title: DIGIT regulates endoderm differentiation of human embryonic stem cells

first: Chan

last: Zhou

state: Massachusetts

address: 55 Fruit Street

department: gastroenterology

institute: Mass General Hospital, Harvard Medical School

summary: Endoderm differentiation is a critical step leading to development of the gastrointestinal system.  We found that DIGIT is a lncRNA that is required for endoderm differentiation.  We used directional RNA sequencing (RNA-seq) to globally evaluate the effects of loss of DIGIT expression during endoderm differentiation and chromatin immunoprecipitation and sequencing (ChIP-seq) to define the sites occupied by SMAD3 during endoderm diferentiation.

overall_design: Analysis of genome-wide coding and noncoding gene expression using RNA-seq in human embryonic stem cells (hESCs) and DIGiT-deficient (DIGIT KO) hESCs under hESC culture conditions and after four days of endoderm differentiation.  SMAD3 Chip-seq was performed to define enhancers activated during endoderm differentiation.

first: Kaveh

last: Daneshvar

first: Joshua

middle: V

last: Pondick

last: York

first: Alan

last: Mullen


title: MERVL/Zscan4 network activation results in transient genome-wide DNA demethylation of mESCs

status: Public on Oct 03 2016

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

type: Methylation profiling by high throughput sequencing

summary: Mouse embryonic stem cells are heterogeneous and contain rare cells expressing transcripts normally upregulated in pre-implantation embryos, including the Zscan4 cluster and MuERVL endogenous retrovirus. Through single cell transcriptomics and genome-wide chromatin and DNA methylation analyses we uncover the dynamics of the regulation and epigenetic consequences of these transient cells. Transcriptional activation of MuERVL and Zscan4 coincided with a global increase in chromatin accessibility. Through a combination of bulk and single-cell RNA-sequencing, we reveal the dynamics and specificities of a MuERVL driven transcriptional network. Interestingly, in addition to pre-implantation embryos, the MuERVL network is similarly upregulated during somatic cell reprogramming, associating it with dramatic chromatin remodeling events. In MuERVL+ mESCs, upregulation of a cluster of Eif1A-like genes results in inhibition of protein synthesis, uncoupling transcription from translation. Consequently, depletion of proteins including DNA methyltransferases, results in genome-wide DNA demethylation, demonstrating the influence of endogenous retroviral activation on the host epigenome.

overall_design: Bisulfite-seq (3 biological replicates of 2 samples)

first: Mélanie

middle: A

last: Eckersley-Maslin

first: Valentine

last: Svensson

first: Christel

last: Krueger

first: Thomas

last: Stubbs

first: Pascal

last: Giehr

first: Felix

first: Ricardo

last: Miragaia

first: Charalampos

last: Kyriakopoulos

first: Rebecca

last: Berrens

first: Inês

last: Milagre

first: Jörn

last: Walter

first: Sarah

last: Teichmann

first: Wolf

last: Reik


title: TFR Cell Suppression Leads to Durable and Selective Inhibition of B Cell Effector Functions

status: Public on Oct 02 2016

city: Boston

first: Arlene

last: Sharpe

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A novel lncRNA GAS1 promotes gastric carcinogenesis and acts as a modular scaffold of WDR5 and KAT2A complexes to specify the histone modification pattern [RNA-seq]

status: Public on Oct 04 2016

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

summary: To elucidate whether GAS1 plays a role in gastric cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of GAS1 shRNA and control shRNA transfectants.

overall_design: RNA-seq was performed in BGC 823 gastric cancer cells after GAS1 shRNA and control shRNA virus infection

first: Jie

last: Hong


title: Small RNA Sequencing of mouse amygdala after knockdown of miR-15a

status: Public on Oct 01 2016

city: Munich

first: Mareen

last: Engel

address: Kraepelinstr. 2-10

department: Stress Neurobiology and Neurogenetics

country: Germany

institute: Max-Planck-Institute of Psychiatry

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs are important regulators of gene expression and associated with stress-related psychiatric disorders. We report that exposing mice to chronic stress led to a specific increase in microRNA-15a levels in the amygdala-Ago2 complex, and a concomitant reduction in the levels of its predicted target, FKBP51, which is implicated in stress-related psychiatric disorders. Reciprocally, mice expressing reduced levels of amygdalar microRNA-15a following exposure to chronic stress exhibited increased anxiety-like behaviors. Here, we performed small RNA Sequencing of mouse basolateral amygdala after miR15a knockdown using injection of a miR-15a sponge virus or control sponge virus.

overall_design: Small RNA Sequencing of basolateral amygdala of 5 mice injected with a miR-15a sponge virus and 5 mice injected with a control sponge virus.

first: Naama

last: Volk

first: Elisabeth

middle: B

last: Binder

first: Alon


title: Photosynthesis in C3-C4 intermediate Moricandia species

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

summary: Analysis of the metabolism in mature leaves of Moricandia species with C3 and C3-C4 intermediate photosynthesis

sample_organism:
Moricandia arvensis
Moricandia moricandioides
Moricandia suffruticosa

overall_design: Mature leaves from Moricandia moricandioides (C3), M. suffruticosa (C3-C4) and M. arvensis (C3-C4) were grown in a climate controlled chamber and harvested for analysis of mRNA, metabites, anatomy and physiology

first: Urte

last: Schlüter

first: Andrea

last: Bräutigam

first: Udo

last: Gowik

first: Michael

last: Melzer

first: Pascal-Antoine

last: Christin

first: Samantha

last: Kurz

first: Tabea

last: Mettler-Altmann

middle: P


title: Transcriptional analysis of rescue of Tfr-mediated B cell suppression with IL-21

summary: Tfh and B cells were cultured together with or without Tfr cells and IL-21.  After 4 days Tfh and B cells were sorted and prepared for 3' targeted RNA-seq.

overall_design: Examination of transcriptional changes upon IL-21 rescue of B cell suppression

middle: H

first: Peter

middle: T

last: Sage


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and dek2 mutant Transcriptomes

first: Weiwei

last: Qi

address: 333 Nanchen Road

institute: Shanghai University

summary: Analysis of  gene expression level. The hypothesis tested in the present study was that dek2 mutant influence the expression of mitochondrial function associated genes. Results provide important information of the gene expression level regulation of mitochondrial part and oxidative phosphorylation.

overall_design: Endosperm mRNA profiles of 15DAP wild type (WT) and dek2 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

first: Yang

last: Yang


title: Transcriptional analysis of Tfr suppression of Tfh and B cells by RNA-seq

first: Arlene

last: Sharpe

summary: Tfh and B cells were cultured together with or without Tfr cells.  After 4 days Tfh and B cells were sorted and prepared for 3' targeted RNA-seq.

overall_design: Examination of transcriptional changes upon suppression of Tfh and B cells.


title: mRNA Next Generation Sequencing of long-lived C. elegans mutants lacking the replication-independent histone variant H3.3

city: Bonn

first: Daniele

last: Bano

address: Sigmund-Freud-Strasse 27

institute: DZNE

summary: The aim of this stuy was to investigate the effect of H3.3 deficiency on gene transcription in both a wild-type and a long-lived mutant context in C. elegans.

overall_design: Next Generation mRNA sequencing was performed on 5 biological replicates of late L4 wild-type, his-72(tm2066); his-71(ok2289), daf-2(e1370), daf-2(e1370); his-72(tm2066); his-71(ok2289), nuo-6(qm200) and nuo-6(qm200); his-72(tm2066); his-71(ok2289).

first: Antonia

last: Piazzesi

first: Drazen

last: Papic

first: Florian

last: Battke

first: Lisha

last: Mathew

first: Chantal

last: Ulmschneider


title: Genome-wide maps of chromatin state of WDR5 and KAT2A in gastric cancer BGC823 cells [ChIP-seq]

first: Haoyan

last: Chen

summary: we performed ChIP coupled with high-throughput sequencing (ChIP-seq) for WDR5 and KAT2A in BGC823 cells. WDR5 and KAT2A ChIP-Seq data analysis revealed 5449 and 6485 called peaks, respectively in BGC823 cells with control shRNA transfection.

overall_design: Examination of WDR5 and KAT2A genomic bingding efficiency and histone modifications pattern change in gastri cancer cell BGC823 cells after downregulation of GAS1 expression.


title: Evolution of an lncRNA leads to a primate specific modulation of alternative splicing

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: We performed the poly(A)-seq of 293T,Hela,THP-1 and N2a cell treated with si5S-OT,shPTBP1 or siU2AF65

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: There are 18 samples without replicates and 5 of them are control.

first: Xiaolin

last: Wang

first: Shanshan

last: Hu


title: Genome structure and organization in mouse CD8 T cells

city: Philadelphia

first: Bing

last: He

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia


title: Differential DNA Methylation Regions in Adult Human Sperm following Adolescent Chemotherapy:  Potential for Epigenetic Inheritance

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: The potential that adolescent chemotherapy can impact the epigenetic programming of the germ line to influence later life adult fertility and promote epigenetic inheritance was investigated. Adult males approximately ten years after pubertal exposure to chemotherapy were compared to adult males with no previous exposure. Sperm were collected to examine differential DNA methylation regions (DMR) between the exposed and control populations. A statistically significant signature of DMRs was identified in the chemotherapy exposed male sperm. The DMRs, termed epimutations, were found in CpG desert regions of primarily 1 kilobase size. Gene associations and correlations to genetic mutations (copy number variation) were also investigated. Observations indicate adolescent chemotherapy exposure can promote epigenetic alterations that persist in later life. The germline (i.e. sperm) epimutations identified suggest chemotherapy has the potential to promote epigenetic inheritance to the next generation.

overall_design: DNA from the semen samples was isolated and equal amounts of DNA from 3 individuals pooled to generate three different pools of control (no previous chemotherapy) and three different pools of adolescent chemotherapy exposed cancer survivors labeled human sperm pools (HS#) #1 through #6. The pooled DNA was immunoprecipitated with 5 methyl cytosine monoclonal antibody for a methylated DNA immunoprecipitation (MeDIP). The MeDIP DNA was used to generate libraries and bar coded (index primers) separately for analysis by next generation sequencing (MeDIP-Seq).

first: Margarett

last: Shnorhavorian

first: Stephen

middle: M

last: Schwartz

first: Barbara

last: Stansfeld

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck


title: Genome structure and organization in mouse CD8 T cells [Hi-C-seq]

summary: Our experiments aimed to investigate the landscape of enhancers and super-enhancers in naïve, effector and memory CD8+ T cells. Here we mapped four histone modification marks and gene expression in naive, effector, and memory cells after viral infection. Our results suggest that the chromatin environment at regulatory DNA sequences in TCM is more permissive than in TN and TE. We further predicted the enhancers and their targets, and constructed transcriptional regulatory networks (TRNs) in three T cell stages. We have identified a highly dynamic repertoire of the enhancers and their targets during CD8 T cell responses, as 77% of the enhancers and 82% of the enhancer-promoter interactions are stage-specific. Our results suggest the dynamic change of enhancer activity during cell stage transition leads to TRN rewiring, which explains the expression change of the key factors of T cell function.

overall_design: We performed RNA-Seq experiments in WT and Tcf1/Lef1 difficient CD8+ T cells, and performed Hi-C experiments in WT cells.

first: Haihui

last: Xue

first: Kai

last: Tan


title: Histone macroH2A1.2 promotes metabolic health and leanness by inhibiting adipogenesis

city: Baronissi

first: Domenico

last: Memoli

address: s.Allende 1

department: Medicine and Surgery

country: Italy

institute: University of Salerno

summary: Obesity has tremendous impact on the health systems. Its epigenetic bases are unclear. MacroH2A1 is a variant of histone H2A, present in two alternatively exonspliced isoforms macroH2A1.1 and macroH2A1.2, regulating cell plasticity and proliferation, during pluripotency and tumorigenesis. Their role in adipose tissue plasticity is unknown. Here we show evidence that macroH2A1.1 protein levels in the visceral adipose tissue of obese humans positively correlate with BMI, while macroH2A1.2 is nearly absent. We thus introduced a constitutive GFP-tagged transgene for macroH2A1.2 in mice and we characterized their metabolic health upon being fed a standard chow diet or a high fat diet. Despite unchanged food intake, these mice exhibit lower adipose mass and improved glucose metabolism both under a chow and an obesogenic diet. In the latter regimen, transgenic mice display smaller pancreatic islets and significantly less inflammation. Genomic and transcriptomic analyses demonstrated that association of macroH2A1.2 promoter occupancy of key adipogenic genes with their transcripts was gene specific. MacroH2A1.2 overexpression markedly inhibited adipogenesis, while overexpression of macroH2A1.1 had opposite effects. MacroH2A1.2 is an unprecedented chromatin component powerfully promoting metabolic health by modulating anti-adipogenic transcriptional networks in the differentiating adipose tissue. Strategies aiming at enhancing macroH2A1.2 expression might counteract excessive adiposity in humans.

overall_design: Examination of 2 different histone modifications in adipocite cell

first: Pazienza

last: Valerio

first: Manlio

last: Vinciguerra

first: Roberta

last: Tarallo


title: Genome structure and organization in mouse CD8 T cells [RNA-seq]

overall_design: We performed RNA-Seq experiments in WT and Tcf1/Lef1 difficient CD8 cells, and performed Hi-C experiments in WT cells.


title: Gene expression analysis of parental cell lines and cell lines with acquired resistance to compound 3 (C03) and compound 7 (C07).

first: David

last: Sykes

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

summary: Cells were cultured for a period of six months in slowly escalating concentrations of two small molecules (Compound 3 and Compund 7) whose protein target was unknown. Over this six month period, the cells cultured in C03 and C07 became resistant to the differentiation and growth inhibitory effects of the the compounds. Total RNA was harvested for RNA-sequencing.

overall_design: Six samples were analyzed in singlicate by RNA-sequencing.

last: Scadden


title: ChIP-seq and RNA-seq in BGC823 cells after downregulation of GAS1 expression

first: Haoyan

last: Chen


title: Gene expression of MLL/AF9 leukemia cells sorted from mice treated with or without brequinar

summary: Mice bearing an MLL/AF9 leukemia were treated with vehicle or brequinar every three days for a total of four doses. Mice were euthanized for collection of the bone marrow cells. The leukemia cells were purified by FACS (fluorescence activated cell sorting) and total RNA was prepared from the purified leukemia cells.

overall_design: Two samples were analyzed in singlicate by RNA-sequencing.


title: Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae

city: Montpellier cedex 5

first: Elsa

last: Ballini

address: UMR BGPI – TA A-54/K – Equipe ICAP campus International de Baillarguet

department: Biology and ecology

country: France

institute: SupAgro Montpellier

summary: In order to understand the mechanisms of Drought induced susceptibility (DIS) we’ve conducted a dual RNAseq experiment on rice infected tissues by Magnaporthe oryzae. At 4 days post inoculation tissues have been collected on mock inoculated and M. oryzae inoculated plants. Rice were conducted under two type of water regime: DIS Drought during three days before inoculation, NoDIS no drought before inoculation. RNAseq was conducted both on rice and fungal RNA.

sample_organism:
Oryza sativa
Pyricularia oryzae

platform_organism:
Oryza sativa
Pyricularia oryzae

overall_design: shoot tissus mRNA 21-day old rice plant were generated by deep sequencing. Three samples per conditions, Four conditions: NoDIS Mock, NoDIS Inoc, DIS Mock, DIS Inoc. NoDIS = plant were conducted with a normal water regime. DIS = plant received no watering during three days before inoculation. Mock = Plant inoculated with control solution (gelatin 0,5%). Inoc = Plant inoculated with Magnaporthe oryzae isolate Fr13 with gelatin 0,5%.

last: BALLINI

first: Przemyslaw

last: Bidzinski

first: Aurélie

last: Ducasse

first: Corinne

last: Michel

first: Jean-Benoit

last: MOREL


title: REV-ERBα influences stability and nuclear localization of the glucocorticoid receptor

city: Fribourg

first: Sara

middle: S

last: Fonseca Costa

address: Chemin du Musée 5

country: Switzerland

institute: University of Fribourg

summary:
We report here that REV-ERBα influences nuclear localization of the glucocorticoid receptor and vice versa. As a consequence these two nuclear receptors influence each others transcriptome.
REV-ERBα (Nr1d1) is a nuclear receptor that is part of the circadian clock mechanism and regulates metabolism and inflammatory processes. The glucocorticoid receptor (GR, Nr3c1) influences similar processes, but is not part of the circadian clock mechanism although glucocorticoid signaling affects resetting of the circadian clock in peripheral tissues. Because of their similar impact on physiological processes we studied the interplay between these two nuclear receptors. We found that REV-ERBα competes with GR for binding to HSP90, a chaperone responsible for the activation of substrate proteins to ensure survival of a cell. This competition affected stability and nuclear localization of GR, thereby affecting GR target gene expression such as IκB and alcohol dehydrogenase 1 (Adh1). Our findings highlight an important interplay between two nuclear receptors that influence each others transcritpional potential indicating that the transcriptional landscape is strongly dependent on dynamic processes at the protein level.

overall_design:
In this dataset, we isolated livers at Zeitgebertime (ZT) 8 and ZT20 of wild type and Rev-erb alpha knock-out animals. Liver samples were immediately flash frozen in liquid N2 and stored at −80 °C. RNA was extracted using NucleoSpin RNA (Machery-Nagel, Düren, Germany) according to the instructions of the manufacturer. Quality of the RNA samples was analysed with a spectrophotometer, agarose gel electrophoresis and reverse transcription-PCR. Library construction starting from the poly(A)-tail and multiplexing was performed according to the instructions of the manufacturer (Illumina). The samples were organized as follows:
Three replicas (1-WT, 2-WT, 3-WT) correspond to genotype WT at ZT8.
Three replicas (4-Rev, 5-Rev, 6-Rev) correspond to genotype Rev-/- at ZT8.
Three replicas (7-WT, 8-WT, 9-WT) correspond to genotype WT at ZT20.
Three replicas (10-Rev, 11-Rev, 12-Rev) correspond to genotypeRev-/- at ZT20.
For the experiment, complementary DNA (cDNA) libraries were barcoded using Illumina primers and loaded onto one lane of an IlluminaHS2000 machine. cDNA libraries were diluted and loaded onto each lane. The samples were sequenced for a maximum sequencing length of 75 bp.
Sequences were aligned to the mouse genome (UCSC version mm10 database). Numbers of the sequences obtained for each library can be found in Supplementary Table 3. Sequences (fastq format) were mapped with Tophat (Trapnell, C. 2009), uniquely mapped sequences from the output files (bam format) were then used for further analysis, percentage of the mapping obtained for each sample can be found in Supplementary Table 3. For all files the reads were counted with HTSeq-count using the following criteria:
samtools view sample.bam | htseq-count -m union -a 10 -s no -i gene_name Mus_Musculus.gtf > sample_counts.txt
Tests for differential expression between the samples were performed in R software (R Core Team, 2014 http://www.R-project.org/) using the DESeq2 package (Version 1.6.3) (Love, M. 2014). A threshold on the corrected P value was used to call for differentially expressed genes (P.adjust<0.05).

first: Takashi

last: Okabe

first: Rohit

last: Chavan

first: Andrea

last: Brenna

first: Juergen

last: Ripperger

first: Urs

last: Albrecht


title: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

institute: University of Luebeck

summary: The magnitude and determinants of differences in cis-regulation for regulatory sequences residing in episomes versus chromosomes remain almost completely unknown. To address this question in a systematic manner, we developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2,236 candidate liver enhancers in an episomal versus a chromosomally integrated context. We find that the activities of chromosomally integrated sequences are substantially different from the activities of the identical sequences assayed on episomes, and furthermore are correlated with different subsets of ENCODE annotations. The results of chromosomally-based reporter assays are also more reproducible and more strongly predictable by both ENCODE annotations and sequence-based models. With a linear model that combines chromatin annotations and sequence information, we achieve a Pearson's R2 of 0.347 for predicting the results of chromosomally integrated reporter assays. This is substantially better than with either chromatin annotations or sequence information alone and also outperforms predictive models of episomal assays. Our results have broad implications for how cis-regulatory elements are identified, prioritized and functionally validated.

overall_design: We developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2,236 candidate liver enhancers and 204 controls in an episomal versus a chromosomally integrated context. By using integration-competent vs. integration-defective components of the lentiviral system, we directly compared the functional activities of 2,236 candidate liver enhancers in a chromosomally integrated versus an episomal context in the human liver hepatocellular carcinoma cell line, HepG2.

first: Jay

last: Shendure

first: Nadav

last: Ahituv


title: Effects of aged garlic extract (AGE) and FruArg on lipopolysaccharide-induced genetic response in microglial cells using gene expression profiling

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary:
We hypothesized that aged garlic extract, and a pure compound from it, FruArg, can repress the genetic response induced by lipopolysaccharide (LPS).
We applied gene expression profiling to understand the potential mechanisms of the protective effects of AGE and FruArg against LPS stress in BV-2 cells.
Gene expression profiling showed that AGE repressed the transcriptome alteration induced by LPS. FruArg, as an active compound in AGE, accounted for AGE's protective effects. These results suggest that AGE and FruArg are capable of alleviating oxidative and neuroinflammatory responses stimulated by LPS in BV-2 cells.

overall_design:
Using mouse microglia cells BV-2, we treated cells with control solvent, 100ng/mL LPS, LPS+AGE (0.5% v.v), and LPS+FruArg (3mM). 2 biological replicates for each treatment were performed.

See "Effects of aged garlic extract (AGR) and FruArg on lipopolysaccharide induced genetic response in microglial cells using gene expression profiling", Scientific Report 2016.

first: Hailong

last: Song

first: Zhe

last: Qu

first: Valeri

last: Mossine

first: Jie

last: Hou

first: Jilong

last: Li

first: Jianlin

last: Cheng

first: Michael

last: Greenlief

first: Dennis

last: Lubahn

first: Jiankun

last: Cui

first: Grace

middle: Y

last: Sun

first: Linda

last: Randall

first: Frank

middle: J

last: Schmidt

first: Ronald

last: Walter

first: Zezong

last: Gu


title: ChIP-Seq-Data from MEFs overexpressing Fbxl10

city: Freiburg

first: Dominica

last: Willmann

address: Breisacherstr. 66

institute: Uniklinik-Freiburg

summary: Overexpression of Fbxl10 leads to enhanced migration in mouse embryonic fibroblast

overall_design: To analyse the role of histone demethylase Fbxl10 we generated gain of function model overexpressing HA-tagged Fbxl10 and identified target genes by Chip-Seq and transcriptome analysis.

first: Magdalena

last: Rohde

first: Jutta

last: Kirfel


title: Fbxl19 recruits Rnf20 to CpG Islands and promotes H2B mono-ubiquitination

city: Austin

first: Bum-Kyu

last: Lee

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

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

overall_design: Refer to individual Series


title: Dynamic organization and activation of enhancers and super-enhancers dictate effector and memory CD8+ T cell responses

first: Bing

last: He


title: Dynamic organization and activation of enhancers and super-enhancers dictate effector and memory CD8+ T cell responses (ChIP-Seq)

overall_design: We performed ChIP-Seq for 4 histone modification markers and RNA-Seq experiments in three CD8+ T cell differentiation stages.

first: Haihui

last: Xue

first: Kai

last: Tan


title: Fbxl19 recruits Rnf20 to CpG Islands and promotes H2B mono-ubiquitination [ChIP-Seq]

summary: Rnf20 catalyzes lysine 120 mono-ubiquitination of histone H2B (H2Bub1) that has been previously invloved in normal differentiation of embryonic stem (ES) and adult stem cells. However,the mechanims underlying by which Rnf20 is recruited to its target chromosomal loci to generate H2Bub1 is still elusive. Here, we reveal that Fbxl19, a CxxC domain-containing protein, physically interacts with Rnf20, guides it preferentially to CpG island-containing target promoters, and thereby promotes mono-ubiqutination of H2B. We first show that up-regulation of Fbxl19 induces the level of global H2Bub1, while down-regulation of Fbxl19 reduces the level of H2Bub1 in mouse ES cells. Our genome-wide target mapping unveils the preferential occupancy of Fbxl19 on CpG island-containing promoters, and we further show that the binding of Fbxl19 is essential for the recruitment of Rnf20 to its target genes and subsequent H2Bub1. Altogether, our results demonstrate that Fbxl19 plays critical roles in the H2Bub1 pathway by recruiting Rnf20 to CGI target genes specifically and selectively.

overall_design: ChIP sequenicngs were performed for Fbxl19 and H2Bub1 in mouse ES cells. To perform Fbxl19 ChIP-seq we generated Fbxl19-overexpressing flag-biotin tagged clones and selected overexpression (OE)-high (more than 5 fold) and OE-low (sub-endogeous level) clones. Using these two OE-high and OE-low clones, we performed ChIP-seq of Fbxl19 using Streptavidin-conjugated beads. We also conducted H2Bub1 ChIP-seq  under various conditions: normal, differentiation, Fbxl19-OE, Fbxl19-KD, and Fbxl19-KD under differentaiton conditions. Input was also sequenced and used for control.

first: Jonghwan

last: Kim


title: Dynamic organization and activation of enhancers and super-enhancers dictate effector and memory CD8+ T cell responses (RNA-Seq)


title: Epithelial cell RNA-seq in aged skin

city: New York

first: Brice

last: Keyes

state: NY

address: 1230 York Ave, Box 300

institute: The Rockefeller University

summary: Transcriptional analysis of hair follicle stem cells and epidermal cells in young and aged skin.

overall_design: Isolation of murine epithelial keratinocytes for RNA-seq analysis from young (2mo) and aged (24mo) animals

middle: E


title: Salicylic acid accumulation is required for Fe-deficiency responses in Arabidopsis

city: Hangzhou

first: chenjia

last: shen

address: Xuelin

institute: Hangzhou Normal University

summary: Several phytohormones and other small molecules have been demonstrated to be involved in iron (Fe) homeostasis. However, how salicylic acid (SA), an essential hormone in plant immunity and defense responses, participates in Fe-deficiency responses in plants is largely unknown. Here, we took advantage of a SA biosynthesis defect mutant phytoalexin deficient 4 (pad4: T-DNA Salk_089936) to explore the possible effects of endogenous SA on the morphological and physiological responses to Fe deprivation. Under a Fe-deficiency treatment, Col-0 showed more severe leaf chlorosis and root growth inhibition compared with the pad4 mutant. The soluble Fe concentrations were significant higher in pad4 than Col-0 under the Fe-deficiency treatment, suggesting that a mutation in the PAD4 gene may alleviate the Fe-deficiency-induced symptoms by regulating the soluble Fe concentrations. Furthermore, a SA signaling maker line (PR1promoter: GUS) was used to investigate how Fe deficiency affects endogenous SA biosynthesis and metabolism. The data showed that Fe deficiency significantly induced SA accumulation in Col-0, and the loss function of PAD4 blocked this process. The requirement of endogenous SA accumulation for Fe-deficiency responses was confirmed using a series of SA biosynthetic mutants and transgenic lines.

overall_design: To elucidate the molecular and metabolic mechanisms that affect plant SA responses to Fe deficiency, we performed a comparative RNA sequencing analysis of the whole seedling transcriptomes between Col-0 and the pad4 mutant under +Fe and –Fe treatments. The expression levels of many hormone response genes were altered in pad4 compared with Col-0. Hence, Fe acquisition may be under the control of a complex interplay among hormone signaling pathways.

first: Chenjia

last: Shen

first: Huizhong

last: Wang


title: Evaluating Side Effects of Nanoparticle-mediated siRNA Delivery to Mesenchymal Stem Cells Using Next-generation Sequencing and Enrichment Analysis

status: Public on Sep 30 2016

city: Rochester

first: Danielle

middle: SW

last: Benoit

address: 308 Robert B Goergen Hall, Box 270168

department: Biomedical Engineering

institute: University of Rochester

summary: RNA interference (RNAi) has immense potential to modulate cell functions. However, effective delivery of siRNA while avoiding deleterious side effects has proven challenging. This study investigates both intended and unintended effects of diblock copolymer nanoparticle (NP) delivery of siRNA delivery to human mesenchymal stem cells (hMSC). Specifically, siRNA delivery was investigated at a range of NP-siRNA:hMSC ratios with a focus on the effects of NP-siRNA treatment on hMSC functions. Additionally, next-generation RNA sequencing (RNA-seq) was used with enrichment analysis to observe side effects in hMSC gene expression. Results show NP-siRNA delivery is negatively correlated with hMSC density. However, higher NP-siRNA:hMSC ratios increased cytotoxicity and decreased metabolic activity. hMSC proliferation was largely unaffected by NP-siRNA treatment, except for a 3-fold reduction in hMSCs seeded at 4,000 cells/cm2. Flow cytometry reveals that apoptosis is a function of NP-siRNA treatment time and seeding density; ~14% of the treated hMSCs seeded at 8,000 cells/cm2 were annexin V+-siRNA+ 24 h after treatment, while 11% of the treated population was annexin V+-siRNA-. RNA-seq shows that NP-siRNA treatment results in transcriptomic changes in hMSCs, while pathway analysis shows upregulation of apoptosis signaling and downregulation of metabolism, cell cycle, and DNA replication pathways, as corroborated by apoptosis, metabolism, and proliferation assays. Additionally, multiple innate immune signaling pathways such as toll-like receptor (TLR), retinoic acid-inducible gene 1 (RIG-I)-like receptor, and nuclear factor-κB (NF-κB) signaling pathways are upregulated. Furthermore, and consistent with traditional siRNA immune activation, cytokine-cytokine receptor signaling was also upregulated. Overall, this study provides insight into NP-siRNA:hMSC ratios that are favorable for siRNA delivery. Moreover, NP-siRNA delivery results in side effects across the MSC transcriptome that suggest activation of the innate immunity that could alter MSC functions associated with their therapeutic potential.

overall_design: 21 total samples were analyzed from 7 experimental groups, with each group performed in triplicate (S1, S2, S3). Groups: (1) Day 0 samples harvested on day of NP-siRNA treatment administration (D0); (2) Untreated samples 1 day post-treatment (D1_NT); (3) NP-siRNA treated samples 1 day post-treatment (D1_Trxt); (4) Untreated samples 5 days post-treatment (D5_NT); (5) NP-siRNA treated samples 5 days post-treatment (D5_Trxt); (6) Untreated samples 14 days post-treatment (D14_NT); (7) NP-siRNA treated samples 14 days post-treatment (D14_Trxt).

first: Dominic

middle: W

last: Malcolm

first: Janet

last: Sorrells

first: Daniel

last: Van Twisk

first: Juilee

last: Thakar


title: Reprogramming Mouse Fibroblasts into Engraftable Myeloerythroid and Lymphoid Progenitors: Induction and Underlying Mechanisms (ChIP-Seq)

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Here we show that hematopoietic transcription factors Scl, Lmo2, Runx1 and Bmi1 can convert a developmentally-distant lineage (fibroblasts) into “induced hematopoietic progenitors” (iHPs). We analyzed transcriptomic data for cell undergoing the transdifferentiation process at several time-points of the process.

overall_design: We peroformed ChIP-Seq of Lmo2 using cell undergoing conversion from mouse embryonic fibroblasts (MEF) to induced hematopoietic progenitors (iHPs).

first: C

last: EL Farran

first: H

last: Cheng

last: Fang

first: T

last: Liu

first: Y

last: Loh

first: B

last: Lim


title: Reprogramming Mouse Fibroblasts into Engraftable Myeloerythroid and Lymphoid Progenitors: Induction and Underlying Mechanisms


title: Time course of myeloid differentiation in the Lysozyme-GFP ER-HoxA9 cells following estradiol withdrawal

city: Boston

first: David

last: Sykes

summary: Lysozyme-GFP ER-HoxA9 cells were cultured in the presence of estradiol (active ER-HoxA9) or in the absence of estradiol (inactive ER-HoxA9). Samples were taken at 10 time points over a 120 hour time course of myeloid differentiation to examine those gene expression changes that accompany differentiation upon the release of HoxA9 differentiation arrest.

overall_design: RNA Sequencing at 10 different time points done in duplicate

last: Scadden


title: Transcriptome profile of wildtype and Ret homozygote null mouse guts at E11.5 and E12.5

city: Baltimore

first: Sumantra

last: Chatterjee

state: MD

address: 733 N Broadway, Room 572

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: Total mRNA seq was perfomed on widtype and Ret null mouse embryonic gut at 2 stages of devlopment- E11.5 and E12.5

overall_design: Total RNA from 3 replicates each of wildtype and Ret null emryonic gut was converted to cDNA  and run on HiSeq 2000 (75 bp paired end)

first: Aravinda

last: Chakravarti


title: Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton

city: Nanjing

first: Dewei

last: Zheng

state: Jiangsu Province

address: 1 Weigang Road

department: State Key Laboratory of Crop Genetics and Germplasm Enhancement

institute: Nanjing Agricultural University

summary: Histone modifications regulate gene expression in eukaryotes, but their roles in gene expression changes in interspecific hybrids or allotetraploids are poorly understood. Histone modifications can be mapped by immunostaining of metaphase chromosomes at the single cell level and/or by chromatin immunoprecipitation-sequencing (ChIP-seq) for individual genes. Here we examined H3K4me3 density and transcriptome maps in root-tip cells of allotetraploid cotton (Gossypium hirsutum L.). The overall H3K4me3 levels were relatively equal between A and D chromosomes, which were consistent with equal numbers of expressed genes between the two subgenomes. However, intensities per chromosomal area were nearly twice as high in the D homoeologs as in the A homoeologs. Consistent with the cytological observation, ChIP-seq analysis showed more D-homoeologs with biased H3K4me3 levels than A-homoeologs with biased modifications, which correlated with the greater number of genes with D-biased expression than that with A-biased expression in most homoeologous chromosome pairs. Two chromosomes displayed different expression levels compared with other chromosomes probably because of translocations, which may affect the local chromatin structure (hence expression levels) for the genes involved. This example of genome-wide histone modifications that determine expression bias of homoeologous genes in allopolyploids provides a molecular basis for the evolution and domestication of polyploid species including important crops.

overall_design: Examination of H3K4me3 modifications of Gossypium hirsutum root tip cell.

first: Wenxue

last: Ye

first: Qingxin

last: Song


title: Effect daunorubicin treatment on the transcriptome of HCT116 cells [RNA-seq]

city: Sherbrooke

first: Jean-Francois

last: Lucier

state: Quebec

address: 2500, boulevard de l'Université

department: Département de Biologie

country: Canada

institute: Université de Sherbrooke

summary: We used RNA-seq to measure the transcriptome of HCT116 in response to the DNA damaging agent daunorubicin

overall_design: HCT116 cells were treated for 8h with 250 nM daunorubicin or  with vehicle

first: J

middle: F

last: Millau

first: L

last: Gaudreau


title: Effect daunorubicin on the binding of the cohesin subunit Rad21 in HCT116 cells [ChIP-seq]

summary: We used ChIP-seq to measure the binding of the cohesin subunit Rad21 in response to daunorubicin treatment in HCT116 cells


summary: Histone modifications regulate gene expression in eukaryotes, but their roles in gene expression changes in interspecific hybrids or allotetraploids are poorly understood. Histone modifications can be mapped by immunostaining of metaphase chromosomes at the single cell level and/or by chromatin immunoprecipitation-sequencing (ChIP-seq) for individual genes. Here we examined H3K4me3 density and transcriptome maps in root-tip cells of allotetraploid cotton (Gossypium hirsutum L.). The overall H3K4me3 levels were relatively equal between A and D chromosomes, which were consistent with equal numbers of expressed genes between the two subgenomes. However, intensities per chromosomal area were nearly twice as high in the D homoeologs as in the A homoeologs. Consistent with the cytological observation, ChIP-seq analysis showed more D-homoeologs with biased H3K4me3 levels than A-homoeologs with biased modifications, which correlated with the greater number of genes with D-biased expression than that with A-biased expression in most homoeologous chromosome pairs. Two chromosomes displayed different expression levels compared with other chromosomes probably because of translocations, which may affect the local chromatin structure (hence expression levels) for the genes involved. This example of genome-wide histone modifications that determine expression bias of homoeologous genes in allopolyploids provides a molecular basis for the evolution and  domestication of polyploid species including important crops.


title: Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary: Transcription, the copying of genetic information into RNA, is accomplished by multi-subunit RNA polymerases (msRNAPs) in all living organisms. msRNAPs are highly conserved in evolution and invariantly share a ~400 kDa five-subunit catalytic core1,2. A group of hypothetical single-chain proteins of unknown function, present in various bacteria and bacteriophages, was predicted to be distantly related to msRNAPs, having diverged from them before the Last Universal Common Ancestor3. Here, we studied a ~100 kDa protein, YonO, from this group encoded by the bacteriophage SPβ of Bacillus subtilis. We show that despite homology to only several amino acids of msRNAP, and the absence of most of the conserved domains, YonO is a highly processive and fast DNA-dependent RNA polymerase. Unlike msRNAPs, YonO can start specific transcription on double-stranded DNA without additional factors. We show that YonO is a bona fide RNAP of SPβ bacteriophage that transcribes its late genes. This new class of RNAPs may represent an intermediate step in the evolution of an ancestor of all msRNAPs.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: The wildtype and ΔyonO strains were grown in MMB media until exponential phase, at which point the cultures were halved. To one half (the plus sample), mitomycin C was added to induce the SPβ prophage. The other half (the minus sample) was left uninduced. Both cultures were incubated for a further 60 minutes before cells were harvested. Total RNA was purified from harvested cells and used for RNAseq analysis. To provide biological replicates, each strain was grown, induced and harvested in triplicate.

last: Forrest

first: Katherine

last: James

first: Yulia

last: Yuzenkova

first: Nikolay

last: Zenkin


title: mRNA-seq of nuclear RNA extracted from T4 and T5 neurons of D. melanogaster

city: Martinsried

first: Katarina

last: Pankova

address: Am Klopferspitz 18

institute: Max Planck Institute of Neurobiology

summary: T4 and T5 neurons are components of the neuronal circuit for motion vision in flies. To identify genes involved in neuronal computation of T4 and T5 neurons, we perfomed transcriptome analysis. Nuclei of T4 and T5 neurons were immunoprecipitated, total RNA was harvested and used for mRNA-seq with Illumina technology. In two biological replicates, we mapped 154 and 119 million reads to D. melanogaster genome. mRNA-seq provided information about expression levels of 17,468 annotated transcripts in the T4 and T5 neurons.

overall_design: Cell type – specific transcriptome analysis of the RNA isolated from immunoprecipitated nuclei, performed in two biological replicates

first: Alexander

last: Borst


title: REGION-SPECIFIC NEURAL STEM CELL LINEAGES REVEALED BY SINGLE-CELL RNA-SEQ FROM HUMAN EMBRYONIC STEM CELLS [Cel-seq]

city: Seattle

first: Zizhen

last: yao

department: MAT

institute: Allen Institute for Brain Science

summary: During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.

overall_design: The transcriptomes of 2684 single cells were profiled by CelSeq at different timepoints throughout a 54-day differentiation protocol that converted H1 human embryonic stem cells to a variety of brain cell types.

last: Yao

first: John

last: Mich

first: Sherman

last: Ku

first: Vilas

last: Menon

first: Anne-Rachel

last: Krostag

first: Refugio

last: Martinez

first: Joshua

last: Grimley

first: Yanling

last: Wang

first: Sharad

last: Ramanathan

first: Boaz

last: Levi


title: The Protein Non-anchored cell wall protein NCW-1 promotes cellulase production through effects on cellobiose uptake in Neurospora crassa

city: Tianjin

first: liangcai

last: lin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: The mechanism of cellulase induction in the filamentous fungi is still not completely understood, and the components of this pathway are not well characterized. In this study, the mechanism of how the non-anchored cell wall protein NCW-1 (NCU05137) affect the cellulases induction was investigated. Transcriptome analysis of this quadruple deletion strain △3βG△ncw-1 showed that the expression of major cellulase, cellodextrin transporters and cellulase regulators were significantly increased. Taken together, the cellulase expression machinery was dramatically stimulated in Δ3βGΔncw-1. These results make us understanding the ncw-1 function better and deepened our knowledge about the cellulase induction in N. crassa.

overall_design: △3βG△ncw-1 and △3βG were precultured for 20 h in MM, and then transferred into Vogel’s salts containing 1% cellobiose for an additional 4 h. Total RNA from frozen samples was extracted and treated.

first: Liangcai

last: Lin

first: Chaoguang

last: Tian

first: Jingen

last: Li


title: Transcriptome changes due to nuclear penetration of cancer extracellular vesicles

city: Las Vegas

first: Aurelio

last: Lorico

state: NV

address: 10530 Discovery Drive

department: Cancer Research Center

institute: Roseman University of Health Sciences

summary: Extracellular membrane vesicles (EVs) function as vehicles of intercellular communication in autocrine or paracrine manner. We report that cancer-derived EV biomaterials reach nuclei of human melanoma and breast carcinoma cells and multipotent mesenchymal stromal cells  (MSCs) through Rab7+ late endosome subdomains that penetrate into nuclear envelope invaginations. MSCs were exposed to cancer Evs in the presence or absence of drugs that block nucler import or export through the nuclear pores. Depletion of CD9 or inhibition of importin β1, two EV-associated molecules, abrogated the nuclear localization of EV-derived biomaterials and EV-induced early changes in MSC transcriptome notably in genes involved in inflammation. Also inhibition of nuclear export by leptomycin B inhibited early changes in MSC transcriptome. This novel cellular pathway may become a cancer therapeutic target.

overall_design: mRNA-Seq Human mesenchymal stromal cells alone or exposed to cancer Evs in the presence or absence of uptake modulators

first: Yongsheng

last: Bai


title: The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity [FAIRE-Seq]

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

summary: Identification of nucleosome-free, active regulatory regions in in vitro generated CSCs, following the knockdown of the histone linker H1.0

overall_design: FAIRE-seq analysis of biological replicates from SSEA1+ in vitro transformed human skin fibroblasts in the presence or absence of H1.0

first: C

last: Morales Torres

first: A

last: Biran

first: M

last: Burney

first: H

last: Patel

first: T

last: Henser-Brownhill

last: Hashahar

first: Y

first: E

last: Nye

first: B

last: Spencer-Dene

first: R

last: Ben Hamo

first: S

last: Efroni

first: N

last: Matthews

last: Misteli

last: Meshorer

first: P


title: Chromatin decompaction coupled MuERVL endogenous retrovirus activation induces genome-wide DNA demethylation

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Mouse embryonic stem cells are heterogeneous and contain rare cells expressing transcripts normally upregulated in pre-implantation embryos, including the Zscan4 cluster and MuERVL endogenous retrovirus. Through single cell transcriptomics and genome-wide chromatin and DNA methylation analyses we uncover the dynamics of the regulation and epigenetic consequences of these transient cells. Transcriptional activation of MuERVL and Zscan4 coincided with a global increase in chromatin accessibility. Through a combination of bulk and single-cell RNA-sequencing, we reveal the dynamics and specificities of a MuERVL driven transcriptional network. Interestingly, in addition to pre-implantation embryos, the MuERVL network is similarly upregulated during somatic cell reprogramming, associating it with dramatic chromatin remodeling events. In MuERVL+ mESCs, upregulation of a cluster of Eif1A-like genes results in inhibition of protein synthesis, uncoupling transcription from translation. Consequently, depletion of proteins including DNA methyltransferases, results in genome-wide DNA demethylation, demonstrating the influence of endogenous retroviral activation on the host epigenome.

overall_design: Total RNA-seq libraires (3 biological replicates of 2 samples, 4 biological replicates of a third sample); ATAC-seq (4 biological replicates of 3 samples each); Bisulfite-seq (3 biological replicates of 2 samples)

first: Mélanie

last: Eckersley-Maslin

first: Valentine

last: Svensson

first: Christel

first: Pascal

last: Giehr

first: Inês

last: Milagre

first: Ricardo

last: Miragaia

first: Thomas

last: Stubbs

first: Jörn

last: Walter

first: Sarah

last: Teichmann

first: Wolf

last: Reik


title: The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity [ChIP-Seq]

first: Paola

last: Scaffidi

summary: Identification of enrichment for H3K27ac and H3K27me3 in in vitro generated CSCs, following the knockdown of the histone linker H1.0

overall_design: ChIP-seq analysis of biological replicates from SSEA1+ in vitro transformed human skin fibroblasts in the presence or absence of H1.0

first: C

last: Morales Torres

first: A

last: Biran

first: M

last: Burney

first: H

last: Patel

first: T

last: Henser-Brownhill

last: Hashahar

first: Y

last: Li

first: E

last: Nye


first: Dewei

last: Zheng

overall_design: RNA-seq analysis using sequence libraries prepared from the root tip, which was the same tissue used to prepare for metaphase chromosome immune-staining assays. Three independent mRNA-seq libraries were constructed and sequenced by Illumina paired-end reads.

first: Wenxue

last: Ye

first: Qingxin

last: Song


title: REGION-SPECIFIC NEURAL STEM CELL LINEAGES REVEALED BY SINGLE-CELL RNA-SEQ FROM HUMAN EMBRYONIC STEM CELLS [population]

first: Zizhen

last: yao

summary: During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.      During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.     During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.

overall_design: Bulk RNA-seq at different timepoints throughout a 54-day differentiation protocol that converted H1 human embryonic stem cells to a variety of brain cell types.  Each sample was composed of 10^5 or 10^6 cells.

last: Yao

first: John

last: Mich

first: Sherman

last: Ku

first: Vilas

last: Menon

first: Anne-Rachel

last: Krostag

first: Refugio

last: Martinez

first: Joshua

last: Grimley

first: Yanling

last: Wang

first: Sharad

last: Ramanathan

first: Boaz

last: Levi


title: Transcription Factors Sp8 and Sp9 Coordinately Regulate Olfactory Bulb Interneuron Development [ChIP-Seq]

status: Public on Sep 29 2016

city: Shanghai

first: Jiwen

address: NO. 138 Yixueyuan Road

institute: Fudan University

summary: We conducted RNA-Seq and in situ hybridization to identify transcriptional profile changes in the Sp8/Sp9-DCKO olfactory bulb. Simultaneously, we did ChIP-Seq with homemade Sp9 antibody to identify Sp9 binding motifs and which changed genes might be the direct targets of transcription factor Sp9. We found that Sp9 directly binded to key genes which are required for olfactory bulb development. Transcription factors Sp8 and Sp9 belong to the same transcription factor family, so we think Sp8 and Sp9 have very similar binding sites of transcriptional regulation.

overall_design: Chromatin immunoprecipitation reactions were performed in duplicates using one input genomic DNA as control sample.


title: Epistasis between TIFAB and miR-146a, neighboring genes in del(5q) MDS

city: Cincinnati

first: Daniel

last: Starczynowski

state: OH

address: 3333 Burnet Ave

department: Experimental Hematology

institute: CCHMC

summary: Interstitial deletion of a single copy of chromosome 5q is the most frequent cytogenetic alteration in Myelodysplastic Syndromes (MDS), which results in reduced dosage of numerous genes. Furthermore, the extent of the 5q deletion determines disease severity, suggesting cooperation between deleted genes in the proximal and distal regions of del(5q). Although the contribution of individual genes to the pathogenesis of del(5q) MDS has been investigated, less is known about the epistatic interactions and/or cooperation between neighboring deleted genes. Deletion of TRAF-interacting protein with forkhead-associated domain B (TIFAB) and miR-146a, two haploinsufficient genes in del(5q) MDS, has been previously reported to activate the Toll-like receptor (TLR) signaling cascade in hematopoietic stem/progenitor cells (HSPC) by increasing TRAF6 protein stability and mRNA translation, respectively. To investigate the epistasis of TIFAB and miR-146a, we generated a mouse model in which Tifab and miR-146a were simultaneously deleted (Tifab-/-;miR-146a-/-, dKO). Herein, we report that combined hematopoietic-specific deletion of Tifab and miR-146a results in more rapid and severe cytopenia, and progression to a fatal bone marrow (BM) failure-like disease as compared to Tifab- or miR-146adeficiency alone. HSPC from Tifab-/-, miR-146a-/-, and dKO mice exhibit enrichment of gene 69 regulatory networks associated with innate immune signaling. Moreover, a subset of the differentially expressed genes is controlled synergistically following deletion of Tifab and miR-146a. Notably, nearly half of these defined synergy response genes identified in the mouse models were aberrantly expressed in del(5q) MDS HSPC when TIFAB (5q31) and miR-146a (5q33.3) were both deleted. Thus, synergistic control of gene expression following deletion of epistatic haploinsufficient genes in del(5q) MDS may be an underlying mechanism of the diseased state.

overall_design: To determine whether combined deletion of Tifab and miR-146a exaggerates the hematopoietic-specific defects observed in either Tifab- or miR-146a-deficient mice in vivo, bone marrow (BM) cells from WT, Tifab-/-, miR-146a-/-, and dKO mice were transplanted into lethally-irradiated syngeneic recipient mice. All recipient mice efficiently engrafted donor BM cells. To gain insight into the molecular nature and collaborative interplay between TIFAB and miR-146a deficiencies responsible for the exaggerated hematopoietic defect associated with MDS, we examined the gene regulatory networks in HSPC from mice transplanted with WT, Tifab-/-, miR- 146a-/-, and dKO BM. The lineage-Sca-1-c-kit+ (LK) BM fractions were analyzed using whole-genome RNA sequencing. Total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1 ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Amplicon Tagment Mix), incubating at 55C for 10 min. NT Buffer was then added to neutralize the samples. Libraries were prepared by PCR with the Nextera PCR Master Mix, and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle of 72C for 3min, one cycle of 98C for 30s, 12 cycles of 95C for 10s, 55C for 30s, and 72C for 1min, and one cycle of 72C for 5min. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocol

first: Melinda

last: Varney

first: Kwangmin

last: Choi

first: Lyndsey

last: Bolanos

first: Susanne

last: Christie

first: Jing

last: Fang

first: Leighton

last: Grimes

first: Jaroslaw

last: Maciejewsk

first: Jun-ichiro

last: Inoue


title: RNAseq transcriptome analysis reveals developmental heterogeneity among mouse bone marrow monocyte subsets

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

institute: Singapore Immunology Network

summary: Purpose: In our study, we identified a heterogeneity among bone marrow (BM) Ly6Chi monocytes, which can be subdivided the expression of CXCR4. In order to understand the development of BM monocytes, the goal of this experiment is to compare the transcriptome of these 2 BM Ly6Chi monocyte subsets to those of the common monocyte progenitor (cMoP) and Ly6Clo monocytes.

overall_design: 4 BM monocyte subsets (cMoP, Ly6ChiCXCR4hi, Ly6ChiCXCR4lo and Ly6Clo) from 3 different mice were sorted using a BD Aria III. Total RNA was extracted, converted to cDNA and run through deep sequencing using Illumina HiSeq 2500

first: Shu

middle: Z

last: Chong

first: Maximilien

last: Evrard

first: Jinmiao

last: Chen

first: Josephine

last: Lum

first: Michael

last: Poidinger

first: Lai

middle: G

last: Ng


title: A comparison of microRNA expression profiles from splenic hemangiosarcoma, splenic nodular hyperplasia, and normal spleens of dogs

city: Athens

first: Janet

state: GA

address: 2200 College Station Road

department: Small Animal Medicine and Surgery

institute: University of Georgia College of Veterinary Medicine

summary: Splenic masses are common in older dogs and may be malignant, benign, or non-neoplastic; yet diagnosis preceding splenectomy and histopathology remains elusive.  MicroRNAs (miRNAs) are 18-25 nucleotide, single stranded, non-coding RNAs that play a role in post-transcriptional regulation. MicroRNAs in tumor samples have been used to diagnose tumors, provide prognostic information, and aid in targeted treatments in human medicine, but have not been extensively evaluated in veterinary medicine. The objective of this study was to determine differential expression of microRNAs (miRNAs) between canine splenic hemangiosarcoma, canine splenic nodular hyperplasia, and normal canine spleens by use of RNA-sequencing. Eighteen miRNAs were found to be significantly differentially expressed between hemangiosarcoma and nodular hyperplasia only.  The five of these with the largest fold change were mir-193a, mir-450a, mir-503, mir-542, and mir-876.  Four miRNA were significantly differentially expressed between hemangiosarcoma and nodular hyperplasia and also hemangiosarcoma and normal spleen (mir-126, mir-150, mir-203, and mir-452). Findings of this study show that miRNA expression profiles are different between canine splenic hemangiosarcoma, nodular hyperplasia, and normal spleens.  This is a preliminary study with findings of clinical relevance, as masses of the spleen cannot be diagnosed pre-operatively in most cases.  Canine splenic masses are relatively common, and validation these findings is warranted for potential use as a diagnostic test.

overall_design: A total of fifteen samples total were analyzed for miRNA expression. There were 3 experimental condition with 5 replicates in each group.

middle: A

first: Nripesh

last: Prasad

first: Shawn

last: Levy

first: Russell

last: Cattley

first: Stephanie

last: Schleis

first: Harry

last: Boothe

first: Ralph

last: Henderson

first: Bruce

last: Smith


title: Aerobic glycolysis promotes T helper 1 cell differentiation through an epigenetic mechanism

city: New York

first: Ming

last: Li

address: 408 East 69th Street

department: Immunology

institute: Memorial Sloan-Kettering Cancer Center

summary: We analyzed LDHA-regulated genes in mouse Th1 cells through RNA-Seq and ChIP-Seq

overall_design: WT and LDHA-KO Th1 cells were subjected to RNA-Seq and ChIP-Seq analysis

first: Min

last: Peng

last: Yin

first: Sagar

last: Chhangawala

first: Ke

last: Xu

first: Christina

last: Leslie

middle: O


title: Ribosome profiling of human platelets, reticulocytes, and in vitro cell lines

first: Eric

last: Mills

state: Maryland

address: 725 N. Wolfe St

summary: Translation is a fundamental biological process and ribosomes are essential in all  cells, but defects in ribosome biogenesis (ribosomopathies) disproportionately  cause hematopoietic dysfunction of red blood cells and platelets. Here, we  analyze translation in primary human reticulocytes and platelets by ribosome  profiling and uncover dramatic accumulation of post-termination, unrecycled  ribosomes in the 3´UTRs of mRNAs. We then demonstrate that these ribosomes  accumulate as a result of the natural loss of the ribosome recycling factor ABCE1  during terminal differentiation. We find that induction of ribosome rescue factors  PELO and HBS1L is required to maintain translational homeostasis when ABCE1  levels fall. This activation of ribosome rescue mitigates the effects of ribosome  shortage on translational output, including on hemoglobin production. Our  observations suggest that this distinctive loss of ABCE1 in anucleate blood  lineages sensitizes them to defects in ribosome homeostasis and that activation  of a ribosome rescue pathway plays a lineage-specific role in maintaining  ribosome homeostasis during blood cell development.

overall_design: Analysis of ribosome profiling and RNA sequencing data from primary human platelets, primary human reticulocytes, in vitro derived platelet-like particles, and hemin-induced differentiation of K562 cells; manipulation by knockdown and overexpression of Pelota (PELO) and HBS1L in K562 cells and Meg01/platelet-like particles.

first: Wangen

last: Jamie

first: Green

last: Rachel

first: Ingolia

last: Nicholas


title: Comparison of crossbred and purebred cattle by bioinformatics analysis of differentially expressed transcripts

city: Rasht

first: Misagh

last: Moridi

address: Rasht-Qazvin highway

department: Animal Science

country: Iran

institute: University of Guilan

summary:
Background: Transcriptomic variation among cattle breeds and their crossbreds may help to better understanding of consequences of crossbreeding and heterosis. In this study the differences in biological functions and pathways of three crossbreds including 50 and 75 percent Holstein were compared with their purebred parents, Holstein and Taleshi (an indigenous breed) cattle.
Results: Five populations and their ten comparisons were studied by bioinformatics tools for transcriptome analysis. We pooled blood RNA of at least 8 animals of each population prior to RNA sequencing. The obtained results showed that total expressed transcripts in all populations were 72,812 with 22,627 annotated genes. Functional analysis of differentially expressed genes (DEGs) showed that the genetics information processing and metabolism were the most highly-impacted pathways. Among all significantly enriched pathways, eukaryotic translation initiation factor-2 signaling had the highest activation z-score (5.3) in crossbred compared to purebred cattle. The majority of upstream regulators of genes including transcription regulators and cytokines were differentially expressed among populations in which their activation z-score in purebred was more than crossbred cattle.
Conclusions: Crossing of Holstein with Taleshi breed resulted in higher activity of pathways related to genetic information processing and lower activity of pathways related to immunity and inflammatory responses. To the best of our knowledge, this is the first study where the differences in pathways and functions were studied using high throughput sequencing of blood in a cattle crossbreeding program. The analysis revealed that the most important differences between studied genotypes, especially between purebred and crossbred cattle, were related to immune functions and metabolism.

overall_design:
the blood transcriptome of five cattle populations including two purebreds and the three crossbreds of them.

Please note that three crossbreds have different parents and different blood share of their purebred parents;
50CSN is 50 percent crossbred sire Iran native cattle and dam Holstein, 50CSH is 50 percent crossbred sire Holstein and dam Iran native cattle, and 75C is 75 percent Holstein and 25 percent Iran native cattle.

first: Seyed

last: Hosseini Moghaddam

last: Mirhoseini

first: Massimo

last: Bionaz


title: The innate immune protein calprotectin promotes Pseudomonas aeruginosa and Staphylococcus aureus interaction

city: Nashville

last: Skaar

state: TN

address: 1161 21st Avenue South Medical Center North RM# A5104

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University School of Medicine

summary: The goal of this study was to determine the impact of metal deprivation (such as the metal deprivation induced by calprotectin treatment) on the physiology of Pseudomonas aeruginosa under multiple growth conditions. The RNA-seq analysis was designed to reveal the impact of calprotectin treatment on P. aeruginosa physiology during planktonic growth.

overall_design: Six samples total were analyzed. Three were control replicates that had been treated only with the buffer used to suspend the recombinant calprotectin protein. The remaining three were replicate samples treated with 0.25 mg/mL calprotectin. All samples were grown for 18 hours under aerobic growth conditions.

first: Catherine

last: Wakeman

first: Jessica

middle: L

last: Moore

first: Michael

last: Noto

first: Yaofang

last: Zhang

first: Marc

middle: D

last: Singleton

first: Boone

last: Prentice

first: Benjamin

last: Gilston

first: Ryan

last: Doster

first: Jennifer

last: Gaddy

first: Walter

last: Chazin

first: Richard

last: Caprioli


title: Elp3 links tRNA modification to IRES-dependent translation of LEF1 to sustain metastasis in breast cancer

city: LIEGE

first: Sylvain

last: Delaunay

state: BELGIQUE

address: Avenue de l'hôpital 1

department: Molecular biology of diseases

country: Belgium

institute: University of Liège

summary: Quantitative and qualitative changes in mRNA translation occur in tumor cells and support cancer progression and metastasis. Post-transcriptional nucleoside modifications of transfer RNAs (tRNAs) at the wobble U34 base are highly conserved and contribute to translation fidelity. Here, we show that ELP3 and CTU1/2, partner enzymes in U34 mcm5s2-tRNA modification, are upregulated in human breast cancers and sustain metastasis. Elp3 genetic ablation strongly impaired invasion and metastasis formation in the PyMT model of invasive breast cancer. Mechanistically, ELP3 and CTU1/2 support cellular invasion through the translation of the oncoprotein DEK. As a result, DEK promotes the IRES-dependent translation of the pro-invasive transcription factor LEF1. Consistently, a DEK mutant, whose codon composition is independent of U34 mcm5s2-tRNA modification, escapes the ELP3- and CTU1-dependent regulation and restores the IRES-dependent LEF1 expression. Our results demonstrate the key role of U34 tRNA modification to support specific translation during breast cancer progression and highlight a functional link between tRNA modification- and IRES-dependent translation during tumor cell invasion and metastasis.analysis of transcriptomic changes due to Elp3genetic deletion in cells extracted from PyMT mammary tumors.

overall_design: Total RNA obtained from 7 weeks old female isolated primary PyMT control tumors and PyMT Elp3 cKO MMTV-CRE tumor condition.

first: Pierre

last: Close


title: Significant gene expression differences between sessile biofilms and planktonic cells of Clostridium thermocellum

status: Public on Sep 28 2016

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

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

department: Biosciences Division

institute: Oak Ridge National Lab

summary: Clostridium thermocellum forms adherent biofilms on lignocellulosic feedstock in a typical continuous cell-monolayer to efficiently break down and uptake cellulose hydrolysates. The adherent biofilm (i.e., sessile cells) may freely revert to the non-adherent form (i.e., planktonic cells) through generation of offspring cells or microenvironment constraints such as limited surface area. The two interdependent cell populations co-exist and have different contributions to culture activity and growth. We developed a novel bioreactor design to rapidly harvest sessile and planktonic cell populations for omics studies. In RNA-seq analyses, within 3299 protein coding genes, 59% (or 1958 genes) were differentially expressed with a minimum two-fold change between the two cell populations isolated simultaneously at high culture activity. Sessile cells had definitive greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division; planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. Knowledge of these cellular adaptations will aid the engineering of industrially relevant strains for consolidated bioprocessing of solid lignocellulosic biomass.

overall_design: Differential RNA-Seq analyses to investigate sessile and planktonic cell populations for omics studies

first: Alexandru

last: Dumitrache

first: Steven

last: Brown


title: Whole transcriptome splicing analysis in isogenic lung epithelial and adenocarcinoma cell lines with or without a recurrent splicing factor mutation, U2AF1 (S34F)

first: Harold

last: Varmus

address: 1300 York Ave

department: Department of Medicine

institute: Weill Cornell Medicine

summary: The splicing factor gene, U2AF1, is recurrently mutated in a variety of human cancers, including lung adenocarcinomas.  The most frequent U2AF1 mutant, U2AF1 p.Ser34Phe (S34F), induces specific changes in pre-mRNA splicing, but it is unclear how these splicing changes are regulated. We have used genomic editing methods to modify the U2AF1 gene locus in an immortalized human bronchial epithelial cell line (HBEC3kt) and in human lung adenocarcinoma cells with pre-existing U2AF1 alleles, creating a U2AF1 S34F allele in the endogenous locus of HBEC3kts and inactivating U2AF1 S34F alleles in two lung adenocarcinoma cell lines (H441 and HCC78). By comparing global splicing alterations in these isogenic pairs of cell lines, we have identified many splicing alterations that are associated with the U2AF1 S34F mutation. Further, by decreasing the levels of wild-type U2AF1 in the isogenic HBEC3kt cells, we show that the magnitude of mutant-associated splicing is proportional to the ratio of S34F:WT gene products. This observation suggest that wild-type U2AF1 is a negative regulator of splicing alterations induced by U2AF1 S34F.

overall_design: mRNA sequencing for the indicated isogenic cell lines using Illunima HiSeq2000 or HiSeq2500, paired-end 101 bp.

first: Dennis

last: Fei

first: Hayley

last: Motowski

first: Sameer

last: Prasad

first: Jovian

last: Yu

first: James

last: Gao

first: Robert

last: Bradley


title: Transcription Factors Sp8 and Sp9 Coordinately Regulate Olfactory Bulb Interneuron Development

first: Jiwen

last: Li

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

overall_design: Refer to individual Series


title: The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity

city: Jerusalem

first: Eran

last: Meshorer

address: Edmond J. Safra Campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Identification of H1.0 genome wide distribution in in-vitro transformed fibroblast before its silencing in tumor CSCs and the localization of the histone modifications H3K27me3 and H3K4me3.

overall_design: ChIP-seq of H1.0, H1.4, H3K4me3 and H3K27me3 in in vitro-transformed human skin fibroblasts. Two biological replicates each were analyzed.

first: C

last: Morales Torres

first: A

last: Biran

first: M

last: Burney

first: H

last: Patel

first: T

last: Henser-Brownhill

first: A-H

last: Shapira Cohen

first: Y

first: R

last: Ben Hamo

first: E

last: Nye

first: B

last: Spencer-Dene

first: P

last: Chakravarty

first: S

last: Efroni

first: N

last: Matthews

last: Misteli

last: Scaffidi


title: RNAseq liver Glucagon+T3

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

summary: 21 samples of liver RNA coming from mice treated with glucagon (Gluc), thyroid hormone (T3), both, or the conjugated compound (Cp). Each sample comes from a single mice.

overall_design: Examination of mRNA levels in livers extracted from individual male mice maintained on a western diet following daily treatment with glucagon, T3, their combination, or a single molecule hybrid of glucagon and T3 for 16 days.

first: Frederic

last: Flamant

last: Luther

first: Brian

last: Finan

first: Christoffer

last: Clemmensen


title: The methylome of Alu repeats in colon cancer (RNA-Seq)

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

summary: Poly-A messenger RNA data for the NSUMA-based assessment of Alu repeats methylation status in colorectal cancer

overall_design: Two replicates of cell lines

first: Tanya

last: Vavouri

first: Izaskun

last: Mallona


title: Genome-wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear messenger RNA cap-binding complex in plant co-translational RNA decay

first: Xiang

last: Yu

address: 800 DongChuan

institute: Shanghai Jiao Tong University

summary: RNA turnover is necessary for controlling proper mRNA levels post-transcriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5’ end to the 3’ end, such as XRN4, or in the opposite direction by the multi-subunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of co-translational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of co-translational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that co-translational RNA decay is XRN4-dependent. Additionally, studies in plants lacking CAP-BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap-binding complex, reveal a role for this protein in co-translational decay. In total, our results demonstrate the global prevalence and features of co-translational RNA decay in a plant transcriptome.

overall_design: polyA-selected global mapping of uncapped transcripts (GMUCT) in Arabidopsis thaliana.

first: Matthew

middle: R

last: Willmann

first: Steve

last: Anderson

last: Gregory


title: Comparison of Eomes-negative and Eomes-positive human liver NK cells by RNASeq

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

address: Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road

institute: Imperial College London

summary: We sorted Eomes-negative NK cells (CD3- CD56+ CXCR6- CD16-) and Eomes-positive NK cells (CD3- CD56+ CXCR6+) from total leukocytes isolated from the perfusion fluid of five healthy human livers destined for transplantation. Total RNA was extracted from sorted cells, cDNA generated and RNASeq performed.

overall_design: Examination of mRNA levels in paired Eomes-negative/Eomes-positive NK cells from the same donor.


title: A penicillin-binding protein inhibits selection of colistin-resistant, lipooligosaccharide-deficient Acinetobacter baumannii

city: Richardson

first: Joseph

middle: Michael

last: Boll

address: 800 W Campbell

department: Biological Sciences

institute: University of Texas at Dallas

summary: We report the transcriptional expression from wild type, a ponA mutant, and lipooligosaccharide-deficient A. baumannii in order to understand the cellular changes after inactivation of lipid A biosynthesis. Among all strains, genes in the Localization Of Lipoprotein (Lol) transport pathway were upregulated. This study provides a framework to understand how some Acinetobacter baumannii strains can survive without lipid A and lipopolysaccharide/lipooligosaccharide.

overall_design: Examination of the global transcriptome in four different A. baumannii strains.

middle: M

first: M

last: Trent


title: RNA-Seq Analysis of Tetranychus cinnabarinus in Response to Curcumin

city: Chongqing

first: Xuejiao

last: Liu

state: Chongqing

address: Tiansheng

institute: Southwest university

summary: RNA-seq was employed to analyze the transcriptome changes in T. cinnabarinus treated with curcumin or solvent. A total of 105, 706, 297 clean sequence reads were generated from the sequencing with more than 90% of the reads were successfully mapped to the reference sequence. The RNA-seq identified 111 and 96 differentially expressed genes between curcumin and solvent treated mites at 24 h and 48 h post treatment, respectively. GO enrichment analysis showed that differentially expressed genes from 24 h post treatment were categorized into 35 GO functional groups and differentially expressed genes from 48 h post treatment were categorized into 25 GO functional groups. The cellular process under the category of biological process was dominant throughout the GO classification at both time points. Finally, we screened 23 differentially expressed genes that are functionally identical or similar to the targets of common insecticide/acaricides or associated with mite detoxification and metabolism. Overall our results revealed the global transcriptional changes in T. cinnabarinus upon curcumin treatment and will enable the further identification of the targets of curcumin on mite.

overall_design: In this study, RNA-seq was employed to analyze the transcriptome changes in T. cinnabarinus treated with curcumin or solvent treatment 24h and 48h.

first: Wei

last: Ding

first: Dousheng

last: Wu

first: Yongiang

last: Zhang

first: Hong

last: Zhou

first: Ting

last: Lai


title: Spatial proximity to fibroblasts impacts molecular features and therapeutic sensitivity of breast cancer cells influencing clinical outcomes

city: Boston

first: Muhammad

middle: B

last: Ekram

state: MA

address: 450 Brookline Avenue, DA 740A

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Using a 3D co-culture model, we identified significant sub-type-specific changes in the gene expression, metabolic, and therapeutic sensitivity profiles of breast cancer cells in contact with cancer-associated fibroblasts (CAFs). CAF-induced gene expression signatures predicted clinical outcome and immune-related differences in the microenvironment. We found that CAFs strongly protect carcinoma cells from lapatinib, attributable to its reduced accumulation in carcinoma cells and an elevated apoptotic threshold. Using synthetic lethality approaches, we identified molecular pathways whose inhibition sensitizes HER2+ breast cancer cells to lapatinib both in vitro and in vivo including JAK2/STAT3 and hyaluronic acid. Neoadjuvant lapatinib therapy in HER2+ breast tumors lead to a significant increase of phospho-STAT3+ cancer cells and a decrease in the spatial proximity of proliferating (Ki67+) cells to CAFs impacting therapeutic responses. Our studies identify CAF-induced physiologically and clinically relevant changes in cancer cells and offer novel approaches for overcoming microenvironment-mediated therapeutic resistance.

overall_design:
SAGE-Seq: Differential expression analysis of five different cell lines (MCF10DCIS, SUM149PT, MCF7, T47D, and MDA-MB-453) representing three different breast cancer sub-types (triple-negative, luminal estrogen receptor positive, and HER2 positive) that were cultured in the presence and absence of cancer-associated fibroblasts (CAFs).
RNA-Seq: Differential expression analysis of stromal fibroblast cells from different origins (primary breast tumors, normal breast tissue, and brain metastases of breast cancer).

first: Andriy

last: Marusyk

first: Doris

middle: P

last: Tabassum

first: Kornelia

last: Polyak


title: Quantitative profiling of the UGT transcriptome in human drug metabolizing tissues

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

institute: Laval University


title: Transcriptome analysis of effects of various nutrients

city: Deagu, Korea

first: Ji-Yeon

last: Kim

address: 80 Daehakro, Bukgu

country: South Korea

institute: Kyungpook National University

summary: We compared profiling of mRNA of cells grown exponentially in various nutrients. mRNA profiles were generated in duplicate, using Illumina HiSeq 2500. Sequenced reads were mapped to the reference genome sequence (GenBank No. CP14334.1).

overall_design: mRNA of cells exponentially grown carbon or nitrogen sources were generated in duplicate, using Illumina HiSeq 2500.

first: Dong-Woo

last: Lee


title: Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L [miRNA-seq]

city: Lanzhou

first: Yan

last: Qiao

state: Gansu Province

address: No. 1 Yingmen village, Anning District

department: College of Agronomy

institute: Gansu Agricultural University

summary: Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus. A total of 31 and 48 miRNAs were identified to be differentially expressed in the leaves and tubers, respectively. Among the DEGs, 1353 genes in the leaves and 1841 genes in the tubers were upregulated, while 1595 genes in the leaves and 897 genes in the tubers were downregulated by light. Mapman enrichment analyses showed that genes related to MVA pathway, alkaloids-like, phenlypropanoids, flavonoids, and carotenoids metabolism were significantly upregulated, while genes associated with major CHO metabolism were repressed in the leaves and tubers. Integrated miRNA and mRNA profiles revealed that light-responsive miRNAs are important regulators in alkaloids metabolism, UMP-salvage, lipid biosynthesis, and cellulose catabolism. Moreover, several miRNAs may participate in glycoalkaloids metabolism via JA signaling pathway, UDP-glucose biosynthesis and hydroxylation reaction. This study provides a global view of transcriptome response in potato response to light, our results suggest that miRNAs might play important roles in secondary metabolic pathways, especially in glycoalkaloid biosynthesis. The findings will enlighten us on the genetic regulation of secondary metabolite pathways and pave the way for future application of genetically engineered potato.

overall_design:
Four RNA samples were used in this experiment. Eight-week-old plantlets were shifted to the dark 3 day and subsequently exposed to red light (～19.7μmol m−2s−1, 630 nm). Then, the leaves of plantlets were collected and immediately frozen in liquid nitrogen after 12, 24, and 48 h, respectively. Equal amounts of total RNA were pooled at 12, 24 and 48 h time points to produce one sample. Dark-grown plantlets were collected as the control. In vitro generated microtubers were treated under the same conditions as described previously.
Please note that the leaves of plantlets were collected and immediately frozen in liquid nitrogen after 12, 24, and 48 h, respectively and equal amounts of total RNA from three time points were pooled to produce one sample. The pooling strategy was employed to reduce the effect of circadian regulation on genes expression. Microtubers were treated under the same conditions and strategy.

first: Jinwen

first: Jinjin

first: Zhiwei

last: Wang

first: Ran

last: An

first: Haixia

last: Guo

first: Di

first: Junlian


title: Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L [RNA-seq]

overall_design: Four RNA samples were used in this experiment. Eight-week-old plantlets were shifted to the dark 3 day and subsequently exposed to red light (～19.7μmol m−2s−1, 630 nm). Then, the leaves of plantlets were collected and immediately frozen in liquid nitrogen after 12, 24, and 48 h, respectively. Equal amounts of total RNA were pooled at 12, 24 and 48 h time points to produce one sample. Dark-grown plantlets were collected as the control. In vitro generated microtubers were treated under the same conditions as described previously.


title: Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity [ChIP-seq]

city: Singapore

first: Aditi

last: Qamra

address: 60 Biopolis Street, Genome, #02-01

institute: GIS

summary: Regulatory elements in cancer remain poorly characterized in primary solid tumors. Here we applied microscale histone modification profiling to delineate the landscape of somatic promoters and super-enhancers in primary gastric adenocarcinoma, analyzing 94 epigenomic  profiles of primary tumors, normal tissues, and cell lines

overall_design: 14 gastric cancer tumor normal pairs and 14 GC lines are profiled in multiple number of chromatin marks. Study includes re-analysis of 132 primary gastric samples from GSE75898 and 35 primary gastric samples from GSE51776.

first: W

last: Ooi

first: Manjie

last: Xing

first: Patrick

last: Tan


title: Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts

city: Sydney

first: Rachel

last: Levin

state: New South Wales

address: UNSW

country: Australia

institute: University of New South Wales

summary: Symbiodinium, the dinoflagellate photosymbiont of corals, is posited to become more susceptible to viral infections when heat-stressed. To investigate this hypothesis, we mined transcriptome data of a thermo-sensitive and a thermo-tolerant type C1 Symbiodinium population at ambient (27°C) and elevated (32°C) temperatures. We uncovered hundreds of transcripts from nucleocytoplasmic large double-stranded DNA viruses (NCLDVs) and the genome of a novel positive-sense single-stranded RNA virus (+ssRNAV). In the transcriptome of the thermo-sensitive population only, +ssRNAV transcripts had remarkable expression levels in the top 0.03% of all transcripts at 27°C, but at 32°C, expression levels of +ssRNAV transcripts decreased while expression levels of antiviral transcripts increased. In both transcriptomes, expression of NCLDV transcripts increased at 32°C, but thermal-induction of NCLDV transcripts involved in DNA manipulation was restricted to the thermo-sensitive population. Our findings reveal that viruses infecting Symbiodinium are affected by heat stress and may contribute to Symbiodinium thermal sensitivity.

overall_design:
Transcriptional regulation of viral and host antiviral transcripts in response to heat stress by two type C1 Symbiodinium populations was analyzed at three time points.

Please note that this is a follow-up study on the GSE72763 data set for a separate publication. Data were re-processed and re-analyzed using the same raw reads and transcriptome assemblies represented in GSE72763 records. The sample records were duplicated for the convenient retrieval of the complete raw data from SRA and the accession of the corresponding (re-analysis) sample is indicated in each sample title.

*min250_nr.fasta: de novo transcriptome of each Symbiodinium population, non-redundant transcripts (min transcript length 250 bp)

*virus_AnnotationReport.xlsx: virus transcript annotation spreadsheet

*antiviral_AnnotationReport.xlsx: antiviral transcript annotation spreadsheet

Trinity_*report.complete.5.xls: annotation of all transcripts in each transcriptome

*nr.counts.txt: read count matrix for all transcripts in each transcriptome

*TMM.fpkm.matrix.txt: FPKM matrix for all transcripts in each transcriptome


title: Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling

city: Tel Aviv-Yafo

first: Tamir

last: Tuller

department: Biomedical Engineering

institute: Tel Aviv University

summary:
Two novel approaches were recently suggested for genome-wide identification of protein aspects synthesized at a given time. Ribo-Seq is based on sequencing all the ribosome protected mRNA fragments in a cell, while PUNCH-P is based on mass-spectrometric analysis of only newly synthesized proteins.
Here we describe the first Ribo-Seq/PUNCH-P comparison via the analysis of mammalian cells during the cell-cycle for detecting relevant differentially expressed genes between G1 and M phase. Our analyses suggest that the two approaches significantly overlap with each other. However, we demonstrate that there are biologically meaningful proteins/genes that can be detected to be post-transcriptionally regulated during the mammalian cell cycle only by each of the approaches, or their consolidation. Such gene sets are enriched with proteins known to be related to intra-cellular signalling pathways such as central cell cycle processes, central gene expression regulation processes, processes related to chromosome segregation, DNA damage, and replication, that are post-transcriptionally regulated during the mammalian cell cycle. Moreover, we show that combining the approaches better predicts steady state changes in protein abundance.
The results reported here support the conjecture that for gaining a full post-transcriptional regulation picture one should integrate the two approaches.

overall_design: Two Ribo-Seq experiments, which included parallel RNA-Seq, one with 3 replicates, and the other with one replicate, totalling 4 technical replicates for the G1 and M phases of the cell cycle, respectively (totalling 16 samples), were performed.

first: Hadas

last: Zur

first: Ranen

last: Aviner


title: Somatic Promoter Landscape of Primary Gastric Adenocarcinoma Delineated by Epigenomic Profiling

summary: Regulatory elements in cancer remain poorly characterized in primary solid tumors. Here we applied microscale histone modification profiling to delineate the landscape of somatic promoters and enhancers in primary gastric adenocarcinoma, analyzing 94 epigenomic  profiles of primary tumors, normal tissues, and cell lines

overall_design: 14 gastric cancer tumor (T) normal (N) pairs and 14 GC lines are profiled in multiple number of chromatin marks