title: 3’READS+, a sensitive and accurate method for 3’ end sequencing of polyadenylated RNA

city: Newark

first: Bin

last: Tian

email: btian@wistar.org, dinghaiz@gmail.com

address: 205 South Orange Ave., F-Bay 7

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University, New Jersey Medical School

summary: Sequencing of the 3’ end of poly(A)+ RNA identifies cleavage and polyadenylation sites (pAs) and measures transcript expression. We previously developed a method, 3’ region extraction and deep sequencing (3’READS), to address mispriming issues that often plague 3’ end sequencing. Here we report a new version, named 3’READS+, which has vastly improved accuracy and sensitivity. Using a special locked nucleic acid oligo to capture poly(A)+ RNA and to remove bulk of the poly(A) tail, 3’READS+ generates RNA fragments with an optimal number of terminal As that balance data quality and detection of genuine pAs. With improved RNA ligation steps for efficiency, the method shows much higher sensitivity (over two orders of magnitude) compared to the previous version. Using 3’READS+, we have uncovered a sizable fraction of previously overlooked pAs located next to or within a stretch of adenylate residues in human genes, and more accurately assessed the frequency of alternative cleavage and polyadenylation (APA) in HeLa cells (~50%). 3’READS+ will be a useful tool to accurately study APA and to analyze gene expression by 3’ end counting, especially when the amount of input total RNA is limited.

overall_design: Nine 3'READS+ libraries were made with different amounts (100 ng, 200 ng, 400 ng, 1000 ng, 5000 ng, 15000 ng) of input Hela RNA.

first: Dinghai

last: Zheng


title: Single nuclei RNA-seq from adult mouse Hippocampus

status: Public on Aug 16 2016

city: Cambridge

first: Naomi

last: Habib

state: MA

address: 75 Ames st

department: Zhang

country: USA

institute: Broad Institute

type: Expression profiling by high throughput sequencing

summary: We report RNA-seq of single nuclei isolated from the adult C57BL/6 male mouse Hippocampus region. Majority of the nuclei were isolated from 12 weeks old mice (4 different animal), with an additional set of nuclei from 3 months and 2 years old animals. In addition a set of GFP labeled nuclei driven by a VGAT promoter .

overall_design: Microdissections of dentate gyrus, CA1 and CA2/3 regions of the Hippocampus were placed into ice-cold  RNA-later for fixation and stored at 4∘c overnight, then stored in -80∘c. Nuclei were isolated by sucrose gradient centrifugation and kept on ice until sorting using Fluorescence Activated Cell Sorting (FACS) into 96 well plates containing RNA lysis buffer. Single nucleus RNA was first purified then derived cDNA libraries were generated following a modified Smart-seq2 protocol. For VGAT nuclei: high titer AAV1/2 of pAAV-EF1a-DIO-EYFP-KASH-WPRE-hGH-polyA was injected into dorsal and/or ventral Hippocampus, animals were sacrificed two weeks after injections, and GFP labeled nuclei were sorted into plates and processed as described above.


title: Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

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

overall_design: Refer to individual Series


title: Mesp1Cre;Hira-/fl and Mesp1Cre;Hira+/fl in heart at E11.5 and E12.5

status: Public on Aug 12 2016

city: London

first: Daniel

last: Dilg

address: 30 Guilford St

country: United Kingdom

institute: University College London

summary:
Purpose:  The goals of this study are to compare transcriptome profiling (RNA-seq) resulting from a Mesp1Cre driven ablation of Hira in the heart at E11.5 and E12.5.
Methods: RNA extraction was done in triplicate from Mesp1Cre;Hira-/fl and Mesp1Cre;Hira+/fl embryonic hearts at E11.5 and E12.5 using the QIAGEN RNeasy mini kit. RNAseq was processed by the ICH genomics facility, reads were aligned and normalised using BOWTIE and  DEseq R package. Strand NGS 2.5 software was used to re-analyse the aligned files (.bam). By applying the Mann Whitney unpaired test, Benjamini Hochberg False discovery rate (FDR) and filtering the genes using adjusted p-value ≤ 0.05 and absolute fold change ≥ 1.5, 95 % of the results were identical to the DEseq package used by the UCL Genomics facility.
Results: We identified 360 coding transcripts changed in the mutant hearts (Mann Whitney unpaired test, Benjamini Hochberg FDR, p ≤ 0.05, FC ≥ 1.5) with no trend towards up- or down-regulation of global transcription (48.8% down vs 51.2% up) at E12.5.
Conclusions: This work analyses the role of HIRA in mouse cardiac development. It was found that Tnni2 is the most upregulated gene in the absence of Hira. qRT-PCR validation of 25 targets. Little (<5%) or no variation of fold change between RNAseq and qRT-PCR data were observed.

overall_design: Cardiac mRNA profiles of 11-day and 12-day embryonic days Mesp1Cre control (Ctrl) and Mesp1Cre;Hira-/fl (mut) were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Tony

last: Brooks

first: Peter

last: Scambler

first: Ariane

last: Chapgier


title: Genome-wide map of HIRA binding sites in the mouse embryonic heart at E12.5

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIPseq experiment revealed that HIRA binds to GAGA rich DNA sequence in the embryonic heart and is enriched at the common enhancer of Tnni2/Tnnt3 (TTe)

overall_design: HIRA ChIPSeq and HIRA input samples, 30 E12.5 CD1 Wild Type hearts pooled


title: Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [methylation]

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

country: China

institute: Kunming Institute of Zoology

type: Methylation profiling by high throughput sequencing

summary: We report the application of DNA sequencing technology for high-throughput sequencing of mix bis-PCR products totally 38 based on bisulfate treated DNA from human, chimpanzee, gibbon, macaque and crab eating macaque profrontal cortex tissues.

sample_organism:
Macaca fascicularis
Macaca mulatta
Pan troglodytes
Homo sapiens
Hoolock leuconedys

overall_design: Mix bisulfate PCR products from 1 tissues, 23 individula humans, 2 individual chimpanzees, 1 individual gibbons, 7  individual rhesus macaques and 5 crab eating macaques were sequenced by using MiSeq

first: Lei

last: Shi

first: Bing

last: Su


title: Mouse MORC3 is a GHKL ATPase involved in gene silencing and localizes to H3K4me3 marked chromatin

status: Public on Aug 15 2016

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: Microrchidia (MORC) proteins are GHKL ATPases that function in gene silencing in multiple organisms. Animal MORCs also contain CW-type zinc finger domains, which are known to bind to modified histones. We identified mouse MORC3 in a mutant screen for factors required for transgene silencing. We also found that MORC3 localizes to promoters marked by H3K4 trimethylation (H3K4me3) throughout the genome, consistent with its binding to H3K4me3 in vitro. We solved the crystal structure of the MORC3 ATPase-CW domain bound to the nucleotide analog AMPPNP and in complex with a H3K4me3 peptide. The CW domain uses an aromatic cage to bind trimethylated Lys4 and forms extensive hydrogen bonds with the H3 tail. We used native mass spectrometry to show that this region forms ATP dependent dimers, and that dimer formation is enhanced in the presence of non-hydrolyzable ATP analogs. Our work sheds light on aspects of the molecular function of MORC3 and suggests a counterintuitive role of MORC3 in both binding to active promoters and regulating gene silencing.

overall_design: ChIP-seq study on 6 Samples.

first: William

middle: A

last: Pastor


title: Chromatin organization in NPP-13 knockdown C. elegans embryos [seq]

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: C. elegans nuclear pore protein NPP-13 associates with small RNA genes transcribed by RNA Polymerase III. To test if the nuclear pore-chromatin interactions play a role in large-scale chromatin organization, we determined nuclear membrane-genome interactions and RNA Polymerase II localization in C. elegans embryos depleted for NPP-13.

overall_design: Genome-wide ChIP-seq and ChIP-chip for nuclear membrane protein LEM-2, RNA Polymerase II (AMA-1) and H3K4me3 were performed in mixed-stage C. elegans embryos depleted for NPP-13. As a control, ChIP was also performed in wild-type embryos treated with empty vector.


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines Panc-1, FaDu and PC3

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines (pancreatic cancer,  hypopharyngeal squamous cell carcinoma and prostate cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (Panc-1, FaDu and PC3) were treated with miRNAs (miR99a-5p, miR-99a-3p, miR-100-3p, miR-150-5p and miR-150-3p), siRNAs (si-FOXQ1).

first: Keiichi

last: Koshizuka


title: A Coccidioides posadasii CPS1 deletion mutant is avirulent and protects mice from lethal infection

city: Tucson

first: Adam

middle: Scott

last: Buntzman

state: Arizona

address: Keating Bio5 Room 319

department: Medicine

institute: University of Arizona

summary: The CPS1 gene was identified as a virulence factor in the maize pathogen, Cochliobolus heterostrophus. Hypothesizing that the homologous gene in Coccidioides posadasii (Cp) could be important for virulence, we created a deletion mutant, Δcps1, which was unable to cause disease in three strains of mice (C57BL/6, BALB/c, or the severely immunodeficient NOD-scid,γcnull [NSG]). Only a single colony was recovered from one of 60 C57BL/6 mice following intranasal infections of up to 4400 spores. Following administration of very high doses (10,000 to 2.5 x 10^7 spores) to NSG and BALB/c mice, spherules were observed in lung sections at time points from day 3 to day 10 post-infection, but nearly all appeared degraded with infrequent endosporulation. Although the role of CPS1 in virulence is not understood, phenotypic alterations and transcription differences of at least 33 genes in Δcps1 vs. Cp is consistent with both metabolic and regulatory functions for the gene. The in vitro phenotype of Δcps1 showed slower growth of mycelia with delayed and lower spore production compared to Cp, and in vitro spherules were smaller. Vaccination of C57BL/6 or BALB/c mice with live Δcps1 spores either intranasally, intraperitoneally or subcutaneously resulted in over 95% survival with mean residual lung fungal burdens <1000 colony-forming units from an otherwise lethal Cp intranasal infection. Considering its apparently complete attenuation of virulence and the high degree of resistance to Cp infection when used as a vaccine, Δcps1 is a promising vaccine candidate for preventing coccidioidomycosis in humans or other animals.

overall_design: Wild type and CPS1 deletion mutant strains of Coccidioides posadasii strain Silveira spherules grown for 48 hours in Converse medium at 38 degrees celsius in duplicate. RNAseq was performed on an Illumina HiSeq2000 (2x100 paired end).

first: Hema

middle: P

last: Narra

first: Lisa

middle: F

last: Shubitz

first: M

last: Mandel

first: Hien

middle: T

last: Trinh

first: Kurt

last: Griffin

middle: S

first: Jeffrey

last: Frelinger

first: John

last: Galgiani

first: Marc

middle: J

last: Orbach


title: 3´-end sequencing of poly(A)+ RNA in wild-type Saccharomyces cerevisiae and nuclear exosome mutant strains

city: Los Angeles

first: Kevin

last: Roy

state: CA

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

summary: The nuclear exosome performs critical functions in non-coding RNA processing, and in diverse surveillance functions including the quality control of mRNP formation, and in the removal of pervasive transcripts.  Most non-coding RNAs and pervasive nascent transcripts are targeted by the Nrd1p-Nab3p-Sen1p (NNS) complex to terminate Pol II transcription coupled to nuclear exosome degradation or 3´-end trimming. Prior to nuclear exosome activity, the Trf4p-Air2p-Mtr4p polyadenylation complex adds an oligo-A tail to exosome substrates.  Inactivating exosome activity stabilizes and lengthens these A-tails.  We utilized high-throughput 3´-end poly(A)+ sequencing to identify at nucleotide resolution the 3´ ends targeted by the nuclear exosome, and determine the sites of NNS-dependent termination genome-wide.

overall_design: 3´-end mapping of wild-type and various nuclear exosome mutant strains, either using gene knockouts or the anchor away system to conditionally deplete FRB-tagged proteins from the nucleus

first: Guillaume

last: Chanfreau


title: An automatec microwell platform for large-scale single cell RNA-seq.

status: Public on Aug 13 2016

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

summary: We report an automated microwell array platform for single cell RNA-seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Performed single cell RNA-seq on thousands of cells from three cell lines.

first: Jinzhou

last: Yuan


title: Effect of Hotair overexpression in human breast cancer cell lines

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: Study of the transcriptome changes upon Hotair overexpression in wt and Ezh2-/- Human breast cancer cell lines

overall_design: 8 samples, 2 replicates for each

first: Portoso

last: Manuela

first: Vassilev

last: Ivaylo

first: Servant

last: Nicolas

first: Margueron

last: Raphael


title: The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome (single cells)

status: Public on Aug 18 2016

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Innate lymphoid cells (ILCs) are critical modulators of mucosal immunity, inflammation, and tissue homeostasis, but their full spectrum of cellular states and regulatory landscapes remain elusive. Here, we use a combination of genome-wide RNA-seq, ChIP-seq and ATAC-seq to compare the transcriptional and epigenetic identity of small intestinal ILCs, identifying thousands of distinct gene profiles and regulatory elements. Single-cell RNA-seq, cytometry, and imaging analyses reveal functional compartmentalization of cytokine expression and metabolic activity within the three classical ILC subtypes, and highlight transcriptional states beyond the current canonical classification. In addition, using antibiotic intervention and germ-free mice, we characterize the effect of the microbiome on the ILC regulatory landscape, and determine the response of ILCs to microbial colonization at the single-cell level. Together, our work characterizes the spectrum of transcriptional identities of small intestinal ILCs and describes how ILCs differentially integrate signals from the microbial microenvironment to generate phenotypic and functional plasticity.

overall_design: ILC1(CD45+CD3-CD19-GR1-B220-CD127+RORγt-NkP46+), ILC2(CD45+CD3-CD19-GR1-B220-CD127+RORγt-KLRG1+) and ILC3(CD45+CD3-CD19-GR1-B220-CD127+RORγt+) were isolated from small intestine lamina propria of WT C57Bl/6 RORγt-GFP mice, or antibiotics treated mice (vancomycin, ampicillin,kanamycin, and metronidazole)


title: Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

first: Jason

last: Ernst

address: 615 Charles E Young Dr South

department: Biological Chemistry

summary: We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities in K562 and HepG2 cells of more than 15,000 human candidate regulatory regions. The regulatory regions were tiled with overlapping constructs enabling high resolution computational inference of activating and repressive nucleotides.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Reporter mRNA-seq from HepG2 and K562 cells were transfected with a ~54,000-plex MPRA plasmid pool for a 'PilotDesign' and ~244,000-plex pool for a 'ScaleUpDesign'. In the 'PilotDesign' each regulatory region was associated with constructs at nine positions spaced in 30-bp increments with each position linked to 24 10-nt tags. In the 'ScaleUpDesign'  each regulatory region was associated with constructs at 31 positions spaced in 5-bp increments with each position linked to a single 10-nt tag. There were two separate sets of sequences based on the 'ScaleUpDesign'. In the 'PilotDesign' all experiments were conducted with a SV40 promoter, while for the 'ScaleUpDesign' there were separate experiments based on a SV40 and minimal TATA promoter. The reporter mRNA tags facilitate quantitation of their abundances. The same tags were also sequenced from the transfected MPRA plasmid pool to facilitate normalization to plasmid copy numbers. All transfections were done in duplicate. MPRA plasmid pools were amplified and sequenced in replicate for the pilot design and for each design and promoter type for the 'ScaleUpDesign'.

first: Alexandre

last: Melnikov

first: Xiaolan

last: Zhang

first: Li

last: Wang

last: Rogov

first: Tarjei

last: Mikkelsen

first: Manolis

last: Kellis


title: Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp

city: Lausanne

first: Felix

last: Naef

address: Route Cantonale

department: Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

summary: In mammals body temperature fluctuates diurnally around a mean value of 36-37°C. Despite the small differences between minimal and maximal values, body temperature rhythms can drive robust cycles in gene expression in cultured cells and, likely, in, animals. Here we studied the mechanisms responsible for the temperature-dependent expression of Cold- Inducible RNA-Binding Protein (CIRBP). In NIH3T3 fibroblasts exposed to simulated mouse body temperature cycles Cirbp mRNA oscillates about 3-fold in abundance, as it does in mouse liver. This daily mRNA accumulation cycle is directly controlled by temperature oscillations and does not depend on the cells’ circadian clocks. Here, we show that the temperature-dependent accumulation of Cirbp mRNA is controlled primarily by the regulation of splicing efficiency, defined as the fraction of Cirbp pre-mRNA processed into mature mRNA. As revealed by genome-wide “approach-to-steady-kinetics”, this posttranscriptional mechanism is wide-spread in the temperature-dependent control of gene expression.

overall_design: Cultured NIH3T3 cells seeded and kept at 37C degree for 4 hours before being switched to 33C and 38C. After 16 hours of incubation the temperature was shifted to 38C and 33C, respectively. Sample were then taken at 0, 1, 3, 6 and 9 hour after the temperature shift. Paired-end, strand-specific, total RNA-seq was performed over the samples at the respective time points using the Illumina HiSeq2500 platform.

first: Ivana

last: Gotic

first: Saeed

last: Omidi

first: Fabienne

last: Fleury-Olela

first: Nacho

last: Molina

first: Ueli

last: Schibler


title: Genome-wide transcriptome analyses by RNAseq to determine the change that happens in the peripheral taste system with age.

city: Buffalo

first: Jayasha

last: Shandilya

state: New York

address: 619 Cooke Hall

department: Biological Sciences

institute: SUNY at University at Buffalo

summary: To understand the mechanisms that regulate the renewal and maintenance of taste cells we performed RNA-sequencing analysis on isolated taste cells from 2 and 6 month old mice to determine how alterations in the taste cell-transcriptome regulate taste cell maintenance and function in adults. We found that the Activator Protein-1 (AP1) transcription factors (c-Fos, Fosb and c-Jun) and genes associated with this pathway were significantly  downregulated in taste cells from 6 month old mice and further declined at 12 months. We generated conditional c-Fos- knockout mice to target K14-expressing cells, including differentiating taste cells. c-Fos deletion caused a severe perturbation in taste bud structure and resulted in a significant reduction in the taste bud size. c-Fos deletion also affected taste cell turnover as evident by, a decrease in proliferative markers, and upregulation of the apoptotic marker cleaved-PARP. Thus, AP1 factors are important regulators of adult taste cell renewal and their downregulation negatively impacts taste maintenance.

overall_design:
Comparison of genes responsible for peripheral Taste system maintenance at age, 3 and 6 months.
processed_data.txt: List of B vs S gene expression data
gene_exp.diff: cuffdiff data for 2 and 6 month taste cells

first: J

first: Y

last: Gao

first: T

middle: K

last: Nayak

first: S

middle: E

last: Roberts

first: K

last: Medler


title: Effects of Lin28a overexpression on gene expression changes during culturing neural stem cells (NSCs) derived from mouse embryonic ventral midbrain (VM)

status: Public on Aug 11 2016

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: we want to see gene expression changes during in vitro expansion of VM-derived NSCs (VM-NSCs) with cell passges in the absence or presence of Lin28a overexpression. changes upon Lin28 overexpression in P1 and P3 stages of Neural stem cells.

overall_design: RNA-seq, sRNA-seq, and Polysome-seq with/without Lin28 overexpression in P1 and P3 stages of Neural stem cells.

first: Sang-Hun

last: Lee

first: Yong-Hee

last: Rhee


title: Disruption of human-specific synaptogenesis program in autism [RNA-seq]

city: Shanghai

first: Xiling

last: Liu

address: 320 Yue Yang Road

institute: Partner Institute for Computational Biology

summary: To test the connection between the molecular mechanisms underlying autistic disorder and human cognitive evolution, we analyzed the gene expression changes taking place during prefrontal cortex development in autism patients and healthy controls, as well as non-human primates. We found the genes with expression changes in autism are significantly overlapped with genes showing human-specific developmental profile. A major pattern of the overlapped genes reflects the aberrant acceleration of synaptogenesis and synaptic maturation followed by premature synaptic pruning in the prefrontal cortex of autism patients. This pattern involves the same developmental program that controls human-specific extension of cortical synaptogenesis in healthy individuals. Taken together, these findings shed light on the molecular mechanisms underlying autistic phenotype and provide potential targets for clinical intervention.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Compare the gene expression change in autism and the gene expression specificly changed in human.

first: Dingding

last: Han


title: In vivo characterization of Linc-p21 reveals functional cis-regulatory DNA elements

first: Abbie

last: Groff

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

summary: We have sequenced wildtype and mutant heart, liver, lung, and hindlimb from E14.5 embryos of the mutant lncRNA strain Trp53cor1tm1.1Vlcg (lincp21), and performed a massively parallel reporter assay (MPRA) in mouse myoblast cells (C2C12).

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Comparison between wildtype and mutant organ transcriptomes in the Trp53cor1tm1.1Vlcg strain. Additionally, we include a comparison between MPRA signal vector tag distributions and C2C12 tag distributions.

first: A

middle: L

last: Rinn


title: Feedback regulation of ABA signaling and biosynthesis by OsbZIP23 that targets diverse drought resistance related genes in rice

city: Austin

first: Wei

last: Zong

state: Texas

department: Molecular Biosciences

institute: University of Texas at Austin

summary: The OsbZIP23 transcription factor has been characterized for its essential role in drought resistance in rice, but the mechanism is unknown. Here, we performed genome-wide identification of OsbZIP23 targets by immunoprecipitation sequencing (ChIP-seq) and RNA Sequencing (RNA-Seq) analyses in the OsbZIP23-overexpression, osbzip23 mutant, and wild-type rice under normal and drought stress conditions. OsbZIP23 directly regulates a large number of reported genes that function in stress response, hormone signaling, and developmental processes. Among these targets, we found that OsbZIP23 could positively regulate OsPP2C49, and overexpression of OsPP2C49 in rice resulted in significantly decreased sensitivity of the ABA response and rapid dehydration. Moreover, OsNCED4 (9-cis-epoxycarotenoid dioxygenase 4), a key gene in ABA biosynthesis, was also positively regulated by OsbZIP23. Together, our results suggest that OsbZIP23 acts as a central regulator in ABA signaling and biosynthesis, and drought resistance in rice.

overall_design: Genome-wide identification binding sites of OsbZIP23 under drought stress. Examination of mRNA levels in OsbZIP23 mutants and over expressed plants under normal and drought stress condition.

first: W

first: L

last: Xiong


title: Identification of a colitogenic memory CD4+ T cell population that mediates gastrointestinal GVHD

city: Milwaukee

first: William

last: Drobyski

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Using an experimental model of graft versus host disease (GVHD) to examine T cell-mediated inflammation within the colon, we identified a unique CD4+ T cell population that constitutively expresses the β2 integrin, CD11c, has a biased central memory phenotype and memory T cell transcriptional profile, possesses innate-like properties by gene expression analysis, and has increased expression of the gut-homing molecules, α4β7 and CCR9.  Using a number of complementary GVHD mouse models, we show that adoptive transfer of these cells results in TH1-mediated proinflammatory cytokine production, augmented pathological damage in the colon, and increased mortality due to early accumulation of these cells in the GI tract.  The pathogenic effects of this CD4+ T cell population was critically dependent upon co-expression of the IL-23 receptor which was required for maximal inflammatory effects.  Colonic inflammation was regulated by IL-10 that was produced by non-Foxp3-expressing CD4+ T cells which attenuated lethality in the absence of functional CD4+ Foxp3+ T cells.  Thus, coordinate expression of CD11c and the IL-23R defines a novel IL-10 regulated, colitogenic memory CD4+ T cell subset that is poised to initiate inflammation when there is loss of tolerance and breakdown of mucosal barriers as occurs in GVHD as well as other immune-mediated inflammatory bowel disorders.

overall_design: Examination of the transcriptional profile of a novel population of CD4+ CD11c+ T cells that had a central memory T cell phenotype

first: Vivian

last: Zhou

first: Kimberle

last: Agle

first: Xiao

last: Chen

first: Amy

last: Beres

first: Richard

last: Komorowski

first: Ludovic

last: Belle

first: Carolyn

last: Taylor

first: Fenlu

last: Zhu

first: Dipica

last: Haribhai

first: Calvin

middle: B

last: Williams

first: James

last: Verbsky

first: Wendy

last: Blumenschein

first: Svetlana

last: Sadekova

first: Eddie

last: Bowman

first: Christie

last: Ballantyne

first: Casey

last: Weaver

first: David

last: Serody

first: Benjamin

last: Vincent

first: Jonathan

first: Daniel

last: Cua

middle: R


title: Genome-wide analysis of the transcriptional and alternative splicing landscape in intestinal organoids undergoing nutrient starvation or ER stress

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

summary: Our study represents the first detailed analysis of the transcriptional and alternative splicing landscape of intestinal organoids undergoing stress, with biologic replicates, generated by RNA-seq technology. We report significant changes in the expression of genes involved in inflammation, proliferation and transcription, among others. Splicing events commonly regulated by both stresses affected genes regulating splicing and were associated with nonsense-mediated decay (NMD), suggesting that splicing is modulated by an auto-regulatory feedback loop during stress.

overall_design: Murine intestinal organoids were stimulated in triplicate with conditions for either ER stress or nutrient starvation and RNA-seq was conducted to analyze global changes in both gene expression at the transcriptional level and alternative splicing

first: Jessica

last: Tsalikis

first: Stephen

last: Girardin


title: Coevolution of hormone metabolism and signaling networks expands plant adaptive plasticity

city: Cambridge

first: Jing-Ke

last: Weng

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Differential transcriptomic analysis of 10-day-old Arabidopsis seedlings treated with 50 μM ABA, PA, or DPA.

overall_design: 10-day-old Arabidopsis seedlings grown on MS medium was treated with 50 μM ABA, PA, or DPA. Total RNA was extracted from biological duplicates, Illumina RNAseq was performed on each sample.

first: Joseph

last: Noel


title: The landscape of mouse meiotic double-strand break formation, processing and repair

first: Julian

last: Lange

address: 1275 York Avenue

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: SPO11 generates hundreds of DNA double-strand breaks (DSBs) to initiate meiotic recombination. Heritability and genome stability are shaped by the nonrandom distribution of DSBs, but mechanisms molding this landscape remain poorly understood. Here we exploit genome-wide maps of mouse DSBs at unprecedented nucleotide resolution to uncover previously invisible spatial features of recombination. At fine scale, we reveal a stereotyped hotspot structure––DSBs occur within narrow zones between methylated nucleosomes––and identify relationships between SPO11, chromatin, and the histone methyltransferase PRDM9. At large scale, DSB formation is suppressed on non-homologous portions of the sex chromosomes via the DSB-responsive kinase ATM, which also shapes the autosomal DSB landscape at multiple size scales. We also provide the first genome-wide analysis of exonucleolytic DSB resection lengths and elucidate spatial relationships between DSBs and recombination products. Our results paint a comprehensive picture of features that govern successive steps in mammalian meiotic recombination.

overall_design: Five samples total: SPO11-oligo maps from C57BL/6J (one map), Atm+/+ (one map), Atm+/– (map), and Atm–/– (two biological replicate maps) mice

first: Scott

last: Keeney


title: Comparative Methylome Analyses Reveal Human Brain Specific Methylated Regions Implicated in Transcription Regulation

city: Atlanta

first: Soojin

middle: V

last: Yi

state: GA

address: 950 Atlantic Dr

department: School of Biology

institute: Georgia Institute of Technology

summary: To gain further insights into human brain specific epigenetic changes, we generated whole genome bisulfite sequencing methylation maps (methylomes) of rhesus macaque brains. These were then compared to methylomes of human and chimpanzee brains that were previously generated. We then performed validation experiments using targeted bisulfite sequencing.

overall_design: Bisulfite-seq in prefrontal cortext of two male Macaca mulatta

first: Isabel

last: Mendizabal


title: Identification of p63 binding regions in a p63 expressing basal-subtype breast cancer cell line, MCFDCIS.

city: Dallas

first: Xiaoyu

last: Wang

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

summary: p63 ChIP-SEQ in a p63 expressing basal-subtype breast cancer cell line, MCFDCIS and in a p63 deficient claudin-low subtype breast cancer cell line, MDA-MB-231

overall_design: p63 ChIP-SEQ on MCFDCIS and MDA-MB-231 cell lines

first: Gray

middle: W

last: Pearson


title: Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation

first: Fabiana

last: Duarte

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

summary: The coordinated regulation of gene expression at the transcriptional level is fundamental to development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use precision run-on sequencing (PRO-seq) to examine the genome-wide heat shock (HS) response in Drosophila and the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS. We identify the primary HS response genes and the rate-limiting steps in the transcription cycle that GAGA-associated factor (GAF) and HS factor (HSF) regulate. We demonstrate that GAF acts upstream of promoter-proximally paused RNA polymerase II (Pol II) formation (likely at the step of chromatin opening) and that GAF-facilitated Pol II pausing is critical for HS activation. In contrast, HSF is dispensable for establishing or maintaining Pol II pausing but is critical for the release of paused Pol II into the gene body at a subset of highly activated genes. Additionally, HSF has no detectable role in the rapid HS repression of thousands of genes.

overall_design: We used PRO-seq to map the distribution of transcriptionally engaged RNA polymerases in Drosophila S2 cells before (non-Heat Shock) and after 20min of Heat Shock in LacZ-RNAi (control), GAF-RNAi, HSF-RNAi and M1BP-RNAi treated cells. We also performed PRO-seq as a function of time after Heat Shock induction (30sec, 2min, 5min, 10min and 20min) in S2 cells. Furthermore, we used RNA-seq to measure mRNA levels in S2 cells before (non-Heat Shock) and after 30min of Heat Shock. All experiments were performed in two biological replicates.

middle: M

first: Nicholas

last: Fuda

first: Dig

last: Mahat

first: Leighton

last: Core

first: Michael

last: Guertin

first: John

last: Lis


title: 3´-end sequencing of poly(A)+ RNA in wild-type Saccharomyces cerevisiae and a strain carrying a deletion of the RRP6 nuclear exosome catalytic component

first: Kevin

last: Roy

address: 607 Charles E. Young Drive East

summary: The nuclear exosome performs critical functions in non-coding RNA processing, and in diverse surveillance functions including the quality control of mRNP formation, and in the removal of pervasive transcripts.  Most non-coding RNAs and pervasive nascent transcripts are targeted by the Nrd1p-Nab3p-Sen1p (NNS) complex to terminate Pol II transcription coupled to nuclear exosome degradation or 3´-end trimming. Prior to nuclear exosome activity, the Trf4p-Air2p-Mtr4p polyadenylation complex adds an oligo-A tail to exosome substrates.  Inactivating exosome activity stabilizes and lengthens these A-tails.  We utilized high-throughput 3´-end poly(A)+ sequencing to identify at nucleotide resolution the 3´ ends targeted by the nuclear exosome, and determine the sites of NNS-dependent termination genome-wide.

overall_design: 3´-end mapping of wild-type and a nuclear exosome mutant strain by direct RNA sequencing (DRS) (SeqLL, LLC).  RNAs from WT and the RRP6 deletion strain were loaded into four separate channels on the HeliScope single molecule sequencer.

first: Guillaume

last: Chanfreau


title: Nuclear exosome

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

overall_design: Refer to individual Series


title: Ras and TGF-beta signaling aggravates the metastatic and invasive potential of cancer cells through activation of the deltaNp63 alpha transcriptional program

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo


title: Comparison of transcriptomes of sig-7 (RNAi) vs WT C. elegans early stage embryos by RNA-seq

status: Public on Aug 10 2016

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: RNAi targeting a conserved C. elegans cyclophilin, sig-7, causes defective development and embryonic arrest consistent with a global defect in transcription. The goal of this study was to compare the transcript levels in sig-7(RNAi) embryos to those of L4440/RNAi control embryos to examine the global transcriptional effect caused by of loss of sig-7 function

overall_design: Examination of RNA levels using RNAseq in 2 replicate samples each of early embryos from sig-7(RNAi) and RNAi controls

first: William

middle: G

last: Kelly

first: Jeong

last: Ahn

first: Andreas

last: Rechsteiner


title: BCR repertoire analyis of class-switched and non-switched thymic B cells

city: Chicago

first: Zhong

last: Zheng

state: IL

address: 924 E57th ST, Room 402

department: Section of Rheumatology

institute: University of Chicago College of Medicine

summary: We report that a large percentage of thymic B cells undergo class switching intrathymically. Thymic B cell class switching requires cognate T-B interaction. To determine whether B cell specificity was also important for thymic B cell class-switching, we sorted class-switched thymic B cells (CD19+B220+IgM-IgD-), unswitched B cells (CD19+B220+IgM+IgD+) and bulk splenic B cells in 3H9 heavy chain-fixed mice and performed high throughput sequencing analysis of the light chain of these populations. Results of this analysis indicated that class-switched thymic B cells have a distinct repertoire compared with unswitched thymic B cells and splenic B cells. Further reactivity tests indicated that a large part of BCRs enriched in class-switched thymic B cells are autoreactive. These data suggest that autoreactive B cells are selected into class-switched population and expanded in the thymus.

overall_design: Light chain repertoire profiles of class-switched thymic B cells, unswithced thymic B cells and splenic B cells from 3H9 mice were generated by deep sequencing.

first: Jason

last: Perera

first: Haochu

last: Huang


title: Gene expression signatures for primary tumor and tumor-derived exosomes

first: Liu

last: Yanfang

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: To determine the different gene signatures between primary tumor and tumor-derived exosomes, we have employed RNA-sequencing as a discovery platform to identify gene signatures of tumor-derived exosomes, taking the original tumors as a control. We subcutaneously inoculated C57BL/6 mice with Lewis lung carcinoma (LLC). Three weeks later, tumor tissues were cut and tumor-derived exosomes were isolated as described in the "treatment protocol". Then, both exosomal RNA and tumor RNA were extracted and sequenced. From sequencing, we found that exosomal RNAs showed quite different transcript profiles from tumor RNAs.

overall_design: Examination of different gene signatures between primary tumor and tumor-derived exosomes. 2 replicates each.

first: Xuetao

last: Cao

first: Yanfang

last: Liu


title: Alterations in Tissue microRNA after Heat Stress in the Conscious Rat: Potential Biomarkers of Organ-Specific Injury

city: Fort Detrick

first: Matthew

last: Permenter

state: MD

address: 568 Doughten Dr

institute: US Army Center for Environmental Health Research

summary: Heat illness, which remains an occupational and environmental hazard, can be caused by excessive strain or heat load in combination with other factors. In the 10-year period from 1999 to 2009, an average of 658 annual heat-related deaths occurred in the United States. While heat stress at the cellular level has been studied, a paucity of risk assessment and injury biomarkers as well as therapeutic interventions remains.   To identify novel biomarkers and to further understand the molecular mechanisms of heat stress, we identified differentially expressed microRNAs (miRNAs) in the heart, liver, and kidney from a conscious rat model at three time points. We distinguished the effect in animals with histopathological evidence of heart injury from those without evidence of organ injury. In animals without evidence of injury, we identified a total of 45 unique modulated miRNAs, whereas in the three animals with evidence of injury, we identified 171 unique differentially expressed miRNAs. The majority of the perturbed miRNAs were both time and tissue specific. Using the data from a microarray companion study, we identified the mRNAs that are the predicted targets of the differentially expressed miRNAs and performed pathway enrichment analysis. The enrichment analysis suggested that the perturbed miRNAs are involved in biological pathways related to energy metabolism, the unfolded protein response, and organ injury. These miRNAs may serve as organ-specific heat stress biomarkers of exposure or effect, as well as identify potential targets of heat illness prevention.

overall_design: Heart, liver, lung and kidney tissue was collected from rats at Tc,max and at 24 and 48 h for both heat exposed rats (n=4 to 6) or time matched, unheated controls (n= 4 to 6)

first: Young

last: Lee

first: Bonna

middle: C

last: McDyre

first: Danielle

last: Ippolito

first: Taek-Kyun

last: Kim

first: Kai

last: Wang

first: Jonathan

middle: D

last: Stallings


title: HiSeq Chip-seq analysis of whole genomic landscape of G9a and H3K9me2-targeted in CCICs

city: TAIPEI

first: SHIH-TING

last: CHA

address: 6F., No.2, Syu-jhou Road,

country: Taiwan

institute: National Taiwan University

summary:
Purpose: to demonstrate that G9a maintain CCICs functional triats is independent of its methyltransferase activity.
Method: ChIP-seq was applied to CCICs to elucidate the nature of G9a and H3K9me2-regulated differential gene targets by Illumina/Soleza Genome analyzer
Results: It was shown that ghe 4,902 G9a-and H3K9me2-targeted genes are broadly idstributed throughout the genome, and both are co-localized at most of the sites in CCICs.

overall_design: G9a and H3K9me2-targeted in CCICs

first: S

last: Cha


title: p63 binding regions in HaCaT epidermal keratinocyte infected with caRAS/dnRAS and treated with TGF-beta

first: Daizo

last: Koinuma

summary: We evaluated the effect of caRAS/dnRAS expression and TGF-beta on p63 binding in HaCaT cells.

overall_design: p63 binding sites in HaCaT cells were determined by ChIP-seq.

first: Eleftheria

last: Vasilaki

first: Masato

last: Morikawa

first: Anna

last: Mizutani

first: Yudai

last: Hirano

first: Shogo

last: Ehata

first: Anders

last: Sundqvist

first: Hiroyuki

last: Aburatani

first: Aristidis

last: Moustakas

first: Carl-Henrik

last: Heldin

first: Kohei

last: Miyazono


title: PHB Acts as a Member of the HIRA Complex to Control an Epigenetic and Metabolic Circuitry

first: Zhexin

last: Zhu

institute: Chinese Academy of Sciences

summary: Cellular metabolism and chromatin landscape both contribute to cell fate determination. However, their interplay remains poorly understood. Here we show that Prohibitin (PHB), an evolutionarily conserved protein, involves in a histone variant H3.3 chaperon HIRA complex-dependent epigenetic and metabolic circuitry to maintain the identity of human embryonic stem cells (hESCs). We found that silencing of PHB triggers hESC differentiation with concomitant enhancements of histone 3 (H3) lysine (K) methyl modifications as a result of the reduced production of α-ketoglutarate (α-KG), a metabolite required for activities of many dioxygenase and in turn chromatin structure1,2. Mechanistically, PHB acts as a functional member of the HIRA complex3,4. Resembling PHB deficiency, loss of HIRA in hESCs leads to massive differentiation and aberrant histone modifications, although it was previously found not to disrupt the self-renewal in mouse ESCs (mESCs)5. Genome-wide H3.3 ChIP- sequence analyses indicate that reduction of H3.3 deposition caused by PHB knock down is extremely similar to that induced by HIRA knock down. Specifically, silencing either HIRA or PHB leads to repressive chromatin characters at promoters of pluripotency genes and isocitrate dehydrogenases (IDHs), the enzyme responsible for α-KG production, but active chromatin features at promoters of developmental genes, paralleling to transcript levels of these genes. Our results identify PHB as an essential factor not only for hESC self-renewal but also for the proper function of the HIRA complex, linking the HIRA complex-dependent H3.3 deposition to the production of a critical metabolite required for shaping chromatin structure, and demonstrating the importance of the interplay between epigenetic state and metabolic regulation in cell fate determination.

overall_design: Examination of H3.3 deposition in NT, PHB, and HIRA siRNA treated hESCs respectively.

first: Yanwu

last: Zeng

first: Chunliang

last: Li

first: Junjie

last: Gu

first: Laixiang

last: Ge

first: Fan

last: Tang

first: Ying

last: Jin


title: Adrenalectomy plus corticosterone treatment, rat hippocampal RNA-seq

city: Boston

first: Richard

middle: G.

last: Hunter

state: Massachusetts

address: 100 William Morrissey Blvd.

department: Psychology

institute: University of Massachusetts Bo

summary: Male Sprague-Dawley rats 8 weeks old, were adrenalectomized, treated with 300ug/kg corticosterone or vehicle 3 days after surgery then sacrificed 1 hour later. Hippocampi were removed and RNA extracted and processed for sequencing at the Massachusetts General Hospital Nex-Generation Sequening Core.

overall_design: Includes 6 cort treated and 6 control biological replicates


title: HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos

first: Susan

last: Strome


title: Developmental regulation of piRNAs during spermatogenesis in Drosophila melanogaster

city: Singapore

first: Toshie

last: Kai

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: The piRNA pathway is studied in great detail in Drosophila female germline. In this study we show that unlike the female germline where all Piwi proteins are expressed throughout oogenesis, Ago3 - a Piwi family protein shows a spatial expression male germline. To understand dynamics of piRNA pathway during spermatogonia and primary spermatocyte stages of male germline development, we used arrest mutants. The bag of marbles (bam) and benign gonial cell neoplasm (bgcn) mutants have only early mitotic dividing germline cells in the testes due to failure to progress to primary spermatocyte stage, the cannonball (can) and spermatocyte arrest (sa) mutant germline cells cannot progress beyond primary spermatocyte stage. To investigate the dynamics of the piRNA pathway during spermatogenesis in spermatogonia and primary spermatocyte stages, we used testicular tissues from these stage-specific arrested mutants. While we used entire bam and bgcn mutant testes for spermatogonia purification, we while we manually removed the apical regions of can and sa mutant testes to exclude mitotically dividing undifferentiated germline cells for primary spermatocytes purification. Our results show that piRNAs mapping to transposons are more abundant in spermatogonia, whereas those mapping to Suppressor of Stellate [Su(Ste)] and AT-chX are mostly expressed in primary spermatocytes. Furthermore we observed that transposon-mapping piRNAs with ping-pong signature are more abundant in spermatogonia albeit still detectable in primary spermatocytes where Ago3 is not expressed. These results suggest that robust piRNA production via ping-pong cycle takes place in spermatogonia, and to a lesser extent in primary spermatocytes even in the absence of Ago3. Consistently, piRNAs from ago3 mutant testes also exhibit the ping-pong signature, confirming that a non-canonical ping-pong cycle is acting during spermatogenesis. Our study provides a developmental dimension to the piRNA pathway and uncovers a new mechanism used in the male germline to silence transposons.

overall_design: The difference in piRNA from spermatogonia and primary spermatocyte stages was studied by comparing small RNAs from bam and bgcn mutant testis, which represent spermatogonia stages with the small RNAs from apex removed can and sa testis, representing primary spermatocyte stages. In the study we also studied effect of loss of Piwi family proteins Aub and Ago3, which have different spatial expression during male germline development.

first: Amit

last: Anand


title: NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation

status: Public on Aug 09 2016

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

country: Germany

institute: Goettingen University

summary: Mitochondrial gene expression uses a non-universal genetic code in mammals. Besides reading the conventional AUG codon, mitochondrial (mt-)tRNAMet mediates incorporation of methionine on AUA and AUU codons during translation initiation and on AUA codons during elongation. We show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt-tRNAMet to methylate cytosine 34 (C34) at the wobble position. NSUN3 specifically recognises the anticodon stem loop (ASL) of the tRNA, explaining why a mutation that compromises ASL basepairing leads to disease. We further identify ALKBH1/ABH1 as the dioxygenase responsible for oxidising m5C34 of mt-tRNAMet to generate an f5C34 modification. In vitro codon recognition studies with mitochondrial translation factors reveal preferential utilization of m5C34 mt-tRNAMet in initiation. Depletion of either NSUN3 or ABH1 strongly affects mitochondrial translation in human cells, implying that modifications generated by both enzymes are necessary for mt-tRNAMet function. Together, our data reveal how modifications in mt-tRNAMet are generated by the sequential action of NSUN3 and ABH1, allowing the single mitochondrial tRNAMet to recognise the different codons encoding methionine.

overall_design: HEK293 cell lines expressing His-FLAG-tagged NSUN3 or the His-FLAG tag alone were crosslinked using UV or treated with 5-azacytidine and analysed by CRAC

first: Sara

last: Haag

first: Katherine

last: Sloan

first: Namit

last: Ranjan

first: Ahmed

last: Warda

first: Jens

last: Kretschmer

first: Charlotte

last: Blessing

first: Benedikt

last: Hübner

first: Jan

last: Seikowski

first: Sven

last: Dennerlein

first: Peter

last: Rehling

first: Marina

last: Rodnina

first: Claudia

last: Höbartner


title: Using RNA Seq to validate transcriptional profile data obtained by Nanostring analysis

city: Hanover

first: Deborah

middle: A

last: Hogan

state: NH

department: Microbiology and Immunology

institute: Dartmouth College

summary:
Purpose : The goal of this study was to use RNA Seq to validate transcriptional data of two clinical isolates focussing on a subset of 74 transcript that were selected specifically for Nanostring analysis.
Methods : mRNA profiles were generated for the clinical isolates FRD1 and CI224_M, in duplicate, by deep sequencing. Strains were grown for 8 hours in LB medium at 37C prior to RNA harvest. Ribosomal RNA was removed using the Ribi-Zero rRNA Removal Kit (Epicentre). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters.

overall_design: mRNA profiles of liquid cultures grown for 8 hours in LB at 37C were generated for P. aeruginosa clinical isolates FRD1 and CI224_M, each in duplicate, by deep sequencing using Illumina NextSeq.

last: Willger

first: Alex

last: Gifford

first: Heather

last: Bean


title: Cnot3-dependent mRNA deadenylation safeguards the pluripotent state

city: Res Triangle Park

first: Guang

last: Hu

state: NORTH CAROLINA

address: 111 T. W. Alexander dr.

department: ESCBL

institute: NIH/NIEHS

summary: Poly(A)-tail length and mRNA deadenylation play important roles in post-transcriptional gene regulation. Here, we report the regulation of mRNA expression, half-life, and polysome association in mouse embryonic stem cells by the Cnot3 subunit in the Ccr4-Not mRNA deadenylase complex.

overall_design: To determine the consequence of Cnot3 deletion, Cnot3 conditional knockout ESCs were first treated with DMSO (WT) or 0.1μM 4-hydroxytamoxifen (4OHT, KO).   1. In one experiment, cells were collected 3 days after the 4OHT treatment and total RNAs were extracted and sequenced to determine changes in mRNA expression.   2. In the second experiment, cells were collected 3 days after the 4OHT treatment and polysome-associated RNAs were fractionated using a published protocol, purified, and sequenced to determine changes in polysome-association.   3. In the third experiment, cells were further treated with actinomycin D (10ug/ml) 2 days after the initial 4OHT treatment. Cells were collected at 0, 4, 8 hrs after actinomycin D treatment and total RNAs were extracted and sequenced to determine changes in mRNA half-life.  Two biological replicates were carried out for each experiment. RNAs were extracted using RNA purification kits from Life Technologies, and RNA-seq libraries were prepared using Illumina TruSeq RNA library preparation kit.

first: Hu

last: Guang

first: Xiaofeng

last: Zheng


title: Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Three biological replicates of H. volcanii grown under optimal conditions to mid-exponential growth phase were used to determine the primary transcriptome and map 5’-ends of transcripts. In total, 4,749 potential transcriptional start sites (TSS) were detected. A position weight matrix was derived for promoter prediction, showing that 64% of the TSS were preceded by stringent or relaxed basal promoters. 1,851 TSS belonged to protein-coding genes, showing that less than half (46%) of the 4040 protein-coding genes are expressed under optimal growth conditions. 72% of all protein-coding transcripts were leaderless, underscoring that this is the default pathway for translation initiation in haloarchaea. The 5’-UTRs of transcripts with leaders had a widely varying length distribution without any optimum. 2,898 of the TSS belong to potential non-coding RNAs, representing an unexpectedly high fraction (61%) among all transcripts. 2792 of the non-coding TSS had not been described before and were thus novel (59% of all TSS). A large fraction of the potential novel non-coding transcripts are cis-antisense RNAs (1,244 aTSS). There was a strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs, suggesting that negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts correspond to internal transcripts overlapping with mRNAs (1,153 iTSS) and intergenic small RNA (sRNA) candidates (395 TSS).

overall_design: Three biological replicates were performed with slight differences in library preparation. In each case, part of the sample was treated with terminator 5'-phosphate-dependent exonuclease (+TEX), while part of the sample remained untreated (-TEX). Therefore, in total, six samples were analysed by high-throughput sequencing.

first: Julia

last: Babski

first: Karina

last: Haas

first: Daniela

last: Näther-Schindler

first: Matthias

last: Hammelmann

first: Friedhelm

last: Pfeiffer

middle: U

first: Rolf

last: Hilker

first: Anke

last: Becker

first: Cynthia

last: Sharma

first: Anita

last: Marchfelder

first: Jörg

last: Soppa


title: RNAseq changes in fibroblasts after treatment with selected protein(s) or E16.5 skin extract

city: Taipei

first: Mai-Yi

last: Fan

address: No1, Sec. 1, Jen - Ai Rd.

summary:
Purpose: To identify the cellular processes upregulated in fibroblasts after treatment with selected protein(s) or E16.5 skin extract
Methods: To explore the mechanism of extract-induced HF neogenesis, adult dermal fibroblasts were cultured in the presence of E16.5 extract or selected protein(s) for 3 days before being tested.
Results: we determined how the exposure of adult fibroblasts to E16.5 extract, the selected protein mix or each of the selected proteins and compared the resultant transcriptomes with those of adult DP and embryonic dermal fibroblasts.
Conclusions: Gene expression of adult fibroblasts exposed to E16.5 extract and selected proteins mix, the key DP signature genes became upregulated.

overall_design: Fibroblasts mRNA profiles of mouse with different treatments and adult DP and embryonic dermal fibroblasts were generated by next generation sequencing. SRA study accession: SRP081009; BioProject accession: PRJNA337890

first: Sabrina

first: Sung-Jan

last: Lin


title: Elucidation of Transcriptome-Wide MicroRNA Binding Sites in Human Cardiac Tissues by Ago2 HITS-CLIP

city: Iowa City

first: Ryan

last: Boudreau

state: IA

address: 500 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: We deciphered Ago2:RNA interactions in post-mortem human heart tissues using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts.

overall_design: Profiling AGO2-associated RNAs in cardiac tissues obtained from 6 donors with heart diseases of differing etiologies

last: Boureau

last: Spengler


title: Gene expression analysis of CD122HI versus CD122LO Vγ7+ murine small intestinal IEL at 14-17 days of age

city: London

first: Rafael

last: Di Marco Barros

address: 44 Lincolns Inn Fields

institute: Francis Crick Institute

summary:
Background: The neonatal (D14-17) murine small intestinal epithelium is enriched for Vγ7+ IEL displaying an ‘immature’ CD122LO cell surface phenotype. We believe these cells are precursors for signature CD122HI Vγ7+ IEL that predominate among small intestinal IEL from postnatal D21.

Method: To further characterise this potential precursor-product relationship, CD122hi Vg7+ and CD122lo Vg7+ IEL were purified from individual D14-D17 mice on four independent occasions and compared by total RNAseq.

Conclusion: ~3000 genes are differentially expressed between CD122HI and CD122LO murine Vg7+ neonatal IEL

overall_design: 4 independent Paired samples of CD122hi Vg7+ and CD122lo Vg7+ IEL were purified from the small intestinal epithelium of pooled 14-17 day old mice. RNA was isolated from sorted samples. Gene expression analysis was performed by total RNAseq.

first: Natalie

last: Roberts

first: Robin

last: Dart

first: Pierre

last: Vantourout

first: Anett

last: Jandke

first: Oliver

last: Nussbaumer

first: Philip

last: East

first: Livija

last: Deban

first: Sara

last: Cipolat

first: Rosie

last: Hart

first: Maria

last: Iannitto

first: Adam

last: Laing

first: Bradley

last: Spencer-Dene

first: Deena

last: Gibbons

first: Peter

last: Irving

first: Pablo

last: Pereira

first: Ulrich

last: Steinhoff

first: Adrian

last: Hayday


title: The Chromatin-Looping Factor ZNF143 Engages at Looping Promoters to Favor the Estrogen Response in Breast Cancer (ChIP-seq)

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College street

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: Estrogen signaling in breast cancer cells relies on long-range chromatin interactions connecting distal regulatory elements bound by the estrogen receptor 1 (ESR1) to target gene promoters. This ensures stimulus and subtype-specific transcriptional responses. Expanding on the function of CTCF and the cohesin complex in breast cancer, we demonstrate that the chromatin-looping factor ZNF143 binds the promoter of most early-response estrogen target genes connected to distal regulatory elements in ESR1-positive breast cancer cells. Its chromatin occupancy is unaffected by estrogen stimulation, supporting a stable three-dimensional genomic architecture within the early response to estrogen. Its loss abrogates the estrogen-induced transcriptional response and growth of breast cancer cells. When taking into account CTCF, ZNF143 and cohesin complex subunits, we show that chromatin-looping factors are genetically altered in over 20% of ESR1-positive primary breast tumors. Furthermore, the overexpression of ZNF143, CTCF and RAD21, a cohesin complex subunit, in ESR1-positive breast tumors associates with a worse clinical outcome. Overall, our results suggest that ZNF143 is a new critical effector of the estrogen response and highlights the contribution of the chromatin looping machinery to ESR1-positive breast cancer development.

overall_design: Examination of genome-wide ZNF143 binding in MCF-7 cells

first: Aislinn

last: Treloar

first: Xiaoyang

last: Zhang

first: Xue

last: Wu


title: Transcriptome profiling of the human dorsal striatum in bipolar disorder

city: Jupiter

first: Ronald

last: Davis

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: The Scripps Research Institute - Scripps Florida

summary: Bipolar disorder (BD) is a highly heritable and heterogeneous mental illness whose manifestations often include impulsive and risk-taking behavior. This particular phenotype suggests that abnormal striatal function could be involved in BD etiology, yet most transcriptomic studies of this disorder have concentrated on cortical brain regions. We report the first transcriptome profiling by RNA-Seq of the human dorsal striatum comparing bipolar and control subjects. Differential expression analysis and functional pathway enrichment analysis were performed to identify changes in gene expression that correlate with BD status. Further co-expression and enrichment analyses were performed to identify sets of correlated genes that show association to BD.

overall_design: Total RNA samples were isolated from 36 postmortem dorsal striatum subjects (18 bipolar and 18 control) and sequenced. One outlier sample was removed and 35 samples (18 bipolar and 17 control) were analyzed.

first: Rodrigo

last: Pacifico


title: RNA-Seq analysis of wild-type and Brpf1-null fetal liver LSK cells

city: Montreal

first: Xiang-Jiao

last: Yang

state: Quebec

address: 1160 Pine Ave W

department: Medicine

institute: McGill University

summary: To compare the impact of hematopoietic-specific Brpf1 gene inactivation, LSK (Lin-Sca1+cKit1+) cells were sorted from wild-type and Brpf1-null fetal liver cells for RNA-Seq.

overall_design: Four E14.5 embryos were used to pool sufficient LSK cells for total RNA isolation and subsequent sequencing on HiSq2500. Two independent pairs of wild-type and mutant RNA samples (each of which contained LSK cells pooled from four embryos) were used for oligo-dT primed RNA Seq.

first: Linya

last: You

first: Jinfeng

last: Zou

first: Edwin

last: Wang


title: Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes[RNA-Seq]

city: Rochester

first: Jennifer Jane

last: Westendorf

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: Histone deacetylase inhibitors are efficacious epigenetic-based therapies for some cancers and neurological disorders; however, these drugs inhibit multiple Hdacs and have detrimental effects on the pre- and post-natal skeleton.  To better understand how Hdac inhibitors affect the skeleton, we focused on understanding the role of one of their targets, Hdac3, in endochondral bone formation by deleting it in immature murine chondrocyte micro masses with Adeno-Cre. Hdac3-deficient chondrocytes expressed higher levels of pro-inflammatory and matrix degrading genes (e.g., Il-6, Mmp3, Mmp13, Saa3)  and lower levels of genes related to the extracellular matrix production, bone development and ossification (e.g., Acan, Col2a1, Ihh, Col10a1).  Histone acetylation was increased in and around genes with elevated expression.

overall_design: High Throughput RNA sequencing and Chromatin immunopreciptation sequencing experiments were performed in chondrocyte cultures. Differential analysis was conducted on ChIP-seq and RNA-seq data to identify H3K27Ac profile for up and down regulated genes in Hdac3-deficient murine chondrocytes.

first: Jennifer

first: Lomeli

last: Carpio

first: Asha

last: Nair

first: Krutika

last: Gaonkar

first: Jaime

last: Davila


title: Transcriptional profile of Salmonella enterica serovar Typhimurium 4/74 wild-type and mutants using strand-specific RNA-seq

city: Liverpool

first: Jay

last: Hinton

address: Crown Street

department: Institute of Integrative Biology

institute: University of Liverpool

summary: New tools for studying bacterial transcripts at the single nucleotide level offer an unparalleled opportunity to understand the bacterial transcriptome. For the model pathogen Salmonella enterica serovar Typhimurium, it is necessary to identify the regulatory inputs for all RNA transcripts, including small RNAs (sRNAs) and coding genes. Here, we use RNA-seq to define the transcriptomes of mutants lacking 18 global regulatory systems that, among other functions, modulate the expression of the SPI1 and SPI2 Type Three secretion systems in S. Typhimurium strain 4/74. We directly compared the roles of the major regulators of transcription, and reported the effects of the regulatory mutations on expression of sRNAs. We also use this method to describe the impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

overall_design: Transcriptome analysis of S. Typhimurium 4/74 using RNA isolated wild-type and mutants grown under infection-relevant conditions.

first: Aoife

last: Colgan

first: Carsten

last: Kröger

first: Médéric

last: Diard

first: Wolf-Dietrich

last: Hardt

first: José

last: Puente

first: Sathesh

last: Sivasankaran

first: Karsten

last: Hokamp


title: Comparison of RNA Pol II localization in the genomes of sig-7 (RNAi) vs WT C. elegans early stage embryos

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

institute: UC Santa Cruz

summary: RNAi targeting a conserved C. elegans cyclophilin, sig-7, causes defective development and embryonic arrest consistent with a global defect in transcription. The goal of this study was to compare the location of RNA Pol II in sig-7(RNAi) embryos to the localization in L4440/RNAi control embryos to examine the global effect of loss of sig-7 on RNA Pol II regulation and its distribution within gene bodies

overall_design: anti-AMA-1 ChIP in 2 replicates each of sig-7(RNAi) and RNAi control early stage embryos

first: William

last: Kelly

first: Jeong-Hyun

last: Ahn

first: Andreas

last: Rechtsteiner


title: Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes

first: Jennifer Jane

last: Westendorf

summary:
Histone deacetylase inhibitors are efficacious epigenetic-based therapies for some cancers and neurological disorders; however, these drugs inhibit multiple Hdacs and have detrimental effects on the pre- and post-natal skeleton.  To better understand how Hdac inhibitors affect the skeleton, we focused on understanding the role of one of their targets, Hdac3, in endochondral bone formation by deleting it in immature murine chondrocyte micro masses with Adeno-Cre. Hdac3-deficient chondrocytes expressed higher levels of pro-inflammatory and matrix degrading genes (e.g., Il-6, Mmp3, Mmp13, Saa3)  and lower levels of genes related to the extracellular matrix production, bone development and ossification (e.g., Acan, Col2a1, Ihh, Col10a1).  Histone acetylation was increased in and around genes with elevated expression.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
High Throughput RNA sequencing and Chromatin immunopreciptation sequencing experiments were performed in chondrocyte cultures. Differential analysis was conducted on ChIP-seq and RNA-seq data to identify H3K27Ac profiles for up and down-regulated genes in Hdac3-deficient murine chondrocytes.
mm10 was used as reference genome.
Refer to individual Series


title: Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes[ChIP-Seq]

first: Jennifer

first: Lomeli

last: Carpio

first: Huihuang

last: Yan

first: Jinfu

last: Nie

first: Jeong

last: Lee


title: rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

summary: RNA structures are of crucial importance for biological function and gene regulation. Guanine (G)-rich sequences in RNA can assemble to form RNA G-quadruplex (rG4) structures; specific rG4s have been shown to regulate gene expression, and are associated with human diseases. However, no transcriptome-wide method has been reported to map rG4s, limiting our understanding of the rG4 structure and its relationship with function and regulation. Here we introduce a transcriptome-wide rG4 profiling method, rG4-Seq, in which the rG4-mediated reverse transcriptase stalling is read out by next-generation sequencing at nucleotide resolution. We apply this method to human RNA and report the first global map of rG4 structures for any organism. Our analysis identifies over 3,000 rG4s, and increases to over 11,000 upon addition of a rG4 stabilizing ligand Pyridostatin (PDS). Notably, we discover that besides canonical rG4s, many rG4s are non-canonical with novel structural features such as long-loops, bulges, and 2-quartet. We also find that rG4 formation is associated with its stability, Cytosine (C)-content, and the stability of alternative RNA structures. Our data reveals that rG4s can be found in messenger RNAs (mRNAs) and long intergenic noncoding RNAs (lincRNAs). In mRNAs, rG4s are enriched in untranslated regions, and are significantly correlated with microRNA target sites and polyadenylation signals. Remarkably, we found that majority of our in vitro identified rG4s can change the in silico predicted RNA structure to uncover alternative RNA conformation.. Futhermore, the rG4s that have analogues in many ortholog genes across different species show a preferential association with RNA processing and stability. rG4-seq is a broadly applicable method that enables the RNA G4 structurome and its biological roles to be interrogated and can be readily applied in other organisms on a transcriptome-wide scale.

overall_design: 12 samples, 150 bp single-ended RNA-Seq libraries from cell extracts after performing RTS reaction in different buffers (Li, K and K+PDS rich buffer). Each of the 3 conditions has 4 libraries from independent biological replicates.

first: Chun

last: Kwok

first: Aleksandr

last: Sahakyan

first: Vicki

middle: S

last: Chambers

first: Shankar

last: Balasubramanian


title: AroA deficient Salmonella Typhimurium – More than an auxotrophic mutant

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

summary: Recombinant attenuated Salmonella are believed to act as powerful live vaccine carrier able to elicit protection against many infectious agents. ∆aroA exhibits auxotrophy for aromatic amino acids and is commonly used for attenuation. Interestingly, deletion of aroA dramatically increased virulence of the Salmonella. Detailed analyses demonstrate that Salmonella’s physiology is significantly altered, most likely due to osmotic imbalance and stress. The result is a serious influence of lipid and amino acid turn over, possible increasing sensitivity to penicillin, complement and phagocytic uptake. In addition, in concert with other immunomodulating mutations, the phase of flagella expression is changed. Furthermore, virulence associated genes like arnT or ansB were affected. These alterations could explain the increased virulence. Thus, intravenous application of ∆aroA Salmonella to mice significantly increased induction of pro-inflammatory cytokines. We also employed such bacteria in therapy against tumors and realized that ∆aroA strains display an improved anti-tumor activity.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: The samples of Salmonella Typhimurium Wild type strain and derivates (SF100 (ΔlpxR9 ΔpagL7 ΔpagP8), SF101 (ΔaroA), SF102 (ΔlpxR9 ΔpagL7 ΔpagP8 ΔaroA)) were analyzed by RNA-seq. The control samples were cultivated in the LB medium until the exponential phase. Four biological replicas were pooled in pairs to get two replicas for RNA extraction, library preparation and sequencing. Tumor samples were collected from mice infected with Wt Salmonella and SF102. Bacterial RNA was extracted from single tumors. The tumor samples were split into two technical replicas for sequencing library preparation.

first: Sebastian

last: Felgner

first: Michael

last: Frahm

first: Dino

last: Kocijancic

first: Manfred

last: Rohde

first: Agata

last: Bielecka

first: Wolf-Rainer

last: Abraham

first: Roy

last: Curtiss III

first: Susanne

last: Haeussler

first: Marc

last: Erhardt

first: Siegfried

last: Weiss


title: Histone Arginine Methylation in Cocaine Action: Essential Role of Src Signaling in the Nucleus Accumbens

status: Public on Aug 08 2016

city: New York

first: Eric

last: Nestler

state: NY

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: Despite addiction being one of the most prevalent and debilitating disorders worldwide, effective treatments are lacking. Repeated cocaine exposure induces maladaptive transcriptional regulation within the brain’s reward circuitry, such as the nucleus accumbens (NAc), and epigenetic mechanisms, such as histone acetylation or methylation on Lys (K) residues, have been linked to these lasting actions of cocaine. However, in contrast to K methylation, the functional role of histone Arg (R) methylation remains unexplored in addiction models and poorly understood in brain in general. Here we show that protein-R-methyltransferase-6 (PRMT6) and its associated histone mark, asymmetric dimethylation of R2 on histone H3 (H3R2me2a), are decreased in the NAc of mice and rats after repeated cocaine exposure, as well as in the NAc of cocaine-addicted humans. PRMT6 downregulation occurs selectively in NAc medium spiny neurons expressing dopamine D2 receptors (D2-MSNs) and serves to protect against cocaine-induced addictive-like behavioral abnormalities. Using ChIP-seq, we demonstrate that reduced H3R2me2a binding at gene targets in NAc after repeated cocaine is strongly correlated with increased binding of H3K4me3, and identify Src kinase signaling inhibitor 1 (Srcin1 or p140Cap) as a key gene for these chromatin modifications. Cocaine induction of Srcin1 in NAc, which is associated with reduced Src signaling, decreases cocaine reward, the motivation to self administer cocaine, and cocaine-induced changes in NAc MSN dendritic spines. These results suggest that this suppression of Src signaling in NAc D2-MSNs, via PRMT6 and H3R2me2a downregulation, functions as a homeostatic brake to restrain cocaine action, and provide novel candidates for the development of new treatments for cocaine addiction.

overall_design: H3R2me2A ChIP-seq of mouse. Cocaine vs Saline, 3 biological replicates.

first: Diane

last: Damez Werno

first: Ning-Yi

last: Shao

first: Li

last: Shen


title: Foxn1 choreographs both early and late events in thymic lympho-stromal cross-talk

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Normal thymic T cell development is enabled by a stromal microenvironment most importantly composed of distinct epithelial cell populations in cortex and medulla. Their differentiation, growth and function require the expression of the transcription factor Foxn1. Direct targets of Foxn1 have, however, remained largely undefined. Utilizing newly created static and inducible genetic model systems, we now provide a genome wide map of Foxn1 target genes and the sequences bound by this master regulator. Foxn1 controls not only essential steps early in intrathymic lymphoid development including T cell lineage commitment but is also indispensable for later stages in T cell maturation such as the selection of CD4 and CD8 T cells. Thus, Foxn1 function critically choreographs both early and late events in thymic lympho-stromal cross-talk.

overall_design:
Foxn1 ChIP-seq and RNA-seq in mouse models of hypofunctional or conditional knock-out of Foxn1
Brief sample descriptions are shown below:
Foxn1 ChIP-seq (GSM1945905) - chromatin immunoprecipitated using an antibody against FOXN1-FLAG (wt*); 2 samples
Input ChIP-seq (GSM1945906) - input chromatin; 2 samples
42cT (GSM1945907) - RNA-seq on wt*/-::nu/nu cTEC; 3 samples
42mT (GSM1945908) - RNA-seq on wt*/-::nu/nu mTEC; 2 samples
96cT (GSM1945909) - RNA-seq on wt*/wt*::nu/nu cTEC; 3 samples
96mT (GSM1945910) - RNA-seq on wt*/wt*::nu/nu mTEC; 2 samples
NcT (GSM1945911) - RNA-seq on Dox-treated TetO- iFoxn1(del7,8) cTEC; 5 samples
PcT (GSM1945912) - RNA-seq on Dox-treated TetO+ iFoxn1(del7,8) cTEC; 5 samples
C57BL/6 mice (GSM1945913) - ATAC-seq on wild-type cTEC; 1 sample
Please see each sample for more detailed information.

first: Saulius

last: Zuklys

first: Georg

last: Höllander


title: Suppression of ischemia in arterial occlusive disease by JNK-promoted native collateral artery development

city: Worcester

first: Kasmir

last: Ramo

state: MA

address: 273 Plantation Street, Biotech II, Suite 309

department: Molecular Medicine

institute: University of Massachusetts Medical School

summary: Arterial occlusive diseases are major causes of morbidity and mortality. Blood flow to the affected tissue must be restored quickly if viability and function are to be preserved. Collaterals are artery-to-artery or arteriole-to-arteriole interconnections that can bypass an occlusion by providing an alternative route for blood flow to the affected tissue. The increased flow and sheer stress initiate processes that result in the remodeling (arteriogenesis) of these vessels into efficient conductance arteries. Here we report that the mixed-lineage kinase (MLK) pathway activates cJun NH2-terminal kinase (JNK) in endothelial cells. Disruption of Mlk2/3 or Jnk1/2 genes caused severe blockade of blood flow and failure to recover in the femoral artery ligation model of hindlimb ischemia because of abnormal collateral arteries. We show that the MLK-JNK pathway is essential for patterning and maturation of collateral arteries during development, but this pathway is not required for angiogenesis or arteriogenesis in adults. JNK in endothelial cells promotes Delta-like 4-induced Notch signaling and suppresses excessive sprouting angiogenesis during development. This function of the MLK-JNK pathway contributes to normal formation of native collateral arteries. The MLK-JNK pathway is therefore a key regulatory mechanism for vascular development. These data highlight the crucial importance of the collateral circulation in the response to arterial occlusive diseases.

overall_design: RNA-seq analysis of mouse lung endothelial cells (MLEC) of the following genotypes Cdh5-Cre+ Jnk1+/+ Jnk2+/+ Jnk3-/-(ECtrl), Cdh5-Cre- Jnk1LoxP/LoxP Jnk2LoxP/LoxP Jnk3-/- (EfCtrl), and Cdh5-Cre+ Jnk1LoxP/LoxP Jnk2LoxP/LoxP Jnk3-/- (E3KO).  Three separate samples from mouse lung endothelial cells of each genotype were analyzed.

first: Roger

middle: J

last: Davis


title: Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome

city: Houston

first: Rodney

last: Samaco

state: TX

address: 1250 Moursund St.

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The goal of this study was to characterize a novel Mecp2 allele in the laboratory rat, a distinct rodent species from the laboratory mouse with unique features. The allele was created by zinc finger-nuclease (ZFN) targeting (SAGE/Horizon) of the X-linked gene, Methyl-CpG-Binding Protein 2 (Mecp2), resulting in normal Mecp2 RNA abundance, but absent protein in male rats as expected due to the presence of only one copy of mutant Mecp2, and an approximate 50% reduction in female rats as expected from animals that harbor one wild-type copy and one mutant copy of Mecp2. Behavioral characterization of female rats with the Mecp2 ZFN allele and wild-type littermates was conducted, and Mecp2 ZFN/+ female rats showed behavioral phenotypes that were consistent with disease-like features present during the early stages of disease onset in the neurological disorder Rett syndrome. The goal of conducting RNAseq studies was to compare existing gene expression alterations in the Mecp2 rat with one of the most widely studied Mecp2 mouse model. Hypothalami were obtained from males with complete loss of MeCP2 (ZFN/y) and wild-type littermate male rats for RNA-seq studies. Common and unique gene expression alterations among the Mecp2 rodents that were then tested  in human Rett and control postmortem brain revealed the benefit of combining findings from both models, suggesting the predictive validity of this approach for future studies for the identification of potential preclinical outcome measures. QPCR validation in an independent set of rats was conducted with a subset of genes from the Mecp2 ZFN rat RNA-seq data as an additional control measure. Taken together, these findings demonstrate that the Mecp2 rat model is a complementary tool with unique features for the study of RTT and highlight the potential benefit of cross-species analyses in identifying potential disease-relevant preclinical outcome measures.

overall_design: Transcriptional profiles of hypothalamic samples obtained from male rats haboring a novel zinc-finger nuclease Mecp2 loss-of-function allele and corresponding wild-type littermate rats were generated using RNA-seq

first: Surabi

last: Veeraragavan

first: Ying-Wooi

last: Wan

first: Zhandong

last: Liu


title: Interbacterial signaling via Burkholderia contact-dependent growth inhibition proteins

city: Chapel Hill

first: Peggy

last: Cotter

state: NC

address: 125 Mason Farm Rd, 6205 Marsico

institute: University of North Carolina

summary: In prokaryotes and eukaryotes, cell-cell communication and recognition of self are critical to coordinate multicellular functions. While kin and kind discrimination are increasingly appreciated to shape naturally occurring microbe populations, the underlying mechanisms that govern these interbacterial interactions are insufficiently understood. Here we identify a mechanism of interbacterial signal transduction that is mediated by contact-dependent growth inhibition (CDI) system proteins. CDI systems have been characterized by their ability to deliver a polymorphic protein toxin into the cytoplasm of a neighboring bacterium, resulting in growth inhibition or death unless the recipient bacterium produces a corresponding immunity protein. Using the model organism Burkholderia thailandensis, we show that delivery of a catalytically active CDI system toxin to immune (self) bacteria results in gene expression and phenotypic changes within the recipient cells. Termed contact-dependent signaling (CDS), this response promotes biofilm formation and other community-associated behaviors.

overall_design:
Examination of wild-type Burkholderia thailandensis and two mutant strains, each in triplicate (9 samples total).

mutant BtEKA contains two amino acid substitutions (E3064A and K3066A) within the coding sequence of gene Bth_I2723. In mutant PS12-WT, the native promoter of gene Bth_I2723 has been replaced with the strong constitutive promoter of the E264 rpsL gene, PS12.

first: Erin

last: Garcia


title: Global gene expression profiles of cardiac progenitors differentiated from human pluripotent stem cells in 3D culture under simulated microgravity

city: Atlanta

first: Rajneesh

last: Jha

state: Georgia

address: 2015 Uppergate Dr

department: Pediatric Cardiology

institute: Emory University School of Medicine

summary:
Methods: RNA-seq libraries were prepared using the Illumina TruSeq RNA kit and the TrueSeq method was employed for mRNA enrichment. The libraries were quantified and samples were multiplexed in each lane of the flowcell. Cluster generation was performed and then sequenced on the Illumina HiSeq1000 system. Reads were mapped on the Human Genome Reference and normalized expression table was generated.
Results: Among differentially expressed genes, 53 of them were up-regulated and 75 were down-regulated.
Conclusions: Data demonstrate increased expression of genes associated with growth, development, and pro-survival in cardiac progenitors cultured under simulated microgravity compared with those cultured under standard gravity.

overall_design: RNA-sequencing analysis was performed to compare global gene expression profiles of cells at differentiation day 8 under simulated microgravity vs. standard gravity.

first: Mary

last: Wagner

first: Nirav

last: Patel

first: Gregory

last: Tharp

first: Steven

last: Bosinger

first: Chunhui

last: Xu


title: Differentiation and specification of resident tissue macrophages [ID3-KO RNA-seq]

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Tissue resident macrophages are functionally diverse cells that share an embryonic mesodermal origin. However, the mechanism(s) that control their specification remain unclear. We performed transcriptional, molecular and in situ spatio-temporal analyses of macrophage development in mice. We report that Erythro-Myeloid Progenitors generate pre-macrophages (pMacs) that simultaneously colonize the head and caudal embryo from embryonic day (E)9.5 in a chemokine-receptor dependent manner, to further differentiate into tissue F4/80+ macrophages. The core macrophage transcriptional program initiated in pMacs, is rapidly diversified in early macrophages as expression of transcriptional regulators becomes tissue-specific. For example, the preferential expression of the transcriptional regulator Id3 initiated in early fetal liver macrophages appears critical for Kupffer cell differentiation, as inactivation of Id3 causes a selective Kupffer cell deficiency that persists in adults. We propose that colonization of developing tissues by differentiating macrophages is immediately followed by their specification as they establish residence, hereby generating the macrophage diversity observed in post-natal tissues.

overall_design: RNA-sequencing of ID3+/- and ID3-/- Kupffer cells

first: Elvira

last: Mass

first: Ivan

last: Ballesteros

first: Matthias

last: Farlik

first: Florian

last: Halbritter

first: Patrick

last: Gunther

first: Lucile

last: Crozet

first: Christian

middle: E

last: Jacome-Galarza

first: Johanna

last: Klughammer

first: Yasuhiro

last: Kobayashi

first: Elisa

last: Gomez-Perdiguero

first: Joachim

last: Schultze

first: Marc

last: Beyer

first: Frederic

last: Geissmann


title: The Chromatin-Looping Factor ZNF143 Engages at Looping Promoters to Favor the Estrogen Response in Breast Cancer

first: Mathieu

last: Lupien

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

overall_design: Refer to individual Series


title: The Chromatin-Looping Factor ZNF143 Engages at Looping Promoters to Favor the Estrogen Response in Breast Cancer (RNA-seq)

summary: Estrogen signaling in breast cancer cells relies on long-range chromatin interactions connecting distal regulatory elements bound by the estrogen receptor 1 (ESR1) to target gene promoters. This ensures stimulus and subtype-specific transcriptional responses. Expanding on the function of CTCF and the cohesin complex in breast cancer, we demonstrate that the chromatin-looping factor ZNF143 binds the promoter of most early-response estrogen target genes connected to distal regulatory elements in ESR1-positive breast cancer cells. Its chromatin occupancy is unaffected by estrogen stimulation, supporting a stable three-dimensional genomic architecture within the early response to estrogen. Its loss abrogates the estrogen-induced transcriptional response and growth of breast cancer cells. When taking into account CTCF, ZNF143 and cohesin complex subunits, we show that chromatin-looping factors are genetically altered in over 20% of ESR1-positive primary breast tumors. Furthermore, the overexpression of ZNF143, CTCF and RAD21, a cohesin complex subunit, in ESR1-positive breast tumors associates with a worse clinical outcome. Overall, our results suggest that ZNF143 is a new critical effector of the estrogen response and highlights the contribution of the chromatin looping machinery to ESR1-positive breast cancer development.

overall_design: mRNA profiles of MCF-7 cells (siCtl or siZNF143) under vehicle (EtOH) or E2 (10 uM 17-beta oestradiol) stimulation

first: Aislinn

last: Treloar


title: RNA-seq Analysis of Control DPSC and DPSC Derived Neurons

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

summary: A major challenge to the study and treatment of neurogenetic syndromes is the difficulty in gaining access to live neurons from individuals with these disorders. Although other sources of stem cells are currently available for differentiation into neurons, these can involve invasive procedures and be difficult or expensive to generate limiting their use on a broad scale, especially for rare syndromes which may not be well represented in the local population.  Dental pulp stem cells (DPSC) are neural crest derived multipotent stem cells that reside deep the pulp of shed (baby) teeth and have the potential for broad use in the study of neurogenetic disease.  In order to investigate the characteristics of DPSC which make them a valuable resource for the study of neurogenetic syndromes we performed a set of viability, senescence and immortalization studies on control DPSC and DPSC derived neurons. We investigated the basic transport conditions and determined the maximum passage number for primary DPSCs. We then immortalized control DPSC using human telomerase reverse trancriptase (hTERT) and evaluated both neuronal differentiation potential and gene expression changes using RNAseq. Here we show that immortalized DPSC share morphological and electrophysiological properties with non-immortalized DPSC.  We also show that differentiation of DPSC into neurons changes gene expression for 1305 transcripts, while immortalized neurons differ significantly in gene expression for 183 transcripts of which 94 also changed during differentiation. Taken together, these studies indicate that immortalized dental pulp derived neruons may be a new and powerful resource for the study of rare neurological disorders where patient samples are rare or difficult to obtain.

overall_design: RNA-seq Analysis of 3 neurotypical control DPSC, 3 DPSC derived neurons and 3 each immortalized versions of DPSC and DPSC neurons (~3 weeks post maturation)

first: Norra

last: Urraca

first: Rawaha

last: Memon

first: Sarita

last: Goorha

first: Colleen

last: Valdez

middle: T

first: Reese

last: Scroggs

first: Martin

last: Donaldson

first: Dave

last: Bridges

first: Lawrence

last: Reiter


title: Differentiation and specification of resident tissue macrophages [SMART-Seq2]

first: Christoph

last: Bock

overall_design: RNA-sequencing of sorted macrophage cell populations (Mac) and progenitors (EMP, pMac) from various tissues and collected at different time points, including technical and biological replicates

first: Elvira

last: Mass

first: Ivan

last: Ballesteros

first: Matthias

last: Farlik

first: Florian

last: Halbritter

first: Patrick

last: Gunther

first: Lucile

last: Crozet

first: Christian

last: Jacome-Galarza

first: Johanna

last: Klughammer


title: Quantitative analysis of wild type and MeCP2-/y mice hippocampus miRNAs using next generation sequencing

city: Shanghai

first: Zilong

last: Qiu

address: No.320, Rd. Yueyang

institute: Chinese Academic of Science

summary: To determine whether the miRNA expression profile is altered by MeCP2, we performed Solexa-based RNA sequencing(RNA-seq) to assess global changes in the expression pattern of miRNAs caused by the loss of MeCP2 in mecp2 null (knockout[KO]) mice (Chen et al., 2001).

overall_design: Hippocampus miRNA profiles of 30-day old wild type (WT) and MeCP2-/y mice were generated by deep sequencing using Illumina HiSeq 2000

first: Tian-lin

last: Cheng


title: Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

summary: The most common congenital heart disease (CHD) is the ventricular septal defect (VSD), which is also a subfeature of Tetralogy of Fallot (TOF) representing the most common form of cyanotic CHD. The underlying causes for the majority of CHDs are still unclear and most probably consist of combinations of genetic, epigenetic and environmental factors. DNA methylation is the most widely studied epigenetic modification and several cardiac regulators have already been shown to be differentially methylated in CHD patients. Here, we present the first analysis of genome-wide DNA methylation data obtained from cardiac biopsies of TOF and VSD patients. We applied affinity-based enrichment of methylated DNA sequences with methyl-CpG-binding domain proteins followed by next-generation sequencing (MBD-Seq).

overall_design: MBD-seq on cardiac biopsies of patients with Tetralogy of Fallot and ventricular septal defect


title: Negative reciprocal regulation between SIRT1 and Per2 in circadian clock during aging (ChIP-Seq)

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: SIRT1 is involved in both aging and circadian clock regulation, yet the link between the two processes in relation to SIRT1 function is unclear. Analyzing SIRT1-deficient cells and mice, we demonstrated that SIRT1 and Per2 constitute a reciprocal negative regulation loop that plays important roles in modulating circadian rhythmicity, metabolism and aging. SIRT1-deficient mice exhibit profound premature aging and enhanced H4K16 acetylation in the promoter of Per2 leading to its overexpression; in turn, Per2 suppresses SIRT1 transcription through binding to SIRT1 promoter at the CLOCK/BMAL1 site. We further demonstrated that absence of SIRT1 or ectopic overexpression of Per2 in the liver resulted in an accelerated pace of circadian rhythm and dysregulated amplitude, mimicking the natural process of circadian shortening in aged mice. Thus the interplay between SIRT1 and Per2 provides a link between the life-long sequence of aging and circadian clock maintenance.

overall_design: To test whether changes in gene expression induced by Sirt1 KO are associated with changes in H4K16ac level at promoters, we profiled gene expression by using microarray and genomic binding of H4K16ac by using ChIP-Seq for Sirt1 KO mice and wild type control month (3-month).

first: Wang

last: Rui-Hong

first: Zhao

last: Tingrui

first: Cui

last: Kairong

first: Hu

last: Gangqing

first: Chen

last: Qiang

last: Weiping

last: Keji

first: Deng

last: Chu-Xia


title: Gene expression profiles of the respiratory tree of sea cucumber Apostichopus japonicus during aestivation by RNA-seq

city: Yantai

first: Ye

last: Zhao

state: Shandong Province

address: Qingquan Road No.30

institute: Yantai University

summary: Sea cucumbers (Holothuroidea; Echinodermata) cycle annually between aestivation, when water temperature is above about 25°C in the summer, and active life, when temperature is below about 18°C. We used RNA-Seq to determine gene expression profiles of respiratory tree tissue of A. japonicus during non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA).

overall_design: At least 15 individuals per stage, respiratory tree at NA, DA and AA stages were used for our experiments.

first: Muyan

last: Chen