oocyte microinjection in situ (OMIS) stimulates tissue repair responses, but some of microinjected immature oocytes are matured, ovulated and fertilizable. By OMIS-mediated Cas9 approach, ntla and gata5 loci of oocytes arrested at prophase I of meiosis are successfully edited before fertilization. Through OMIS, high efficiency of biallelic mutations in single or multiple loci using Cas9/gRNAs allows immediate manifestation of mutant phenotypes in F0 embryos and multiple transgenes can co-express the reporters in F0 embryos with patterns similar to germline transgenic embryos. Our approach opens a door to efficient modification of the genome and provides a possibility to repair defective oocytes in situ.

overall_design: Following OMIS with rhodamine B, 10-15 microinjected oocytes (still arrested at prophase I) were isolated from the ovary at 5 hours post-OMIS (hpO) or 14 hpO, while uninjected oocytes were isolated at the same time points from the other ovary of the same female.The RNA-seq were performed in these oocytes.

first: Weimin

last: Shen

first: Bingjie

first: Anming

last: Meng


title: Intercellular transfer of small RNAs from astrocytes to lung tumor cells induces resistance to chemotherapy.

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Brain metastases are highly resistance to chemotherapy and have a poor prognosis for cure. Tumor cells are surrounded by activated astrocytes and exploit their cyto-protective properties for protection from apoptosis induced by chemotherapy. The mechanism by which astrocytes protect tumor cells is poorly understood. An important non-mutational mechanism of chemotherapy resistance is regulation of gene translation mediated by small non-coding RNAs (sRNAs), in particular, microRNAs (miRNAs). Here we studied the role of astrocytic sRNAs in promoting resistance of the human lung tumor PC14 cells to apoptosis induced by chemotherapy. To this end we compared the sRNA profile of human lung tumor cells that were cultured with or without astrocytes by miRNA microarray. The results show that sRNAs are transferred from astrocytes to PC14 cells in a contact-dependent manner. This transfer is fast and reached plateau already after six hours of co-culturing. Carbenoxolone, a broad-spectrum gap junction antagonist, inhibited the sRNAs transfer indicating that the sRNAs are transferred via gap-junction, maybe via survival pathways.  Enforced expression of these sRNA in PC14 cells increased their resistance to the chemotherapy agent Taxol. In light of these results, we offer novel findings that may be clinically relevant to treatment  development for brain metastases.

overall_design: In the current study we focus on the potential transfer of smallRNAs from astrocytes to metastatic lung tumor cells and its outcome on the resistance of tumor cells to chemotherapy. Our experimental system comprised of co-culturing conditioned immortalized mice astrocytes (H-2K b-tsA58 mice, herein astrocytes) and human lung adenocarcinoma PC14 cell line.

first: Assaf

last: Menachem

first: Victoria

last: Makovski

first: Or

last: Bodner

first: Reuven

last: Stein

first: Noam

last: Shomron

first: Yoel

last: Kloog


title: Genome wide analysis of overexpression of miR-203 in primary mouse cortical neurons

status: Public on Aug 28 2018

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

summary:
Effect of lentiviral mediated overexpression of miR-203 in mouse cortical neurons at different days in vivo
Total RNA isolated from E15 cortical cultures using QIAGEN miRNeasy mini kit (QIAGEN; 217004) were processed on an Illumina mouse Ref8 v2 beadchip microarrays following the manufacture’s protocol.  Microarray data analysis was performed using R and Bioconductor packages. Raw expression data were log2 transformed and normalized by quantile normalization. Probes were considered robustly expressed if the detection P value was 0.05 for at least half of the samples in the data set. Probes were re-mapped to mouse Ensembl gene IDs (v67; May 2012 data freeze) for comparison with RNA-sequencing data.

overall_design: Mouse primary cortical neurons were overexpressed with miR-203 or scrambled miRNA (Control) using lentiviral construct. Untreated cells were used as unt controls. Cells were infected at DIV0 and RNA isolated at various time points - DIV6, DIV8, DIV10 and DIV13. 4 independent replicates (biological) were used for the study.

first: Daniel

middle: H

last: Geschwind


title: Comparative Transcriptomics in Ebola-Makona infected Ferrets, Non-human Primates, and Humans

status: Public on Aug 26 2018

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

summary: The domestic ferret has recently been described as a uniformly lethal model of infection for three species of Ebolavirus known to be pathogenic to humans.  Reagents to systematically analyze the ferret host response to infection are lacking; however, the recent publication of a draft ferret genome has opened the potential for transcriptional analysis of ferret models of disease.  In this work, we present comparative analysis of longitudinally sampled blood taken from ferrets and non-human primates infected with lethal doses of the Makona strain of Zaire ebolavirus.   Strong induction of proinflammatory and prothrombotic signaling programs were present in both ferrets and non-human primates and both transcriptomes were similar to previously published datasets of fatal cases of human Ebola virus infection.

overall_design: Whole blood RNA-Sequencing from ferrets infected with Ebola Virus Makona variant

first: Robert

middle: W

last: Cross

first: Viktoria

last: Borisevich

first: Steve

middle: G

last: Widen

first: Thomas

last: Wood

first: Rebecca

middle: S

last: Shim

first: Ricky

last: Adams

first: Dawn

last: Gerhardt

first: Richard

last: Bennet

first: Anna

middle: N

last: Honko

first: Joshua

middle: C

last: Johnson

first: Lisa

last: Hensley

last: Geisbert

first: John

last: Connor


title: The tumor suppressor menin prevents effector CD8 T cell dysfunction by targeting mTORC1-dependent metabolic activation [Agilent]

status: Public on Aug 30 2018

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

summary: While menin plays an important role in preventing T-cell dysfunction, such as senescence and exhaustion, the regulatory mechanisms remain unclear. We found that menin prevents the induction of dysfunction in activated CD8 T cells by restricting the cellular metabolism. mTOR complex 1 (mTORC1) signaling, glycolysis, and glutaminolysis are augmented by menin deficiency. Rapamycin treatment prevents CD8 T-cell dysfunction in menin-deficient CD8 T cells. Limited glutamine availability also prevents CD8 T-cell dysfunction induced by menin deficiency, and its inhibitory effect is antagonized by α-ketoglutarate (α-KG), an intermediate metabolite of glutaminolysis. α-KG-dependent histone H3K27 demethylation seems to be involved in the dysfunction in menin-deficient CD8 T cells. We also found that α-KG activates mTORC1-dependent central carbon metabolism. These findings suggest that menin maintains the T-cell functions by limiting mTORC 1 activity and subsequent cellular metabolism.

overall_design: Gene expression of WT, Menin KO, Utx KO or Menin/Utx dKO CD8 T cells

first: Masakatsu

last: Yamashita


title: Smed-myb-1 specifies early temporal identity during planarian epidermal differentiation

status: Public on Aug 18 2018

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: The planarian epidermis provides an excellent model to explore adult stem cell (ASC) lineage development due to well-characterized and distinct spatiotemporal phases during lineage progression.  Using flow cytometry-isolated cells enriched in epidermal progenitors, we performed transcriptional profiling and RNAi screening to uncover regulators of epidermal differentiation.  We identified a MYB-type transcription factor (Smed-myb-1) required for specification of the first temporal phase of post-mitotic maturation.  Knockdown of myb-1 abolished the early progenitor phase of differentiation without ceasing production of subsequent epidermal progenitors or homeostatic turnover and regeneration of the epidermis.  Further examination revealed accelerated maturation of ASC descendants, with premature entry into subsequent progeny phases and ultimately the epidermis.  These results demonstrate that a spatiotemporal shift in lineage progression occurs in the absence of the early progenitor state after myb-1 RNAi, and identify myb-1 as a critical regulator of the early temporal window in the step-wise specification during planarian epidermal differentiation.

overall_design: control(RNAi) and Smed-myb-1(RNAi) animals were fed 3 times over 1 week. RNA was collected 6 days after the last feed. Samples were sequenced to a depth of >40 million reads.  Each condition was biologically triplicated.

first: Shu

last: Zhu


title: Multi-tissue transcriptome profiling of North American derived Atlantic salmon

status: Public on Aug 22 2018

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

summary: The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing is enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analysed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from brain, pituitary, ovary and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors present in each tissue-specific gene cluster were identified. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.

overall_design: The goal of this study is to catalogue gene expression in multiple tissues in Atlantic salmon. Key tissues important for understanding salmon biology and important traits related to their aquaculture industry were chosen namely; brain, pituitary gland, ovary and liver. RNA was isolated and 16 RNA-Seq libraries (4 tissues x 4 replicates) were sequenced on Illumina Nova-Seq sequencing platform. Samples were analysed to infer differential gene expression. Hierarchical clustering of those differentially expressed genes (DEGs) were performed and tissue-specific gene clusters were extracted and analysed for functional categories using the Gene Ontology database.

first: Harry

last: King

first: Bradley

last: Evans

first: Antonio

last: Reverter

first: James

last: Kijas


title: Whole blood RNA-Sequencing from 12 Rhesus Macaques following  Ebola Makona Infection

first: Emily

last: Speranza

overall_design: 12 Rhesus macaques were infected with 1000 PFU of Ebola virus  Makona. Blood samples were taken at pre-infection times as well as 3, 5, and 7 days post infection. Whole blood was collected, inactivated in Trizol, and RNA was extracted for use in RNA-Sequencing.

first: Robert

last: Cross

first: Viktoria

last: Borisevich

first: Steve

last: Widen

first: Thomas

last: Wood

first: Rebecca

last: Shim

last: Adams


title: Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos [161 cells]

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

summary: To explore the dynamic change of transcriptome in pre-implantation of rhesus monkey, we collected single cells for RNA-sequencing.

overall_design: We collected 161 ICM single cells from rhesus monkey early embryos encompassing the stages of early blastocyst, middle blastocyst, late blastocyst and hatching blastocyst.

first: Xinyi

last: Wang

first: Dajian

last: He

first: Chunli

last: Sun


title: Microfluidic enrichment, isolation and characterization of disseminated melanoma cells from lymph node samples

status: Public on Aug 14 2018

city: Regensburg

first: Giancarlo

last: Feliciello

address: Am Biopark 1

institute: Fraunhofer ITEM

type: Genome variation profiling by genome tiling array

summary: For the first time in melanoma, novel therapies have recently shown efficacy in the adjuvant therapy setting, which makes companion diagnostics to guide treatment decisions a desideratum. Early spread of disseminated cancer cells (DCC) to sentinel lymph nodes (SLN) is indicative of poor prognosis in melanoma and early DCCs could therefore provide important information about the malignant seed. Here, we present a strategy for enrichment of DCCs from SLN suspensions using a microfluidic device (ParsortixTM, Angle plc). This approach enables the detection and isolation of viable DCCs, followed by molecular analysis and identification of genetic changes. By optimizing the workflow, the established protocol allows a high recovery of DCC from melanoma patient-derived LN suspensions with harvest rates above 60%. We then assessed the integrity of the transcriptome and genome of individual, isolated DCCs. In LNs of melanoma patients, we detected the expression of melanoma-associated transcripts including MLANA (encoding for MelanA protein), analysed the BRAF and NRAS mutational status and confirmed the malignant origin of isolated melanoma DCCs by comparative genomic hybridization. We demonstrate the feasibility of epitope-independent isolation of LN DCCs using ParsortixTM for subsequent molecular characterization of isolated single DCCs with ample application fields including the use for companion diagnostics or subsequent cellular studies in personalized medicine.

overall_design: The analysis aimed to indentify profiles of copy number changes in genomic DNA of disseminated cancer cells (DCCs) in lymph nodes (LNs). For this, DCCs were enriched using the ParsortixTM system. After harvest, cells were collected and transferred on chamber slides, enabling manual isolation of single cells using a micromanipulator. For further molecular downstream analysis, isolated single cells were subjected to simultaneous whole transcriptome amplification (WTA) and whole genome amplification (WGA). Subsequently, single-cell DNA was amplified using the Ampli1 WGA Kits and subjected to single-cell aCGH analysis according to previously published protocol (Czyz ZT et al., PLoS One. 2014 Jan 21;9(1):e85907). The analysis included 4 single DCCs obtained from 2 melanoma patients. The reference sample used for all aCGH experiments consisted of a pool of four single-cell WGA products generated from WBCs of a healthy male donor.

first: Kathrin

last: Weidele

first: Nataša

last: Stojanović

first: Aleksandra

last: Markiewicz

first: Sebastian

last: Scheitler

first: Barbara

last: Alberter

first: Philipp

last: Renner

last: Haferkamp

first: Christoph

middle: A

last: Klein

first: Bernhard

last: Polzer


title: Ex Vivo Lung Perfusion as a Human Platform for Preclinical Small Molecule Testing

status: Public on Aug 16 2018

city: Pittsburgh

first: Josiah

last: Radder

state: Pennsylvania

address: 200 Lothrop St

department: Pulmonary, Allergy, and Critical Care Medicine

institute: University of Pittsburgh

summary: We report mRNA expression from human lung homogenate samples taken during Ex Vivo Lung Perfusion during an acute challenge with LPS and an intervention with the small molecule BC1215

overall_design: Examination of tissue gene expression changes in response to LPS and the effect of BC 1215 on this LPS response

first: Nathaniel

last: Weathington

first: Mauricio

last: Rojas


title: Cell type and species-specific methylation patterns in neuronal and non-neuronal cells of human and chimpanzee cortex

city: Würzburg

first: Christian W.

last: Remmele

address: Am Hubland

department: Department of Bioinformatics

institute: University of Wuerzburg

type: Methylation profiling by high throughput sequencing

summary: Using reduced representation bisulfite sequencing (RRBS), we have compared the methylomes of neuronal and non-neuronal cells from three female human and three chimpanzee cortices (Brodmann area 10). Differentially methylated regions (DMRs) with genome-wide significance were enriched in specific chromosomal regions. Intraspecific methylation differences between neuronal and non-neuronal cells were approximately three times more abundant than interspecific methylation differences between human and chimpanzee cell types. The vast majority (>90%) of human intraspecific DMRs (including DMRs with retrotransposons) were hypomethylated in neurons, compared to glia. Intraspecific DMRs were enriched in genes that have been associated with different neuropsychiatric disorders. Interspecific DMRs were enriched in genes showing human-specific brain histone modifications. Methylation differences between human and chimpanzee non-neuronal cells (N=666) were much more frequent than neuronal interspecific DMRs (N=96). More than 95% of interspecific non-neuronal DMRs were hypermethylated in humans.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Comparison of methylation of 3 human neuronal cell, 3 human non-neuronal, 3 chimpanzee neuronal cell and 3 chimpanzee non-neuronal cell RRBS libraries

first: Julia

last: Böck

first: Christian

first: Marcus

last: Dittrich

first: Tobias

last: Müller

first: Ivanela

last: Kondova

first: Stephan

last: Persengiev

first: Ronald

last: Bontrop

first: Carsten

last: Ade

first: Theo

middle: F

last: Kraus

first: Armin

last: Giese

first: Nady

last: El Hajj

first: Eberhard

last: Schneider

first: Thomas

last: Haaf


title: SIRT1 Activation Disrupts Maintenance of Myelodysplastic Syndrome Stem and Progenitor Cells by Restoring TET2 Function [microarray expression profiling]

status: Public on Aug 13 2018

city: Duarte

first: Sun

last: Jie

state: CA

address: 1500 East Duarte Road

institute: City of Hope

summary:
Improved understanding of mechanisms regulating myelodysplastic syndrome (MDS) hematopoietic stem/progenitor cell (HSPC) growth and self-renewal is critical for developing MDS therapy. We revealed a novel regulatory axis that SIRT1-deficiency induced TET2 hyperacetylation promotes MDS HSPC functions, and provide an approach to target MDS HSPCs by activating SIRT1 deacetylase.
Four Groups: Group1: MDS-L cells transduced with lentiviral vector targeting non-silence squence (control shRNA for SIRT1); Group2: MDS-L cells transduced with lentiviral vector containing interference squence targeting SIRT1  (SIRT shRNA); Group 3: MDS-L cells transduced with lentiviral vector targeting non-silence squence (control shRNA for TET2); Group 4: MDS-L cells transduced with lentiviral vector containing interference squence targeting TET2 (TET2 shRNA).

overall_design: Expression profiling data in SIRT1 KD or TET2 KD MDS-L cells was compared to control shRNA transduced MDS-L cells by using an HlncOA 1.0 array

first: Ling

last: Li

first: Jie

last: Sun


title: Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [RNA-Seq]

status: Public on Aug 09 2018

city: Cincinnati

first: Caitlin

last: Dunn

state: Ohio

address: 3333 Burnet Avenue

department: Division of Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary: The purpose of the study was to identify mRNA transcripts in human placenta that contained a THE1B element.

overall_design: mRNA-seq from two human placentas with and without pre-amplification enrichment for THE1B-containing trancripts

last: Dunn-Fletcher

first: Louis

last: Muglia

first: Gernot

last: Wolf

first: Todd

last: Macfarlan


title: The Miniature-chemostat Aging Device: A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of replicatively aging yeast

city: Boston

first: David

last: Hendrickson

address: 725 Parsons

institute: Harvard

summary: WT and mutant strains (fob1delta,sir2delta,ubr2delta) of Saccharomyces cerevisiae were grown and replicatively aged in mini-stat aging devices for transcriptional (RNA-seq) and chromatin accessibility (ATAC-seq) profiling.

overall_design: Yeast cells were collected during exponential growth and labeled with biotin for retention of mother cells using magnetic streptavidin beads in specialized growth vessels. Aging mothers were sampled over time for collection of RNA and DNA for RNA-seq and ATAC-seq respectively.

first: Ilya

last: Soifer


title: Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [ChIP-Seq]

summary: The purpose of the study was to examine histone marks H3K27ac and H3K4me1 at THE1B elements in human placenta.

overall_design: ChIP-seq for H3K27ac and H3K4me1 on human placenta at full term


title: Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation

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

overall_design: Refer to individual Series


title: Integrated regulation of apical hook development by transcriptional coupling of EIN3/EIL1 and PIFs in Arabidopsis

status: Public on Aug 02 2018

city: Durham

first: xing

last: zhang

address: FFSC Bldg., 124 Science Drive

institute: duke university

summary: A dual-core processor, composed of EIN3/EIL1 and PIFs, mediates both positive and negative regulation of apical hook development by multiple hormones and light signals.

overall_design: Three-day-old etiolated seedlings of Col-0, hls1, pifq, ein3 eil1, and pifq ein3 eil1 plants (not including roots) were collected and ground into a fine powder in liquid nitrogen. Two biological replicates were prepared for each genotype. Total RNA was extracted using the RNeasy Plant Mini kit (QIAGEN). The RNA sequencing and differential gene expression analysis were performed at the Bionova company. RNA quality was evaluated on a Bioanalyzer 2100 instrument (Agilent, Santa Clara, CA). Sequencing libraries were prepared following the protocol for the Directional RNA Library Prep Kit (NEB), and 150 nt paired-end high throughput sequencing was performed on an Illumina Hiseq X Ten system. Low quality sequencing reads were removed.

first: Xing

last: Zhang

first: Yusi

last: Ji

first: Chang

last: Xue

first: Honghao

last: Ma

first: Yulin

last: Xi

first: Peixin

last: Huang

first: Huan

last: Wang

first: Fengying

last: An

first: Bosheng

first: Yichuan

first: Hongwei

last: Guo


title: Plant miRNA profile from  pooled human serum samples

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

summary: Our previous studies have demonstrated that stable microRNAs (miRNAs) in mammalian serum and plasma are actively secreted from tissues and cells and can serve as a novel class of biomarkers for diseases, and act as signaling molecules in intercellular communication. Here, we report the surprising finding that exogenous plant miRNAs are present in the sera and tissues of various animals and that these exogenous plant miRNAs are primarily acquired orally, through food intake.

overall_design: 8 pooled samples (each pooled from 10 healthy Chinese subjects, mean age 50.9 ± 7.9) was conducted in the Healthy Physical Examination Center of the Jinling Hospital.

first: Lin

first: Dongxia

last: Hou


title: Reframing gene essentiality in terms of adaptive flexibility

status: Public on Jul 19 2018

city: La Jolla

first: Adam

last: Feist

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California, San Diego

summary: Essentiality assays are commonly practiced as important tools for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are often utilized to test the predictive power of genome-scale models. False positive predictions occur when computational analysis predicts a gene to be non-essential, however experimental screens deem the gene to be essential. One explanation for this inconsistency is that the model contains the wrong information, possibly an incorrectly annotated alternative pathway or isozyme reaction. Inconsistencies could also be attributed to experimental limitations, such as growth tests with arbitrary time cut-offs. The focus of this study was to resolve such inconsistencies to better understand isozyme activities and gene essentiality. Gene-deletion strains associated with false positive predictions of gene essentiality on defined minimal medium for Escherichia coli were targeted for extended growth tests followed by population sequencing.

overall_design: RNAseq was performed on various Keio collection gene-deletion populations and clones adapted for growth on D-glucose. The genes that were knocked out of these strains were thrA, ptsI, and serB. Differentially expressed genes were examined comparing gene-deletion strains to the wild type strain.

first: Gabriela

middle: I

last: Guzman


title: RNA-dependent epigenetic silencing directs transcriptional down regulation caused by intronic repeat expansions

status: Public on Jul 25 2018

city: Melbourne

first: Avilash

last: Singh Yadav

state: Victoria

address: Innovation Walk 18, Monash University Clayton Campus

department: School of Biological Sciences

institute: Monash University

summary: Transcriptional down regulation caused by intronic triplet repeat expansions underlies diseases such as Friedreich?s ataxia.  This down regulation of gene expression is coupled with epigenetic changes but the underlying mechanisms are unknown. Here, we show that an intronic TTC/GAA triplet expansion within the IIL1 gene of Arabidopsis thaliana results in accumulation of 24-nt siRNAs and repressive histone marks at the IIL1 locus, which in turn causes its transcriptional down regulation and an associated phenotype. Knocking down DICER LIKE-3 (DCL3), which produces 24-nt siRNAs, suppressed transcriptional down regulation of IIL1 and the expansion-associated phenotype. Furthermore, knocking down additional components of the RNA-dependent DNA Methylation (RdDM) pathway, also suppressed both transcriptional down regulation of IIL1 and the repeat expansion associated phenotype. Thus our results show that triplet repeat expansions can lead to local siRNA biogenesis, which in turn down regulates transcription through an RdDM-dependent epigenetic modification.

overall_design: Comparison of the small RNA profile of 45 day old Arabidopsis thaliana accessions Col-0, Bur-0 and NS15 grown at 23°C or 27°C SD.

first: Hannes

last: Eimer

first: Sridevi

last: Sureshkumar

last: Yadav

first: Calvin

last: Kraupner-Taylor

first: Champa

last: Bandaranayake

first: Andrei

last: Seleznev

first: Tamblyn

last: Thomason

first: Stephen

last: Fletcher

first: Stephanie

last: Gordon

first: Bernard

last: Carroll

first: Sureshkumar

last: Balasubramanian


title: Transcriptomic analysis of A. thaliana roots in response to carbenicillin

city: Madrid

first: Federico

last: Navarro-García

state: Madrid

address: Plaza de Ramón y Cajal

department: Microbiología y Parasitología

country: Spain

institute: Universidad Complutense de Madrid

summary: A. thaliana plants were grown in 1/2 MS medium in the presence of carbenicillin (10 µg·mL-1) for 1 or 7 days and RNA from their roots extracted and sequenced in Illumina HiSeq 2000/5000 (2x50 bp).

overall_design: Total RNA obtained from A. thaliana roots grown in the absence (mock) or presence of carbenicillin  (10 µg·mL-1) for 1 or 7 days. Three replicas per experiment.

first: Marco

last: Gudiño

first: Noel

last: Blanco-Touriñán

first: Miguel

last: Blázquez


title: Identification of human genes of which expression are induced by 4MU-xyloside treatment

status: Public on Aug 01 2018

city: Ako

first: Hiderou

last: Yoshida

state: Hyogo

address: Kamigori, Koto 3-2-1

department: Life Science

institute: University of Hyogo

summary: The Golgi stress response is a homeostatic mechanism that augments the functional capacity of the Golgi apparatus when Golgi function becomes insufficient (Golgi stress). Three response pathways of the Golgi stress response have been identified in mammalian cells, the TFE3, HSP47 and CREB3 pathways, which augment the capacity of specific Golgi functions such as N-glycosylation, anti-apoptotic activity and pro-apoptotic activity, respectively. On the contrary, glycosylation of proteoglycans (PGs) is another important function of the Golgi, although the response pathway upregulating expression of glycosylation enzymes for PGs in response to Golgi stress remains unknown. Here, we found that expression of glycosylation enzymes for PGs was induced upon insufficiency of PG glycosylation capacity in the Golgi (PG-Golgi stress), and that transcriptional induction of genes encoding glycosylation enzymes for PGs was independent of the known Golgi stress response pathways and ER stress response. Promoter analyses of genes encoding these glycosylation enzymes revealed the novel enhancer element PGSE, which regulates their transcriptional induction upon PG-Golgi stress. From these observations, the response pathway we discovered is a novel Golgi stress response pathway, which we have named the PG pathway.

overall_design: Three control samples (DMSO-treated) and three 4MU-xyloside treated samples

first: Kanae

last: Sasaki

first: Mai

last: Taniguchi

first: Sachiko

last: Midori

first: Mayu

last: Yamamoto


title: Argonaute-miRNA complexes reveal concerted action in disease related pathways of a human, glioblastoma cell line

status: Public on Jul 18 2018

city: Düsseldorf

first: Pablo

last: Landgraf

address: Moorenstraße 5

department: Clinic of Pediatric Oncology, Hematology and Clinical Immunology

institute: Heinrich-Heine University Düsseldorf

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

summary: Glioblastoma is the most common primary malignant brain tumor occurring in the central nervous system and is characterized by rapid proliferation, genetic aberrations and poor response to treatment. The classical genetic alterations in glioblastoma target pathways governing cellular proliferation, cellular survival, invasion and angiogenesis. In this study, the regulation of glioblastoma-relevant pathways by small non-coding RNAs was analyzed by identification of Argonaute protein-associated microRNAs and mRNAs. We utilized a highly controlled method termed PAR-CLIP-Array by biochemical isolation of cross-linked ribonucleoprotein complexes with monoclonal antibodies specific for individual Argonaute proteins followed by microarray detection. We demonstrate here that the different Argonaute proteins bind different subsets of miRNAs and mRNAs in a glioblastoma cell line model. By extending our study generating miRNA-mRNA network interaction models we could further show, that different Argonaute proteins act in concert to regulate glioblastoma-relevant pathways. We therefore provide novel insights into glioblastoma regulation by microRNAs.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Co-immunoprecipitation in the glioblastoma cell line model SNB19 of three different Argonaute complexes using monoclonal antibodies and stringent washing conditions. We performed photo-activated UV cross-linking using 4'-thioruidine before cell lysis. Unspecific binding to the bead matrix and to the Fc part of the monoclonal rat antibody were recorded and corrected by an antibody isotype control and empty bead controls. Argonaute-associated miRNAs/mRNAs and uspecific bound miRNAs/mRNAs of the isotype control were identified by microarray hybridization. The empty bead controls were not hybridized to the microarrays, but only used for correction of unspecific RNA binding to the bead matrix during Western Blot and RT-PCR validation. The total RNA of SNB19 cells was hybridized to microarrays for comparison with Ago-associated RNAs. These experiments were performed in triplicates.

first: Svenja

last: Daschkey

first: Arndt

last: Borkhardt

first: Gunter

last: Meister


title: Ruxolitinib inhibits Cyclosporine-induced proliferation of cutaneous squamous cell carcinoma

city: NEW YORK

first: Melody

last: Abikhair

state: NY

address: 550 FIRST AVENUE

institute: NYU School of Medicine

summary:
Organ transplant recipients (OTRs) on Cyclosporine A (CSA) are prone to catastrophic cutaneous squamous cell carcinoma (SCC). Allograft-sparing, cancer-targeting systemic treatments are unavailable. We have shown increased risk for catastrophic SCC in OTRs via CSA-mediated induction of Interleukin-22 (IL-22). Herein, we found CSA drives SCC proliferation and tumor growth through IL-22 and JAK/STAT pathway induction. We in turn inhibited SCC growth with an FDA-approved JAK 1/2 inhibitor, Ruxolitinib.  In human SCC cells, greatest proliferative response to IL-22 and CSA treatment occurred in non-metastasizing lines. IL-22 treatment upregulated JAK1 and STAT1/3 in A431 SCC cells. JAK/STAT pathway genes were highly expressed in tumors from a cohort of CSA-exposed OTRs, and in SCC with high risk for metastasis. Compared to immunocompetent SCC, genes associated with innate immunity, response to DNA damage and p53 regulation were differentially expressed in SCC from OTRs.  In nude mice engrafted with human A431 cells, IL-22 and CSA treatment increased tumor growth and upregulated IL-22 receptor, JAK1 and STAT 1/3 expression.  Ruxolitinib treatment significantly reduced tumor volume and reversed the accelerated tumor growth.  CSA and IL-22 exacerbate aggressive behavior in SCC. Targeting the IL-22 axis via selective JAK/STAT inhibition may reduce the progression of aggressive SCC in OTRs, without compromising immunosuppression.
In this study, microarray data was used to compare normal skin to immunocompetent SCC, to transplant associated SCC (TSCC)

overall_design: Total RNA was extracted from tissue samples of normal skin (n = 10), immunocompetent SCC (n = 8) and SCC from OTRs (n = 5)

last: Abikhair Burgo

first: John

last: Carucci


title: Structural, physiological and regulatory analysis of maltose transporter genes in Saccharomyces eubayanus CBS12357T.

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Saccharomyces pastorianus lager brewing yeasts are domesticated hybrids of  Saccharomyces cerevisiae and cold-tolerant Saccharomyces eubayanus. To better understand the contribution of both parental genomes to maltose metabolism in brewing wort, this study focuses on maltose transport in the S. eubayanus type strain CBS12357T/FM1318T. To obtain complete sequences of the MAL loci of this strain, a near-complete genome assembly was generated using the Oxford Nanopore Technology MinION sequencing platform. Except for CHRXII, all sixteen chromosomes were assembled as single contigs. Four loci harboring putative maltose transporter genes (SeMALT1-4), located in subtelomeric regions of CHRII, CHRV, CHRXIII and CHRXVI, were completely resolved. The near-identical loci on CHRV and CHRXVI strongly resembled canonical S. cerevisiae MAL loci, while those on CHRII and CHRXIII showed different structures suggestive of gene loss. Functionality of the SeMALT1-4-encoded transporters was confirmed by their ability to restore growth on maltose, but not on maltotriose, of a maltose-transport-deficient S. cerevisiae strain. Simultaneous CRISPR-Cas9-assisted deletion of SeMALT2 and SeMALT4, which shared 99.7 % sequence identity, eliminated growth of S. eubayanus CBS12357T on maltose. Transcriptome analysis of S. eubayanus CBS12357T established that, in maltose-grown cultures, SeMALT2 and SeMALT4 were expressed at much higher levels than SeMALT1 and SeMALT3, thus resolving the apparent discrepancy between heterologous expression and deletion studies. These results represent a first genomic and physiological characterization of maltose transport in S. eubayanus CBS12357T and provides a valuable resource for further industrial exploitation of this yeast.

overall_design: Compare expression of glucose and maltose grown cells of S. eubayanus CBS12357. For each condition duplicate experiments were performed.

first: Marcel

last: van den Broek


title: Effect of 8-oxoguanine DNA glycosylase 1 (OGG1) inhibitor on pro-inflammatory gene expression.

status: Public on Jul 10 2018

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

summary:
Balbc J mouse received vehicle (solvent) or OGG1 inhibitor 1 h prior to treatment via intraperitoneal route.
Tumor necrosis factor alpha (TNFa, 20 ng per ml) was installed into lungs via intranasal route in 60 microliters of solvent).
One hour after TNFa challenge mice were sacrificed, lungs were removed and RNAs were isolated from individual lungs (n=6)
After reverse transcription cDNAs were pooled and changes in gene expression was determined by using SABiosciences Mouse Inflammatory Cytokines & Receptors PCR Array (PAMM-011Z)

overall_design: Total pooled (n=6) cDNAs generated  Superscript® III First Strand Synthesis System (Invitrogen), mixed with equal amounts of 2X SYBR Green Supermix (Qiagen) and 20 μl of reaction mixture was added to each well of the PAM-011Z array. The reaction was evaluated using an ABI PRISM® 7000 Sequence Detection System using recommended settings by SABiosciences.

first: Leopoldo

last: Aguilera-Aguirre

first: Wenjing

last: Hao


title: Real-time quantitative PCR analysis of mouse lung epithelial cells 12 (MLE-12)

status: Public on Jul 06 2018

summary:
MLE12 cells were treated with 8-oxoguanine DNA glycosylase 1 (OGG1) inhibitor with or without TNF to evaluate its effect on pro-inflammatory gene expression.
We used SA Biosciences Mouse Inflammatory Cytokines & Receptors PCR Array (PAMM-011Z) to quantitate inflammatory gene expression dependent on OGG1 .

overall_design: Triplicate cultures of cells (-/+OGG1 inhibitor, solvent) were TNF exposed for 30 minutes, RNAs were isolated, pooled (n=3), cDNA were synthesized using Superscript® III First Strand Synthesis System (Invitrogen), mixed with equal amounts of 2X iTaq Universal SYBR Green Supermix (Bio-Rad) and 20 μl of reaction mixture was added to each well of the PAMM-011ZA array. The qRT-PCR was performed using an ABI PRISM® 7000 Sequence Detection System as recommended by SA Biosciences.


title: Expression data of whole genome from new diagnostic AML patients (with or without EMI) and healthy volunteers

status: Public on Jul 04 2018

city: Harbin

first: Zhibo

last: Guo

state: Heilongjiang

address: No.23 Street

institute: Harbin Medical University

summary: Whole Genome microarray was conducted to further explore the underlying gene expression alterations in extramedullary infiltration (EMI) of AML. 4 matched samples from EMI, non-EMI AML patients and healthy volunteers were selected. Mononuclear cells from 12 bone marrow samples were separated according to protocols. RNA was then extracted and hybridization for further microarray analysis.

overall_design: EMI-related genes were selected by comparing with non-EMI AML patients and healthy controls. 4 independent experiments were performed using different donors for each experiment.

first: Yinghua

last: Li


title: Transcriptome analysis of Mycobacterium tuberculosis post 24 hours VapC11 overexpression.

status: Public on Jul 11 2018

city: Chandigarh

first: Amar

last: Deep

state: Chandigarh

address: C/o Dr.krishan Gopal , IMTech

department: Protein Science and Engineering

country: India

institute: Institute of Microbial Technology

summary: We report the effects of VapC11 overexpression on Mycobacterium tuberculosis H37Rv strain. VapC11 is a tRNase which specifically cleaves tRNA-Leu^CAG (leuT).Cells harbouring either pTetR (Control) or pTetR-vapC11 was used to understand the effect of VapC11 toxin overproduction on cellular transcriptome.

overall_design: Cells harbouring pTetR (Vector only) or pTetR-vapC11 were used for RNA-Seq analysis. Experiments were repeated twice for each strain. Data: Control samples were 1A and S8 (1A_R1 & 1A_R2; S8_R1 & S8_R2) ; Toxin overexpressing samples were 2A and S9 (2A_R1 & 2A_R2; S9_R1 & S9_R2).

first: Ramandeep

last: Singh

first: Krishan

last: Gopal

first: Prabhakar

last: Tiwari


title: Identification and validation of circHIPK3 is upregulated in colorectal cancer and characterization of its role in promoting carcinogenesis

city: GuangZhou

first: Ying

last: Wei

address: JuQuanLu 3

institute: Geneseed Biotech Co.,Ltd

summary: In order to confirm that circHIPK3  in colorectal cancerand characterization of its role in carcinogenesis, verified the expression level of circHIPK3 in additon 18 samples, and further collected 30 health controls and 30 colorectal cancer patients for exosome detection. The present study identified circHIPK3 is higher expression in CRC tissues and exosome of CRC patients.

overall_design: Total circRNAs were detected in two colorectal cancer biopsies and corresponding para-cancer tissues

first: Fanghua

last: Qiu

first: Jiewen


title: Transcriptional profiling of Mms21 deleted (mms21Δ/Δ) mutant Candida albicans strains

status: Public on Jul 03 2018

city: Montreal

first: Yuan

last: Sun

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology Department

country: Canada

institute: Concordia University

summary:
Mms21 deleteion in Candida albicans resulted in invasveness and filamentatation in YPD media at 30 degrees Celsius. Wild type SN148 do not make any Filaments in YPD at 30 degrees Celsius. The aim was to look for transcription profiling mms21 dleleted mutant against wild type to find genes up and down regulated in the mutant especially thoseones critical for filamentation.
Mms21 deleteion in Candida albicans resulted in invasveness and filamentatation in YPD media at 30 degrees Celsius. Wild type SN148 do not make any Filaments in YPD at 30 degrees Celsius. The aim was to look for transcription profiling mms21 dleleted mutant against wild type to find genes up and down regulated in the mutant especially thoseones critical for filamentation.

overall_design: 2 samples were analyzed. Cells were grown in YPD media at 30 degrees celcius to OD 0.8. MMS21 deleted strain (mms21Δ/Δ) vs wild type (SN148) were hybridized, dye swap was done. One replica per array.

first: Islam

last: Amjad

first: Tebbji

last: Faiza


title: Transcriptional responses of inbred lines B73, B75 and B96 and resulting F1 lines to herbivory by Tetranychus urticae

city: Salt Lake City

first: Richard

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

summary: The extreme generalist two-spotted spider mite, Tetranychus urticae, which is documented to feed on more than 1100 plant hosts, is becoming an increasingly important agricultural pest. Historically, as studies of plant-herbivore interactions have focused largely on insects, considerably less research has investigated plant responses to spider mite herbivores, especially in grasses. To identify intraspecific differences in maize response to T. urticae, we collected RNA-seq data from three maize (Zea mays) inbred lines (B73, B75 and B49) as well as two F1 lines arising from crosses between B73 x B75 and B73 x B96. For each maize line, RNA-seq data was collected from uninfested leaves (control) and leaves infested with T. urticae for 24 hours.

overall_design: The experiment was performed with four or eight (in the case of B73 only) biological replicates across each of the following (48 samples in total): control uninfested B73 (B73-C), T. urticae infested B73 (B73-T), control uninfested B75 (B75-C), T. urticae infested B75 (B75-T), control uninfested B96 (B96-C), T. urticae infested B96 (B96-T), control uninfested B73xB75 F1s (F1-B73-B75-C), T. urticae infested B73xB75 F1s (F1-B73-B75-T), control uninfested B73xB96 F1s (F1-B73-B96-C) and T. urticae infested B73-B96 F1s (F1-B73-B96-T). B73 replicates 1-4 should be used as references for all samples related to B96, while B73 replicates 5-8 should be used as references for all samples related to B75.

first: Huyen

last: Bui

first: Robert

last: Greenhalgh


title: Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation [miRNA]

status: Public on Jun 29 2018

city: London

first: John

middle: Alexander

last: McGrath

address: Great Maze Pond

department: St John's Institute of Dermatology

institute: King's College London

summary: Keloids represent a common form of exaggerated wound scarring that cause considerable morbidity. Moreover, there are limited data on molecular mechanisms underlying keloids and effective therapies are lacking. To gain new insight in the transcriptomic alterations of wound healing in keloid-prone individuals, we followed an integrative approach of RNA-Seq and miRNA expression data analysis in serial skin biopsies of the same site (baseline and six weeks after wounding) in keloid-prone (n=8) and healthy matched control individuals (n=6). Bioinformatic analysis identified 37 miRNAs and 1449 genes that are differentially expressed specifically in keloid-prone individuals during wound healing. Pathway enrichment analysis was undertaken in the RNA-Seq data and identified NOTCH signaling, MAPK signaling, and Toll-like receptor pathways to be altered in keloid-prone individuals after wounding. In addition, dysregulation of DNA repair, p53 signalling and metabolic pathways (RNA, protein, fructose, mannose and glycerophospholipid metabolism) was highlighted during keloid formation. Gene association network analysis demonstrated divergent average expression profiles of cytokine signaling genes, as well as lipid metabolism genes between keloid-prone and healthy individuals during wound healing. In summary, our study provides a comprehensive and integrative analysis of the keloid transcriptome and miRNAome and highlights biological pathways that feature during keloid formation.

overall_design: miRNA gene expression profiling skin biopsies at baseline and 6 weeks after wounding in keloid-prone and healthy individuals.

first: Alexandros

last: Onoufriadis

first: Chao-Kai

last: Hsu

first: Chrysanthi

last: Ainali

first: Chuin

middle: Y

last: Ung

first: Ellie

last: Rashidghamat

first: Hsing-San

last: Yang

first: Hsin-Yu

last: Huang

first: Umar

last: Niazi

first: Jui-Chu

first: Rosamond

last: Nuamah

first: Alka

last: Saxena

first: Emanuele

last: de Rinaldis


title: LGP2 virus sensor regulates gene expression network mediated by TRBP-bound microRNAs.

city: Bunkyo-ku

first: Kumiko

last: Ui-Tei

state: Tokyo

institute: The University of Tokyo

summary: To reveal the fuction of cytoplasmic virus sensor protein, LGP2, on RNA silencing, we analyzed gene expression profiles on HeLa WT and LGP2 knockout cells, which were generated with CRISPR/Cas system.

overall_design: Total RNAs were extracted form HeLa WT and LGP2 knockout cells and performed microarray analysis.

first: Tomoko

last: Takahashi


title: The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing [BS-Seq]

status: Public on Jun 21 2018

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: We found PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing.

overall_design: Examination of the DNA methylation level in Arabidopsis

first: Lianmei

last: Tan

first: Cuijun

last: Zhang

first: Xinjian


title: Analysis of differential gene expression in the Streptococcus sanguinis brpL mutant

status: Public on Jun 14 2018

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

summary: Gene expression profile of the Streptococcus sanguinis transcription regulator, brpL, deletion mutant compared to the wild-type strain SK36

overall_design: Experiment: brpL mutant vs. wild-type SK36. Biological replicates independently grown and prepared for each sample.

first: Bin

last: Zhu


title: Tbx5 paralogues during zebrafish development

status: Public on Jun 12 2018

city: Chicago

first: Erin

last: Boyle Anderson

state: IL

department: Committee on Development, Regeneration and Stem Cell Biology

institute: University of Chicago

summary:
Purpose: The goals of this study were to compare the effect on the transcriptome of loss of the Tbx5 paralogues in zebrafish.
Methods: Whole embryos were injected with morpholinos targetting either Tbx5a, Tbx5b, or both at the single cell stage. At either 18 or 21 hpf, embryos were pooled and RNA was extracted from the whole embryo. Transcriptomes were generated using Illumina HiSeq 2500.
Results: The preliminary experiment produced 632 million reads and a list of 494 differentially expressed genes (detected using Cuffdiff), of which 454 were unique. This final triplicate sequencing gave 309.4 million reads. When using Cuffdiff to produce differential gene expression lists, a list of 162 differentially expressed genes were identified.
Conclusions: This study is a detailed analysis of the different transcriptomes of zebrafish deficient in the Tbx5 paralogues and the differential gene expression that occurs as a result of downregulation of the paralogues, both individually and separately.

overall_design: Whole embryo RNA sequencing of pooled zebrafish embryos at 18hpf and 21hpf in wildtype, Tbx5a- and Tbx5b-deficient embryos.

first: Robert

middle: K

last: Ho


title: Transcriptional profiling of HT-29 cells with different treatments

status: Public on Jun 04 2018

city: Shanghai

first: Zaijun

last: Ma

address: Qiuyue Road 26

institute: Chinese Academy Science

summary: Through RNA-seq, we investigated the transcriptional changes of necroptotic cell induced by TNF-α, SM-164 and zVAD. We report here that necroptosis leads to transcriptional activation of a large set of genes including pro-inflammatory cytokines, which is much stronger than that triggered by TNF-α alone. Furthermore, the robust induction of cytokine expression could be blocked by necroptotic inhibitor Nec-1s. Thus, we show that necroptosis exerts a profound effect on transcription, and activate the expression of pro-inflammatory genes, providing insights into the mechanism by which necroptosis promotes inflammation in human diseases.

overall_design: Examination of the transcriptional changes of HT-29 cell with different treatments

first: Junying

last: Yuan

first: Lihui

last: Qian

first: Kezhou


title: Salicylic acid inhibits transcriptional repression activities of its receptors to promote defense gene expression

status: Public on Jun 08 2018

city: Vancouver

first: Yuelin

state: BC

address: 6270 University Blvd

department: Department of Botany

institute: University of British Columbia

summary: Salicylic acid (SA) is a plant defense hormone required for immunity. Arabidopsis NPR1 and NPR3/NPR4 were previously shown to bind SA and proposed as SA receptors. However, unlike NPR1, loss of NPR3/NPR4 does not block SA-induced defense gene expression.  Here we report that NPR3/NPR4 function as transcriptional repressors and SA inhibits their activities to promote the expression of key immune regulators. npr4-4D, a newly identified gain-of-function allele that renders NPR4 unable to bind SA, constitutively represses SA-induced immune responses. In contrast, the equivalent mutation in NPR1 abolishes its function in promoting SA-induced defense gene expression. Further analysis revealed that npr4-4D and npr1-1 have additive effect on blocking SA-induced defense gene expression, suggesting that NPR4 and NPR1 function in parallel to regulate SA-induced immune responses. Our study reveals the molecular functions of SA receptors NPR3/NPR4 and uncovers a brand new mechanism of SA perception.

overall_design: RNA-seq analysis of WT, npr1-1, npr4-4D, and npr1-1 npr4-4D arabidopsis seedlings untreated or treated with SA. 4 genotypes and 2 conditions, each with 2 biological replicates resulting in a total of 16 samples.

first: Yuli

last: Ding

first: Tongjun

last: Sun

first: Kevin

last: Ao

first: Yaxi

first: Xin

last: Li


title: Intragraft molecular pathways associated with tolerance induction in renal transplantation

status: Public on May 07 2018

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
Complications associated with immunosuppression, specifically nephrotoxicity and infection risk, significantly affect graft and patient survival after kidney transplantation.
We previously showed that tolerance could be induced and full donor chimerism, as well as immunosuppression withdrawal, was obtained in highly mismatched allograft recipients using a bioengineered stem cell product (FCRx).

overall_design: Gene expression profiles in renal biopsy samples from tolerance-induced FCRx recipients, paired donor organs before implant, and subjects under standard immunosuppression (SIS) without rejection and with acute rejection were compared.

first: Valeria

last: Mas

first: Sai

middle: V

last: Bontha


title: Transcriptomic analysis of immunity in rainbow trout (Oncorhynchus mykiss) gills infected by Ichthyophthirius multifiliis

status: Public on Jun 13 2018

city: Copenhagen

first: Khairul

last: Syahputra

address: Stigbøjlen 7

department: Veterinary and Animal Science

country: Denmark

institute: University of Copenhagen

summary:
Purpose: a transcriptomic analysis was performed to extend our understanding on the immune response picture of rainbow trout exposed to I. multifiliis.
Methods: Gill samples were collected from fish in each tank (control and infected group) at day 8 after infection. Total RNA was extracted using RTN350 (Sigma-Aldrich), according to the manufacturer’s instruction and subsequently, DNase treated with DNase I (Thermo Scientific, USA). Quality and integrity of the total RNA were checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent, Amstelveen, Netherlands). Illumina RNAseq libraries were prepared from 500 ng total RNA using the Illumina TruSeqTM Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions (Illumina Inc. San Diego, CA, USA). All RNAseq libraries (150-750 bp inserts) were sequenced on an Illumina HiSeq2500 sequencer as 1 x 50 nucleotides single-end reads according to the manufacturer’s protocol. Image analysis and base calling were done using the Illumina pipeline. Reads were aligned to the Rainbow trout reference genome (http://www.genoscope.cns.fr/trout/data/) using TopHat (version 2.0.5) and on average 53.4% of the RNAseq reads could be mapped. The resulting files were filtered using SAMtools (version 0.1.18) to exclude secondary alignment of reads. For statistical comparison of gene expression levels between groups, aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9). To make comparisons across samples possible, these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scalling factor, we employed library size estimates determined using the R/Bioconductor (release 2.11) package DESeq. Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Correction for false positives is included in the statistical analysis of gene expression through DESeq. The cut-off for significance was set to adjusted p<0.05 and at least 2-fold change.
Results: a transcriptomic analysis was performed on infected rainbow trout gills and it showed that a total of 3,352 (7.2%) out of 46,585 identified genes were revealed significantly expressed after parasite infection. Of differentially expressed genes, 1.796 genes were up-regulated and 1.556 genes down-regulated. These were classified into 61 Gene Ontology (GO) terms and mapped to 282 reference canonical pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Infection of I. multifiliis induced a clear differential expression of immune genes, related to both innate and adaptive immunity. A total of 268 (6.86%) regulated genes was known to take part in 16 immune-related pathways. These involved pathways related to the innate immune system such as Chemokine signaling pathway, Platelet activation, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and Leukocyte transendothelial migration.
Conclusion: a transcriptomic profile of rainbow trout gills exposed to the parasitic I. multifiliis was reported for the first time. A total of 3,355 differentially expressed unigenes were identified. Of these were 1,184 unigenes (mapped to 952 genes) annotated 282 KEGG pathways and 268 unigenes were associated with 16 immune pathways. Most unigenes were related to innate immune system pathways (Chemokine signaling pathway, Platelet activation, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and Leukocyte transendothelial migration) although a number of unigenes was related to adaptive responses (antigen processing and presentation, T and B cell receptor signaling pathway). The present study gave a far better resolution of the immune response of rainbow trout exposed to a parasitic protozoan than has ever been presented previously. The identification of a series of immune genes involved in several but important was useful for understanding of immune mechanism of the rainbow trout responding to the parasite I. multifiliis. Our results provide tools to link innate and adaptive immune elements in the process and present basic information which will be useful in the future studies related to immunoprophylaxis.

overall_design: Transcriptome profiling of rainbow trout exposed to I. multifiliis was generated by Next Generation Sequencing, in 10 replicates, using Illumina HiSeq2500 sequencer.

first: Per

last: Kania

first: Azmi

last: Al-Jubury

first: Rezkar

last: Jafaar

first: Ron

middle: P

last: Dirks

first: Kurt

last: Buchmann


title: Expression data from Arabidopsis shoots and roots

status: Public on May 01 2018

city: Bochum

first: Scott

last: Sinclair

address: Universitaetstrasse 150

institute: Ruhr Universitaet Bochum

summary:
Regulation of genes in shoots and roots and Arabidopsis in response to Zn-deficiency in wild-type and hma2 hma4 mutants plants
We used microarrays to determine co-regulated genes in the roots of Zn deficient wild-type plants with hma2 hma4 plants from control conditions. These co-regulated genes are candidates for regulation by a systemic signal

overall_design: Shoots and roots of wild-type plants grown in control and Zn-deficient conditions were harvested at 7 weeks of age, 3 weeks after transfer to -Zn or control media. Shoot and roots of wild-type and hma2 hma4 plants were harvested after 21 days of growth

first: S

first: T

last: Senger

first: I

last: Talke

first: M

last: Haydon

first: U

last: Kraemer


title: Histone H3.3 G34 mutations alter histone H3K36 and H3K27 methylation in cis

status: Public on Apr 26 2018

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

summary: High-throughput sequencing of numerous patient samples has identified a myriad of frequent mutations of epigenetic regulators in human cancers, including recently discovered mutations in histone-encoding genes. Lysine-to-methionine mutations such as H3K27M and H3K36M share a common mechanism of inhibiting methylation pathways at the genome-wide level to promote tumorigenesis. However, the mechanism underlying the molecular and cellular changes due to H3G34 alterations is yet to be determined. H3G34 itself is not post-translationally modified; however, G34 lies in close proximity to K36, which undergoes methylation during transcriptional elongation. In Hela cells, H3.3G34L/W mutations have no effect on global levels of methylation on H3K36, H3K27, or other major methylation sites on endogenous histone H3, which include both H3.3 and the canonical H3.1/H3.2 proteins. However, long exposures of the blots revealed that methylation on the ectopic Flag-H3.3 proteins are affected by G34 mutations: with di- and trimethylation on H3K36 and H3K27ac reduced whereas H3K27me3 increased in the G34L and G34W mutated H3.3 compared to the WT H3.3. ChIP-seq results showed that mutations of H3.3G34 affect methylation on H3K36 and H3K27 in cis. G34L/W mutants abolish SETD2 methylation of H3K36. In contrast, the enzymatic activities of both EZH2 and p300 on H3K27 are not affected by G34 mutations. Consistent with changes in H3K27me3 and H3K36m3 levels, we found increased binding of PRC2 (EZH2, SUZ12 and EED) and PRC1 complex components (CBX8 and RING2) and reduced binding of H3.3K36me3 reader such as ZMYND11 to the G34 mutants. In summary, our study revealed that histone H3.3 G34 mutations alter histone K36 and K27 methylation in cis, and affect the binding of readers specific to K36 or K27 methylation.

overall_design: ChIP-seq of H3.3, Flag-H3.3, H3K27ac, H3K27me3, H3K36me2, and H3K36me3 were applied in HeLa cells stably expressing WT or mutant (G34L/G34W) H3.3 and control vector (Ctrl). ChIP-seq of Flag-H3.3, H3K36me2, and H3K36me3 were also applied in HeLa cells stably expressing mutant K36M H3.3.

first: Leilei

first: Xiaobing


title: Discovery of YAP target genes with TNFa or IL-1b induction

status: Public on Jun 02 2018

city: Hangzhou

first: Qiong

last: Zhang

address: 866 YuHangTang Rd, Medical Research Building A212, ZiJinGang Campus, Zhejiang University

institute: Zhejiang University

summary: Proper inflammatory responses are vital to restore tissue homeostasis against offending factors. However, it is largely under explored whether inflammatory responses are modulated by the Hippo effectors YAP/TAZ. To identify the transcription targets related to inflammatory reponses for YAP, we utilized human bronchioalveolar carcinoma cells H358 expressing YAP(5SA) or GFP (as a control) and treated with vehicle, TNFa or IL-1b, respectively. Our work disclosed the complex features of YAP/TAZ’s role in inflammatory responses.

overall_design: H358 GFP and H358 YAP(5SA) are generated. Each cell line was treated with 10 g/ml TNF-a, 10 g/ml IL-1b or vehicle for 1 hour. This makes 6 samples. The expression data from H358 GFP treated with vehicle serve as control.

first: Zongping

last: Xia


title: DNA replication origins in whole Arabidopsis seedlings

status: Public on Apr 15 2018

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

institute: Centro de Biologia Molecular Severo Ochoa

summary: Full genome replication in eukaryotes depends on the function of thousands of DNA replication origins (ORIs). The genome-wide identification of ORI location, achieved for animal and plant cells in culture, has been important to define their DNA and chromatin features. A major challenge in the field is to approach the biology of ORIs in whole organisms to understand their developmental plasticity. Here, we have determined the ORI location, activity and chromatin landscape in two developmental stages of Arabidopsis thaliana. We found that ORIs associate with multiple chromatin signatures including the most frequent at TSS but also at proximal and distal gene regulatory regions or repressed Polycomb domains. In constitutive heterochromatin, a high fraction of ORIs colocalize with GC-rich retrotransposons. Quantitative analysis of ORI activity led us to conclude that strong ORIs possess high scores of local GC content and clusters of GGN trinucleotides that may form G quadruplexes and other G-rich structures. We also found that development primarily influences ORI firing strength rather than the location of ORIs in different genomic loci. Moreover, ORIs that preferentially fire at early vegetative stages colocalize with GC-rich heterochromatin whereas those at later stages associate with transcribed genes. Our results provide the first identification of ORI features in a whole organism, opening new ways of studying DNA replication in different cell types in the context of development under normal and mutant conditions.

overall_design: We isolated replication intermediates to purify short nascent strands of increasing size (Fractions 3, 4 and 5+6+7) from two developmental stages of Arabidopsis seedlings (4 and 10 day-old). For each developmental stage we processed three independent biological replicates and two genomic controls. A total of 20 samples were sequenced. We also did RNA-seq of 4 day-old seedlings in duplicate (2 samples).

first: J

last: Sequeira-Mendes

first: R

last: Peiró

first: Z

last: Vergara

last: Morata

last: Aragüez

first: C

last: Costas

last: Mendez-Giraldez

middle: M

last: Casacuberta

last: Bastolla


title: Arabidopsis thaliana leaf parallel analysis of RNA ends

status: Public on Jun 25 2018

city: Norwich

first: Josh

last: Thody

state: Norfolk

address: Norwich Research Park

institute: University of East Anglia

overall_design: Three Arabidopsis thaliana leaf degradome replicates were constructed using wild type Columbia (Col-0) plants

first: Joshua


title: Direct control of SPEECHLESS by PIF4 in the high temperature response of stomatal development

status: Public on Apr 05 2018

city: Stanford

first: Jessica

middle: Kay

last: Chang

address: 300 Pasteur Drive, Alway Building M311

department: Genetics

institute: Stanford University

summary: Environmental factors shape the phenotypes of multicellular organisms. The production of stomata—the epidermal pores required for gas exchange in plants—is highly plastic, and provides a powerful platform to address environmental influence on cell differentiation [1-3]. Rising temperatures are already impacting plant growth, a trend expected to worsen in the near future [4]. High temperature inhibits stomatal production but the underlying mechanism is not known [5]. Here, we show that elevated temperature suppresses the expression of SPEECHLESS (SPCH), the bHLH transcription factor that serves as the master regulator of stomatal lineage initiation [6,7]. Our genetic and expression analyses indicate that the suppression of SPCH and stomatal production is mediated by the bHLH transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a core component of high temperature signaling [8]. Importantly, we demonstrate that upon exposure to high temperature, PIF4 accumulates in the stomatal precursors and binds to the promoter of SPCH. In addition, we find SPCH feeds back negatively to the PIF4 gene. We propose a model where the high temperature-activated PIF4 binds and represses SPCH expression to restrict stomatal production at high temperature. Our work identifies a molecular link connecting high temperature signaling and stomatal development, and reveals a direct mechanism by which production of a specific cell lineage can be controlled by a broadly-expressed environmental signaling factor.

overall_design: Gene expression profiles following 12 hr Dex-induction of control and ML1p:SPCH1-4A-expressing Arabidopsis plants grown in liquid culture. Four replicates per line at 0 and 12 hr.

first: Kelli

last: Davies

first: On

last: Lau

first: Dominque

last: Bergmann


title: Sequencing of human chain specific ribosome transcriptional group

status: Public on Apr 13 2018

city: Guangzhou

first: Tan

last: yi

address: No.7 West Street, Yuancun, Guangzhou, P. R. China

institute: South China Institute of Environmental Science (SCIES), Ministry of Environmental Protection (MEP)

summary: The purpose of this study is to investigate whether the expression profile of long chain non coding RNA (lncRNA) in different concentrations of PM2.5 after treatment of normal human bronchial cells is changed. The total RNAs were extracted from 16HBE cells after exposure to either PM2.5, at concentration of 50 μg/mL and 100μg/mL, or PBS (control group) for 48h. lncRNA-sequencing, detection and analysis was performed. Fold change ≥ 2 and p ≤ 0.05 were used as a cutoff values to determine significant differential expression Further, cluster analyses were performed to classify lncRNAs based on their distinguishable expression in different samples.

overall_design: Detection of a long chain noncoding RNA treated with cell type and different concentrations of PM2.5

first: Yi

last: Tan

first: YuYu

last: Wang

first: XiaoWu

last: peng


title: IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors [mRNA]

status: Public on Mar 19 2018

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: The oncofetal IGF2 mRNA binding protein (IGF2BP) family modulates tumor cell properties but IGF2BP paralogue-specific roles remain poorly understood. We demonstrate that phenotypic roles of IGF2BPs vary in a cancer cell-dependent manner. However, only IGF2BP1 shows oncogenic potential in all cancer cells analyzed. Consistently, only IGF2BP1 expression is associated with poor prognosis in ovarian carcinoma and promotes all oncogenic properties analyzed in ovarian cancer-derived tumor cells. Despite a substantial overlap of candidate target mRNAs of IGF2BP paralogues proposed by CLIP analyses, the paralogue-specific depletion of IGF2BPs induces strikingly distinct deregulation of mRNA abundance. Transcripts decreased by IGF2BP1 depletion or knockout are enriched for IGF2BP1- as well as AGO-CLIP hits conserved in distinct cell lines, are prone to targeting by highly abundant miRNAs and comprise significantly longer 3’UTRs. Downregulation of target mRNAs upon IGF2BP1 depletion is abrogated when miRNAs are expressed at low levels or depleted by DICER/DROSHA knockdown. Strikingly, the depletion of all 12 randomly selected miRNA-prone target mRNAs impairs at least one analyzed IGF2BP1-modulated tumor cell property. These findings indicate that IGF2BPs serve distinct roles in cancer-derived cells and suggest that IGF2BP1’s main role is the post-transcriptional, miRNome-dependent enhancement of factors promoting oncogenic tumor cell properties.

overall_design: total RNA-Seq of ES-2 cells transfected with either control siRNAs (siC) or siRNAs directed against IGF2BP1/IGF2BP2/IGF2BP3.

first: Simon

last: Müller

first: Nadine

last: Bley

first: Bianca

last: Busch

first: Vanessa

last: Rousseau

first: Danny

last: Misiak

first: Tommy

last: Fuchs

first: Marcell

last: Lederer

first: Stefan

last: Hüttelmaier


title: RNA-seq to identity genes expressed in dissected inflorescence meristems of Col-0 Arabidopsis thaliana plants.

status: Public on May 25 2018

city: Lyon

first: Antoine

last: Larrieu

address: 46 allée d'Italie

institute: ENS Lyon

summary: The shoot apical meristem of higher plants continuously generates new tissues and organs through complex changes in growth rates and directions of its individual cells. Cell growth, driven by turgor pressure, largely depends on the cell walls, which allow cell expansion through synthesis and structural changes. A previous study revealed a major contribution of wall isotropy in organ emergence, through the disorganization of cortical microtubules. We show here that this disorganization is coupled with the transcriptional control of genes involved in wall remodelling. Some of these genes are induced when microtubules are disorganized and cells shift to isotropic growth. Mechanical modelling shows that this coupling has the potential to compensate for reduced cell expansion rates induced by the shift to isotropic growth. Reciprocally, cell wall loosening induced by different treatments or altered cell wall composition promotes a disruption of microtubule alignment. Our data thus indicate the existence of a regulatory module activated during organ outgrowth, linking microtubule arrangements to cell wall remodelling.

overall_design: 3 Col-0 samples

first: Teva

last: Vernoux


title: The response of Streptococcus pneumoniae to antibiotic stress on the transcriptome of a competence negative strain

status: Public on Mar 09 2018

city: Lausanne

first: Arnau

last: Domenech

address: Biophore building

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

summary:
The aim of this study is to identify the rapid (RR) and adaptative (AR) response of S. pneumoniae to aztreonam and clavulanic acid stress on transcriptional level
Streptococcus pneumoniae is able to acquire antibiotic resistance by activation of competence and subsequent DNA uptake. Several antibiotics induce competence by disrupting protein-quality control or perturbing DNA replication. Here, we demonstrate that aztreonam (AZT) and clavulanic acid (CLA) also promote competence. We show that AZT and CLA induce cell chain formation by targeting the D,D-carboxypeptidase PBP3. In support of the hypothesis that chain forming promotes competence, we demonstrate that an autolysin mutant (𝞓lytB) is hypercompetent. As competence is initiated by the binding of a small extracellular peptide (CSP) to a membrane-anchored receptor (ComD), we wondered if chain formation alters CSP diffusion and thereby sensing by ComD. Indeed, the presence of AZT or CLA affects competence synchronization. Artificially reducing CSP diffusion by increasing culture medium viscosity also triggers competence. Together, our data show that AZT and CLA effectively switch CSP-based quorum sensing to autocrine-like signalling, as CSP is now retained to chained cells and no longer shared in a common pool.

overall_design: The different conditions were compared to each other. With or withour the short (rapid response) or long (adaptative response) presence of the compounds. The slide configuration also contained 6 replicate spots for each gene.

first: Jelle

last: Slager

first: Jan-Willem

last: Veening


title: Genome-wide characterization of cis-acting DNA targets of Opaque11 in maize

status: Public on Apr 09 2018

first: Liming

last: Xu

address: 333 Nanchen Road

institute: Shanghai University

summary: Opaque11 (O11) is a bHLH transcription factor that plays important roles in maize endosperm development, nutrient metabolism, and stress response.

overall_design: Examination of 15 days after pollination(DAP) wild type maize kernels with O11 specific antibody.  o11 mutant seeds which have no accumulation of O11 protein were used as negtive control.Two independent biological replicates prepared at different times were used in this study.

first: Fan

last: Feng

first: Rentao

last: Song


title: RNA Sequencing facilitates the identification of transcriptional targets of Pitx1 in Xenopus laevis

status: Public on Mar 07 2018

city: Flushing

first: Ye

last: Jin

address: 6530 Kissena Blvd

department: Biology

institute: Queens College-CUNY

summary: The cement gland in Xenopus laevis has long been used as a model to study the interplay of cell signaling and transcription factors during embryogenesis. The homeodomain-containing transcription factor Pitx1 has been linked to cement gland development. However, the downstream transcriptional targets of Pitx1 remain unknown. Here, we utilize RNA Sequencing to identify transcripts whose expression are affected by Pitx1 misexpression in animal cap explants.

overall_design: mRNA profile of pitx1-injected or control animal cap explants at neurula stages were generated by deep sequencing, in duplicate, using Illumina HiSeq2500 by Genewiz.

first: Daniel

last: Weinstein


title: IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors [small RNA]

first: Markus

last: Glaß

summary: The oncofetal IGF2 mRNA binding protein (IGF2BP) family modulates tumor cell properties but IGF2BP paralogue-specific roles remain poorly understood. We demonstrate that phenotypic roles of IGF2BPs vary in a cancer cell-dependent manner. However, only IGF2BP1 shows oncogenic potential in all cancer cells analyzed. Consistently, only IGF2BP1 expression is associated with poor prognosis in ovarian carcinoma and promotes all oncogenic properties analyzed in ovarian cancer-derived tumor cells. Despite a substantial overlap of candidate target mRNAs of IGF2BP paralogues proposed by CLIP analyses, the paralogue-specific depletion of IGF2BPs induces strikingly distinct deregulation of mRNA abundance. Transcripts decreased by IGF2BP1 depletion or knockout are enriched for IGF2BP1- as well as AGO-CLIP hits conserved in distinct cell lines, are prone to targeting by highly abundant miRNAs and comprise significantly longer 3’UTRs. The downregulation of target mRNAs observed upon IGF2BP1 depletion is abrogated when miRNAs are expressed at low levels or depleted by DICER/DROSHA knockdown. Strikingly, the depletion of 10 randomly selected miRNA-prone target mRNAs impairs at least one analyzed IGF2BP1-modulated tumor cell property. These findings indicate that IGF2BPs serve distinct roles in cancer-derived cells and suggest that IGF2BP1’s main role is the post-transcriptional, miRNome-dependent enhancement of factors promoting oncogenic tumor cell properties.

overall_design: small RNA-Seq of ES-2 cells transfected with either control siRNAs (siC) or siRNAs directed against IGF2BP1, IGF2BP2 or IGF2BP3. Two or three replicates per condition.

first: Simon

last: Müller

first: Nadine

last: Bley


title: RNA expression in MDA-MB-231 cells transfected with scramble, LSD1 or HDAC5 shRNA (HG-U133A_2)

status: Public on Mar 30 2018

city: Pittsburgh

first: Yi

last: Huang

state: Pennsylvania

address: 204 Craft Ave

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh Cancer Institute

summary: We performed gene expression microarray to examine the potential effect that depletion of HDAC5 (an important HDAC isozyme) or LSD1 (an FAD-dependent histone lysine demethylase) has on the triple-negative breast cancer transcriptome.

overall_design: Twelve samples were subject to microarray anaylsis:  3 biological replicates were treated with 1) scramble shRNA, 2) HDAC5 shRNA, 3) scramble shRNA, or 4) LSD1 shRNA.

first: Shauna

last: Vasilatos

first: Chunyu

last: Cao