title: Changes in ovarian gene expression profiles in maturing European eel (Anguilla anguilla) (responders and non-responders)

first: Ron

last: Dirks

summary: The goal of this study was to gain a better understanding of the genetic background of gonadal maturation of the European eel and to use gene expression profiles to identify predictive markers for broodstock selection that can be measured in blood samples. Three-year-old farmed silver female European eels were injected with 20 mg salmon pituitary extract (SPE) once per week and sampled after 4 weekly hormone injections. Four responders (gonadosomatic index > 1.5) and two non-responders (gonadosomatic index < 1.0) were selected for Illumina RNAseq analysis to identify early markers of responsiveness to gonadotropin treatment.

overall_design: Deep-sequencing transcriptome analysis of ovarian samples derived from four responsive and two non-responsive eels after four weekly injections with gonadotropins.

first: Hans

middle: J

last: Jansen


title: RNA sequencing of mouse littermate wild-type and Shh null E10.5 forelimbs [Illumina]

status: Public on Jul 01 2015

city: Cambridge

first: Jordan

last: Lewandowski

state: MA

address: 7 Divinity Ave

country: USA

institute: Harvard University

type: Expression profiling by high throughput sequencing

summary: We wanted to identify differentially expressed genes in wild-type and Shh null E10.5 mouse forelimbs

overall_design:
Used two wild-type technical replicates and two Shh null  technical replicates
UT-Genome and Analysis Facility

first: Fang

last: Du


title: ABL Tyrosine Kinase Phosphorylates DGCR8 to Stimulate MicroRNA Processing in DNA Damage Response

city: La Jolla

first: Jean

middle: YJ

last: Wang

state: CA

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: University of California San Diego

type: Non-coding RNA profiling by high throughput sequencing

summary: miR-seq to find miRs that are induced by DNA damage and whose induction requires ABL kinase activity

overall_design: Use p53-inactive HEK293T cells. Use doxorubicin to induce DNA damage. Use imatinib co-treatment to inhibit ABL kinase activity

first: Chi-Chiang

last: Tu


title: Integrated genomics of Crohn’s disease risk variant identifies a role for CLEC12A in antibacterial autophagy

status: Public on Jun 30 2015

city: Boston

first: Ramnik

last: Xavier

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Using integrated genomics we identify a role for CLEC12A in antibacterial autophagy. Clec12a-/- mice are more susceptible to bacterial infection and CLEC12A deficient cells exhibit impaired antibacterial autophagy. We used transcriptional profilinf to understand the role of CLEC12A in the response to Salmonella and Listeria.

overall_design:
Bone marrow-derived macrophages from WT or Clec12a-/- mice were infected with Salmonella enterica serovar Typhimurium or Listeria monocytogenes. Cells were harvested at 0,3,6, and 24hours post-infection for RNA analysis.

Please note that single-end sequencing was performed but two files: R1 files that contained the sample barcodes (19 or 17bp reads) and R2 files that contained the single-end-sequenced 46bp cDNA reads were generated. Since the barcode info is mostly redundant, only R2 reads were submitted (described in 'raw_file_readme.txt').

first: K

last: Lassen

first: G

last: Goel

first: R


title: Allele-selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-coding and Noncoding RNAs, and RNA Isoforms

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

type: Genome variation profiling by high throughput sequencing

summary:
Purpose:  mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. Analysis of allelic RNA ratios at heterozygous SNPs served to reveal genetic factors in ribosomal loading.
Methods: RNA-seq was performed on cytosolic extracts and polysomal fractions (3 ribosomes or more) from three lymphoblastoid cell lines.  As each RNA fraction was amplified (NuGen kit), and relative contributions from various RNA classes differed between cytosol and polysomes, the fraction of any given RNA species loaded onto polysomes was difficult to quantitate. Therefore, we focused on relative recovery of the various RNA classes and rank order of single RNAs compared to total RNA.
Results: RNA-seq of coding and non-coding RNAs (including microRNAs) in three LCLs revealed significant differences in polysomal loading of individual RNAs and isoforms, and between RNA classes. Moreover, correlated distribution between protein-coding and non-coding RNAs suggests possible interactions between them. Allele-selective RNA recruitment revealed strong genetic influence on polysomal loading for multiple RNAs. Allelic effects can be attributed to generation of different RNA isoforms before polysomal loading or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Several variants and genes identified by this approach are also associated with RNA expression and clinical phenotypes in various databases.
Conclusions:  These results provide a novel approach using complete transcriptome RNA-seq to study polysomal RNA recruitment and regulatory variants affecting protein translation.

overall_design: cells from 3 samples were grown to 5x105 cells/mL density in T75 tissue culture flask and harvested, total RNA and polysome bound RNA was sequenced by Ion Proton

last: Webb

first: Roshan

last: Mascarenhas

first: Maciej

last: Pietrzak


title: A global comparative analysis of gene expression in ovules and leaves based on integrated De Novo transcriptome assembly of Ginkgo biloba L.

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

country: China

institute: Yangzhou University

summary: We sequenced mRNA from mature ovules and fully expanded leaves of female G. biloba to generate a  comprehensive gene expression profile. These results provide valuable gene expression information, which will contribute to facilitate our understanding of various biological mechanisms between ovules and leaves and uncover a more important molecular insight toward ovule evolution in early seed plants.

overall_design: Examination of mRNA levels in ovules and leaves

first: Zhao

middle: G

last: Lu


title: small RNA-seq of Physcomitrella patens small RNA mutants

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

summary: To investigate the effects of dcl3,dcl4,mDCL,rdr2,rdr6,nrpd1b, and nrpd1c mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.

overall_design: Total RNA samples were obtained from the indicated mutants and subject to small RNA-seq using the Illumina TruSeq Small RNA protocol, and analyzed on a HiSeq2500 instrument


title: RNA-sequencing of Postnatal Day 10 Wild-type and Nfix KO Subventricular Zone-derived Primary Monolayer-cultured Neural Stem Cells

city: Buffalo

first: Bo

last: Zhou

state: NY

address: 701 Ellicott st

department: Biochemistry

institute: University at Buffalo

summary:
Purpose: To study the mechanisms involved in the regulation by NFIX on neural stem cell development and to examine the transcriptome changes associated with the loss of NFIX in neural stem cells.
Methods: Subventricular zones of 10-day-old wild-type and Nfix KO mice were sectioned and dissociated into single cells. Cells were cultured in proliferation condition for 10 days. RNA was purified and poly-A selected to build the library for RNA-seq.
Conclusions: Our study represents the first detailed analysis of transcriptome changes in primary monolayer-cultured neural stem cells associated with the loss of NFIX.

overall_design: Cells dissociated from 10-day-old wild-type and nuclear factor I-X (Nfix KO) mice subventricular zone were cultured in DMEM/F12 with B27, Glutamine, EGF and bFGF for 10 days. RNA was harvested with Norgen RNA purification micro kit and then prepared with illumina TruSeq kit. Samples from 6 mice (3 vs. 3) were loaded on one lane. 50-cycle single-read run was performed on Hiseq 2000. The sequence reads were analyzed by TopHat 2.0.7 followed by Cufflinks 1.3.0 with the mm9 UCSC annotation files.

first: Sujith

last: Valiyaparambil

first: Jonathan

last: Bard

first: Richard

last: Gronostajski


title: Gata6 potently initiates reprogramming of pluripotent and differentiated cells to extraembryonic endoderm stem cells

city: London

first: Kathy

last: Niakan

address: Mill Hill

country: United Kingdom

institute: The Francis Crick Institute

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: dsRNA-seq of Physcomitrella patens rdr mutants

summary: To investigate the effects of rdr2 and rdr6 mutations upon the strucutred component of the Physcomitrella patens transcriptome, dsRNAseq performed. The accumulation of dsRNAseq reads within known small RNA (microRNA and siRNA) loci was quantified and compared between wild-type and the two mutants.

overall_design: Total RNA samples were obtained from wild-type, rdr2, and rdr6, and subject to dsRNAseq via the protocol described by Zheng et al. (2010) (PMID: 20941385)

first: Brian

middle: D

last: Gregory


title: piRNAs and transgenerational RNA interference protect essential genes from RNA silencing in C. elegans

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

summary: This data series contains small RNA high-throughput sequencing data derived from cell lysates and FLAG::HRDE-1 immunoprecipitates (IP) after resetting RNAi in the presence or absence of piRNAs in C. elegans.

overall_design: Small RNAs were isolated from adult wild type and mutant or transgenic C. elegans and subjected to Illumina HiSeq sequencing. The series contains fastq and tab-separated files for 10 libraries.


title: small RNA-seq of Physcomitrella patens rdr mutants

summary: To investigate the effects of rdr2 and rdr6 mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.

overall_design: Total RNA samples were obtained from wild-type, rdr2, and rdr6, and subject to small RNA-seq via the protocol described by Zheng et al. (2010) (PMID: 20941385)


title: The novel functional effects of exogenous EBV-miR-BARTs on NPC progression

city: Guangzhou

first: Xin

last: Li

state: Province

address: Southern medical university

department: Cancer research institute

institute: Southern medical university

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Betapolyomavirus macacae

first: Yanfen

last: Ye


title: Next Generation Sequencing Facilitates Quantitative Analysis of CNE1-mock, CNE1-BART1, CNE-BART3, CNE1-BART7 cells

summary: By using  NGS-derived retinal transcriptome profiling (RNA-seq) to compare the gene expression profiling between 4 differently treated NPC cells

overall_design: Examination of different gene expression in EBV-miRNA-BART1/3/7 lentivirus and their control infected nasopharyngeal carcinoma cells.


title: HEB associates with PRC2 and SMAD2/3 to regulate developmental fates

city: Stanford

first: Se-Jin

last: Yoon

address: 300 Pasteur Drive, Alway M311

department: Genetics

institute: Stanford University


title: Small RNA genes of Physcomitrella patens

summary: Small RNA-seq from 10 day-old wild-type Physcomitrella patens was performed using 5 biological replicates. Replicates were grown in three batches at different times.  Batch 1 had one replicate from strain "old WT", Batch 2 had two replicates from strain "old WT", and batch 3 had two replicates from strain "2009 WT".  Old WT and 2009 WT were collected from Gransden wood, England; "old" has been in lab cultivation for at least 10 years, while "2009" was more recently collected from the wild (in 2009.)

overall_design: Annotation and quantification of small RNA-producing genes in Physcomitrella patens

first: M

first: B


title: IFN-g Regulates mTORC1, Cellular Metabolism and mRNA Translation to Potentiate Inflammatory Macrophage Activation [RNA-Seq]

status: Public on Jun 29 2015

city: New York

first: Xiaodi

last: Su

address: 535 East 70th Street

department: Arthritis and Tissue Degeneration Program

institute: Hospital for Special Surgery

summary: IFN-g primes macrophages for enhanced inflammatory activation by TLRs and microbial killing, but little is known about the regulation of cell metabolism or mRNA translation during priming. We found that IFN-g regulates macrophage metabolism and translation in an integrated manner by targeting mTORC1 and MNK pathways that converge on the selective regulator of translation initiation eIF4E. Physiological downregulation of the central metabolic regulator mTORC1 by IFN-g was associated with autophagy and translational suppression of repressors of inflammation such as HES1. Genome-wide ribosome profiling in TLR2-stimulated macrophages revealed that IFN-g selectively modulates the macrophage translatome to promote inflammation, further reprogram metabolic pathways, and modulate protein synthesis. These results add IFN-g-mediated metabolic reprogramming and translational regulation as key components of classical inflammatory macrophage activation.

overall_design: RPF and RNAseq libraries were generated from mock or IFN-g-primed human macrophages. Cells were stimulated with Pam3Cys and harvested at 4 hours. Libraries were generated using protocol modified from Illumina Truseq technology.

first: Yingpu

last: Yu

first: Yi

last: Zhong

first: Eugenia

last: Giannopoulou

first: Xiaoyu

last: Hu

first: Hui

last: Liu

first: Justin

middle: R

last: Cross

first: Gunnar

last: Rätsch

first: Charles

middle: M

last: Rice

first: Lionel

middle: B

last: Ivashkiv


title: Genome-wide mapping of DNA hydroxymethylation in osteoarthritic chondrocytes [methylation]

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

type: Methylation profiling by high throughput sequencing

summary:
Examination of the genome-wide distribution of 5hmC in osteoarthritic chondrocytes compared to normal chondrocytes in order to elucidate the effect on OA-specific gene expression.
5hmC-sequencing was performed and data was compared with microarray gene expression data to identify genes with differential expression between normal and OA chondrocytes that are potentially under epigenetic regulation.

overall_design: High-throughput sequencing of 5hmC in 4 normal and 4 OA chondrocyte samples.

first: Sarah

middle: E

last: Taylor

first: Ye

middle: H

first: Wing

last: Wong


title: Characterizing the interactions between a naturally-primed IgA (mAb 260.8) and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice

city: St. Louis

first: Joseph

last: Planer

state: Missouri

address: 4444 Forest Park Ave

department: Pathology

institute: Washington University School of Medicine

platform_organism:
Bacteroides thetaiotaomicron
Phocaeicola vulgatus
Parabacteroides distasonis
Methanobrevibacter smithii
Lachnospira eligens
Agathobacter rectalis


title: Characterizing the interactions between a naturally-primed IgA and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice [RNA-Seq]

summary: We report the mid-log phase transcriptional profile of the human gut symbiont Bacteroides thetaiotaomicron, grown in the presence of mouse monoclonal IgAs with species- and strain-level specificity (mAb 260.8 and mAb 225.4, respectively).

overall_design: mRNA expression profiling of the type strain of Bacteroides thetaiotaomicron (NC_004663) grown in vitro in the presence of either (i) PBS (carrier control), (ii) mAb 225.4 alone, (iii) mAb 260.8 alone, (iv) an equal combination of mAbs 225.4 and 260.8, or (v) a nonbinding control mouse mAb IgA (JC63.1)


title: IFN-g Regulates mTORC1, Cellular Metabolism and mRNA Translation to Potentiate Inflammatory Macrophage Activation


title: Genome-wide mapping of DNA hydroxymethylation in osteoarthritic chondrocytes


title: HEB associates with PRC2 and SMAD2/3 to regulate developmental fates [ChIP-Seq]

first: Se-Jin

summary: We report the interaction between HEB and PRC2 components in mouse embryonic stem cells (ESCs)

overall_design: ChIP-Seq of HEB and SMAD2/3 in mouse ESC and derived endoderm

middle: W

last: Foley

first: Julie

middle: C

last: Baker


title: HEB associates with PRC2 and SMAD2/3 to regulate developmental fates [RNA-Seq]

last: Yoon

overall_design: We profiled gene expression for biological triplicate shControl- and shHEB-infected ESCs and differentiated embryoid body (EB) in serum-free defined culture system with or without activin treatment


title: Gene expression analysis in WT-AG-haESCs, DKO-AG-haESCs and round spermatids

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: RNA seq result shows that WT-AG-haESCs and DKO-AG-haESCs samples are clustered together using hierarchical cluster both in the all expression genes and imprinting genes. This suggests that DKO of DMRs of H19 and Gtl2 do not change the overall gene expression patterns in AG-haESCs.

overall_design: We used round spermatids as control. Using RNA-seq, profile of all the expression genes and imprinting genes beteween different samples were analysed.

first: Rui

last: Dong

first: Cuiqing

first: Yu-Hang

last: Xing

first: Hua-Hong

last: Fang

first: Ling-Ling

last: Chen

first: Jinsong

last: Li


title: IFN-g Regulates mTORC1, Cellular Metabolism and mRNA Translation to Potentiate Inflammatory Macrophage Activation [miRNA-Seq]

first: Xiaodi

last: Su

overall_design: microRNA-seq libraries were generated from mock or IFN-g-primed human macrophages. Cells were stimulated with or without Pam3Cys and harvested at 4 hours Libraries were generated using Illumina Truseq small RNA technology.

first: Yingpu

last: Yu

first: Yi

last: Zhong

first: Eugenia

last: Giannopoulou

first: Xiaoyu

last: Hu

first: Hui

last: Liu

first: Justin

last: Cross

first: Gunnar


title: From glacier to sauna: RNAseq of the human pathogen Exophiala dermatitidis

city: Vienna

first: Hakim

last: Tafer

address: Muthgasse 18

country: Austria

institute: University of Natural Resources and Life Sciences Vienna

summary: We report the transcriptome response of Exophiala dermatitidis submitted to different temperature conditions

overall_design: 2 Temperature conditions (45C, 1C), 2 exposition length (1 hour, 1 week) compared to optimal condition (37C)

first: Barbara

last: Blasi

first: Tafer

last: Hakim

first: Donatella

last: Tesei

first: Katja

last: Sterflinger


title: DNA methylation profiling in WT-AG-haESCs, DKO-AG-haESCs and round spermatids

first: Li

last: Yang

summary: We generated RRBS data to analyse the DNA methylation profiling among WT-AG-haESCs, DKO-AG-haESCs and round spermatids, we found deletion of H19 and Gtl2 DMRs do not change the methylation patterns in AG-haESCs base on all detected CpG sites.

overall_design: We used round spermatids as control and analysed the DNA methylation profiles of all the cell lines were by RRBS.

first: Rui

last: Dong

first: Cuiqing

first: Yu-Hang


title: Molecular Basis for RNA Polymerase II to Sense the DNA Demethylation Status during Transcription Elongation

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: DNA methylation at selective cytosine residues (5mC) and their removal by TET-mediated DNA demethylation are critical for setting up pluripotent states in early embryonic development. TET enzymes successively convert 5mC to 5hmC, 5fC, and 5caC, the later two of which are subject to removal by thymine DNA glycosylase (TDG) in conjunction with base excision repair. Early reports indicate that 5fC and 5caC could be stably detected on enhancers, promoters, and gene bodies with distinct effects on gene expression, but the mechanisms have remained elusive. Here we determined the X-ray crystal structure of elongating Pol II in complex with DNA template containing oxidized 5-methylcytosines (oxi-mCs), revealing specific hydrogen bonds between the 5-carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase. This causes a positional shift for incoming NTP, thus compromising nucleotide addition. To test the in vivo significance of this structural insight, we determined the global effect of increased 5fC/5caC levels on transcription, finding that such DNA modifications indeed retarded Pol II elongation on gene bodies. These results demonstrate the functional impact of oxi-mCs on gene expression and suggest a novel role for Pol II to function as a specific and direct epigenetic sensor during transcription elongation.

overall_design: Time-course GRO-seq in mESC cells w/o TDG knockout

first: Lanfeng

last: Wang

first: Yu

last: Zhou

first: Liang

last: Xu

last: Xiao

first: Xingyu

last: Lu

first: Jenny

last: Chong

first: Hairi

first: Chuan

last: He

first: Dong


title: Transcriptional responses of Bdtf1-deletion mutant to the phytoalexin brassinin in the necrotrophic fungus Alternaria brassicicola

city: Honolulu

first: Yangrae

last: Cho

state: HI

address: 3190 Maile Way, St John 317

department: Plant and Environmental Protection Sciences

institute: University of Hawaii at Manoa

summary: Brassica species produce antifungal indolyl compounds, brassinin and its derivatives, during microbial infection.  The fungal pathogen Alternaria brassicicola detoxifies brassinin and possibly its derivatives.  This ability is an important property for the successful infection of brassicaceous plants.  Previously, we identified a transcription factor, Bdtf1, essential for the detoxification of brassinin and full virulence.  To discover genes that encode putative brassinin-digesting enzymes, we compared gene expression profiles between a mutant strain of the transcription factor and wild-type A. brassicicola under two different experimental conditions.  A total of 170 and 388 genes were expressed at higher levels in the mutants than the wild type during the infection of host plants and saprophytic growth in the presence of brassinin, respectively.  In contrast, 93 and 560 genes were respectively expressed at lower levels in the mutant than the wild type under the two conditions.  Fifteen of these genes were expressed at lower levels in the mutant than in the wild type under both conditions.  These genes were assumed to be important for the detoxification of brassinin and included Bdtf1 and 10 putative enzymes.  This list of genes provides a resource for the discovery of enzyme-coding genes important in the chemical modification of brassinin.

overall_design: Examination of downstream genes regulated by a transcrition factor under two test conditions


title: Gene expression analysis and DNA methylation profiling in WT-AG-haESCs, DKO-AG-haESCs and round spermatids

overall_design: Refer to individual Series


title: Selection for improved energy efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes

status: Public on Jun 28 2015

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University


title: Selection for improved energy efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes [RNA-Seq]

summary: Integrated breeding strategies are used to increase both the yield potential and stability of crops.  Most of these approaches have a direct genetic basis.  The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear.  A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance.  These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions.  Moreover, these characteristics were transgenerational inheritable.  Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance.  Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines.   The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance.  This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding.

overall_design: SRA study accession: SRP052946, Bioproject: PRJNA273932. Two canola (Brassica napus L. spp. oleifera (Metzg) Sinsk. f. biennis) epilines with low respiration and high NAD(P)H content were selected. Grinded leaf material from 26 day-old control and both epilines was collected in triplicate and served as input for deep sequencing on Illumina GAIIx.

first: Aurine

last: Verkest

first: Marina

last: Byzova

first: Cindy

last: Martens


title: LncPHx2 RNA-interactome

status: Public on Jun 27 2015

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: LncPHx2 RNA-interactome study realed that LncPHx2 is associated with multiple RNAs

overall_design: Biotinylated DNA probes targeting LncPHx2 were used to precipitate endogenous LncPHx2 and associated RNAs from Hepa 1-6 cells. The associated RNAs were sequenced and 415 unique transcripts were identified.

first: Lulu

last: Huang

first: Shuling

last: Guo


title: Oncogene-dependent regulation of tumor cells via stromal reciprocal signalling

city: Manchester

first: Hui Sun

last: Leong

address: Wilmslow Road

department: The University of Manchester

institute: Cancer Research UK Manchester Institute

summary: Cancer is a heterocellular disease composed of tumor cells and stromal cells. Although stromal cells are known to regulate cancer progression, oncogene-dependent signalling through heterocellular cancer systems remains poorly elucidated. Here, we describe KRASG12D-dependent ‘reciprocal’ signalling across tumor and stromal Pancreatic Ductal Adenocarcinoma (PDA) cells. Heterocellular multivariate phosphoproteomics demonstrates how an oncogenic cue (KRASG12D), a trans-cellular signal (SHH), and stromal cells drive a reciprocal response in tumor cells. KRASG12D-dependent reciprocal signalling regulates the tumor cell phosphoproteome, total proteome, and mitochondria activity via an IGFR1/AXL-AKT axis. The reciprocal KRASG12D signalling state requires a heterocellular context and is unreachable by cell-autonomous oncogenic KRAS alone. These findings provide evidence that oncogenic KRAS regulates tumor cells via heterocellular reciprocation.

overall_design: Comparison between FACS resolved iKRAS cells (previously in co-culture with PSCs) pertubed with a SHH antibody

first: Christopher

last: Tape

first: Stephanie

last: Ling

first: Jonathan

last: Worboys

first: Hui

first: Kelly

last: McMahon

first: Ida

last: Norrie

first: Crispin

last: Miller

first: Douglas

last: Lauffenburger

first: Claus

last: Jørgensen


title: Using RNA Seq to define the regulon of the Pseudomonas aeruginosa transcription factor Anr in low-oxygen colony biofilms.

city: Hanover

first: Deborah

last: Hogan

state: NH

address: Vail Building Rm 208

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

summary:
Purpose : The goal of this study was to use RNA Seq to define the regulon of the transciption factor Anr by comparing global transcriptional profiles of Pseudomonas aeruginosa strain PAO1 and a clinical isolate with their isogenic ∆anr mutants, grown in colony biofilms at 1% oxygen.
Methods : mRNA profiles were generated for laboratory strain PAO1 and for a clinical isolate J215, as well as for ∆anr derivatives of each strain, in duplicate, by deep sequencing. Strains were grown for 12 hours in colony biofilms at 1% O2, 5% CO2 prior to RNA harvest. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas aeruginosa PAO1

overall_design: mRNA profiles of 12 hour colony biofilms were generated for P. aeruginosa strains PAO1 WT, PAO1 ∆anr, clinical isolate J215, and J215 ∆anr, each in duplicate, by deep sequencing using Illumina HiSeq.

first: John

last: Hammond

first: Sabin

last: Bhuju


title: Protein kinase C is essential for viability of the rice blast fungus Magnaporthe oryzae

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

institute: University of Exeter

summary: A strain of M. oryzae was constructed in which the native PKC1 gene was replaced with an analogue-sensitive PKC1 allele (pkc1AS). This allele could be inhbited by the analogue 1NA-PP1. Global transcriptional profiling of mycelium following selective PKC inhibition identified significant changes in gene expression associated with cell wall re-modelling, autophagy, signal transduction and secondary metabolism.

overall_design: Mycelium was grown in the presence and absence (control) of the inhibitor 1NA-PP1 for a number of different times up to 24 hours.

first: Tina

last: Penn

first: Nicholas

last: Talbot


title: Landscape of Hematopoiesis Described in Induced Pluripotent Stem Cells and Human Bone Marrow

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: Granulopoietic differentiation of myeloid progenitor cells derived from control iPSCs  was performed in a two-step liquid culture. At the end of culture, stages of differentiation were identified by morphological analysis and submitted for RNA-sequencing analysis in order to provide insight into the genomic landscape of myeloid lineage hematopoiesis as modeled by the in vitro induced differentiation of iPSCs as compared to in vivo bone marrow-derived promyelocytes.

overall_design: Peripheral blood from healthy controls was obtained and iPSC were generated from peripheral blood mononuclear cells.  Hematopoietic progenitors generated from control iPSCs when cultured in myeloid expansion medium containing 50ng/mL SCF, 10ng/mL IL-3 and 10ng/mL GM-CSF for 5 days at which point cells were stained for CD45-Pacific blue, CD34-PECy7, CD33-AP, CD11b-APC-Cy7, CD15-FITC.  7-AAD was used to eliminate the dead cells. The promyelocytic population (CD45+CD34-CD33+CD11b-CD15+/lo) was sorted and the RNA from control iPSC promyelocytes was isolated using QIAGEN RNAeasy mini kit. The RNA samples were processed for RNA-seq analyses using RNA-seq protocol from NuGEN and Illumina. The amplified products were sequenced to analyze the gene expression profile of each replicate sample.  A total of 20 samples were used in this analysis to characterize and compare iPSC in vitro differentiated myeloid cells with those isolated from human bone marrow.

first: Ramesh

last: Nayak

first: Jose

last: Cancelas

first: Carolyn

last: Lutzko

first: H

middle: L

last: Grimes

first: Phillip

last: Dexheimer

first: Bruce

last: Aronow


title: Partial Hepatectomy Induced Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration

status: Public on Jun 26 2015

first: Sagar

last: Damle

summary: Gene expression analysis showed that LncPHx2 depletion resulted in upregulation of mRNAs encoding proteins known to promote cell proliferation, including MCM components, DNA polymerases, histone proteins, and transcription factors

overall_design: RNA-seq analysis was performed on livers of mice subjected to PHx or to sham surgery after treatment with LncPHx2_ASO1 or with PBS. Gene expression profiling was done at 48 hours post-surgery

first: Lulu

last: Huang

first: Shuling

last: Guo


title: damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

summary: DamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with normalisation based on read-counts alone can lead to high background and the loss of bound signal. DamID-seq thus presents novel challenges in terms of normalisation and background minimisation. We describe here damidseq_pipeline, a software pipeline that performs automatic normalisation and background reduction on multiple DamID-seq FASTQ or BAM datasets.

overall_design: Single replicate profiling of pol II occupancy in 3rd instar larval neuroblasts of Drosophila

first: Andrea

last: Brand


title: Bcl3 target genes in mESCs

status: Public on Jun 25 2015

city: Taipei

first: Chen-Yun

last: Chen

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Science

country: Taiwan

institute: Acdemia Sinica

summary: Bcl3 is expressed in mESCs. ChIP-seq was used to identify its binding pattern and target genes.

overall_design: ChIP of Bcl3 in mESCs under conventional culture condition


title: ncRNA (non-coding RNA) signature in endothelial cells during hypoxia

city: Hannover

first: Jan

last: Fiedler

address: Carl-Neuberg-Str. 1

department: Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx

country: Germany

institute: Hannover Medical School

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


title: Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration


title: Mapping nucleosome resolution chromosome folding in yeast by Micro-C

city: Berkeley

first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: We describe a Hi-C based method, Micro-C, in which micrococcal nuclease is used instead of restriction enzymes to fragment chromatin, enabling nucleosome resolution chromosome folding maps. Analysis of Micro-C maps for budding yeast reveals abundant self-associating domains similar to those reported in other species, but not previously observed in yeast. These structures, far shorted than topologically-associating domains in mammals, typically encompass one to five genes in yeast. Strong boundaries between self-associating domains occur at promoters of highly transcribed genes, and regions of rapid histone turnover that are typically bound by the RSC chromatin-remodeling complex. Investigation of chromosome folding in mutants confirms roles for RSC, “gene looping” factor Ssu72, Mediator, H3K56 acetyltransferase Rtt109, and N-terminal tail of H4 in folding of the yeast genome. This approach provides detailed structural maps of a eukaryotic genome and our findings provide insights into the machinery underlying chromosome compaction.

overall_design:
Chromatin is fragmented by Mnase, subsequenct nucleosomal end repair, and a modified two-step method for purfiying ligation products. Using Illumina paired-end sequencing maps Micro-C library and generates nucleosome resolution contact maps.

The readme.txt file contains additional description of how each processed data file was generated.

first: Oliver

last: Rando

first: Tsung-Han

last: Hsieh


title: The H3K4-methyl epigenome regulates MLL leukemia stem cell oncogenic potential

first: Stephen HK

last: WONG

address: G2035 SIM1 Bldg

institute: Stanford University

summary: The genetic programs that maintain leukemia stem cell (LSC) self-renewal and oncogenic potential have been well defined, however the epigenetic landscape that determines their cellular identity and functionality has not been established.  We report that LSCs in MLL-associated leukemia are maintained in an epigenetic state defined by relative genome-wide high-level H3K4me3 methylation and low level H3K79me2.  LSC differentiation is associated with dynamic reversal of these broad epigenetic profiles and concomitant down-regulation of the LSC maintenance transcriptional program.  LSCs also share with embryonic stem cells a large subset of genes with bivalent histone marks related to embryonic development.  The histone demethylase KDM5B negatively regulates MLL-induced leukemogenesis demonstrating the crucial role of the H3K4 global methylome for determining leukemia stem cell fate.

overall_design: Investigation of multiple histone modification marks and RNA Pol II in ckit+ and ckit- cells isolated and fractionated from MLL leukemia mice.

first: Stephen

first: Michael

last: Cleary


title: RNA-seq analysis reveals significant effects of EGFR signaling on mesenchymal stem cells (MSC)

city: Naples

first: Nicola

last: Normanno

address: via Mariano Semmola

country: Italy

institute: INT PASCALE

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to analyse the whole transcriptome of MSCs stimulated with TGFα in order to comprehensively assess the genes regulated by EGFR signalling
Methods: Libraries of cDNA were obtained from poly(A)-RNA fractions from not-stimulated or TGFα-stimulated MSCs and sequenced with a SOLiD 5500xl platform. Whole-transcriptome reads were aligned to the version 19 of the human genome (hg19) with the SOLiD LifeScope Genomic Analysis Software version 2.5 (Life Technologies) using the parameters recommended in the user’s manual. The number of observed counts (number of reads/gene) was normalized for the length of the transcript and the number of mapped reads (RPKM) (Reads Per Kilobase per Million of mapped reads). DESeq tool in R package was used to obtain a statistical evaluation of differential gene expression.
Results: 1,640 genes resulted highly differentially regulated: 967 genes up-regulated with Fold Induction (FI)≥1.50, and 673 genes down-regulated with FI≤0.50. When highly regulated genes were categorized into enriched categories according to GO molecular function classification and KEGG pathways analysis, a large number of genes coding for potentially secreted proteins or for surface receptors resulted enriched following TGFα treatment. In particular, significant  up-regulation of VEGFA, IL6, EREG, HB-EGF, LIF, NGF, NRG1, CCL19, CCL2, CCL25 and CXCL3 was observed.
Conclusions: Taken together these findings suggest that EGFR activation in MSCs leads to a significant change in the expression of a wide array of genes coding for secreted proteins that can significantly enhance tumor progression by acting on several mechanisms within the tumor microenvironment

overall_design: mRNA profiles of MSCs starved overnight in serum free medium and treated for 1 hour with recombinant at a concentration of 10 ng/ml by deep sequencing, in quadruplicate, using SOLiD 5500xl.

first: Antonella

last: DeLuca

first: Francesca

last: Bergantino

first: Susan

last: Costantini


title: Functional analysis of chicken IRF7 in response to dsRNA analog poly(I:C) by integrating overexpression and knockdown

city: Davis

first: Huaijun

last: Zhou

address: Meyer 3307, One shields Ave.

institute: UC Davis

summary: In this study, an integrative high-throughput functional genomics approach was applied by combining overexpression and knockdown assays with RNA-seq; this side-by-side approach was taken in an effort to obtain corroboration and complementary support in the identification of potential genes that are under the control of IRF7.

overall_design: Transcriptiome analysis of Poly(I:C) induced IRF7 overexpression & knockdown DF-1 cell lines and their respective controls

first: Tae

last: Kim


title: Selection for improved energy efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes [ChIP-Seq]

first: Patrick

last: Willems

overall_design: To investigate the epigenetic effect on histone mark distribution of the EUE/PEG selection we performed ChIP-seq analyses. Native ChIP using an anti-H3K4me3 and no antibody (background control) was done on PEG1 and control plants.

first: Aurine

last: Verkest

first: Marina

last: Byzova

first: Cindy

last: Martens


title: Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells

status: Public on Jun 24 2015

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: Glioblastoma (GBM) is the most common and most aggressive primary brain tumor in adults. The existence of a small population of stem-like tumor cells that efficiently propagate tumors and resist cytotoxic therapy is one proposed mechanism leading to the resilient behavior of tumor cells and poor prognosis.  In this study, we performed an in-depth analysis of the DNA methylation landscape in GBM-derived cancer stem cells (GSCs). Parallel comparisons of primary tumors and GSC lines derived from these tumors with normal controls (a neural stem cell (NSC) line and normal brain tissue) identified groups of hyper- and hypomethylated genes that display a trend of either increasing or decreasing methylation levels in the order of controls, primary GBMs, and their counterpart GSC lines, respectively. Interestingly, concurrent promoter hypermethylation and gene body hypomethylation were observed in a subset of genes including MGMT, AJAP1 and PTPRN2. These unique DNA methylation signatures were also found in primary GBM-derived xenograft tumors indicating that they are not tissue culture-related epigenetic changes. Integration of GSC-specific epigenetic signatures with gene expression analysis further identified candidate tumor suppressor genes that are frequently down regulated in GBMs such as SPINT2, NEFM and PENK. Forced re-expression of SPINT2 reduced glioma cell proliferative capacity, anchorage independent growth, cell motility, and tumor sphere formation in vitro. The results from this study demonstrate that GSCs possess unique epigenetic signatures that may play important roles in the pathogenesis of GBM.

overall_design: The reduced representation bisulfite sequencing (RRBS) approach (Meissner et al., 2008) was used to generate genome-wide single-base resolution CpG methylation profiles of three primary GBMs (1063T, 1133T, and 1142T) and three GSC lines (1063S, 1133S, 1142S) derived from these primary GBM tumors. The NSC line and the normal brain (NB) tissue sample were used as controls for comparison purposes. In addition, we analyzed three GBM xenograft tumor tissue samples (Mayo22, Mayo39, Mayo59) developed by Dr. Jann N. Sarkaria of Mayo Clinic.


title: Allele-specific expression in A. thaliana hybrids grown under control and drought stress conditions

city: Versailles

first: Francisco

middle: A.

last: Cubillos

address: Route de St Cyr

country: France

institute: INRA-IJPB

summary: We estimate Allele-specific expression in F1 hybrids between Col-0 and Cvi-0 accessions grown under well watered and drought stress conditions. We found that ~90% of the genes showed similar ASE under both stresses. Trans-effects were less robust across environments, however its effect was milder compared to cis-variation.

overall_design: Assessment of ASE in different environments

first: Olivier

last: Loudet


title: Genome-wide maps of chromatin state in wild-type and SetDB1 induced knockout mESCs

city: Suzhou

first: Xiaoqin

last: Yang

address: No. 199, Ren'ai Road

institute: Suzhou Medical College of Soochow University

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells and characterized genome-wide SetDB1 binding and H3K9 trimethylation (H3K9me3) profiles in mouse ES cells and uncovered two distinct classes of SetDB1 binding sites, termed solo and ensemble peaks. The solo peaks were devoid of H3K9me3 and enriched near developmental regulators while the ensemble peaks were associated with H3K9me3.  A subset of the SetDB1 solo peaks, particularly those near neural development related genes, was found to be associated with Polycomb Repressive Complex 2 (PRC2) as well as PRC2-interacting proteins Jarid2 and Mtf2.  Genetic deletion of Setdb1 dramatically reduced Ezh2 binding as well as histone 3 lysine 27 (H3K27) trimethylation level at SetDB1 solo peaks and facilitated neural differentiation. Furthermore, we found that H3K27me3 inhibits SetDB1 methyltransferase activity in vitro.  The currently identified reciprocal action between SetDB1 and PRC2 reveals a novel mechanism underlying ES cell pluripotency and differentiation regulation.

overall_design: Examination of 2 different histone modifications in 2 cell status.

first: Yong

last: Zhang


title: The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer

city: La Jolla

first: Christopher

last: Benner

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

overall_design: Refer to individual Series


title: Induction of circular RNA in fetal heart development recapitulated in in vitro differentiation

city: Stanford

first: Linda

last: Szabo

address: Beckman Center, B400 279 W. Campus Dr. MC: 5307

department: Biochemistry

summary: We discovered induction of circular RNA in human fetal tissues, including the heart. In this study, we were able to recapitulate this induction by in vitro directed differentiation of hESCs to cardiomyocytes, paving the way for future studies into circular RNA regulation.

overall_design: We harvested hESCs at sequential stages of differentiation: undifferentiated (day 0), mesoderm (day 2), cardiac progenitor (day 5) and definitive cardiomyocyte (day 14). We performed RNA sequencing in biological triplicate, with 3-8 technical replicates each.


title: Tissue-specific circular RNA induction during human fetal development

summary: The pervasive expression of circular RNA from protein coding loci is a recently discovered feature of many eukaryotic gene expression programs.  Computational methods to discover and quantify circular RNA are essential to the study of the mechanisms of circular RNA biogenesis and potential functional roles they may play.  In this paper, we present a new statistical algorithm that increases the sensitivity and specificity of circular RNA detection.by discovering and quantifying circular and linear RNA splicing events at both annotated exon boundaries and in un-annotated regions of the genome  Unlike previous approaches which rely on heuristics like read count and homology between exons predicted to be circularized to determine confidence in  prediction of circular RNA expression, our algorithm is a statistical approach. We have used this algorithm to discover general induction of circular RNAs in many tissues during human fetal development.  We find that some regions of the brain show marked enrichment for genes where circular RNA is the dominant isoform. Beyond this global trend, specific circular RNAs are tissue specifically induced during fetal development, including a circular isoform of NCX1 in the developing fetal heart that, by 20 weeks, is more highly expressed than the linear isoform as well as beta-actin. In addition, while the vast majority of circular RNA production occurs at canonical U2 (major spliceosome) splice sites, we find the first examples of developmentally induced circular RNAs processed by the U12 (minor) spliceosome, and an enriched propensity of U12 donors to splice into circular RNA at un-annotated, rather than annotated, exons.  Together, our algorithm and its results suggest a potentially significant role for circular RNA in human development.

overall_design: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit.


title: Morphological and Genetic Mechanisms of Regeneration in Hemichordates

city: Kansas City

first: Alejandro

last: Sánchez Alvarado

address: 1000 E 50th Street

institute: The Stowers Institute for Medical Research

summary: Analysis of gene expression level changes during the regeneration of the hemichordate posterior during the first 96 hours of regeneration.

overall_design: Animals were bisected, then collected at eight experimental timepoints - 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, with a minimum of four replicates for each timepoint. Additionally, four healthy and intact animals were bisected and immediately collected to serve as reference controls.

first: Shawn

last: Luttrell

first: Kirsten

last: Gotting

first: Eric

last: Ross

first: Billie

last: Swalla


title: Integrative transcriptome profiling of cognitive aging and its preservation through Ser/Thr protein phosphatase regulation

city: Chicago

first: C. Sehwan

last: Park

state: IL

address: 375 East Chicago Ave

department: Pritzker School of Law

institute: Northwestern University

summary: Environmental enrichment has been reported to delay or restore age-related cognitive deficits, however, a mechanism to account for the cause and progression of normal cognitive decline and its preservation by environmental enrichment is lacking. Using genome-wide SAGE-Seq, we provide a global assessment of differentially expressed genes altered with age and environmental enrichment in the hippocampus. Qualitative and quantitative proteomics in naïve young and aged mice was used to further identify phosphorylated proteins differentially expressed with age. We found that increased expression of endogenous protein phosphatase-1 inhibitors in aged mice may be characteristic of long-term environmental enrichment and improved cognitive status. As such, hippocampus-dependent performances in spatial, recognition, and associative memories, which are sensitive to aging, were preserved by environmental enrichment and accompanied by decreased protein phosphatase activity. Age-associated phosphorylated proteins were also found to correspond to the functional categories of age-associated genes identified through transcriptome analysis. Together, this study provides a comprehensive map of the transcriptome and proteome in the aging brain, and elucidates endogenous protein phosphatase-1 inhibition as a potential means through which environmental enrichment may ameliorate age-related cognitive deficits.

overall_design: 4 groups with 3 biological replicates per group: aged in environmental enrichment (EA), aged in standard housing (SA), young in environmental enrichment (EY), and young in standard housing (SY).

first: C

first: Hubert

last: Rehrauer


title: Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq

city: Madison

first: Ning

last: Leng

state: WI

address: 330 N Orchard St

institute: Morgridge Institute for Research

summary: Oscillatory gene expression is fundamental to mammalian development, but technologies to monitor expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applications to a number of data sets, include a single-cell RNA-seq data set of human embroyonic stem cells (hESCs), demonstrate advantages of the approach and also identify a potential artifact in the Fluidigm C1 platform.

overall_design: Total 213 H1 single cells and 247 H1-Fucci single cells were sequenced. The 213 H1 cells were used to evaluate Oscope in identifying oscillatory genes. The H1-Fucci cells were used to confirm the cell cycle gene cluster identified by Oscope in the H1 hESCs. Normalized expected counts are provided in GSE64016_H1andFUCCI_normalized_EC.csv.gz

first: Leng

last: Ning

first: Chu

last: Li-Fang


title: The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (ChIP-Seq)

status: Public on Jun 23 2015

city: Cleveland

first: Chia-Feng

last: Liu

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Lerner Research Institute

summary: SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We used RNA-seq to charatierize a rat chondrosarcoma (RCS) cells as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes and ChIP-seq to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio.

overall_design: ChIP-seq for SOX9,  SOX6 and histone modifications were carried out using RCS cells

middle: F

first: Veronique

last: Lefebvre


title: Transcriptomics and Metabolomics of 10 - 28 day post anthesis cotton fiber from Gossypium hirsutum and Gossypium barbadense

city: Raleigh

first: Candace

middle: Hope

last: Haigler

state: NC

address: 101 Derieux Place

department: Crop Science

institute: North Carolina State University

summary:
Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter.
Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics.
Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed.
Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: See Bioproject PRJNA263926 and SRA accession SRP049330 for study design and raw sequencing data and Bioproject PRJNA269608 and TSA accession GBYK00000000 for Gossypium arboreum assembled contig sequences used for transcriptome mapping - Cotton fiber mRNA from 10,15,18,21 and 28 day post anthesis fiber from either Gossypium hirusutm or Gossypium barbadense was sequenced and differential gene expression analysis was conducted between species for each timepoint and between adjacent timepoints. Each timepoint was representative of fiber from 9 individual plants processed as 3 biological replicate pools (material from 3 individual plants per pool).

first: J

last: Tuttle

first: Gyoungju

last: Nah

first: Mary

last: Duke

first: Xueying

last: Guan

first: Qingxin

last: Song

first: Z

middle: J

last: Chen

first: Brian

last: Scheffler


title: The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis


title: Critical role of histone turnover in neuronal transcription and plasticity [RNA-seq]

city: New York

first: Li

last: Shen

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Turnover and exchange of nucleosomal histones and their variants, a process long believed to be static in post-replicative cells, remains largely unexplored in brain. Here, we describe a novel mechanistic role for HIRA (histone cell cycle regulator) and proteasomal degradation associated histone dynamics in the regulation of activity-dependent transcription, synaptic connectivity and behavior. We uncover a dramatic developmental profile of nucleosome occupancy across the lifespan of both rodents and humans, with the histone variant H3.3 accumulating to near saturating levels throughout the neuronal genome by mid-adolescence. Despite such accumulation, H3.3 containing nucleosomes remain highly dynamic–in a modification independent manner–to control neuronal- and glial- specific gene expression patterns throughout life. Manipulating H3.3 dynamics in both embryonic and adult neurons confirmed its essential role in neuronal plasticity and cognition. Our findings establish histone turnover as a critical, and previously undocumented, regulator of cell-type specific transcription and plasticity in mammalian brain.

overall_design: All RNA-seq samples were generated to test the impact of neuronal activity/adult physiological plasticity on histone turnover turnover mediated alterations in mRNA expression in the central nervous system. This was tested in cultured neurons and astrocytes, and embryonic/adult brain tissues

first: Ian

last: Maze


title: Critical role of histone turnover in neuronal transcription and plasticity [ChIP-seq]

overall_design: All ChIP-seq samples were generated to test the impact of neuronal activity/adult physiological plasticity on histone turnover in the central nervous system. This was tested in cultured neurons and astrocytes, FACS purified neurons or FACS purified Glia.


title: The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer (RNA-seq)

first: Christopher

last: Benner

summary: This study was aimed at understanding the genome-wide binding and regulatory role of the DAXX transcriptional repressor, recently implicated in PCa. ChIP-Seq analysis of genome-wide distribution of DAXX in PC3 cells revealed over 59,000 DAXX binding sites, found at regulatory enhancers and promoters. ChIP-Seq analysis of DNA methyltransferase 1 (DNMT1), which is a key epigenetic partner for DAXX repression, revealed that DNMT1 binding was restricted to a small number of DAXX sites. DNMT1 and DAXX bound close to transcriptional activator motifs. DNMT1 sites were found to be dependent on DAXX for recruitment by analyzing DNMT1 ChIP-Seq following DAXX knockdown (K/D), corroborating previous findings that DAXX recruits DNMT1 to repress its target genes. Massively parallel RNA sequencing (RNA-Seq) was used to compare the transcriptomes of WT and DAXX K/D PC3 cells. Genes induced by DAXX K/D included those involved in autophagy, and DAXX ChIP-Seq peaks were found close to the transcription start sites (TSS) of autophagy genes, implying they are more likely to be regulated by DAXX.

overall_design: Determine changes in gene expression levels between WT and DAXX K/D prostate cancer cells by RNA-Seq (PC3 Cells).

first: Lorena

last: Puto

first: Tony

last: Hunter


title: Critical role of histone turnover in neuronal transcription and plasticity

status: Public on Jun 22 2015

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


title: DNA methylation analysis by RRBS in germ cells of mice exposed to Vinclozolin

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

summary: We provide quantitative maps of cytosine methylation at single base resolution by RRBS in E13.5 primordial germ cells and adult sperm purified from mice exposed to Vinclozolin.

overall_design: Pregnant F0 female mice were exposed to two doses (a low dose VD1=1 mg/kg bw/d and a high dose VD2=100mg/kg bw/d) of Vinclozolin in the drinking water during pregnancy. We isolated primordial germ cells at E13.5 and mature sperm from adult F1 males obtained from control and exposed mothers. For PGCs, we sequenced RRBS libraries prepared from one pool isolated from F1 embryos exposed to the low dose, one pool isolated from F1 embryos exposed to the high dose, and two control pools isolated from unexposed embryos. For sperm, we sequenced three RRBS libraries prepared from a pool of sperm isolated from F1 males exposed to the high dose, and five RRBS libraries prepared from control pools isolated from unexposed animals.

first: Sylvain

last: Guibert


title: Upstream Anti-sense Promoters Act as Local Enhancers of Mammalian Protein-coding Genes

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Anti-sense transcription originating upstream of mammalian protein-coding genes is a well-documented phenomenon, but remarkably little is known about the function or regulation of these anti-sense promoters or the non-coding RNAs they generate. Here we define at nucleotide resolution the divergent transcription start sites (TSSs) near mouse mRNAs. We find that coupled sense and anti-sense TSSs form the boundaries of an evolutionarily conserved and nucleosome-depleted regulatory region with dramatically enriched transcription factor (TF) occupancy. Notably, as the distance between sense and anti-sense TSSs increases, so does the level of TF binding and signal-dependent gene activation. We further discover a cluster of anti-sense TSSs in macrophages with an enhancer-like chromatin signature. Remarkably, this signature identifies promoters that are selectively and rapidly activated during immune challenge. We conclude that anti-sense TSSs can serve as potent, local enhancers of sense-strand gene expression by facilitating TF binding and deposition of activating histone modifications.

overall_design:
ChIP-seq, Start-RNA-seq, and MNase-seq from mouse bone marrow-derived macrophages (BMDMs), and Start-RNA-seq from mouse embryonic fibroblasts (MEFs) are included.
For ChIP-seq, two biological replicates are included for each of three treatment conditions; untreated, 30 minutes lipopolysaccharide (LPS), and 2 hours LPS. Each biological replicate for all ChIP conditions was sequenced in two lanes for depth, creating two technical replicates for each biological replicate. Raw files for paired technical replicates are labeled as repX.1 and repX.2, where repX.1 is technical replicate 1 and repX.2 is technical replicate 2.
For Start-RNA-seq in BMDMs, two biological replicates are included for each of three treatment conditions; untreated, 30 min LPS, and 2 hr LPS.
For MNase-seq, data from three biological replicates of untreated BMDMs are included. Four technical replicates of biological replicate 1, two technical replicates of biological replicate 2, and four technical replicates of biological replicate 3 are included. Raw files for paired technical replicates are labeled as repX.1, repX.2, repX.3, etc.
For Start-RNA-seq in untreated MEFs, two biological replicates are included. Two technical replicates for each of the MEF Start-RNA-seq biological replicates are included. Paired technical replicates are labeled as repX.1 and repX.2.

first: Benjamin

last: Scruggs

first: Daniel

last: Gilchrist

first: Sergei

last: Nechaev

first: Ginger

last: Muse

first: Adam

last: Burkholder

first: David

last: Fargo


title: Promoter nucleosome dynamics regulated by signaling through the CTD code

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

country: Spain

institute: Instituto de Biología Funcional y Genómica (IBFG)

summary: Sequencing of mononucleosomal DNA from asynchronous cells of Schizosaccharomyces pombe WT and S2A mutant

overall_design: Mononucleosomal DNA from asynchronous S. pombe WT (1 sample) and S2A mutant cells (2 samples) were sequenced (Illumina HiSeq 2000) using the single-end read protocol

first: Philippe

last: Materne

first: Jayamani

last: Anandhakumar

first: Valerie

last: Migeot

first: Ignacio

last: Soriano

first: Carlo

last: Yague-Sanz

first: Elena

last: Hidalgo

first: Carole

last: Mignion

first: Francisco

last: Antequera

first: Damien

last: Hermand


title: Cell cycle analysis of histone marks and 4C in human Fucci ESCs

city: Athens

first: Stephen

last: Dalton

state: Georgia

address: Paul D. Coverdell Center, Rm. 245/276, 500 DW Brooks Drive

department: Department of Biochemistry and Molecular Biology

institute: Univ. of Georgia

summary: Using the Fucci cell cycle indicator system in hESCs, we evaluated the patterns of bivalent histone marks and enhancer histone marks during the cell cycle by ChIP-seq.  We further evaluated how the chromatin architecture changed during the cell cycle.  We found that bivalent domains are cell cycle regulated, and H3K4me3 specifically peaks during the late G1 stage of the cell cycle.  H3K27me3, however, is largely unchanged during the cell cycle.  Cell cycle-regulated bivalent domains interact with enhancers and form cell cycle regulated chromatin interactions.

overall_design: FACS-isolated cell cycle fractions (DN, early G1; KO2, late G1; AzL, S-phase; and AzH, G2/M) from Fucci hESCs were subject to ChIP-seq for H3K4me3, H3K27me3, H3K27ac and H3K4me1, and used for sequencing along with input controls for each of the 4 cell cycle fractions (20 samples total), using Illumina platform, or 4C-seq for each cell cycle fraction using viewpoints neighboring the GATA6 or SOX17 promoters.

first: Amar

last: Singh

first: Li

last: Li


title: Towards understanding the molecular basis of cockroach tergal gland morphogenesis. A transcriptomic approach

city: Barcelona

first: Guillem

last: Ylla

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37

institute: Institute of Evolutionary Biology

summary: The tergal gland is a structure exclusive of adult male cockroaches that produces substances attractive to the female and facilitates mating. It is formed de novo in tergites 7 and 8 during the transition from the last nymphal instar to the adult. Thus, the tergal gland can afford a suitable case study to investigate the molecular basis of a morphogenetic process occurring during metamorphosis. Using Blattella germanica as model, we constructed transcriptomes from male tergites 7-8 in non-metamorphosing specimens, and from the same tergites in metamorphosing specimens. We performed a de novo assembly all available transcriptomes to construct a reference transcriptome and we identified transcripts by homology. Finally we mapped all reads into the reference transcriptome in order to perform analysis of differentially expressed genes and a GO-enrichment test. A total of 5,622 contigs appeared to be overrepresented in the transcriptome of metamorphosing specimens with respect to those specimens that did not metamorphose. Among these genes, there were six GO-terms with a p-value lower than 0.05 and among them GO: 0003676 (“nucleic acid binding”) was especially interesting since it included transcription factors (TFs). Examination of TF-Pfam-motifs revealed that the transcriptome of metamorphosing specimens contains the highest diversity of these motifs, with 29 different types (seven of them exclusively expressed in this stage) compared with that of non-metamorphosing specimens, which contained 24 motif types. Transcriptome comparisons suggest that TFs are important drivers of the process of tergal gland formation during metamorphosis.

overall_design: We sequenced the mRNA from the tergites 7-8 (where the tergal gland appears in the male adult individuals) with Roche 454 GS Junior System, in 4 different developmental stages; in nymph 5 during the ecdysone peak when flat tergites are being produced; in nymph 6 day 1 when the adult program its being initiated; nymph 6 day 1 treated with Juvenil Hormone that inhibits the adult program; and in nymph 6 during the ecdysone peak when tergal gland its being formed. Different transcription factors were found to play a crucial role in TG morphogenesis.

first: Xavier

last: Belles


title: RNA-seq analysis of gene expression after exposure to hot and cold stress in WT cells of Thermosynechococcus elongatus, BP-1

city: Austin

first: Rebecca

last: Knight

state: TX

address: 1 University St. A6700

department: Plant Biology

institute: University of Texas

summary: To investigate the temperature response in Thermosynechococcus elongatus (BP-1) and look for coordinated control in the cell, transcriptomes of BP-1 were measured using RNAseq following exposure to low and high temperature stress. The amount of temperature increase (53 to 61 °C) and decrease (53 to 45 °C) was based on the allowable range of continuous growth.  The cells were growth in three separate culture tubes under LED light in a temperature-controlled submersible chamber under batch growth conditions.  The temperature shift was conducted once the cells reached their target concentration of 1.5E7 cells/ml.  A control experiment was conducted, in which the temperature remained at 53 °C, ensuring that the cellular physiology and light attenuation were comparable and that the only difference between the hot and cold treatments relative to the control treatment was temperature.

overall_design: Heat stress 61°C and cold stress 45°C samples taken at time 0, 0.5hr, 3hr, 10hr, and 24hr.  A control experiment, in which the temperature remained at 53 °C samples taken at time 3hr, 10hr, and 24hr. Each sample timepoint consisted of three biological replicates.


title: BMP signaling differentially regulates distinct hematopoietic stem cell types

city: Edinburgh

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

department: MRC Centre for Inflammation Research

institute: University of Edinburgh

summary: In BRE-GFP transgenic mice BMP activated cells are marked by GFP expression. Analysis of GFP+ and GFP- LSK-SLAM HSC enriched fractions from fetal liver and adult bone marrow shows the interinsic differences in the genetic program of these two HSC enriched fractions.

overall_design: RNAseq of GFP+ and GFP- LSK-SLAM cells from BRE-GFP transgenic mice Fetal liver and adult bone marrow

first: Mihaela

last: Crisan


title: Individuality and variation of personal regulomes in human T cells

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: We surveyed the variation and dynamics of active regulatory elements genome-wide in CD4+ T cells, using Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq) in longitudinal samples from healthy volunteers and during T cell activation. We created robust pipelines that enable accurate single molecule counting and allelic discrimination from clinical material. Over 4000 regulatory elements (7.2%) showed reproducible personal variation in activity. Gender was the most significant attributable source of regulome variation. ATAC-seq revealed novel elements that escape X chromosome inactivation and predicted gender-specific gene regulatory networks across autosomes, which coordinately impact genes with immune function. Noisy regulatory elements with personal variation in accessibility are significantly enriched for autoimmune disease loci. Over one third of regulome variation lacked genetic variation in cis, suggesting contributions from environmental or epigenetic factors. These results refine concepts of human individuality and provide foundational reference to compare disease-associated regulomes.

overall_design: We examined chromatin structure using ATAC-seq in purified human CD4+ T cells in 33 samples from 12 healthy donors and 15 samples from 3 patients with cutaneous T cell leukemia (CTCL). For T cell activation (TCA) time course, CD4+ cells from healthy donor 1 isolated as above were stimulated with ionomycin (1 ug/mL) and Phorbol Myristate Acetate (PMA; 20 ng/mL) and collected at 0, 1, 2, 4 hours in duplicate.

first: Lisa

last: Zaba

first: Paul

middle: G

last: Giresi

first: Rui

first: Michelle

last: Longmire

first: Youn

last: Kim

first: Willian

last: Greenleaf

first: Howard

middle: Y

last: Chang


title: Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape of ESCs revealing changes in lineage specification and chromosomal stability

city: Houston

first: Hyunjae

address: 1102 Bates Ave

department: Pediatric Oncology

institute: Baylor College of Medicine

overall_design: Refer to individual Series


title: Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape of ESCs revealing changes in lineage specification and chromosomal stability (RNA-Seq)

summary: Histone modifications and DNA methylation represent two distinct modes of varying epigenetic landscapes, but whose exact interrelationship remains unclear. Previous studies have shown that histone H3 lysine 4 trimethylation (H3K4me3) inhibits the binding of de novo DNA methyltransferases (Dnmt) through the ATRX-DNMT3-DNMTL (ADD) domain, thus protecting H3K4me3 marked CpG islands (CGI) from DNA methylation. In addition to H3K4me3, we identified antagonistic relationship between H3T3 phosphorylation and the binding of the ADD domain to the unmodified H3 N-terminus. To assess the physiological relevance of these restrictions, we engineered the wild-type ADD domain of Dnmt3a (WT) to permit additional binding to either H3K4me3 (WWD) or H3T3ph (R) and stably introduced FLAG-tagged, full-length normal or mutant Dnmt3a2 into ESCs lacking all Dnmts (TKO; triple knock-out of Dnmt1, Dnmt3a, and Dnmt3b) using the PiggyBac transposon system. For each WT-, WWD-, and R-Dnmt3a2, we generated bulk and clonally-derived ESC lines. We then employed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) to identify the genomic distribution of full-length WT-, WWD-, R-Dnmt3a2, and the H3K4me3 distribution. In parallel, we quantitatively measured genome-wide CpG (cytosine) methylation at base-pair resolution using an enhanced form of reduced representation bisulfite sequencing (RRBS), and performed RNA-seq to assess transcription in matched ESC lines.

overall_design: Examination of mRNA profiles in Dnmt TKO-ESCs expressing wild-type/mutant Dnmt3a2.

first: Kyung-Min

last: Noh


title: Transcriptional landscape of transkingdom communication between Candida albicans and Streptococcus gordonii

city: Aberdeen

first: Sophie

last: Shaw

state: Aberdeen City

address: 23 St. Machar Drive

department: Centre for Genome Enabled Biology and Medicine

institute: University of Aberdeen

summary: Recent studies have shown that the transcriptional landscape of the pleiomorphic fungus Candida albicans is highly dependent upon growth conditions. Here using a dual RNA-seq approach we identified 299 C. albicans and 72 Streptococcus gordonii genes that were either up- or down-regulated specifically as a result of co-culturing these human oral cavity microorganisms. Seventy five C. albicans genes involved in responses to chemical stimuli, regulation, homeostasis, protein modification and cell cycle were statistically (P ≤0.05) upregulated, while 36 genes mainly involved in transport and translation were down-regulated. Upregulation of filamentation-associated TEC1 and FGR42 genes, and of ALS1 adhesin gene, concurred with previous evidence that the C. albicans yeast to hypha transition is promoted by S. gordonii. Increased expression of genes required for arginine biosynthesis in C. albicans was potentially indicative of a novel oxidative stress response. The transcriptional response of S. gordonii to C. albicans was less dramatic, with only eight S. gordonii genes significantly (P ≤0.05) up-regulated ≥ twofold (glpK, rplO, celB, rplN, rplB, rpsE, ciaR, and gat). The expression patterns suggest that signals from S. gordonii cause a positive filamentation response in C. albicans, while S. gordonii appears to be transcriptionally less influenced by C. albicans.

sample_organism:
Streptococcus gordonii
Candida albicans

platform_organism:
Streptococcus gordonii
Candida albicans

overall_design: Five Samples; Sample 1 - Candida albicans cells grown in hypha inducing conditions for two hours; Sample 2 - Candida albicans cells grown in hypha-inducing conditions for two hours before co-culture with Streptococcus gordonii cells for one hour in a 2:1 rato; Sample 3 - Candida albicans cells grown in hypha-inducing conditions for two hours before culture in Streptococcus gordonii media for one hour; Sample 4 - Candida albicans cells grown in hypha inducing conditions for two hours, filtered to remove Candida albicans cells and media added to Streptococcus gordonii cells for one hour; Sample 5 - Streptococcus gordonii cells alone for one hour. All samples extracted and sequenced in biological triplicate using Illumina HiSeq2500. Samples 1, 2 and 3 aligned to the reference genome for Candida albicans and Samples 2, 4 and 5 aligned to the reference genome for Streptococcus gordonii.

first: Lindsay

last: Dutton

first: Konrad

last: Paskiewicz

first: Richard

last: Silverman

first: Peter

last: Splatt

first: Angela

last: Nobbs

last: Lamont

last: Jenkinson

first: Mark

last: Ramsdale


title: Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape of ESCs revealing changes in lineage specification and chromosomal stability (ChIP-Seq)

overall_design: Examination of wild-type/mutant Dnmt3a2 and matched H3K4me3 distributions in TKO-ESCs.


title: Nuclear HNRNPA2B1 HITS-CLIP and RNA-seq

status: Public on Jun 20 2015

first: Claudio

last: Alarcon

state: New York

address: 1230 York Ave

department: Systems Cancer Biology

institute: The Rockefeller University

summary: To identify HNRNPA2B1 binding sites on endogenous nuclear RNAs, we performed HITS-CLIP for endogenous HNRNPA2B1 and RNA-seq to analyze the nuclear RNA under either METTL3 or HNRNPA2B1 depletion.

overall_design: Wild type MDA-MB-231 cells were subjected to the HITS-CLIP procedure on immunoprecipitated HNRNPA2B1 associated RNA obtained from the nuclear fraction (Licatalosi D, et al. 2008, Nature 456:464-U22). For RNA-seq, nuclear RNA was extracted from MDA-MB-231 or Hela cells knocked down for METTL3 or HNRNPA2B1.

first: Hani

last: Goodarzi

first: Hyeseung

last: Lee

first: Xuhang

last: Liu

first: Saeed

last: Tavazoie

first: Sohail


title: Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape of ESCs revealing changes in lineage specification and chromosomal stability (Bisulfite-Seq)

last: Kim

overall_design: Examination of DNA methylation levels in Dnmt TKO-ESCs expressing wild-type/mutant Dnmt3a2.


title: Survival rate and transcriptional response upon infection with the generalist parasite Beauveria bassiana in a world-wide sample of Drosophila melanogaster

status: Public on Jun 19 2015

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

institute: University of Munich

summary: The ability to cope with infection by a parasite is one of the major challenges for any host species and is a major driver of evolution. Parasite pressure differs between habitats. It is thought to be higher in tropical regions compared to temporal ones. We infected Drosophila melanogaster from two tropical (Malaysia and Zimbabwe) and two temperate populations (the Netherlands and North Carolina) with the generalist entomopathogenic fungus Beauveria bassiana to examine if adaptation to local parasite pressures led to differences in resistance. Contrary to previous findings we observed increased survival in temperate populations. This, however, is not due to increased resistance to infection per se, but rather the consequence of a higher general vigor of the temperate populations. We also assessed transcriptional response to infection within these flies eight and 24 hours after infection. Only few genes were induced at the earlier time point, most of which are involved in detoxification. In contrast, we identified more than 4,000 genes that changed their expression state after 24 hours. This response was generally conserved over all populations with only few genes being uniquely regulated in the temperate populations. We furthermore found that the American population was transcriptionally highly diverged from all other populations concerning basal levels of gene expression. This was particularly true for stress and immune response genes, which might be the genetic basis for their elevated vigor.

overall_design: mRNA profiles of whole Drosophila melanogaster adult males from an African, American, Asian and European population after infection with Beauveria bassiana. Samples include uninfected controls, 8h after infection and 24h after infection. 3 biological replicates each (2 in the case of American controls).

first: Francesco

last: Paparazzo

first: Aurélien

last: Tellier

first: Wolfgang

last: Stephan


title: Regulatory mechanisms on the early process of mouse spermatogenesis investigated by digital gene expression tag profiling analysis

city: Beijing

first: lili

last: hao

address: Beichen west road

institute: BIG

summary: A detailed understanding of the gene regulation mechanisms in premeiosis cells is germane to understanding normal spermatogenesis. The genome-wide expression profiles of type B spermatogonia and primary spermatocytes in mouse were investigated using Solexa/Illumina’s digital gene expression (DGE) system, a tag based high-throughput transcriptome sequencing method, and the developmental process of early spermatogenesis was analyzed systematically. The results suggested that the expression pattern of mouse type B spermatogonia and primary spermatocytes was changed dramatically, especially the genes related to junction assembly, regulation of actin cytoskeleton and pluripotency. The change of the expression levels of these pathways’ main components may be affected by corresponding miRNAs through post-transcriptional regulation. The analysis results will benefit for better understanding the molecular mechanism of early spermatogenesis process.

overall_design: Using DGE technology to examine gene expression pattern's change between mouse type B spermatogonia and primary spermatocytes cell types.

first: Xiujun

last: Zhang

first: Lili

last: Hao

first: Lijun

last: Meng

first: Songnian

last: Hu

first: Mengchun

last: Jia


title: The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer (ChIP-seq)

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

overall_design: To determine DAXX binding sites in the prostate cancer (PCa) genome, the PC3 cell line was used. A stable DAXX shRNA knockdown (K/D) PC3 cell line and a control shRNA counterpart, were compared in a ChIP-Seq study.

first: Lorena

middle: A

last: Puto

first: Tony

last: Hunter


title: Nucleoporin Nup153 Regulates Stem Cell Pluripotency through Gene Silencing

summary: Nucleoporins (Nups) are a family of proteins best known as the constituent building blocks of nuclear pore complexes (NPCs), the transport channels that mediate nuclear transport. Recent evidence suggest that several Nups have additional roles in controlling the activation and silencing of developmental genes, however, the mechanistic details of these functions remain poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem cells (mESCs) causes the de-repression of developmental genes and induction of early differentiation. This loss of pluripotency is not associated with defects in global nucleo-cytoplasmic transport activity. Instead, Nup153 binds to the transcriptional start site (TSS) of developmental genes and mediates the recruitment of the polycomb repressive complex 1 (PRC1) to its target loci. Our results reveal a nuclear transport-independent role of Nup153 in maintaining stem cell pluripotency and introduce a role of NPC proteins in mammalian epigenetic gene silencing.

overall_design: RNA-seq, ChIP-Seq, and DamID-Seq for Nup153, Oct4, and key chromatin regulators in mouse ES cells and neural progenitors

first: Filipe

middle: V

last: Jacinto

first: Martin

last: Hetzer


title: renal cell carcinoma

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic


title: Mutational activation of a mechanosensitive megachannel drives metastatic cell survival.

first: David

last: Soong

state: NY

address: 1305 York Avenue

department: Institute for Computational Biomedicine

institute: Weill Cornell Medical College

summary: Next-generation sequencing has revolutionized cancer biology by accelerating the unbiased discovery of novel mutations across human cancers. Transforming such discoveries into a conceptual framework of cancer progression requires narrowing the vast number of mutations down to the driver elements, and further reducing these to mutations that govern cancer progression as opposed to tumor initiation. By integrating next-generation RNA-sequencing (RNA-seq) with in vivo selection, we devise an approach that identifies a series of novel recurrent non-synonymous amino acid mutations that are enriched in metastatic breast cancer cells and predicted to significantly alter protein function. These mutations, found in PANX1, RBFA, REST, KRIT1 and ZSWIM6, are detected at higher frequencies in the transcriptomes of two patients’ highly metastatic sub-lines relative to their poorly metastatic parental lines. We functionally characterize the cellular and molecular roles of one of these mutations—a nonsense alteration that yields a truncated pannexin-1 (PANX11-89) plasma membrane megachannel subunit—in metastatic progression. PANX11-89 interacts with full-length PANX1 and augments PANX1 channel activity to promote the survival of cancer cells as they are mechanically deformed. Protection from deformation-induced cell death requires PANX1 channels to release ATP, which acts as a cell autonomous survival signal during mechanical stress. Functional characterization of additional nonsense and missense PANX1 mutations detected in epithelial cancers of the colon, lung, and prostate reveals that these mutants also enhance PANX1-mediated ATP release. In vivo testing of one such truncating mutation detected in a metastatic colorectal tumor also enhances early survival, dissemination and liver metastatic colonization by human colon cancer cells. Finally, pharmacological inhibition of PANX1 inhibits breast cancer metastasis, implicating PANX1 as a novel therapeutic target in cancer. Our findings reveal that ATP release through mechanosensitive PANX1 channels enables cancer cells to overcome a major metastasis suppressive barrier—deformation-induced death in the microvasculature.

overall_design: To systematically identify base-pair mutations present in metastatic cells that may drive cancer progression, we performed whole-transcriptome RNA-sequencing (RNA-seq) of in vivo-selected, highly metastatic human breast cancer cell sub-lines, CN-LM1A and MDA-LM2, as well as the CN34 and MDA-MB-231 parental lines from which they were derived. To minimize the false positive rate and allow for subsequent statistical analysis, we sequenced biological replicates of each cell line. Mutations conferring enhanced metastatic capacity should be enriched in the transcriptomes of highly metastatic cells relative to their less metastatic parental populations.

first: Paul

last: Furlow

first: Steven

first: Nils

last: Halberg

first: Creed

last: Mangrum

first: Olivier

last: Elemento

first: Sohail

last: Tavazoie


title: The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (RNA-Seq)

first: Chia-Feng

last: Liu

state: OH

address: 9500 Euclid Avenue,

institute: Cleveland Clinic Lerner Research Institute

summary: SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We used RNA-seq to charatierize a rat chondrosarcoma (RCS) cells as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes and ChIP-seq to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio.

overall_design: RNAs were isolated  from three bioogical replicatse of rat chondrosarcoma (RCS) cells and rib samples for RNA-seq experiments.

first: Veronique

last: Lefebvre


title: Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells [DNase-Hypersensitivity]

first: Yu-Xiang

last: Zhang

address: Fengtai-District,You-An-Men-Wai

department: Biochemistry

institute: Capital Medical University, China

summary: Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100-500bp. Therefore, we have modified the double-hit method and use short DNA fragments to generate DNA libraries for next generation sequencing. We call this method Short DHS Assay (Short DNAse I Hypersensitive Site assay). The short segments are 100-300bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by the Short DHS assay are consistent with those identified by longer fragments in previous studies.

overall_design: HeLa S3 Nuclear extraction and DNase I digestion

first: Yuxiang

first: Yamei

last: Wang

first: Ping

last: Zhou

first: Liyong


title: Genome-wide DNA methylation profiling reveals epigenetic changes in the rat nucleus accumbens associated with cross-generational effects of adolescent THC exposure

first: Yasmin

last: Hurd

address: 1470 Madison Avenue, Room 105 (Office)

department: Departments of Psychiatry; Neuroscience; Pharmacology and Systems Therapeutics

institute: Icahn School of Medicine at Mount Sinai

summary: Drug exposure during critical periods of development is known to have lasting effects, increasing one’s risk for developing mental health disorders. Emerging evidence has also indicated the possibility for drug exposure to even impact subsequent generations. Our previous work demonstrated that adolescent exposure to Δ9-tetrahydrocannabinol (THC), the main psychoactive component of marijuana (Cannabis sativa), in a Long-Evans rat model affects reward-related behavior and gene regulation in the subsequent (F1) generation unexposed to the drug. Questions, however, remained regarding potential epigenetic consequences. In the current study, using the same rat model, we employed Enhanced Reduced Representation Bisulfite Sequencing to interrogate the epigenome of the nucleus accumbens, a key brain area involved in reward processing. This analysis compared 16 animals with parental-THC exposure and 16 without to characterize relevant systems-level changes in DNA methylation. We identified 1,027 differentially methylated regions (DMRs) associated with parental THC exposure in F1 adults, each represented by multiple CpGs. These DMRs fell predominantly within introns, exons, and intergenic intervals, while showing a significant depletion in gene promoters. From these, we identified a network of DMR-associated genes involved in glutamatergic synaptic regulation, which also exhibited altered mRNA expression in the nucleus accumbens. These data provide novel insight into drug-related cross-generational epigenetic effects, and serve as a useful resource for investigators to explore novel neurobiological systems underlying drug abuse vulnerability.

overall_design: Study consisted of a total of 32 F1 individuals (Long-Evan rats); 16 animals (8 female, 8 male) were offspring from THC-exposed parents, and the remaining 16 animals (8 female, 8 male) were offspring from saline-exposed parents ("controls"; "VEH-exposed").

first: Corey

middle: T

last: Watson

first: Henrietta

last: Szutorisz

first: Paras

last: Garg

first: Qammarah

last: Martin

first: Joseph

last: Landry

first: Andrew

last: Sharp


title: Comparison of glucocorticoid receptor (NR3C1) binding in wild type and Klf15-/- MEFs

status: Public on Jun 18 2015

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

institute: University of Colorado, Denver

summary: The objective of this study was to dertemine GR binding patterns within wild type murine embryonic fibroblasts in comparison to embryonic fibroblasts derived from mice containing a null mutation for Klf15.

overall_design: This study utilized duplicate samples and the following conditions.  Wild type cells treated with ethanol (pooled single sample secondary to low starting material); wild type cells treated with dexamethasone for 1 hour (2 samples); Klf15-/- cells treated with ethanol (2 samples); Klf15 -/- cells treated with dexamethasone (2 samples). Samples treated with ethanol served as controls.

first: Sarah

last: Sasse

first: Mukesh

middle: K

last: Jain

first: Tzu

first: Anthony

middle: N

last: Gerber


title: Small RNA-seq during the ecdysone and heat-shock response in Drosophila Kc167 cells

status: Public on Jun 17 2015

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

summary: Small RNA sequencing libraries at 0 h, 3 h, and 48 h time points after ecdysone treatment and 20min heat shock (37 degrees celcius) in Drosophila cell culture

overall_design: Examination of small RNA dynamics during differentiation

first: Victor

last: Corces


title: Chromatin signature identifies monoallelic gene expression across mammalian cell types

first: Sebastien

last: Vigneau

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

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


title: gammaH2Av ChIP-seq in Drosophila stage 10B and 13 follicle cells

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: We analyzed gamaH2Av ChIP-seq from hand dissected stage 10B and 13 follicle cell nuclei. Egg chambers were dissected from wild-type (OrR) or H2Av[ΔCT] ovaries to assess binding at the Drosophila Follicle Cell Amplicons and across the genome.

overall_design: ChIP-seq of gammaH2Av bound to follicle cell DNA from stage 10B and 13 egg chambers, collected from wild-type (OrR) and  H2Av[ΔCT] Drosophila ovaries. Sequences analyzed by Illumina sequencing. Two replicates are included for each ChIP reaction.

first: Jessica

last: Alexander

first: M

middle: I

last: Barrasa


title: Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells

first: Yu-Xiang

last: Zhang

overall_design: Refer to individual Series


title: Chromatin signature identifies monoallelic gene expression across mammalian cell types (RNA-seq)

summary: Monoallelic expression of autosomal genes (MAE) is a widespread epigenetic phenomenon which is poorly understood, due in part to current limitations of genome-wide approaches for assessing it. Recently, we reported that a specific histone modification signature is strongly associated with MAE, and demonstrated that it can serve as a proxy of MAE in human lymphoblastoid cells (Nag et al. Elife. 2013 Dec 31;2:e01256). Here, we use murine cells to establish that this chromatin signature is conserved between mouse and human, and is associated with MAE in every tested cell type. Our analyses reveal extensive conservation in the identity of MAE genes between the two species. By applying MAE chromatin signature analysis to a large number of cell and tissue types, we show that the MAE state remains consistent during terminal cell differentiation and is predominant among cell-type specific genes, suggesting a link between MAE and specification of cell identity.

overall_design: PolyA RNA purification and subsequent high-throughput sequencing were performed on two independent B-lymphoid clonal cell line, derived from 129S1/SvImJ x CAST/EiJ F1 mice and immortalized with Abelson murine leukemia virus, and on two independent fibroblast clonal cell lines, derived from 129S1/Sv x CAST/EiJ F1 and immortalized with SV40.

first: Nag

last: Anwesha

first: Vigneau

last: Sébastien

first: Savova

last: Virginia

first: Zwemer

middle: M

last: Lillian

first: Gimelbrant