title: Transcriptional profile of brain TRM in Toxoplasma gondii infection

city: Riverside

first: Emma

last: Wilson

address: 900 University Ave

department: Biomedical Sciences

institute: University of California, Riverside

summary: During chronic infection memory T cells acquire a unique phenotype and become dependent on different survival signals than those needed for memory T cells generated during an acute infection. The distinction between the role of effector and memory T cells in an environment of persistent antigen remains unclear. Here, in the context of chronic Toxoplasma gondii infection we demonstrate that a population of CD8 T cells exhibiting a tissue resident memory (TRM) phenotype persists in the brain.  We show that this population is distributed throughout the brain in both parenchymal and extraparenchymal spaces.  Furthermore, this population is transcriptionally distinct and exhibits a transcriptional signature consistent with the TRM observed in acute viral infections.

overall_design: Differential gene expression analysis with the following specified comparisons: 1) brain CD103+ CD8 T cells to brain CD103- CD8 T cells 2) brain CD103+ CD8 T cells to spleen CD103+ CD8 T cells 3) brain CD103+ CD8 T cells to spleen CD103- CD8 T cells

first: Tyler

middle: A

last: Landrith

first: Suhas

last: Sureshchandra

first: Andrea

last: Rivera

first: Jessica

middle: C

last: Jang

first: Maham

last: Rais

first: Meera

middle: G

last: Nair

first: Ilhem

last: Messaoudi


title: A high-resolution map of transcriptional repression by Ikaros

status: Public on Jun 12 2017

city: London

first: Thomas

middle: Samuel

last: Carroll

address: Hammersmith Hospital, Du Cane Rd

department: Bioinformatics

country: United Kingdom

institute: MRC Clinical Sciences Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcription factor Ikaros is essential for early B cell development, which involves precise control of the transcription program. Gene repression is less well understood compared to gene activation. The purpose of this study was to characterise the chromatin changes mediated by Ikaros, which could shed light on how Ikaros mediates transcriptional silencing.

overall_design: We carried out RNA polymerse II (RNAP2) chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) in B3 cells after 6h of control carrier ethanol (EtOH) treatment or 4-hydroxytamoxifen (4-OHT) treatment to induce Ikaros translocation. We also carried out MNase-seq in B3 cells after 6h of EtOH or 4-OHT treatment.

first: Ziwei

last: Liang

first: Matthias

last: Merkenschlager


title: Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing.

overall_design: mRNA, lncRNA and circRNA profiles of the mouse spermatogonial stem cells (SSCs) and  female germline stem cells (FGSCs) by strand- specific RNA- seq

first: Xiaoyong

last: Li


title: Host genetic background strongly affects pulmonary miRNA expression before and during evolution of influenza A virus infection

city: Braunschweig

last: Preusse

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz Centre for Infection Research

summary:
Background: The role of host encoded microRNAs in genetically determined host susceptibility to influenza A virus (IAV) infection has not been explored. We therefore compared changes in pulmonary miRNA expression during IAV infection in two inbred mouse strains with differential susceptibility to IAV infection.

Results: miRNA expression profiles were determined in lungs of the more susceptible mouse strain DBA/2J and the less susceptible strain C57BL/6J within 120 hours post infection (hpi) with IAV (H1N1) PR8. Even the miRNomes of uninfected lungs differed substantially between the two strains. After a period of relative quiescence, major miRNome reprogramming was detected in both strains by 48 hpi and increased through 120 hpi. Distinct groups of miRNAs regulated by IAV infection could be defined: (1) miRNAs (n= 39) whose expression correlated with HA mRNA expression and represented the general response to IAV infection independent of host genetic background; (2) miRNAs (n=20) whose expression correlated with HA mRNA expression but differed between the two strains; and (3) remarkably, miRNAs (n=8) whose abundance even in uninfected lungs differentiated nearly perfectly (area under the ROC curve >0.99) between the two strains throughout the time course. Higher abundance of miRNAs with anti-apoptotic functions and lower abundance of miRNAs regulating the PI3K-Akt pathway were associated with the more susceptible DBA/2J strain.

Conclusions: These results suggest that differences in host miRNA abundance before and during IAV infection are in part determined genetically and contribute to susceptibility to IAV infection in this experimental mouse model, and likely in humans.

overall_design: Influenza A virus infection timecourse in two mouse strains (C57BL/6J, DBA/2J) with different susceptibility to the virus.

first: Klaus

last: Schughart

first: Frank

last: Pessler


title: Identification of heptanal receptors in mouse olfactory epithelium by a high-throughput in vivo method

city: Durham

first: Kentaro

last: IKEGAMI

address: 213 Research Drive

country: USA

institute: Duke University

summary: We present heptanal receptors identified using a high-throughput in vivo method (Jiang et al., 2015)

overall_design: pS6-IP RNA-Seq in heptanal stimulated vs wild type mice olfactory epithelium

first: Hiroaki

last: Matsunami

first: Yue

last: Jiang

last: Ikegami

first: Xiaoyang

middle: S

last: Hu


title: Gene resistance to transcriptional reprogramming following nuclear transfer is directly mediated by multiple chromatin repressive pathways

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: Understanding the mechanism of resistance of certain genes to reactivation will help improving the success of nuclear reprogramming. Here, in a Xenopus oocyte nuclear transfer assay we identify mouse genes that are resistant to reprogramming by oocyte factors. By using MEF nuclei with WT or reduced DNA methylation in combination with chromatin modifiers able to erase H3K9me3, H3K27me3, and H2Aub from transplanted nuclei, we reveal the basis for resistance to transcriptional reprogramming. We observe a complex relationship between loss of resistance and chromatin modifiers treatment as a majority of gene is affected by more than one type of treatment, suggesting that resistance requires simultaneous repression through multiple epigenetic mechanisms. Existence of synergistic as well as adverse mechanism of action of chromatin modifiers on removal of resistance is revealed by the classification of resistant genes according to their sensitivity to chromatin modifiers treatments. We further demonstrate that removal of H2Aub from transplanted chromatin explain loss of resistance upon USP21 expression. Finally, we provide evidence that H2A ubiquitylation is also contributing to resistance to transcriptional reprogramming in mouse nuclear transfer embryos.

sample_organism:
Xenopus laevis
Mus musculus

platform_organism:
Xenopus laevis
Mus musculus

overall_design: 36 samples, single-ended RNA-seq libraries from MEF or mES nuclei transplanted to Xenopus oocytes; 8 samples, single-ended RNA-seq libraries from mES  cloned two-cell stage embryos; 4 samples single-ended ChIP-seq librarys (H2Aub antibody) from MEF transplanted to Xenopus oocytes.

first: Jerome

last: Jullien

first: Munender

last: Vodnala

first: George

middle: E

last: Allen

middle: R

first: Vincent

last: Pasque

first: Nathalie

last: Beaujean

first: Stan

last: Wang

first: Haruhiko

last: Koseki

first: Vitorio

last: Sartorelli

first: John

middle: B

last: Gurdon


title: Next Generation Sequencing of Pkd1 mutant kidneys

city: Dallas

first: Ronak

last: Lakhia

state: Texas

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UTSW

summary: This study sough to understand the differential gene expression profile of Pkd1 mutant mice kidneys in the setting of miR 17~92 deletion

overall_design: 3 Pkd1 knockout mice and 3 Pkd1 miR-17 knockout mice were analyzed

first: R

first: V

last: Patel


title: Genome-wide identification and characterization of miRNAome from tomato roots (Solanum lycopersicum) and root-knot nematode (Meloidogyne incognita) during susceptible and resistant interactions.

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

country: India

institute: Delhi University

summary: RKNs are economically most damaging, obligate sedentary endoparasites that form giant cells within host roots to obtain nutrition and complete their life cycle. We report genome-wide identification of miRNAs from both host and RKN using RKN-infected susceptible tomato roots through high-throughput sequencing. Eleven small RNA libraries were made from five disease development stages, their five corresponding uninfected development stages and uninfected development stage 0. A total of 52 conserved miRNAs, 4 variants of conserved miRNAs and 281 novel miRNAs of host were identified. A significantly upregulated expression of majority of the miRNAs was observed during susceptible response and downregulated expression during resistance response through qRT-PCR. The miRNA targets were predicted and validated through 5’RLM-RACE. Furthermore, correlation between the expression profile of selected conserved miRNAs viz., miR164, miR156, miR396, miR159, and novel Sly_miRNA996 with their target transcription factors viz., NAC, SBP, GRF1, GAMYB-like, and MYB-like, respectively was also determined. This study suggests a potential role of host miRNAs in regulating transcription factor genes involved in plant developmental processes and defense responses during RKN infection. Additionally, 328 RKN miRNAs including 38 conserved miRNAs, 106 novel miRNAs, and 184 candidate novel miRNAs were identified from same dataset. The differential expression of conserved and RKN-specific miRNAs at different development stages of nematode in tomato roots suggests their probable role during nematode development and adaptation to parasitic behavior. This is the most comprehensive study reporting the identification and characterization of miRNAs from both tomato and RKN in five different disease development stages under soil grown conditions and their potential roles during RKN infection in tomato roots.

overall_design: Total eleven small RNA libraries of root {Stage 0 uninfected (SO UI), Stage 1 uninfected (S1 UI), Stage 1 infected (S1 I), Stage 2 uninfected (S2 UI), Stage 2 infected (S2 I), Stage 3 uninfected (S3 UI), Stage 3 infected (S3 I), Stage 4 uninfected (S4 UI), Stage 4 infected (S4 I), Stage 5 uninfected (S5 UI), stage 5 infected (S5 I)} were constructed and high-throughput sequencing was performed using HiSeq 200 sequencing system.

first: Pritam

last: Kaur

first: Neha

last: Shukla

first: Arun

last: Jagannath

first: Manu

last: Agarwal

first: Shailendra

last: Goel

first: Amar

last: Kumar


title: Epigenetic profiling of aorta macrophages of mice exposed to intermittent hypoxia (CD11ME)

city: Chicago

first: David

last: Gozal

state: Illinois

address: KCBD, Room 4100, 900 E. 57th Street, Mailbox 4

department: Department of Pediatrics

institute: University of Chicago

summary: ChIP-seq targeting H3K9ac and H3K27me3 histone modifications was carried out on macrophages isolated from aortas of mice exposed to intermittent hypoxia or room air conditions.

overall_design: One replicate was generated for each histone mark in each condition for a total of 4 immunoprecipitated samples and no input or control sample.

first: Rene

last: Cortese

first: Tzintzuni

middle: I

last: Garcia


title: Genome-wide primary transcriptome landscape reveals the diversity of regulatory elements in archaeal genomes

city: Daejeon

first: Yujin

last: Jeong

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: We show the transcriptomic landscape of the H2-producing archaeon Thermococcus onnurineus NA1 in response to different growth conditions using primary and whole transcriptome sequencing. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA boxes, A-rich B recognition elements (BREs), and promoter proximal element (PPE) motifs in promoter regions, a high pyrimidine nucleotide content (T/C) at the −1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs). In addition, along with differential transcript levels, 117 leaderless genes and 86 non-coding RNAs (ncRNAs) were identified, representing diverse cellular functions and potential regulatory functions during hydrogen production. Further comparative analysis of T. onnurineus upstream regulatory sequences with those of closely related archaeal genomes demonstrated that orthologous genes are expressed from highly conserved promoter sequences, however their upstream sequences for transcriptional and translational regulation are largely diverse. This study suggests that closely related archaea maintain orthologous gene functions, but may diversify the elements that regulate them to adapt to their unique environmental habitats.

overall_design: Profiles of primary transcripts and whole transcripts of Thermococcus onnurineus NA1 were generated by deep sequencing using Illumina Miseq and Illumina Genome Analyzer IIx.

first: Suhyung

last: Cho

first: Min-Sik

last: Kim

first: Bo-Rahm

last: Lee

first: Jung-Hyun

first: Sung

last: Kang

first: Byung-Kwan


title: Direct Generation of Human Neuronal Cells from Adult Astrocytes by Small Molecules

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Astrocytes, due to the proximity to neuronal lineage and capability to proliferate, are ideal starting cells to regenerate neurons. Human fetal astrocytes have been successfully converted into neuronal cells by small molecules, which offer a broader range of further applications than transcription factor-mediated neuronal reprogramming. Here we report human adult astrocytes could also be converted into neuronal cells by a different set with fewer small molecules. These induced neuronal cells exhibited typical neuronal morphologies, expressed neuronal markers, and displayed neuronal electrophysiological properties. Genome-wide RNA-sequencing analysis showed the gene expression profile of induced neuronal cells resembled that of human embryonic stem cell-differentiated neurons. When transplanted into postnatal mouse brains, these induced neuronal cells could survive in vivo. Altogether, our study provides a new strategy to directly generate transgene-free neurons from human adult astrocytes by small molecules.

overall_design: In this data set, we include RNA-Seq data of human astrocytes treated with small molecules (Valproic acid, Chir99021, Repsox, forskolin, i-Bet151 and ISX9) for 0, 2, and 30 days, as well as neurons derived from human embryonic stem cells

first: Longfei

last: Gao

first: Wuqiang

last: Guan

first: Min

last: Wang

first: Huihan

first: Jiali

last: Yu

first: Qing

last: Liu

first: Binlong

last: Qiu

first: Yongchun

first: Yifang

last: Ping

first: Xiuwu

last: Bian

first: Gang

last: Pei


title: Fetal metabolic programing increases the susceptibility of cardiovascular diseases in the offspring due to maternal high-fat-diet during diabetic pregnancy

city: Brookings

first: Moul

last: Dey

state: South Dakota

address: SWG 440, Rotunda Lane

department: Health and Nutritional Sciences

institute: South Dakota State University

summary: Increasing trends of obesity in childbearing women with a concurrent gestational diabetes are often associated with adverse fetal metabolic cues. Not only the carbohydrates but also fats are considered to contribute additional dietary fuels to the fetal hearts. To examine the hitherto unknown epigenetic mechanisms on the offspring’s cardiometabolic health due to maternal high-fat (HF) diet (40% kcal) or streptozotocin (STZ)-induced diabetic pregnancy, or both, we carried out an epigenetic characterization of neonatal heart tissue using chromatin immunoprecipitation (ChIP) sequening and a previously validated rat model. Chromatin landscape of offspring’s heart tissue revealed differential peaks distribution on various promoter regions mapped to the rat genome due to histone (H3) modifications by acetylation (H3Ac) or trimethylations of lysine 4 and 27 (H3K4me3 and H3K27me3, respectively). Ongoing evaluations include gene ontology and disease ontology analyses. Together, it is expected that the findings will show that maternal HF-diet with or without gestational diabetes changes the cardiac histone signature in rat offspring, potentially leading to development of novel disease prevention strategies.

overall_design: Examination of 3 different histone modifications in rat heart tissues.

first: Michelle

middle: L

last: Baack


title: Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of citrus (Poncirus trifoliata L. Raf.) by RNA sequencing

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

institute: Huazhong Agricultural University

summary: To investigate the role of lncRNAs in citrus flowering, paired-end strand-specific RNA sequencing was performed between precocious trifoliate orange and its wild-type. Total 6,584 potential lncRNAs were identified, 51.6% of which came from intergenic regions. It was also observed that 555 lncRNAs were significantly up-regulated, and 276 lncRNAs were down-regulated in precocious trifoliate orange, indicating that lncRNAs could be involved in the regulation of citrus flowering.

overall_design: Two samples, the terminal bud and the five following buds (the major node position for flower formation) from spring flushes of the MT and the WT 2-year-old trees were collected at flower initiation (after self-pruning).  And then subjected to RNA-seq.

first: Chun-Gen

last: Hu

first: Jin-Zhi

last: Zhang


title: Identification of Sc and Esg chromatin-binding sites by ChIP-Seq analysis in progenitor cells of Drosophila midgut

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: To study the antagonism between Esg and Sc, we compared their direct binding sites identified by 3HA-esg and 3HA-sc ChIP-Seq. Through ChIP-Seq analysis, 14347 binding sites of Sc and 2765 binding sites of Esg were identified through p-value cutoff 1.00e-05. Among Sc binding sites, 10675 were protein-coding genes and 2678 localized to promoter region. For Esg, 2036 were protein-coding genes and 846 localized to promoter region. Through comparison, 2153 common binding sites were identified, and among these, 1620 were protein-coding genes and 659 localized to promoter region. A common binding region at the promoter of pros was identified.

overall_design: 3HA-esg or 3HA-sc transgenes were expressed in progenitor cells by esg-Gal4. Anti-HA antibody was used for ChIP, followed by deep sequencing analysis.

first: Yumei

last: Li

first: Rongwen

last: Xi

first: Huanwei

last: Huang


title: PNET animal model: new insights

first: Yingtao

last: Bi

state: IL

address: 750 North Lake shore drive

institute: Northwestern University

summary: Recently, we described a new animal model of CNS primitive neuroectodermal tumors (CNS-PNET), which was generated by orthotopic transplantation of human Radial Glial (RG) cells into NOD-SCID mice’s brain sub- ventricular zone. In the current study we conducted comprehensive RNA-Seq analyses to gain some insights on the mechanisms underlying tumorigenesis in this mouse model of CNS-PNET. Here we show that the RNA-Seq profiles derived from these tumors cluster with those reported for patients’ PNETs.

overall_design: RNA-seq of tumors from central nervous system primitive neuroectodermal tumor (CNS PNET) animal model

first: Sergey

last: Malchenko


title: Specific and novel human microRNAs are regulated as response to fungal infection

city: Jena

first: Andreas

last: Dix

address: Beutenbergstraße 11a

institute: Hans-Knöll-Institut

summary: Within the last decades, invasive fungal infections have gained increasing significance. They are characterized by high mortality rates and are often caused Candida albicans and Aspergillus fumigatus. The increasing number of infections underlines the necessity for additional anti-fungal therapies, which require an extended knowledge of gene regulations during fungal infection. MicroRNAs are regulators of important cellular processes, including immune response. By analyzing their regulation and impact on target genes, novel therapeutic approaches may be developed. Here, we examine the role of microRNAs in human dendritic cells during fungal infections. Dendritic cells represent the bridge between the innate and the adaptive immune systems. Therefore, analysis of gene regulation of dendritic cells is of particular significance. By applying next-generation sequencing of small RNAs, we quantify microRNA expression in monocyte-derived dendritic cells after 6 and 12h of infection with C. albicans and A. fumigatus as well as treatment with LPS. We use two different tools and an online database to determine potential target genes. We identified 29 microRNAs that are differentially regulated after infection by the fungi or LPS. Two and five of them are specific for fungal infections after 6h and 12h, respectively. We further validated interactions of miR-132-5p and miR-212-5p with immunological relevant target genes, such as FKBP1B, KLF4, and SPN, on both RNA and protein level. Our results indicate a fine-tuning function of these microRNAs during fungal infections. Beyond that, we identified previously undiscovered microRNAs. We validated three novel microRNAs via qRT-PCR. A comparison with known microRNAs revealed possible relations with the miR-378 family and miR-1260a/b for two of them, while the third one features a unique sequence with no resemblance to known microRNAs. In summary, this study analyzes the effect of known microRNAs in dendritic cells during fungal infections and proposes novel microRNAs that could be experimentally verified.

overall_design: The microRNA expression in human dendritic cells stimulated with Aspergillus fumigatus, Candida albicans, and LPS was compared to unstimulated controls. For each condition, the expression was measured after 6h and 12h of co-cultivation. 31 samples were generated, comprising three to four replicates for each time point and condition.

first: Kristin

last: Czakai

first: Ines

last: Leonhardt

first: Karin

last: Schäferhoff

first: Michael

last: Bonin

first: Reinhard

last: Guthke

first: Hermann

last: Einsele

first: Oliver

last: Kurzai

first: Jürgen

last: Löffler

first: Jörg

last: Linde


title: Chronic nicotine differentially affects murine transcriptome profiling in isolated cortical interneurons and pyramidal neurons

city: chongqing

first: jie

last: yang

address: 1 Youyi Road

institute: Chongqing Medical University

summary: Nicotine differentially affected subset of genes in Sst- and Thy1- neurons, which might contribute to the distinct effect of nicotine on interneuron and pyramidal neuron activities. Meanwhile, the altered transcripts associated with mitochondrial activity were found between interneurons and pyramidal neurons after chronic nicotine.

overall_design: We assessed the differentially expressed genes (DEGs) by nicotine in Sst- or Thy1- neurons, respectively, and then compared DEGs between Sst- and Thy1- neurons in the absence and presence of nicotine.

first: Jie

last: Yang

first: Guo-Jun

last: Chen


title: Grapevine grafting: scion transcript profiling and defense-related metabolites induced by different rootstocks.

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

summary: Genotype, climate, soil qualities, and rootstocks are among the main factors that influence grape development as well as fruit and wine composition. In this work, the rootstock/scion interactions were studied using transcriptomic and metabolic approaches on leaves of Gaglioppo variety, grafted onto thirteen different rootstocks growing in the same locations. The experiments were performed in a vineyard in the south of Italy, characterized by the Mediterranean climate with warm and dry summers. Whole leaf transcriptome of ‘Gaglioppo’ grafted on five selected rootstocks showed high variability in gene expression. In particular, significant modulation of transcripts linked to primary (e.g. carbohydrate and transport) and secondary metabolism (e.g.  phenylpropanoids pathways and response to stress) was observed. Interestingly, genes involved in the priming defense responses (e.g stilbenes and defense genes) were strongly activated in some graft combinations. These results were further confirmed by the quantification of stilbene contents. According with these observations, the leaves of ‘Gaglioppo’ grafted on 1103 Paulsen showing the lowest levels of stilbene synthase transcripts and stilbene metabolites, reveal the greater sensitivity to downy mildew in in vitro assay. This study carrying out an extensive analysis of rootstock effects to scion leaves open a useful way to unravel this complex interaction

overall_design: Differential expression analysis of Gaglioppo variety grafted onto five different rootstocks

first: Walter

last: Chitarra

first: Irene

last: Perrone

first: Carla

last: Avanzato

first: Paolo

last: Boccacci

first: Deborah

last: Santini

first: Giovanna

last: Gilardi

first: Ilenia

last: Siciliano

first: Maria

last: Gullino

first: Massimo

last: Delledonne

first: Franco

last: Mannini

first: Giorgio

last: Gambino


title: Analysis of Human Airway epithelial cells transcriptome after transfection of small RNAs from miR-34/449 family

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Since the seed sequence is shifted between canonical and isomer variant of hsa-miR-34b-5p and hsa-miR-449c-5p, we examine whether the transfection of the different forms of these miRNAs results in distinct targetomes

overall_design: Transfection of proliferating Human Airway Epithelial Cells with all the miR-34/449  5-p members and isomirs (mirbase reference for hsa-miR-34b-5p and hsa-miR-449c-5p) at a final concentration of 10nM

first: B

last: Marcet

first: O

last: Mercey

first: K

first: P

last: Barbry


title: Integrator complex subunit 12 is a key regulator of human protein synthesis pathways

first: Alexander

last: Kheirallah

state: Cambridgeshire

address: Hills Road

department: Stem Cell Institute

summary: Genome wide association studies of human lung function have identified a signal on 4q24 but the mechanistic basis for this signal is unclear. This region contains the Integrator Complex subunit 12 gene (INTS12) and nearby polymorphisms associated with lung function correlate with INTS12 expression. We aimed to define INTS12 function in human bronchial epithelial cells. RNAseq pathway analyses of INTS12 depleted cells revealed robust downregulation of several protein synthesis related pathways, including the aminoacyl tRNA synthetases and PERK regulated gene expression. Indeed, INTS12 knockdown using mRNA silencing repressed cellular translation and proliferation. ChIPseq gene-centric analyses revealed INTS12 binding to be near transcriptional start sites. The binding was found to be enriched for differentially expressed loci identifying the genes it regulates, a finding previously unknown for this particular member of Integrator complex. These findings contribute to the biology behind genetic association

overall_design: INTS12 depletion was induced in human bronchial epithelial cells from both donors. RNAseq gene expression profiling was performed 48h and 120h since the initiation of knockdown in the first and second donor respectively. Silencing was achieved with two independent D-siRNAs and experiments included scambled D-siRNA transfected and un-transfected cells. Experiments were performed in three biological replicates. Genome-wide INTS12 binding sites were inferred by INTS12 ChIPseq in two donor cells. ChIPseq experiment included input control pooled from both sequenced donors.

middle: K


title: Sequencing of synthetic small RNAs hsa-miR-34b-5p, hsa-miR-449c-5p and their isomir variant

summary: The aim of this small RNA Seq is to determine if the sequence reads observed for hsa-miR-34b-5p and hsa-miR-449c-5p represent library artifacts or sequencing artifacts

overall_design: Each mature miRNA isomer has been sequenced alone in a complex mixture of RNA. The two forms of hsa-miR-34b-5p and hsa-miR-449c-5p were sequenced with a 1:1 ratio (mix)


title: Differential gene expression analysis of Wildtype and NMD deficient mutants grown at 23°C Long day condition

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

institute: Korea University

summary: We sequenced mRNA of WT, upf1-5, upf3-1 and their double mutant seedlings grown at 23°C, day 8 after germination, ZT 16

overall_design: Examination of mRNA level in WT and NMD deficient mutant seedling grown at 23°C

first: Muhammad

last: Fahim

first: Jeong-Hwan

last: Lee

first: Ji-Hoon

last: Ahn


title: Characterizing isomer variants in the microRNA-34/449 family

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

overall_design: Refer to individual Series


title: Low-cost, low-bias and low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

summary: We developed a new method on sequencing low-input RNA. This method shows much low-bias with the advantage of semiconductor while competing with smart-seq2. In order to analyze the low-input RNA datasets sensitively, we also develop FANSe2splice with high experimental verification rate as the analysis tool in our method.

overall_design: The RNA of HBE and A549 were sequenced in our method. And smart-seq2 was also examined in HBE RNA.

first: Zhibiao

last: Mai


title: Deletion of Lsd1 triggers Senescence in Trophoblast Stem Cells by Induction of Sirt4

city: Freiburg

middle: Josefina

last: Castex

address: BreisacherStrasse 66

institute: Freiburg Uniklinik


title: The role of Sgf73 occupancy

city: La Jolla

first: Albert

middle: R.

last: La Spada

state: California

address: 2880 Torrey Pines Scenic Dr.

department: Pediatrics

institute: University of California San Diego

summary: Sgf73, a core component of the SAGA (Spt-Ada-Gcn5 Acetyltransferase) co-activator complex, is the yeast orthologue of ataxin-7, which in humans undergoes CAG ? polyglutamine repeat expansion to produce the neurodegenerative disease spinocerebellar ataxia type 7 (SCA7).   We recently documented that deletion of SGF73 dramatically extends replicative lifespan (RLS) in yeast.  To define the basis for Sgf73-mediated RLS extension, and to further explore the molecular function of Sgf73/ataxin-7 we performed ChIP-Seq for Sgf73 in yeast to identify its regions of DNA binding. The aim of the study was to uncover the underlying mechanisms controlled by Sgf73. This information will be used to understand the role of Sgf73 target genes in yeast aging pathways and possibly highlight pathways of mammalian aging regulation and SCA7 neurodegeneration in humans.

overall_design: Examination of Sgf73 occupancy in wildtype S. cerevisiae

first: Amanda

last: Mason

first: Renee

middle: M

last: Garza

first: Mark

last: McCormick

first: Brian

last: Kennedy

first: Lorraine

last: Pillus


title: ChIP-seq verifiy KDM3B recruitment on Wnt target gene promoters

city: Los Angeles

first: Cunyu

last: Wang

state: CA

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

summary: Histone demethylase Epigenetically Controls Wnt target Transcription

overall_design: Identification of genome-wide binding sites of KDM3B, and examination of H3K9me2 upon KDM3A and KDM3B depletion in HCT116 cells

first: Jiong

last: Li

first: Bo

last: Yu

first: Peng

last: Deng

first: Yongxin

first: Cun-Yu


title: Effects of narciclasine treatment on major metabolic organs of C57BL/6 mice

first: Wei

last: Xie

address: zhongguancun beidajie

institute: Tsinghua University

summary: To test the effects of narciclasine treatment on major metabolic organs of C57BL/6 mice, we first fed the mice with a high fat diet (HFD) then gavaged them with the narciclasine weekly. After 7 weeks of narciclasine treatment, the four major metabolic organs WAT, BAT, Liver and muscle were harvested and the total RNA was prepared for RNA sequencing analysis. By analyzing the RNA-seq data sets, we found that the primary target of this narciclasine is skeletal muscle.

overall_design: Examinaton of expression profile upon narciclasine trearment on different tissues

first: Sofi

last: Julien

first: Jingyi

last: Wu

first: Feng

last: Xu


title: H3K9ac occupancy of Nedd4- or control-knockdown Hep3B cells

city: New York

first: Xian

last: Zhang

address: 580 main st apt 138

institute: MSKCC

summary: H3 Nedd4

overall_design: ChIP seq using anti-H3K9ac antibody

first: Hui-Kuan

last: Lin


title: Lsd1 ChIP-Seq in trophoblast stem cells

first: Maria

last: Castex

summary: ChIP-Seq for Lsd1 in TSCs in stemness conditions

overall_design: Examination of Lsd1 chromatin localization in TSCs

first: Laura

last: Arrigoni

first: Josefina


title: Multiple targeted metabolic effects of an oriental herb medicine “Taeeumjowuitang” with transcriptional response in diet-induced obesity; comparison with green tea extract

city: Gwangju

first: Ji-Young

last: Choi

address: 30, Chosundae 3-gil, Dong-gu

department: Food and Nutrition

institute: Chosun University

summary: We investigated the effect of an oriental herbal medicine “Taeeumjowuitang” on phenotype characteristics and elucidated anti-obesity mechanism based on RNA-seq transcriptomic profiles in an obesity animal model comparison with green tea extract.

overall_design: Total RNA of epididymal adipose tissues was obtained from normal diet, high-fat diet and Taeeumjowuitang (TJ) or green tea extract (GT) added high-fat diet-fed mice and mRNA expression-associated with lipid, and glucose metabolism was measured.

first: Myung-Sook


title: Profiles of Long Noncoding RNAs in Human Naive and Memory T Cells

status: Public on Jun 11 2017

city: Nashville

first: Charles

middle: F

last: Spurlock III

state: Tennessee

address: 1161 21st Avenue South

department: Medicine

institute: Vanderbilt University School of Medicine

summary: We employed whole-genome RNA-sequencing to profile mRNAs and both annotated and novel long noncoding RNAs (lncRNAs) in human naive, central memory, and effector memory CD4+ T cells. Loci transcribing both lineage-specific annotated and novel lncRNA are adjacent to lineage-specific protein-coding genes in the genome. Lineage-specific novel lncRNA loci are transcribed from lineage-specific typical- and supertranscriptional enhancers and are not multiexonic, thus are more similar to enhancer RNAs. Novel enhancer-associated lncRNAs transcribed from the IFNG locus bind the transcription factor NF-κB and enhance binding of NF-κB to the IFNG genomic locus. Depletion of the annotated lncRNA, IFNG-AS1, or one IFNG enhancer-associated lncRNA abrogates IFNG expression by memory T cells, indicating these lncRNAs have biologic function.

overall_design: We extracted RNA from CD4+ naïve, central memory, and effector memory cell populations in healthy control subjects to assess expression levels of protein-coding and non-coding genes.

first: Guzel

last: Shaginurova

first: John

middle: T

last: Tossberg

first: Jonathan

middle: D

last: Hester

first: Nathaniel

last: Chapman

first: Yan

last: Guo

first: Philip

last: Crooke III

first: Thomas

last: Aune


title: Gene expression profiling and H3K9ac occupancy in Nedd4 knockdown Hep3B cells


title: Identification of microRNAs in response to blue light irridiation by high-throughput sequencing in Saccharina japonica

city: Qingdao

first: Wei

last: Li

state: Shandong

address: No 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Blue light (BL) is an important environmental factor that plays critical role in algae growth and development. Saccharina japonica, as a typical brown alga, showed greatly affected by BL. However, little has been known about the regulation pathway of BL response in algae. microRNAs (miRNAs) participated in great number of life process regulation and may be also involved in the BL response in plants. To identify miRNAs from S. japonica and characterize their probable roles in BL response, we sequenced and compared small RNA libraries under BL irradiation and dark conditions. 20 potential novel miRNAs were identified from S. japonica. Bioinformatics analysis of the miRNAs indicated that their potential targets were involved in various biological processes. Based on differential expression analysis and qRT-PCR experiment, some probable miRNAs related to BL responses were selected for further verification of their function, such as miR398. Our results demonstrated that miRNAs might play vital roles in metabolism of S. japonica, including BL responses.

overall_design: microRNA profiling of two samples treated by blue light (BL) and dark (DK) by high-throughput sequencing

first: Delin

last: Duan


title: Distribution of p27- and PCAF binding sites (BS) on the chromatin of HCT116 cell line

status: Public on Jun 10 2017

city: Barcelona

first: Oriol

last: bachs

address: Casanova 143

country: Spain

institute: University of Barcelona

summary: We analyzed the transcriptional programs regulated by PCAF and p27 in the colon cancer cell line HCT116 by ChIP-seq. We identified 269 protein-encoding genes that contain both p27 and PCAF binding sites being the majority of these sites different for PCAF and p27

overall_design: 4 samples were analyzed in total. 2 input samples: asynchronously growing (input PCAF) and G0 synchronized (input p27) HCT116 cells. 2 reference samples: PCAF_ChIPseq and p27_ChIPseq

last: Bachs

first: Serena

last: Orlando


title: Lipid catabolism inhibition sensitizes prostate cancer cells to antiandrogen blockade

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: Prostate cancer (PCa) is the most common malignancy among western men and the second leading-cause of cancer related deaths. For men who develop metastatic, castration-resistant PCa (mCRPC), survival is limited, making the identification of novel therapies for mCRPC critical. Deficient lipid oxidation via carnitine palmitoyltransferase (CPT1) results in decreased growth and invasion, underscoring the role of lipid catabolism to fuel PCa growth. In fact, the CPT1A isoform is abundant in PCa, especially in those with high-grade tumors. Since lipid oxidation is stimulated by androgens, we have evaluated the synergistic effects of combining CPT1A inhibition and anti-androgen therapy. Mechanistically, we have found that decreased CPT1A expression is associated with decreased AKT content and activation, likely driven by a breakdown of membrane phospholipids and activation of the INPP5K phosphatase. This results in increased AR content and increased sensitivity to the anti-androgen enzalutamide. To better understand the clinical implications of this findings, we have evaluated fat oxidation inhibitors (etomoxir, ranolazine and perhexiline) in combination with enzalutamide in PCa cell models. We have observed a robust inhibitory effect of the combinations, including in enzalutamide-resistant cells and mouse TRAMPC1 cells, a more neuroendocrine PCa model. Lastly, using a xenograft mouse model, we have observed decreased tumor growth with a systemic combination treatment of enzalutamide and ranolazine. In conclusion, our results show that improved anti-cancer efficacy can be achieved by co-targeting the AR axis and fat oxidation via CPT1A, which may have clinical implications, especially in the mCRPC setting.

overall_design: Prostate cancer LNCaP cells with two different shRNAs for CPT1A were compared to non-targetting  shRNA controls.

middle: W

last: Flaig

first: Maren

last: Salzmann-Sullivan

first: Lih-Jen

last: Su

first: Zhiyong

last: Zhang

first: Molishree

last: Joshi

first: Miguel

middle: A

last: Gijon

middle: J

last: Arcaroli

first: Adrie

last: van Bokhoven

first: Lucia

last: La Rosa

first: Isabel

last: Schlaepfer


title: Trophoblast stem cells (TSC) global transcriptome in stemness conditions after treatment with Lsd1 inhibitor or induction of Lsd1 depletion [RNA-seq]

first: Maria

last: Castex

summary: RNA-Seq for  Lsd1-deficient TSCs or treated with Lsd1 inhibitor for 24hrs

overall_design:
TSC were treated with Lsd1 inhibitor or DMSO in stemness conditions for 24hrs; media and inhibitor where replaced every 12hrs along the duration of the experiment; 2 replicates were used for treatment  together with 2 control replicates in stemness; DFKZ genomics and proteomics.

Please note that strain and targeting strategy had been described in the previous PMID: 24448552 publication

first: Günthger

last: Thomas

first: Castex

last: Josefina


title: Genomic Regulation of Invasion by STAT3 in Triple Negative Breast Cancer

city: Huntsville

first: Joy

last: Agee

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Breast cancer is a heterogeneous disease comprised of four molecular subtypes defined by whether the tumor-originating cells are luminal or basal epithelial cells. Breast cancers arising from the luminal mammary duct often express estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth receptor 2 (HER2). Tumors expressing ER and/or PR are treated with anti-hormonal therapies, while tumors overexpressing HER2 are targeted with monoclonal antibodies. Immunohistochemical detection of ER, PR, and HER2 receptors/proteins is a critical step in breast cancer diagnosis and guided treatment. Breast tumors that do not express these proteins are known as  “triple negative breast cancer” (TNBC) and are typically basal-like. TNBCs are the most aggressive subtype, with the highest mortality rates and no targeted therapy, so there is a pressing need to identify important TNBC tumor regulators. The signal transducer and activator of transcription 3 (STAT3) transcription factor has been previously implicated as a constitutively active oncogene in TNBC. However, its direct regulatory gene targets and tumorigenic properties have not been well characterized. By integrating RNA-seq and ChIP-seq data from 2 TNBC tumors and 4 cell lines, we discovered novel gene signatures directly regulated by STAT3 that were enriched for processes involving inflammation, immunity, and invasion in TNBC.  Functional analysis revealed that STAT3 has a key role regulating invasion and metastasis, a characteristic often associated with TNBC. Our findings suggest therapies targeting STAT3 may be important for preventing TNBC metastasis.

overall_design: ChIP-seq and RNA-seq experimentation were performed in TNBC cell lines: HCC70, MDA-MB-231, MDA-MB-468, MDA-MB-157, HCC1143.  ChIP-seq was performed after 1hr vehicle control indcution (ethanol).  RNA-seq was performed after 96hr knockdown of STAT3 or non-targeting siRNA.  Tissue ChIP-seq was performed in two TNBC tumor samples: A139 and A137.

first: R

last: Myers


title: Globally construct ceRNA regulation network based on comparison with SHEE and SHEEC cell lines (RNA-Seq)

city: Luoyang

first: Jiachun

last: Sun

state: Henan

address: 24 Jinghua road, Jianxi district

institute: Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology

summary: Long non-coding RNAs (lncRNAs), new star ncRNA class of mRNA-like transcripts, play complicate and critical roles in regulating various key biological processes including chromatin modification, transcription and post-transcriptional processing. Remarkably, some lncRNAs serve as a miRNA “sponge” to inhibit mediation of the differentiation of miRNA target in post-transcriptional regulation. Here, we firstly constructed the putative ceRNA network by integrating lncRNAs, miRNAs and mRNAs expression in compared with SHEE and SHEEC cell lines based on the high-though RNA sequencing data and microarray data. Though the biology function analysis, the result showed that ceRNA network mainly participate in PI3K-Akt pathway and may play a modulating role in regulation of essential signal molecules including SYK, FGF11, IL7R, MET, LAMB3, PRS6KB1, ITGB6, ITGB4, ITGA2, ITGA6, EPHA2, SOS2, VEGFA, GRB2, KRAS, CCDN1 and TP53 in primary ESCC. These results could provide us more essential clues for the development of novel therapeutic strategies and efficient drugs target in primary ESCC.

overall_design: The SHEEC and SHEE cell lines were pooled with 5 cell lines respectively.


title: RISC factor MOV10 is required for normal development and viability in both mouse and Xenopus

city: Urbana

first: Stephanie

last: Ceman

address: 601 S. Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois-Urbana Champaign

summary: MOV10 is an RNA helicase that functions in the miRNA pathway. Our study shows that a knockdown of MOV10 in mouse is embryonic lethal. To determine the cause of this developmental phenotype, we knocked down maternal MOV10 in Xenopus eggs at the one cell stage. We observe a defective Maternal to Zygotic Transition (MZT) phenotype in the MOV10 knockouts that leads to abnormal neural tube formation. We are carrying out this RNA seq in order to ascertain the mRNA changes caused on maternal MOV10 knockdown

overall_design: The analysis includes 5 samples. Three of these are control morpholino injected stage 10.5 embryos. The remaining 2 are MOV10 morpholino treated embryos from the same stage. The samples are biological replicates.

first: Geena

last: Skariah


title: Genome-wide binding profile of Dlx5 in mouse T cell lymphoma

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

summary: Homeobox gene Dlx5 induces T-cell lymphoma in transgenic mice. To find the target oncogene implicated in this lymphoma genesis, we immunoprecipitated Dlx5 and sequenced the bound DNA fragments.

overall_design: ChIP using a MycTag anbibody which binds to MycTagged Dlx5 protein

first: Yinfei

last: Tan

first: Joseph

last: Testa


title: Oncogene-Expressing senescent melanocytes upregulate MHC Class II, re-localize to the lymph nodes and activate T cells

status: Public on Jun 09 2017

city: Glasgow

first: Neil

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

summary: OIS is characterized by a stable proliferation arrest and secretion of pro-inflammatory cytokines and chemokines, the senescence-associated secretory phenotype (SASP). Proliferation arrest and the SASP collaborate to enact tumor suppression, the former by blocking cell proliferation and the latter by recruiting immune cells to clear damaged cells. However, the interactions of OIS cells with the immune system are still poorly defined. Here we show that engagement of OIS in primary human melanocytes, specifically by melanoma driver mutations NRASQ61K and BRAFV600E, causes expression of the MHC class II antigen presentation apparatus, via secreted IL1ß signaling and expression of CIITA, a master regulator of MHC class II gene transcription.

overall_design: We quantify transcription via high throughput RNA sequencing in nevus melanocytes in cross FVB/NJ mice with Cre inducible NRAS61K  with an MHCII cross

first: John

last: van Tuyn

first: Farah

last: Jaber-Hijazi

first: Douglas

last: Mackenzie

last: Cole

first: Simon

last: Milling

first: Peter

last: Adams


title: Small RNA-sequencing from apple in phase transition

city: college station

first: Xiuren

last: Zhang

address: 2123 tamu

department: biochemistry & biophysics

institute: texas a&m university

summary: We performed Illumina sequencing of sRNA libraries prepared from juvenile and reproductive phase buds from the apple trees. A large number of sRNAs exemplified by 33 previously annotated miRNAs and 6 novel members displayed significant differential expression (DE) patterns in juvenile and reproductive stages. The study provides new insight into our understanding of fundamental mechanism of poorly studied phase transitions in apple and other woody plants and important resource for future in-depth research in the apple development.

overall_design: Juvenile phase buds and Reproductive phase buds

first: Xinwei

last: Guo

first: Zeyang

last: Ma

first: Zhonghui

first: Lailiang

last: Cheng

first: Tianhong

last: Li


title: hnRNP Q1 targeting RNA in colorectal cancer cell line SW480

city: Tainan

first: Liang-Yi

last: Hung

address: No.1, University Rd.

department: Institute of Bioinformatics and Biosignal Transduction

country: Taiwan

institute: National Cheng Kung University

summary: In order to study the potential targeting RNA of hnRNP Q1 in colorectal cancer, RNA immunoprecipitation were used for collecting hnRNP Q1-associated RNA.

overall_design: GFP-tag hnRNP Q1 were overexpressed in SW480 cells, then the cytoplasmic lysate was harvested for RNA immunoprecipitation by anti-GFP antibody. Total RNA was extracted from immunoprecipitate and submitted for RNA-seq.

first: Chien-Hsien

last: Lai


title: Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1

city: Cambridge

first: Amy

last: Keating

state: Massachusetts

department: Biology and Biological Engineering

institute: Massachusetts Institute of Technology

summary: We used computational models to design focused combinatorial libraries to identify BH3 peptides that bind tightly and selectively to Bfl-1. The final library was predicted to be Bfl-1 selective by PSSMSPOT and STATIUM (DeBartolo et. al. J Mol Biol. 2012). As a design control, we designed similar libraries to be selective for Bcl-xL and Mcl-1. The libraries were transformed into yeast for surface display, pooled, and screened for tight and selective binding to Bfl-1. Five rounds of positive, negative, and/or competition FACS screening were used to isolate cells that expressed the tightest and most selective peptides. To analyze enrichment trends and to assess the success of our library design, we deep sequenced samples from the naïve pool and from pools collected after 3, 4, 5, and 6 rounds of sorting. Additional detail is available in our corresponding publication.

overall_design: DNA samples from yeast-surface display peptide libraries were deep sequenced before and after screening for Bfl-1 selective binding using Illumina NextSeq.

first: Justin

last: Jenson


title: ALOX5 exhibits anti-tumor and drug-sensitizing effects in MLL-rearranged leukemia

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: MLL-rearranged acute myeloid leukemia (AML) remains a fatal disease with a high rate of relapse and therapeutic failure due to chemotherapy resistance. In analysis of our Affymetrix microarray profiling of human AML and normal control samples, we found that ALOX5 is especially down-regulated in MLL-rearranged AML. Our colony forming/replating and bone marrow transplantation (BMT) assays showed that Alox5 exhibited a moderate anti-tumor effect both in vitro and in vivo. Strikingly, leukemic cells with Alox5 overexpression showed a significantly higher sensitivity to the standard chemotherapeutic agents, i.e., doxorubicin (DOX) and cytarabine (Ara-C). The drug-sensitizing role of Alox5 was further confirmed in human and murine MLL-rearranged AML cell models in vitro, as well as in the in vivo MLL-rearranged AML BMT model coupled with treatment of “5+3” (i.e. DOX plus Ara-C) regimen. Our RNA-seq analysis showed that Stat and K-Ras signaling pathways were negatively correlated with Alox5 overexpression in MLL-AF9-leukemic blast cells, implying targeting those pathways likely contributes to Alox5’s functions. Collectively, our work shows that ALOX5 plays a moderate anti-tumor role and functions as a drug sensitizer, with a therapeutic potential, in MLL-rearranged AML.

overall_design: To delineate the potential molecular mechanism underlying the anti-tumor and drug-sensitizing effects of Alox5, we performed RNA sequencing (RNA-seq) of two pairs (4 samples) of mouse BM leukemic blast cells collected from the MA9_Ctrl and MA9_Alox5 mice in secondary BMT assays.

first: Lei

last: Dong


title: Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of BET inhibitor JQ1

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: We analyzed anti-proliferative dominant-negative Brd4 mutants that compete with the function of distinct Brd4 domains. We used these Brd4 mutants to compare the Brd4-specific transcriptome with the transcriptome of JQ1 treated cells.

overall_design: We performed polyA RNA-seq of Raji cells expressing Brd4 constructs f3 and f9 (dnBrd4_f3/f9) and Raji cell expressing the luciferase control vector treated with JQ1 (luc_JQ1) or DMSO as control (luc_DMSO).

first: Tim-Michael

last: Decker

first: Michael

last: Kluge

first: Stefan

last: Krebs

first: Nilay

last: Shah

first: Helmut

last: Blum

middle: C

first: Dirk

last: Eick


title: Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment

city: santiago

first: Romilio

last: Espejo

state: REGIÓN METROPOLITANA

address: C Antunez 2243, providencia

country: Chile

institute: University of Chile

summary: Using high-throughput sequencing of RNA obtained from triplicate samples, we compared the differential gene expression of V. parahaemolyticus when growing at 37°C, 0.9% NaCl, and 0.04% bile salts with that at 12°C, 3% NaCl without bile salts, a condition similar to that prevailing in the ocean.

overall_design: Examine differential expression in to two different condition (six samples)

first: Katherine

last: Garcia

first: Cristian

last: Yáñez

first: Nicolás

last: Plaza

first: Francisca

last: Peña

first: Pedro

last: Sepulveda

first: Diliana

last: Perez


title: The long noncoding RNA SPRIGHTLY acts as an intra-nuclear organizing hub for pre-mRNA molecules.

city: St. Petersburg

first: Bongyong

last: Lee

state: Florida

address: 501 6th Ave S

institute: The Johns Hopkins University

summary: We report the application of domain-specific chromatin isolation by RNA purification (dChIRP) to identify RNA binding partners of long coding RNA, SPRIGHTLY. We demonstrate by SHAPE-Seq and dChIRP that SPRIGHTLY RNA secondary structure has a core pseudo-knotted domain. This lncRNA interacts with the intronic regions of six pre-mRNAs: SOX5, SMYD3, SND1, MEOX2, DCTN6, and RASAL2, all of which have cancer related functions. Hemizygous knockout of SPRIGHTLY by CRISPR/Cas9 in melanoma cells significantly decreases SPRIGHTLY lncRNA levels, simultaneously decreases the levels of its interacting pre-mRNA molecules, decreases anchorage-independent growth rate of cells, and the rate of in vivo tumor growth in mouse xenografts. These results provide the first demonstration of a lncRNA’s 3-dimensional coordinating role in facilitating cancer-related gene expression in human melanomas.

overall_design: Three sets of probes corresponding to three regions of SPRIGHTLY were desiged to pull-down target RNA SPRIGHTLY. Melanoma cell line, A375, cells were treated with 0.3% formaldehde. Chromatin were prepared and subjected to pull-down with three sets of probes separately. Pull-downed RNAs were extracted and subjected to RNA-sequencing using a HiSeq 2500 (Illumina).

first: Ranjan

last: Perera


title: Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

summary: We undertook four mammalian transcriptomics experiments to compare the effect of read mapping, feature counting and differential expression analysis using single-end (SE) and paired-end (PE) protocols. For three of these experiments we also compared a non-stranded (NS) and a strand-specific approach to mapping the paired-end data.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Each of the four RNA-Seq experiments had a simple but typical design, comprised of three biological controls and three treated samples. The six samples in each of the experiments were independent biological replicates. Experiments 1 and 2 were from mouse tissue or primary cells whereas Experiments 3 and 4 involved human primary cells and a cell line respectively.  In all four experiments sequencing was performed on both ends of the cDNA fragment (paired-end reads). We mapped both ends (see Methods) to produce our paired-end data set (PE data). We also mapped only the first read to produce our single-end read datasets for each experiment (SE data).  Sequencing for Experiment 1 occurred in 2012 and used a non-strand-specific protocol for library preparation (Illumina TruSeq kit). The other three experiments were sequenced more recently with the Illumina TruSeq Standed library preparation kit [13]. For these three experiments we looked at the effect of analyzing the paired-end data with a protocol that recognizes the strand-specific nature of the reads (PE data) and also with a protocol that does not recognize this (NS data). In this way we could assess the difference that a strand-specific protocol makes to gene expression analysis.

first: Karen

last: MacKenzie

first: Zara

last: Ali

first: Annemiek

last: Beverdam

first: Veroinica

last: Mendoza Reinoso

first: Louise

last: Roddam

first: Phoebe

last: Griffin

first: Joanne

last: Pagnon

first: Marc

last: Wilkins


title: PPARD is a critical inhibitor of cartilage growth in external ears [RNA-Seq]

city: Nanchang

first: Yanyu

last: Dean

address: Lushanzhong888, Changbei district

institute: Jiangxi Agricultural University

summary: In this study, we uncover the molecular mechanism that PPARD transactive-deficient pigs have large-eared feature. Evidently from this work, PPARD plays a vital role on inhibiting cartilage growth by regulating the transcription of critical genes for chondrogenesis in ligand dependent manner; the activation of sPPARD speeds up apoptosis in CSPCs, terminal differentiation of chondroblasts and matrix degradation in auricular cartilage. The transactive-deficient PPARD has not the capability to slow down cartilage growth and consequently causes that ear size of carried animals increases at a high growth rate. As the role of PPARD in cartilage is similar in pigs, mice and humans, and since cartilage development is well-conserved in animals, our data helps to better understanding of cartilage development and treatment of cartilage-related diseases.

overall_design: Auricular cartilage primary cells  were obtained from external ears of a 4-month-old Duroc × (Landrace × Large White) hybrid pig  (DLL pig) with the wild-type PPARD using enzymatic digestion. Cells were incubated with PPARD agonist (GW0742) and DMSO (as a control) for 24 hours, then total RNA were extracted and generated by deep sequencing, in triplicate, using Ion proton sequencer.

first: Zhen

last: Zhang

last: Duan

first: Zhongping

last: Wu

first: Hui

first: Lusheng

last: Huang

first: Jun

last: Ren


title: Rpph1 regulated Cdc42 and modulated hippocampal pyramidal neurons by competing endogenous miR-330-5p

city: Shenzhen

first: Yifei

last: Cai

address: No. 1120 Lianhua Road

institute: Shenzhen Peking University the Hong Kong University of Science and Technology Medical Center

summary: To build up competing endogenous RNA regulatory network based on APP/PS1 transgenic mice model and verify Rpph1, miR-330-5p and Cdc42 interaction

overall_design: Cortex samples were isolated from two pairs of APP/PS1 transgenic mice and wild type mice control

first: Ziling

last: Sun

first: Hongxue

last: Luo

first: Xiaoyang

last: Ye

first: Qi

first: Yanfen

last: Zou

last: Wan


title: Serum miRNAs from Drug-induced liver injury, Hepatitis B, Liver cirrhosis and Type 2 Diabetes patients

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

summary: The dataset comprises of circulating miRNAs in human subjects with various types of liver impairments. In our study, we analyzed a total 48 serum samples from a group of 42 subjects that included  subjects with accidental acetaminophen overdose (APAP), hepatitis B infection (HBV), liver cirrhosis (LC) and type 2 diabetes mellitus (T2DM) subjects with alanine amino transference (ALT) elevation. As a control 16 sex and age matched healthy controls from subjects with no evidence of liver disease were analyzed. The miRNA profiles were measured using next-generation sequencing platform.

overall_design: small RNA profiles of serum form 3 APAP patients, 9 LC patients, 7 HBV patients, 7 T2DM patients with ALT elevation and 16 healthy control (HC) subjects

first: Jos

last: Kleinjans


title: Genome-scale Activation Screen Identifies a LncRNA Locus Regulating a Gene Neighborhood [RNA-Seq]

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

summary: The mammalian genome contains thousands of loci that transcribe long noncoding RNAs (lncRNAs), some of which are known to play critical roles in diverse cellular processes through a variety of mechanisms. While some lncRNA loci encode RNAs that act non-locally (in trans), emerging evidence indicates that many lncRNA loci act locally (in cis) to regulate expression of nearby genes—for example, through functions of the lncRNA promoter, transcription, or transcript itself. Despite their potentially important roles, it remains challenging to identify functional lncRNA loci and distinguish among these and other mechanisms. To address these challenges, we developed a genome-scale CRISPR-Cas9 activation screen targeting more than 10,000 lncRNA transcriptional start sites (TSSs) to identify noncoding loci that influence a phenotype of interest. We found 11 novel lncRNA loci that, upon recruitment of an activator, each mediate BRAF inhibitor resistance in melanoma. Most candidate loci appear to regulate nearby genes. Detailed analysis of one candidate, termed EMICERI, revealed that its transcriptional activation results in dosage-dependent activation of four neighboring protein-coding genes, one of which confers the resistance phenotype. Our screening and characterization approach provides a CRISPR toolkit to systematically discover functions of noncoding loci and elucidate their diverse roles in gene regulation and cellular function.

overall_design: RNA-seq on A375 cells overexpressing candidate lncRNA or protein-coding gene.

first: Feng


title: PPARD is a critical inhibitor of cartilage growth in external ears

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

overall_design: Refer to individual Series


title: RNA sequencing to identify common targets for regulation of cognition

city: Miami

first: Eleonore

last: Beurel

state: FL

address: 1011 NW 15th Street Gautier room 415

department: Psychiatry

institute: University of Miami, Miller School of Medicine

summary: siRNA  BDNF and siRNA HDAC4 treatment impaired cognition

overall_design: mice were treated with siRNA for BDNF or HDAC4, and sacrificed, RNA were extracted from hippocampus and analyzed using RNA-seq

first: Richard

last: Jope


title: Transcriptional profile of human iPSC and HIOs with APC mutations

city: Boston

first: Ignacio S.

last: Caballero

address: 620 Albany St., NEIDL 401V

department: NEIDL/Microbiology

institute: Boston University School of Medicine

summary:
Background and Aims: mutations in the gene Adenomatous Polyposis Coli or APC appear in most sporadic cases of colorectal cancer and it is the most frequent mutation causing hereditary Familial Adenomatous Polyposis. The detailed molecular mechanism by which APC mutations predispose to the development of colorectal cancer is not completely understood. This is in part due to the lack of accessibility to appropriate models that recapitulate the early events associated with APC mediated intestinal transformation.
Methods: we have established a novel platform utilizing human induced Pluripotent Stem cells or iPSC from normal or FAP-specific APC mutant individuals and evaluated the effect of the mutation in the cells before and after differentiation into intestinal organoids. In order to minimize genetic background effects we also established an isogenic platform using TALEN-mediated gene editing.
Results: comparison of normal and APC mutant iPSC revealed a significant defect in cell identity and polarity due to the presence of APC in heterozygosity as well as chromosomal aberrations including abnormal anaphases and centrosome numbers. Importantly, upon specification into intestinal progeny, APC heterozygosity was responsible for a major change in the transcriptional identity of the cells with dysregulation of key signaling pathways, including metabolic reprogramming, abnormal lipid metabolism and intestinal-specific cadherin expression.
Conclusions: we have developed a novel iPSC/intestinal model of APC mutagenesis and provide strong evidence that APC in heterozygosity imparts a clear phenotypic and molecular defect, affecting basic cellular functions and integrity, providing novel insights in the earlier events of APC-mediated tumorigenesis.

overall_design: Four independent biological replicates of each (APC+/+ vs APC+/-) were analyzed in triplicates, before and after differentiation into intestinal organoids, for a total of 48 samples

first: Cesar

last: Sommer

first: Francisco

last: Molina-Estevez

first: Amalia

last: Capilla Villanueva

first: Nicholas

last: Skvir

first: Sanjib

last: Chowdhury

first: Gustavo

last: Mostoslavsky


title: PPARD is a critical inhibitor of cartilage growth in external ears [ChIP-Seq]

first: Yanyu

last: Dean

overall_design: Examination of PPARD binding sites in auricular-derived primary cartilage cells from a 4-month-old Duroc × (Landrace × Large White) hybrid pig  (DLL pig).

first: Zhen

last: Zhang

last: Duan

first: Zhongping

last: Wu

first: Hui

first: Lusheng

last: Huang

first: Jun

last: Ren


title: Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [ChIP-exo]

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

summary: A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the defense system for osmotic stress in bacteria. However, its full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level under OmpR knock-out condition. We find that OmpR tends to regulate mostly membrane-located gene products of diverse fundamental biological processes, such as narU, ompX, and nuoN. Investigating co-regulation of entire set of genes regulated by other stress-response TFs unveils that they are surprisingly independently regulated by TF(s) responding to each stress. Additionally, detailed investigation of physiological roles of newly discovered OmpR regulon reveals that activation of narU encoding nitrate/nitrite transporter is a relatively unique strategy of E. coli K-12 MG1655 to significantly improve cellular tolerance toward osmotic stress.

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

overall_design: A total of two samples were analyzed. ompR-8myc tagged cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation.

first: Sang-Woo

last: Seo


title: ALG-5 is a miRNA-associated Argonaute required for proper developmental timing in the Caenorhabditis elegans germline

city: FORT COLLINS

first: Taiowa

last: Montgomery

state: CO

address: 1878 Campus Delivery

institute: Colorado State University

summary: Caenorhabditis elegans contains twenty-five Argonautes, of which, only ALG-1 and ALG-2 are known to interact with miRNAs. ALG-5 belongs to the AGO subfamily of Argonautes that includes ALG-1 and ALG-2, but its role in small RNA pathways is unknown. We analyzed by high-throughput sequencing the small RNAs associated with ALG-5, ALG-1, and ALG-2, as well as changes in mRNA expression in alg-5, alg-1, and alg-2 mutants.

overall_design: We analyzed by high-throughput sequencing miRNA-Argonaute interactions in C. elegans and their impact on mRNA levels. The data in this series includes mRNA sequencing of loss-of-function mutants, small RNA sequencing of loss-of-function mutants, and sequencing of small RNAs that co-immunoprecipitate with each Argonaute protein.

first: Kristen

last: Brown

first: Joshua

last: Svendsen


title: RNA-seq analysis of differential gene expression in rumen papillae from Holstein Friesian bulls undergoing diet restriction and compensatory growth

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: The objective of this study was to examine the effect of dietary restriction and subsequent re-alimentation induced compensatory growth on the global gene expression profile of ruminal epithelial papillae. Holstein Friesian bulls (n=38) were assigned to one of two groups: restricted feed allowance (RES; n=19) for 125 days (Period 1) followed by ad libitum access to feed for 55 days (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n=19).  All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependent on each treatment group. At the end of Period 1, 9 animals from each treatment group were slaughtered, with 10 animals from each treatment slaughtered at the end of Period 2. Rumen epithelium was collected from all animals within thirty minutes of slaughter. RNA was extracted and rumen epithelium gene expression was examined using RNAseq technology on all samles collected (end of Period 1: 9 samples each from ADLIB and RES groups; end of Period 2: 10 samples each from ADLIB and RES groups). Genes identified as differentially expressed in response to both dietary restriction and subsequent compensatory growth included those involved in processes such as cellular interactions and transport, protein folding and gene expression, as well as immune response. This information can be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction.

overall_design:
38 rumen epithelium RNA samples were analyzed in total.
Purebred Holstein Friesian bulls were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=9) followed by ad libitum access to feed for a further 55 days (n=10) or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=19).  The first 125 days of the trial were denoted as Period 1, during which treatment groups were fed differentially. The subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial, with the amount of feed provided different dependent on each treatment group. Restricted fed animals were fed to grow at 0.6 kg /day during Period 1, with ad libitum animals expected to gain in excess of 1.5 to 2 kg/day.

first: Sinead

last: Waters

first: Paul

last: Cormican

first: Alan

last: Kelly

first: Emma

last: O'Shea

first: David

last: Kenny


title: Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]

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

overall_design: A total of four samples were analyzed. WT and ΔompR  mutant cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation.


title: Changes in Gene Expression between Soybean F1 Hybrids and their Parents are Associated with Agronomically Valuable Traits

city: Raleigh

first: Earl

middle: William

last: Taliercio

state: NC

address: 3127 Ligon St

institute: USDA/ARS

summary: Gene expression of the F1 Hybrids between two soybean parents (NMS4-44-329 and N7103) were compared. Changes in gene expression were correlated with agronomic traits.

overall_design: RNA was isolated from leaf matrial harvested from the field in july of 2015. Four replicates were grown at two location in a random complete block design. Each samples is represented from three or four replications form each location


title: Menin Enhances c-Myc-mediated Transcriptional Activity To Promote Cancer Progression

city: Hefei

first: Ping

last: Gao

state: Anhui

address: Huangshan Road 443

department: Innovation Center for Cell Biology

institute: School of Life Science, University of Science and Technology of China

summary: MYC is a master regulator of transcription in growing cells. Menin is an enigmatic protein that displays unique ability to either suppress or promote tumorigenesis in a context dependent manner. It's interesting to ask is there any relationship between MYC and menin.Here, we used RNA-seq to study global transcriptomic expression of MYC or MEN1 knockdown HT1080 cells to investigate whether there are any correlations between MYC- and menin- regulated gene expression. Besides, we performed ChIP-seq assays for MYC and Menin binding sequences to address whether Menin and MYC share some common binding sites on chromatin.

overall_design: Human fibrosarcoma HT1080 cells were transfected with MYC shRNAs, MEN1 shRNAs or non-targeting control shRNA followed by RNA extraction and sequenced on Illumina HiSeq 4000 (Homo sapiens). And also we performed MYC ChIP-seq and Menin ChIP-seq to address whether Menin and MYC share some common binding sites on chromatin.RNA Pol II ChIP-seq for NTC and shMEN1 HT1080 cell samples were used to study the effect of Menin on RNA Pol II-mediated elongation.

first: Gongwei

first: Shenqi

last: Shen

first: Huafeng

last: Zhang


title: Multi-site Neurogenin3 phosphorylation controls pancreatic endocrine differentiation: transcriptomic analysis of pancreatic organoids overexpressing wild type and phosphomutant Neurogenin3

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: The proneural transcription factor Neurogenin3 (Ngn3) plays a critical role in pancreatic endocrine cell differentiation. While previous studies have focused on Ngn3 gene function, little is known about the regulation of Ngn3 protein.  Here we demonstrate that Ngn3 protein undergoes cyclin-dependent kinase (cdk)-mediated phosphorylation on multiple serine-proline sites. Replacing wild-type protein with a phosphomutant form of Ngn3 increases α-cell generation, the earliest endocrine cell type to be formed in developing pancreas. Mechanistically, preventing multi-site phosphorylation enhances Ngn3 stability and DNA binding, and promotes the expression of target genes that drive differentiation. In addition to perturbing embryonic endocrine differentiation, un(der)phosphorylated Ngn3 contributes to maintaining adult β-cell differentiation in the presence of pro-proliferation cue. Here we perform transcriptomic analysis of a low number of pancreatic organoid cells expressing wild type and phosphomutant Ngn3. Analysis of the endocrine differentiation programme activated by Ngn3 in this context revealed the cell fate plasticity of the system and demonstrated that preventing Ngn3 phosphorylation enhances endocrine gene expression.

overall_design: RNA-sequencing of pancreatic organoid infected with GFP-WT Ngn3 and GFP-6S-A Ngn3 (phosphomutant version of Ngn3) at 2days and 8days after induction. Control: GFP only. Samples at 2days: 3 biological replicates and 6 technical replicates. Samples at 8days: 3 biological replicates and 1-2-3 technical replicates depending on the sample

first: Roberta

last: Azzarelli

first: Sonia

last: Nestorowa

first: Steffen

last: Rulands

first: Berthold

last: Gottgens

first: Philpott

last: Anna


title: Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655

first: Donghyuk

last: Kim


title: Gene expression profiling of papillary thyroid cancer from central and invasive regions

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

institute: Ajou University School of Medicine

summary: We analyzed the gene expression profile of papillary thyroid cancer from central and invasive regions.

overall_design: Examination of 3 different papillary thyroid cancer groups and analysis of each group between central and invasive regions.

first: Tae

first: Young

middle: H


title: BMP (Bone morphogenetic protein) signaling network regulates mesenchymal stem cell lineage commitment during tooth development

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

summary: Mesenchymal stem cells (MSCs) are multipotent progenitor cells present in various mesenchymal tissues that undergo strict lineage-specific differentiation programs, faithful to their unique tissue origins. However, the key regulators that activate dental pulp MSC commitment to odontogenesis remain unclear. In this study, we utilized an inducible Cre/loxP system to interrupt BMP signaling in apical MSCs at the onset of molar root formation in order to investigate the functional requirement for BMP signaling and its downstream targets in MSC cell fate determination during tooth morphogenesis.

overall_design: mRNA profiling of  MSC to study role of BMP signaling in tooth morphogenesis

first: Jifan

last: Feng

first: Junjun

last: Jing

first: Jingyuan

last: Li

first: Hu

last: Z

first: Tingwei

first: Xu

last: T

first: Yang

last: Chai


title: RNA sequencing reveals differential expression of genes associated with an altered morphology of rumen papillae in lactating dairy cows fed diets with various forage sources

city: Hangzhou

first: Diming

last: Wang

address: 866 yuhangtang RD

institute: Zhejiang University

summary: Total RNA from rumen epithelial tissues of cows fed alfalfa hay (AL),Rice straw (RS) or Corn stover (CS)diet were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR.

overall_design: We performed a differential analysis of transcriptomes of rumen epithelial tissues collected from cows fed AL, RS or CS diets, to study molecular mechanisms of forage source changing rumen papillae thickness and shape.

first: G

last: Leluo

first: D


title: Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours [RNA-seq]

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

summary: Here we compared the performance of Affymetrix HTA 2.0 microarray and Illumina 2000 RNA-sequencing techniques on the clinical samples collected from patients with lung squamous cell carcinoma.

overall_design: Comparison of transcriptome (9 tumor and 9 adjacent tissue samples) in RNA-seq and microarray.

first: Petr

middle: V

last: Nazarov

first: Tony

last: Kaoma

first: Nathalie

last: Nicot

first: Christelle

last: Ghoneim

first: Laurent

last: Vallar


title: Genome and transcriptome profiling of fibrolamellar carcinoma [RNA-Seq]

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare variant of HCC that most frequently affects young adults. Because of its rarity and an absence of preclinical models, the molecular biology of FL-HCC remains unclear. Our objective was to analyze chromosomal alterations and dysregulated gene expression in tumor specimens collected at a single center during two decades of experience with FL-HCC.

overall_design:
We analyzed 38 specimens from 26 patients by array comparative genomic hybridiziation (aCGH) and 35 specimens from 16 patients by transcriptome sequencing (RNA-seq).
This submission represents transcriptome component of study.

first: Eric

last: Sorenson

first: Raya

last: Khanin

first: Zubin

last: Bamboat

first: Michael

last: Cavnar

first: Teresa

middle: S

last: Kim

first: Eran

last: Sadot

first: Shan

last: Zeng

first: Jonathan

middle: B

last: Greer

first: Adrian

last: Seifert

first: Noah

last: Cohen

first: Megan

last: Crawley

first: Benjamin

last: Green

first: David

last: Klimstra

first: Ronald

middle: P

last: DeMatteo


title: Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours

first: Arnaud

last: Muller


title: Identification and Characterization of a Class of MALAT1-like Genomic Loci

status: Public on Jun 08 2017

city: Dunedin

first: Sarah

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary: The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a non-coding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using a RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3’-end triple helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a coevolution of the 3’-end module. MALAT1-like genes in Anolis carolinensis are highly expressed in adult testis, thus we named them testis-abundant long noncoding RNAs (tancRNAs). TancRNA loci produce multiple small RNA species, including piRNAs, from the antisense strand. The coevolved 3’-end of tancRNAs serve as potential targets for the PIWI-piRNA complex. Thus, we have identified an evolutionarily conserved class of lncRNAs with similar structural constraints, post-transcriptional processing, subcellular localization and a distinct function in spermatocytes.

overall_design: 4 RNA-Seq datasets analyzing gene expression in Anolis carolinensis. NSR-Seq of brain and testis, small RNA-Seq of testis (19-33 nt), small RNA-Seq of testis (52-68 nt).

first: Bin

last: Zhang

middle: L

last: Spector


title: Transcriptomes of 102 soybean accessions

city: Athens

first: Scott

middle: A.

last: Jackson

state: Georgia

address: 111 Riverbend Rd.

department: Center for Applied Genetic Technologies

institute: University of Georgia

summary: A comparison of RNA expression profiles across a diverse set of soybean genotypes

overall_design: RNA-seq of 41 soyNAM parental lines and 61 milestone cultivars

first: Kyung-Do

first: Robert

last: Schmitz


title: Integrating transcriptome and proteome profiles of prenatal muscle tissue to reveal the postnatal growth differences in pigsof Pig Muscle Tissue

city: Beijing

first: Liyuan

last: Wang

state: China

address: No.2 of Yuanmingyuan West Road, Haidian District

department: Animal Sciencie and Technology

institute: China Agricultura University

summary: We using RNA sequences (from RNA-seq) from the prenatal muscle tissues of three pig breeds (Tibetan pig [TP], Wujin pig [WJ], and Large White pig [LW]) were analyzed to compare the differentially expressed genes related to embryonic myogenesis and to identify the genes related to postnatal growth rate and growth potential in pigs. We obtained 38.7-50.1 million clean data through the RNA-seq and detected that 19,626 genes were positively expressed and 13,660 of them were co-expressed in the muscle tissues of the four samples. The 3,626 unique DEGs in TP were mainly enriched in 76 GO terms and 35 KEGG pathways.The GO terms mainly included ATP binding, calcium ion binding, negative regulation of transcription from RNA polymerase II promoter, and cell components of cytoplasm, nucleus, and extracellular exosome . The top 20 KEGG pathways mainly included metabolic, insulin signaling, FoxO signaling, and AMPK signaling pathways that are mostly involved in muscle development and growth.

overall_design: RNA sequences from the tissues of  embryonic longissimus dorsi muscle of  three pig breeds (Tibetan pig [TP], Wujin pig [WJ], and Large White pig [LW]) were examined using HiSeq 4000.

first: Peng

last: Shang

first: Zhixiu

first: Hao


title: FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers [RNA-seq]

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

summary: This work sought to identify endothelial-specific enhancer elements by applying ATAC-Seq to nuclei isolated from Tg(fli1a:egfp) transgenic zebrafish embryos.

overall_design: for comparison of cell type specific gene expression and ATAC-Seq datasets, we performed parallel RNAseq in duplicate on GFPplus and minus cells isolated from Tg(fli1a:egfp) zebrafish embryos


title: bulk RNAseq of uninjured and 18 hours post-methyl bromide lesion FACS Horizontal basal cells (HBCs)

first: Brian

last: Lin

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

summary: RNAseq analysis of uninjured vs 18hpl injured HBCs show heterogeneous modulation of pathways associated with quiescent stem cell activation. HBCs are the trp63 expressing, quiescent basal stem cell in the olfactory epithelium.

overall_design: Illumina HiSeq of triplicates of uninjured vs 18hpl FACS HBC samples isolated from Krt5-CreER;Ai9 Fl(stop)TdTomato lineage trace animals, induced with Tamoxifen 2 weeks prior to FACS. Each triplicate contains pooled cells from multiple animals, followed by standard differential gene expression

first: James

middle: E

last: Schwob

first: Daniel

last: Herrick


title: FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers

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

overall_design: Refer to individual Series


title: FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers [ATAC-seq]

summary:
Fluorescence-Activated Nuclei Sorting (FANS)-assisted Assay for Transposase Accessible Chromatin sequencing (ATAC-seq)
This work sought to identify endothelial-specific enhancer elements by applying ATAC-Seq to nuclei isolated from Tg(fli1a:egfp) transgenic zebrafish embryos.

overall_design: ATAC-Seq performed on GFPplus and GFPminus nuclei isolated from Tg(fli1a:egfp) embryos.  Separate ATAC-Seq libraries were constructed from GFPplus and minus nuclei isolated on three separate occasions to give biological triplicate samples and 6 total samples.


title: Differential gene expression of Pseudomonas aeruginosa ΔPA14_22470 (ΔPA3225) versus UCBPP-PA14 wildtype in planktonic and biofilm cells

city: Ottawa

first: Thien-Fah

last: Mah

state: ON

address: 451 Smyth Road

department: Biochemistry, Microbiology, and Immunology

country: Canada

institute: University of Ottawa

summary: PA3225 is a LysR-type transcriptional regulator, and the ΔPA3225 deletion mutant is more resistant to various antibiotics than the wild-type PA14 strain in both planktonic and biofilm cells.  In order to characterise the regulon of PA3225, we compared the transcriptomes of biofilm and planktonic ΔPA3225 to biofilm and planktonic PA14 wild-type by RNA-seq.

overall_design: RNA was isolated from planktonic and biofilm PA14 wild-type and ΔPA3225 cells (3 biological replicates for each condition = 12 samples) and submitted to McGill University and Genome Quebec Innovation Centre for library preparation, RNA-seq, and data processing.

first: Clayton

last: Hall

first: Li


title: Depicting early human development and germ cell origin with porcine embryos

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Human primordial germ cells (hPGCs), the precursors of sperm and eggs, originate in early postimplantation embryos. Since early human embryos cannot be investigated directly, we extended our recent in vitro model for hPGC fate, alongside direct analysis of early porcine embryos, which develop in a highly similar manner.  Here we show that porcine PGCs (pPGCs) originate from the posterior pre-primitive streak epiblast in response to WNT and BMP-pSMAD signalling, followed by sequential induction of SOX17–BLIMP1 expression. This is reminiscent of our observations for the human in vitro counterpart. Mechanistic analysis in the culture model for hPGC specification and gastrulation shows that a balanced SOX17-BLIMP1 gene dosage is critical and sufficient for PGC specification; SOX17 subsequently induces definitive endoderm during gastrulation. We demonstrate that porcine embryos when combined with a tractable human model system can provide insights on early human development and mechanisms of early cell fate decisions.

overall_design: RNA-Seq analysis to investigate transcriptomes of hESCs and hPGCs induced from hESCs with cytokines or with overexpression of SOX17 and BLIMP1

first: Toshihiro

last: Kobayashi

first: Haixin

first: Walfred

last: Tang

first: Naoko

last: Irie

last: Withey

first: Doris

last: Klisch

first: Anastasiya

last: Sybirna

first: David

last: Contreras

last: Webb

first: Cinzia

last: Allegrucci

first: Ramiro

last: Alberio

first: M

last: Surani


title: Structure-seq2: Sensitive and accurate genome-wide profiling of RNA structure in vivo

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

summary: We present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity and data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. Structure-seq2 can employ a biotinylated nucleotide to facilitate the protocol. We have benchmarked Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa) and apply Structure-seq2 to provide evidence of hidden breaks in chloroplast rRNA and a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded rRNA.

overall_design: 14 Structure-seq2 libraries are generated via MiSeq. Two replicates are included each of the standard Structure-seq2 protocol (both + and - DMS), and of the biotin variation.

first: Laura

last: Ritchey

last: Su

first: Yin

last: Tack

first: Sarah

middle: M

last: Assmann

first: Philip

last: Bevilacqua


title: High-dose maternal folic acid supplementation before conception impairs reversal learning in offspring mice

city: Bonn

first: Kristin

middle: Simone

last: Henzel

address: Ludwig-Erhard-Allee 2

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Folic acid supplements prior to and during gestation are recommended and necessary to prevent neural tube defects in developing embryos. But there are also studies suggesting possible adverse effects of high-dose folic acid supplementation. Here, we address whether maternal dietary folic acid supplementation at 40 mg/kg chow (FD), restricted to a period prior to conception, affects gene expression in the offspring generation.

overall_design: Total RNA extracted from hippocampi of 6 control (CD) F1 mice and 5 FD F1 mice at the age of 14 weeks.

first: Devon

last: Ryan

first: Susanne

last: Schröder

first: Marco

last: Weiergräber

first: Dan

last: Ehninger


title: RNA-Sequencing of Stat3 silenced oligodendrocyte progenitor cells.

status: Public on Jun 07 2017

city: Rochester

first: John

last: Mariani

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

summary: We examine the role of Stat3 in oligodendrocyte progenitor cells and determine that direct binding of Stat3 to the Etv6 promoter, and subsequent upregulation, in part, promotes differentiation.

overall_design: Examination of gene expression in Stat3 silenced OLP in the presence or absence of CNTF

middle: N

first: Gareth

middle: R

last: John


title: ATX3, ATX4, and ATX5 encode putative H3K4 methyltransferases and are critical for plant development

first: Yan

last: He

state: Beijing

address: 2 Yuanmingyuan West Road

department: Plant Genetics and Breeding

institute: China Agricultural University

summary: Methylation of lysine residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily-conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related (ATXR) proteins. Here we examined three until-now-unexplored ATX proteins, ATX3, ATX4, and ATX5. We found that they exhibit similar domain structures and expression patterns, and are redundantly required for vegetative and reproductive development. Concurrent disruption of the ATX3, ATX4, and ATX5 genes caused marked reduction in H3K4me2 and H3K4me3 levels genome-wide, and resulted in thousands of genes expressed ectopically. Furthermore, atx3/atx4/atx5 triple mutants resulted in exaggerated phenotypes when combined with the atx2 mutant but not with atx1. Together, we conclude that ATX3, ATX4, and ATX5 are redundantly required for H3K4 di- and trimethylation at thousands of sites located across the genome, and genomic features associated with targeted regions are different from the ATXR3/SDG2-controlled sites in Arabidopsis.

overall_design: ChIP-seq and RNA-seq technologies were undertaken to investigate genomic regions or genes targeted by three uncharacterized H3K4me2/3 genes in Arabidopsis.


title: Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis [22PC RNA-seq]

first: Rohit

last: Bose

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Half of prostate cancers are caused by a gene-fusion that enables androgens to drive expression of the normally silent ETS transcription factor ERG in luminal prostate cells1-4.  Recent prostate cancer genomic landscape studies5-10 have reported rare but recurrent point mutations in the ETS repressor ERF11.  Here we show these ERF mutations cause decreased protein stability and ERF mutant tumours are mostly exclusive from those with ERG fusions.  ERF loss recapitulates the morphologic and phenotypic features of ERG gain in primary mouse prostate tissue, including expansion of the androgen receptor (AR) transcriptional repertoire, and ERF has tumour suppressor activity in the same genetic background of PTEN loss that yields oncogenic activity by ERG.  Furthermore, in a human prostate cancer model of ERG gain and wild-type ERF, ChIP-seq studies indicate that ERG inhibits the ability of ERF to bind DNA at consensus ETS sites.  Consistent with a competition model, ERF loss rescues ERG-positive prostate cancer cells from ERG dependency. Collectively, these data provide evidence that the oncogenicity of ERG is mediated, in part, by displacement of ERF and raise the larger question of whether other gain-of-function oncogenic transcription factors might also inactivate endogenous tumour suppressors.

overall_design: CWR22Pc cells  were infected with shNT or shERF and selected with antibiotics.  Subsequently, cells were treated with 1nM DHT  x 16hrs, or vehicle, in charcoal-stripped media.  Subsequently RNA was extracted and RNA-seq performed.  For each condition, 3 sets of equal numbers of cells were plated and then processed independently.

first: Charles

last: Sawyers