title: An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example

city: Nanjing

first: Jinke

last: Wang

state: Jiangsu

address: Sipailou 2

department: Biomedicine

institute: Southeast Uiniversity

summary: We provided an improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor. We valided the strategy by characterzing the DNA-binding specificty of NF-κB p50 dimer.

overall_design: Proteins of the Nf-kappab family were bound to DNA oligonucleotides containing a degenerate region. The protein-DNA complexes were selected after one or multiple rounds of SELEX and the DNA molecules were deep sequenced.

first: Guangming

last: Gu

first: Tingting

first: Yang

last: Yang

first: Hinxin

last: Xu


title: Digital Gene Expression Tag Profiling after Wt1 deletion in Sertoli cell

status: Public on May 06 2014

city: Beijing

first: wang

last: xiaona

address: Bei Chen Xi Lu #1

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology,Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: The Wilms tumor gene, Wt1, is specifically expressed in Sertoli cells (SCs) which support spermatogenesis. Germ cell loss was found in Wt1 knockout mice. In  vitro  studies  demonstrated  that  Wt1  was  essential  for  cell  polarity maintenance  in  SCs. We used Digital Gene Expression Tag Profiling to detail the global programme of gene expression after Wt1 deletion in sertoli cell and identified 710 gene expression level change more than 2 times.

overall_design: Digital Gene Expression Tag Profiling  analysis  were  performed  using  mRNA  from  control  and Wt1-deficient   Primary Sertoli cells, every group primare sertoli cell were from more than 30 mice.

first: Xiaona

first: Fei

last: Gao


title: Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers

status: Public on May 08 2014

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: In mammalian cells transcription factors (TFs) preferentially bind sites contained in regions of high nucleosomal occupancy, as determined by nucleotide-dependent computational analysis. This observation suggests that nucleosomes may act as gatekeepers of TF binding sites. We hypothesized that in mammalian genomes the information controlling nucleosome assembly may partially coincide with the information that enables TFs to recognize cognate sites in cis-regulatory elements while ignoring the myriad of non-functional, randomly occurring consensus binding sites. This way, nucleosome-mediated masking would be coupled to TF binding site functionality. The hematopoietic master regulator Pu.1 maintained nucleosome depletion at macrophage-specific enhancers that were otherwise occupied by nucleosomes in other cell types and in reconstituted chromatin. We identified a minimal set of DNA sequence and shape features that predicted Pu.1 binding with 78% accuracy. The same features predicted nucleosome occupancy in cells where Pu.1 was not expressed with higher accuracy than specifically designed models. Control of nucleosome deposition by DNA sequence and shape features that also specify TF consensus site functionality may allow maintaining the gatekeeper function of nucleosomes during evolution of cis-regulatory elements.

overall_design:
Chromatin immuno-precipitations of the transcription factor Pu.1 followed by multiparallel sequencing performed in murine bone marrow-derived macrophages. Experiments carried out in cells infected either with a retroviral vector containing  a short hairpin targeting Pu.1 or with the empty vector as control. The shPU.1 hairpin (sequence available upon request)  was selected among five designed using a publicly available software (http://katahdin.mssm.edu/siRNA) and  was cloned in a modified version of TtRMPVIR inducible retroviral vector (Genbank HQ456318) in which the puromycin resistance gene was inserted. The empty vector, containing an sh-Renilla sequence, was used as control.
Chromatin immuno-precipitations of the transcription factor PU.1 binding to in vitro reconstituted chromatin followed by multiparallel sequencing
Micrococcal nuclease digestion of chromatin extracted from bone marrow derived macrophages followed by multiparallel sequencing . Experiments were carried out in untreated cells (4 replicates) and cells infected either with a retroviral vector containing a short hairpin targeting Pu.1 or with  the empty vector as control (2 replicates). The shPU.1 hairpin (sequence available upon request)  was selected among five designed using a publicly available software (http://katahdin.mssm.edu/siRNA) and  was cloned in a modified version of TtRMPVIR inducible retroviral vector (Genbank HQ456318) in which the puromycin resistance gene was inserted. The empty vector, containing an sh-Renilla sequence, was used as control.
Micrococcal nuclease digestion of in vitro reconstituted chromatin followed by multiparallel sequencing

first: Marta

last: Simonatto

first: Silvia

last: Bonifacio

first: Serena

last: Ghisletti

first: Lin

first: Remo

last: Rohs

first: Gioacchino

last: Natoli


title: Rapid evolution of phenotypic plasticity and shifting thresholds of genetic assimilation in the nematode Caenorhabditis remanei

status: Public on May 04 2014

city: Eugene

first: Patrick

middle: C.

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

country: USA

institute: University of Oregon

summary: Many organisms can acclimate to new environments through phenotypic plasticity, a complex trait that can be heritable, subject to selection, and evolve. However, the rate and genetic basis of plasticity evolution remain largely unknown. We experimentally evolved outbred populations of the nematode Caenorhabditis remanei under an acute heat shock during early larval development. When raised in a non-stressful environment, ancestral populations were highly sensitive to a 36.8°C heat shock and exhibited high mortality. However, initial exposure to a non-lethal high temperature environment resulted in significantly reduced mortality during heat shock (hormesis). Lines selected for heat shock resistance rapidly evolved the capacity to withstand heat shock in the native environment without any initial exposure to high temperatures, and early exposure to high temperatures did not lead to further increases in heat resistance. This loss of plasticity would appear to have resulted from the genetic assimilation of the heat induction response in the non-inducing environment. However, analyses of transcriptional variation via RNA-sequencing from the selected populations revealed no global changes in gene regulation correlated with the observed changes in heat stress resistance. Instead, assays of the phenotypic response across a broader range of temperatures revealed that the induced plasticity was not fixed across environments, but rather the threshold for the response was shifted to higher temperatures over evolutionary time. These results demonstrate that apparent genetic assimilation can result from shifting thresholds of induction across environments and that analysis of the broader environmental context is critically important for understanding the evolution of phenotypic plasticity.

overall_design: mRNA profiles of ancestral and two experimentally evolved populations of C. remanei at 20°C or 30°C, 6 replicates/temperature for each population

first: Kristin

middle: L

last: Sikkink

first: Rose

middle: M

last: Reynolds

first: Catherine

last: Ituarte

first: William

middle: A

last: Cresko

middle: C


title: A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions

city: Stanford

first: Robert

middle: B.

last: West

state: CA

address: 300 Pasteur Drive

department: Pathology

institute: Stanford School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: The earliest recognizable stages of breast neoplasia are lesions that represent a heterogeneous collection of epithelial proliferations currently classified based on morphology. Their role in the development of breast cancer is not well understood but insight into the critical events at this early stage will improve efforts in breast cancer detection and prevention. These microscopic lesions are technically difficult to study so very little is known about their molecular alterations.  To characterize the transcriptional changes of early breast neoplasia, we sequenced 3'- end enriched RNAseq libraries from formalin-fixed paraffin-embedded tissue of early neoplasia samples and matched normal breast and carcinoma samples from 25 patients. We find that gene  expression patterns within early neoplasias are distinct from both normal and breast cancer patterns and identify a pattern of pro-oncogenic changes, including elevated transcription of ERBB2, FOXA1, and GATA3 at this early stage. We validate these findings on a second independent gene expression profile data set generated by whole transcriptome sequencing. Measurements of protein expression by immunohistochemistry on an independent set of early neoplasias confirms that ER pathway regulators FOXA1 and GATA3, as well as ER itself, are consistently upregulated at this early stage. The early neoplasia samples also demonstrate coordinated changes in long non-coding RNA expression and microenvironment stromal gene expression patterns.  This study is the first examination of global gene expression in early breast neoplasia, and the genes identified here represent candidate participants in the earliest molecular events in the development of breast cancer.

overall_design: 3SEQ was performed on 72 FFPE human breast samples from 25 patients:  24 normal, 25 early neoplasia, 9 carcinoma in situ, and 14 invasive cancer

first: Alayne

last: Brunner

first: Jun

last: Li

first: Xiangqian

last: Guo

middle: T

last: Sweeney

first: Sushama

last: Varma

first: Shirley

middle: X

last: Zhu

first: Rui

last: Tibshirani

middle: B


title: Glycogen synthase kinase (GSK) 3β phosphorylates and protects nuclear myosin 1c from proteasome-mediated degradation to activate rDNA transcription in early G1 cells

status: Public on May 02 2014

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Nuclear myosin 1c (NM1) mediates RNA polymerase I (pol I) transcription activation and cell cycle progression by facilitating PCAF-mediated H3K9 acetylation, but the molecular mechanism by which NM1 is regulated remains unclear. Here, we report that at early G1 the glycogen synthase kinase (GSK) 3β phosphorylates and stabilizes NM1, allowing for NM1 association with the chromatin. Genomic analysis by ChIP-Seq showed that this mechanism occurs on the rDNA as active GSK3β selectively occupies the gene. ChIP assays and transmission electron microscopy in GSK3β-/- mouse embryonic fibroblasts indicated that at G1 rRNA synthesis is suppressed due to decreased H3K9 acetylation leading to a chromatin state incompatible with transcription. We found that GSK3β directly phosphorylates the endogenous NM1 on a single serine residue (Ser-1020) located within the NM1 C-terminus. In G1 this phosphorylation event stabilizes NM1 and prevents NM1 polyubiquitination by the E3 ligase UBR5 and proteasome-mediated degradation. We conclude that GSK3β-mediated phosphorylation of NM1 is required for pol I transcription activation.

overall_design: Examination of GSK3beta with the genome in mouse embryonic fibroblasts

first: Aishe

last: Sarshad

first: Martin

last: Corcoran

first: Bader

last: Almuzzaini


title: Dual and separable roles for Ezh2 in neurogenic astroglia

city: San Francisco

first: Daniel

last: Lim

address: 35 Medical Center Way RMB 933B

department: Neurological Surgery

institute: University of California, San Francisco

summary: The epigenetic mechanisms that enable specialized astrocytes to retain neurogenic competence throughout adult life are still poorly understood. Here we show that astrocytes that serve as neural stem cells (NSCs) in the adult mouse subventricular zone (SVZ) express the histone methyltransferase EZH2. This Polycomb repressive factor is required for neurogenesis independent of its role in SVZ NSC proliferation, as Ink4a/Arf-deficiency in Ezh2-deleted SVZ NSCs rescues cell proliferation, but neurogenesis remains defective. Olig2 is a direct target of EZH2, and repression of this bHLH transcription factor is critical for neuronal differentiation. Furthermore, Ezh2 prevents the inappropriate activation of genes that specify non-SVZ neuronal subtypes. In the human brain, SVZ cells including local astroglia also express EZH2, correlating with postnatal neurogenesis. Thus, EZH2 is an epigenetic regulator that distinguishes neurogenic SVZ astrocytes, orchestrating distinct and separable aspects of adult stem cell biology, which has important implications for regenerative medicine and oncogenesis.

overall_design: Examination of histone modifications (H3K27me3 and H3K4me3) in subventricular zone neural stem cells

middle: W

last: Hwang

first: Ryan

middle: D

last: Salinas

middle: N

last: Delgado


title: Genomic expression analysis of human monocyte-derived DCs and monocytes

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

summary: To identify the functional non-coding RNAs in human DC development, we explored the gene expression profiles during DC development from peripheral monocytes. Using RNA-seq, we identified many annotated lncRNAs with markedly altered expressions during human DC differentiation and maturation.

overall_design: RNA samples from human peripheral blood monocytes and monocyte-derived DCs were collected. RNAs from 3 donors were pooled together to form monocyte sample or DC sample and then these two samples were subjected to RNA-seq and analysis.

first: Pin

last: Wang

first: Yiquan

last: Xue

first: Cong

last: Wu

first: Yanmei

last: Han

first: Li

last: Lin

first: Zhengping

last: Jiang

first: Yizhi

last: Yu

first: Xuetao

last: Cao


title: Antidiabetic Rosiglitazone Remodels the Adipocyte Transcriptome by Redistributing Transcription to PPARg-Driven Enhancers [HTS]

city: Cincinnati

first: Hee-Woong

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Rosiglitazone (rosi) is a powerful insulin sensitizer, but serious toxicities have curtailed its widespread clinical use.  Rosi functions as a high-affinity ligand for PPARg, the adipocyte-predominant nuclear receptor (NR).  The classic model, involving binding of ligand to the NR on DNA, explains positive regulation of gene expression, but ligand-dependent repression is not well understood.  We have now addressed this issue by studying the direct effects of rosiglitazone on gene transcription, using global run-on sequencing (GRO-seq). Rosi-induced changes in gene body transcription were pronounced after 10 minutes and correlated with steady-state mRNA levels as well as with transcription at nearby enhancers (eRNAs).  Upregulated eRNAs occurred almost exclusively at PPARg binding sites, to which rosi treatment recruited the coactivator MED1. By contrast, transcriptional repression by rosi involved a loss of MED1 from eRNA sites devoid of PPARg and enriched for other TFs including AP-1 factors and C/EBPs. Thus, rosi activates and represses transcription by fundamentally different mechanisms that could inform the future development of antidiabetic drugs.

overall_design: 3T3-L1 matuer adipocyte were treated with rosi, and nascent transcripts were measured at various time points using GRO-seq. ChIP-seq experiments for various coactivators, corepressor, and transcription factors also have been done to monitor initial occupancy or change before and after treatment.

first: Sonia

middle: E

last: Step

first: Jill

last: Marinis

first: Andreas

last: Prokesch

first: David

middle: J

last: Steger

first: Seo-Hee

last: You

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Antidiabetic Rosiglitazone Remodels the Adipocyte Transcriptome by Redistributing Transcription to PPARg-Driven Enhancers

last: Lim

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

overall_design: Refer to individual Series


title: Impacts of the Ubiquitous Factor Zelda on Bicoid-dependent DNA-binding and Transcription in Drosophila

city: New York

first: Stephen

last: Small

state: NY

address: 100 Washington Square East

department: Biology

institute: New York University

summary: In vivo crosslinking studies suggest that the Drosophila transcription factor Bicoid (Bcd) binds to several thousand sites during early embryogenesis, but it is not clear how many of these binding events are functionally important. In contrast, reporter gene studies have identified more than 60 Bcd-dependent enhancers, all of which contain clusters of the consensus binding sequence TAATCC. These studies also identified clusters of TAATCC motifs (inactive fragments) that failed to drive Bcd-dependent activation. In general, active fragments showed higher levels of Bcd-binding in vivo, and were enriched in predicted binding sites for the ubiquitous maternal protein Zelda (Zld). Here we test the role of Zld in Bcd-mediated binding and transcription. Removal of Zld function and mutations in Zld sites caused significant reductions in Bcd-binding to known enhancers, and variable effects on the activation and spatial positioning of Bcd-dependent expression patterns. Genome-wide binding experiments in Zld mutants showed variable effects on Bcd-binding peaks, ranging from strong reductions to significantly enhanced levels of binding. Increases in Bcd binding caused the precocious Bcd-dependent activation of genes that are normally not expressed in early embryos, suggesting that Zld controls the genome-wide binding profile of Bcd at the qualitative level, and is critical for selecting target genes for activation in the early embryo. These results underscore the importance of combinatorial binding in enhancer function, and provide data that will help predict regulatory activities based on DNA sequence.

overall_design:
1-3 hour wild type and zelda mutant embryos were examined for Bicoid binding using Illumina HiSeq 2000.
The Bcd antibody is a rabbit polyclonal antiserum raised against full length Drosophila Bcd protein (Ochoa-Espinosa et al. 2009 PNAS). The antiserum was further purified using the Protein A Antibody Purification Kit (Sigma) for ChIP-seq.

first: Zhe

last: Xu

first: Hongtao

last: Chen

first: Jia

last: Ling

first: Danyang

first: Paolo

last: Struffi


title: H3K27me3 ChIP-seq experiment in fruitfly testis somatic gonadal cells

city: baltimore

first: Xin

state: MD

address: 3400 N Charles St

institute: The Joihns Hopkins University

summary: In many metazoans, germ cells are separated from somatic lineages early in development and maintain their identity throughout life. Here we show that a Polycomb group (PcG) component, Enhancer of Zeste [E(z)] H3K27me3-specific methyltransferase, maintains germline identity in Drosophila adult testes. We find excessive early-stage somatic gonadal cells in E(z) mutant testes, which originate from both over-proliferative cyst stem cells and germ cells turning on an early-stage somatic cell marker. Using complementary lineage-tracing experiments in E(z) mutant testes, a portion of excessive early-stage somatic gonadal cells are found to derive from early-stage germ cells, including germline stem cells. Interestingly, knocking down E(z) specifically in somatic cells caused this germline-to-soma change, suggesting a non-cell autonomous role of E(z) to antagonize somatic identity in germ cells.

overall_design: Using fly testis specifically expressing E(z) shmiR RNAi in germ cells by nos promoter driven GAL4>UAS system, ChIPseq with H3K27me3 antibody was performed, where H3K27me3 is only detected in somatic cells.

first: Suk

middle: H

last: Eun

first: Zhen

last: Shi

first: Kairong

last: Cui

first: Keji

last: Zhao


title: RUNX3 Facilitates Growth of Ewing Sarcoma Cells

status: Public on May 01 2014

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Ewing sarcoma is an aggressive pediatric small round cell tumor that predominantly occurs in bone.  Approximately 85% of Ewing sarcomas harbor the EWS/FLI fusion protein, which arises from a chromosomal translocation, t(11:22)(q24:q12). EWS/FLI interacts with numerous lineage-essential transcription factors to maintain mesenchymal progenitors in an undifferentiated state. We previously showed that EWS/FLI binds the osteogenic transcription factor RUNX2 and prevents osteoblast differentiation. In this study, we investigated the role of another Runt-domain protein, RUNX3, in Ewing sarcoma.  RUNX3 participates in mesenchymal-derived bone formation and is a context dependent tumor suppressor and oncogene.  RUNX3 was detected in all Ewing sarcoma cells examined, whereas RUNX2 was detected in only 73% of specimens. Like RUNX2, RUNX3 binds to EWS/FLI via its Runt domain. EWS/FLI prevented RUNX3 from activating the transcription of a RUNX-responsive reporter, p6OSE2.  Stable suppression of RUNX3 expression in the Ewing sarcoma cell line A673 delayed colony growth in anchorage independent soft agar assays and reversed expression of EWS/FLI-responsive genes.  These results demonstrate an important role for RUNX3 in Ewing sarcoma.

overall_design: RNA-seq to compare transcriptiome of control A673 ewing sarcoma cells stably expression a non-target or RUNX3 shRNA

first: Krista

last: Bledsoe

first: Meghan

last: McGee-Lawrence

first: Emily

last: Camilleri

first: Xiaoke

last: Wang

first: Andre

last: van Wijnen

last: Oliveira

first: Jennifer

last: Westendrof


title: TAL1 in human Endothelial Colony-Forming Cells

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute


title: RNA-seq transcriptome profiling of equine inner cell mass and trophectoderm

city: Davis

first: James

middle: Lee

last: Chitwood

address: 1 Shields Avenue

department: Animal Science

institute: University of California, Davis

summary: Transcriptomic analysis of ICM and TE from in vivo-derived equine blastocysts using Illumina sequencing technology

overall_design: RNA was extracted from individual equine blastocyst ICM and TE (Arcturus Picopure), cDNA was synthesized and amplified (Nugen Ovation V2) and indexed libraries were created for sequencing (TruSeq DNA V1)

first: Pablo

last: Ross


title: Genome-wide maps of Usp16, ubH2A and gene expression profiles in wild type and Usp16 knock out mouse embryonic stem cells (ESCs) and embryoid bodies (EBs)

city: Birmingham

first: Hengbin

state: AL

address: 720 20th St S Kaul Bldg 430

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Polycomb Repressive Complex 1 and histone H2A ubiquitination (ubH2A) contribute to embryonic stem cell (ESC) pluripotency by repressing lineage-specific gene expression. However, whether active deubiquitination co-regulates ubH2A levels in ESCs and during differentiation is not known. Here, we report that the histone H2A deubiquitinase Usp16 regulates H2A deubiquitination and gene expression in ESCs, and importantly, is required for ESC differentiation. Usp16 knockout is embryonic lethal in mice, but does not affect ESC viability or identity. Usp16 binds to the promoter regions of a large number of genes in ESCs and Usp16 binding is inversely correlated with ubH2A levels and positively correlated with gene expression levels. Intriguingly, Usp16-/- ESCs fail to differentiate due to ubH2A-mediated repression of lineage-specific genes. Finally, Usp16, but not the enzymatically inactive mutant, rescues the differentiation defects of Usp16-/- ESCs. Therefore, this study identifies Usp16 and H2A deubiquitination as critical regulators of ESC gene expression and differentiation.

overall_design: Examination of binding pattern of H2A deubiquitinase Usp16 and ubH2A in mouse embryonic stem cells and embroid bodies

first: Wei

last: Yang

first: Yun-Hwa

last: Lee

first: Amanda

last: Jones

first: Jessica

last: Woolnough

first: Dewang

last: Zhou

first: Qian

last: Dai

first: Keith

last: Giles

first: Qiang

last: Wu

first: Tim

last: Townes


title: Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish

city: Oakland

first: Ravi

last: Sachidanandam

address: 2945 Webster St

institute: Girihlet Inc.

summary: ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase (FASN).

overall_design: Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tg(fabp10:nls-mCherry) control larvae, 2 batches of ethanol-treated Tg(fabp10:nls-mCherry) larvae, and 1 batch of Tg(fabp10:nAtf6-cherry; cmlc2:GFP). Each batch was purified for preparation of high-throughput sequencing libraries.

first: Deanna

last: Howarth

first: Claudia

last: Lindtner

first: Ana

last: Vacaru

first: Orkhontuya

last: Tsedensodnom

first: Taisa

last: Vasilkova

first: Christoph

last: Buettner

first: Kirsten

last: Sadler


title: Gene repression by sigmaS: sigma competition for binding to RNA polymerase or more?

status: Public on May 05 2014

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: The alternative subunit of RNA polymerase RpoS/σS controls a global adaptive response allowing many Gram-negative bacteria to survive nutrient deprivation and various stresses and contributes to biofilm formation and virulence of Salmonella enterica serovar Typhimurium. We have addressed an important but poorly understood aspect of σS-dependent control; that of a repressor. The general assumption is that negative regulation of gene expression by σS is mainly a passive phenomenon, due to competition between σS and other sigma factors for binding to a limited amount of core RNA polymerase (RNAP). Genome expression profiling and physiological characterization of mutants of Salmonella ser. Typhimurium deleted for rpoS or producing a σS protein efficient for binding to RNAP, but not to the -10 promoter element, revealed that gene repression by σS requires its binding to DNA. Therefore, gene repression by σS is an active phenomenon rather than the sole cause of σS competing with other sigma factors for RNAP binding.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA profiles of the wild type strain and two rpoS mutants of Salmonella enterica serotype Typhimurium were generated by RNA sequencing, using three biological replicates. One rpoS mutant is deleted for rpoS (delta-rpoS), while the other (rpoSdb) contains two point mutations in rpoS (C421A and G469A) and produces an σS protein inefficient for binding to the -10 promoter element.

first: Françoise

last: Norel

first: Corinne

last: Lévi-Meyrueis

first: Bernd

last: Jagla

first: Odile

last: Sismeiro

first: Marie

last: Dillies

first: Marc

last: Monot


title: Microfluidic single-cell whole-transcriptome sequencing

first: Xiannian

last: Zhang

address: Yiheyuan Road No.5

institute: Peking University

summary: Single-cell whole-transcriptome analysis is a powerful tool for quantifying gene expression heterogeneity in populations of cells. Many techniques have, thus, been recently developed to perform transcriptome sequencing (RNA-Seq) on individual cells. To probe subtle biological variation between samples with limiting amounts of RNA, more precise and sensitive methods are still required. We adapted a previously developed strategy for single-cell RNA-Seq that has shown promise for superior sensitivity and implemented the chemistry in a microfluidic platform for single-cell whole transcriptome analysis. In this approach, single cells are captured and lysed in a microfluidic device, where mRNAs with poly(A) tails are reverse-transcribed into cDNA. Double-stranded cDNA is then collected and sequenced using a next-generation sequencing platform. We prepared 94 libraries consisting of single mouse embryonic cells and technical replicates of extracted RNA and thoroughly characterized the performance of this technology. Microfluidic implementation increased mRNA detection sensitivity as well as improved measurement precision compared with tube-based protocols. With 0.2M reads per cell, we were able to reconstruct a majority of the bulk transcriptome with 10 single cells. We also quantified variation between and within different types of mouse embryonic cells and found that enhanced measurement precision, detection sensitivity, and experimental throughput aided the distinction between biological variability and technical noise. With this work, we validated the advantages of an early approach to single-cell RNA-Seq and showed that the benefits of combining microfluidic technology with high-throughput sequencing will be valuable for large-scale efforts in single-cell transcriptome analysis.

overall_design: We investigated gene expression in mouse embryonic cells using microfluidic-facilitated RNA-Seq to analyze 56 single mouse ES cell (mESC) transcriptomes and 6 single mouse embryonic fibroblast (MEF) transcriptomes. To quantitatively evaluate the sensitivity and precision of our technique, we also sequenced 23 libraries from extracted mESC RNA, representing three sets of technical replicates with varying starting amounts of material.

first: Yanyi

last: Huang

first: Aaron

last: Streets

first: Fuchou

last: Tang

first: Liang

last: Zhao


title: Effects of methylprednisolone on Aspergillus fumigatus 293 gene expression

city: Utrecht

first: Erik

last: Bathoorn

address: Heidelberglaan 100

department: MMB

country: Netherlands

institute: UMC Utrecht

summary: Corticosteroid use has epidemiologically been associated with invasive aspergillosis.  We found that hydrocortisone and MP in physiological concentrations cause a change in morphology of A. fumigatus 293 growth with a less dense core, and straighter outgrowth of longer hyphae. Treated with MP, we found a differential expression of genes annotated to cell wall structure, and to cell cycle programme compared to untreated control, which could explain the changes in morphology. The up-regulation of genes encoding for toxins, iron acquisition, and cell wall components enforcing oxidative stress resistance would theoretically result in a more pathogenic A. fumigatus phenotype. Upregulation of pathways involved in DNA-repair might indicate on genotoxic effects of MP.

overall_design: Examination of test setting with 0.5 microM methylprednisolone versus control setting without methylprednisolone. Identification of differentially expressed genes (DEGs) was performed on the pooled data of the 3 samples treated with MP versus the 3 untreated control samples, with correction for the total number of reads per group.

first: Pieter-Jan

last: Haas


title: Cell cycle dependence of neuroprogenitor fate determination regulated by Trrap-mediated histone acetylation

city: Beijing

first: Zechen

last: Chong

address: NO. 7 Beitucheng West Road

institute: Beijing Institute of Genomics

summary: Epigenetic control of neural stem/progenitor cell fate is fundamental to achieve a fully brain architecture. Two intrinsic programs regulate neurogenesis, one by epigenetic-mediated gene transcription and another by cell cycle control. Whether and how these two are coordinated to determine temporally and spatially neural development remains unknown. Here we show that deletion of Trrap (Transcription translation associated protein), an essential cofactor for HAT (histone acetyltransferase), leads to severe brain atrophy due to a combination of cell death and a blockade of neuron production. Specifically, Trrap deletion forces differentiation of apical progenitor (AP) fate into basal progenitors (BP) and neurons thereby limiting the total neurogenic production. Despite Trrap’s general role in transcriptional regulation, a genome-wide transcriptome analysis of neuroprogenitors identified the cell cycle regulators that are specifically affected by Trrap deletion. Furthermore, E2F-dependent recruitment of HAT and transcription factors to the promoter of cell cycle regulators is impaired in Trrap-deleted neuroprogenitors. Consistent with these molecular changes, Trrap deletion lengthens particularly G1 and S phases in APs in vivo. Therefore, our study reveals an essential and a distinct function of Trrap-HAT in regulation of cell cycle progression that is required for proper determination of neuroprogenitor fate.

overall_design: Determine gene transcriptions by comparing Trrap-deleted and wild type samples

first: Zhao-Qi

last: Wang


title: Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance

city: South San Francisco

first: Vikram

last: Agarwal

address: 1130 Veterans Blvd

institute: Calico Life Sciences

summary: Recent studies have reported that competitive endogenous RNAs (ceRNAs) can act as sponges for a miRNA through their binding sites and that changes in ceRNA abundances from individual genes can modulate the miRNA’s activity. Consideration of this hypothesis would benefit from knowing the quantitative relationship between a miRNA and its endogenous target sites. Here, we altered intracellular target-site abundance through expression of a miR-122 target in hepatocytes and livers, and analyzed the effects on miR-122 target genes. Target repression was released in a threshold-like manner at high target-site abundance (≥1.5x10^5 added target sites per cell), and this threshold was insensitive to the effective levels of the miRNA. Furthermore, in response to extreme metabolic liver disease models, global target-site abundance of hepatocytes did not change sufficiently to affect miRNA-mediated repression. Thus, modulation of miRNA target abundance is unlikely to cause significant effects on gene expression and metabolism through a ceRNA effect.

overall_design: Seventeen mRNA profiles were generated of 1) primary hepatocytes of mice expressing variable levels of a recombinant Adenovirus expressing the transcript of AldolaseA (Ad-AldoA), containing either 1 or 3 sites matching miR-122 or a mutated miR-122 site (no site), 2) primary hepatocytes derived from mice treated with Antagomir-122 (treatment group) or Antagomir-122mm (control group), 3) livers originating of a genetic model (Ldlr deficient mice) causing severe pathological changes in cholesterol metabolism, 4) livers of mice perfused with Insulin or PBS, and 5) livers of mice fed a high-fat or chow diet; most samples were sequenced in duplicate or triplicate by an Illumina HiSeq 2000. One small RNA profile was also generated from livers of mice fed a chow diet by Solexa sequencing.

first: Remy

last: Denzler

first: Joanna

last: Stefano

first: David

middle: P

last: Bartel

first: Markus

last: Stoffel


title: Transcriptomics of a novel trophoblast differentiation protocol applied to human embryonic stem cells

city: Singapore

first: Paul

last: Robson

address: 60 Biopolis Street, Genome

department: Developmental biology

country: Singapore

institute: Genome Institute of Singapore

summary: We report the transcriptomic dynamics and novel transcriptomic events discovered by using a novel protocol which differentiates human embryonic stem cells to the trophoblast lineage. We used five timepoints (day 0, 2, 4, 6, 8) to see the progression of differenciation. At each timepoint RNA was extracted, and poly A RNA-Seq was performed using ABI SOLiD technology.

overall_design: Human embrynoic stem cells , exposed to the differenciation medium at five time points (day 0, 2,4,6,8)

first: Wishva

last: Herath

first: Wen

last: Luo

last: Huss


title: Triptolide alters the miRNA expression profiles in human hepatocellular carcinoma HepG2 cells

first: Changquan

last: Ling

state: Shanghai

address: No. 800,Xiangyin Road

department: Department of Traditional Chinese Medicine

institute: Second Military Medical University

summary: We compared miRNA expression profiles among 5 groups of HepG2 cells treated with various concentrations (0,100,200 nM) of triptolide for 12 h or 24 h.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two-condition experiment, triptolide intervention vs. without intervention. Biological replicates: 3 control, 3 treated, independently grown and harvested. One replicate per array.

first: Ling

last: Changquan

first: Li

last: Shuguang


title: Illumina Sequencing data of the influence on gene expression of insulator protein co-factor dMes-4

status: Public on Apr 30 2014

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

institute: CNRS

summary: The Drosophila insulator-binding proteins (IBPs) dCTCF/Beaf32 mark the physical borders of chromosomal domains involving co-factors that participate in long-range interactions. Chromosomal borders are further enriched in specific histone modifications yet the implication of histone modifiers and nucleosome dynamics remains largely unknown in such context. Here, we show that IBP depletion impairs nucleosome dynamics over genes flanked by their binding sites. Biochemical purification identifies a key histone methyltransferase of H3K36, NSD/dMes-4, as a novel co-factor of IBPs involved in chromatin accessibility, which specifically co-regulates hundreds of genes flanked by Beaf32/dCTCF. dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-mediated H3K36me3, RNA splicing and nucleosome positioning. Our results unveil a model for how IBPs regulate gene expression and nucleosome dynamics through NSD/dMes-4, which may contribute to regulate H3K27me3 spreading. Together, our data suggest a division of labor for how IBPs may dynamically regulate chromatin organization depending on distinct co-factors.

overall_design: mRNA profiles of Beaf32-depleted or Wild-Type control Drosophila S2 cells by RNASeq (Illumina)

first: Priscillia

last: Lhoumaud

first: Gael

last: Micas

first: Adrien

last: Gamot

first: Dany

last: Severac


title: Illumina Sequencing data of the influence of Insulator Proteins on chromatin

overall_design: Nucleosome profiles of  Beaf32-depleted or Wild-Type control Drosophila S2 cells by MNase-Seq (Illumina/TruSeq) for total/bulk nucleosomes or following immunoprecipitation with anti-H3K27me3 antibodies

first: Suresh

last: Cuddapah

first: Magali

last: Hennion

first: Keji

last: Zhao


title: Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

summary: Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned (phased) in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors influence nucleosome phasing in regions that are not close to genes. We performed a combinational mapping of nucleosome positioning and DNase I hypersensitive sites (DHSs) across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Our results support the barrier model for nucleosome organization as a general feature of eukaryote genomes, including plant genomes, and not limited to TSSs. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome. We propose that genome-wide nucleosome positioning in the eukaryotic genomes is orchestrated by genomic regions associated with regulatory proteins.

overall_design: Rice chromatin was digested by micrococcal nuclease (MNase) into mono-nucleosome size. Mono-nucleosomal DNA was isolated and sequenced (MNase-seq) using Illumina sequencing platforms. We obtained a total of 38 million (M) single-end reads from our first MNase-seq experiment and mapped ~26 M to unique positions in the rice genome. We also conducted pair-end sequencing of an independent MNase-seq library, obtained 274 M paired-end reads, and mapped ~231 M read pairs to unique positions in the rice genome.We applied a strategy of combinational mapping of nucleosome positioning and DHSs (GSE26610) to examine whether nucleosome positioning is associated with all cis-regulatory elements in the rice genome. All datasets used in the analysis were developed using rice leaf tissue in the same developmental stage

first: Wenli

last: Zhang

first: Jiming

last: Jiang


title: Sorghum nitrogen stress tolerance

city: Lincoln

first: Chi

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk).

overall_design: RNAseq deep sequencing

first: Malleswari

last: Gelli

first: Yongchao

last: Duo

first: Anji

middle: R

last: Konda

first: David

last: Holding

first: Ismail

last: Dweikat


title: Illumina Sequencing data of  Insulator Proteins and the co-factor dMes-4

first: Olivier

overall_design: ChIP-Seq profiles of H3K36 methylation and RNA Pol II in Drosophila S2 cell line (wild-type) cells


title: Improved tagmentation-based whole genome bisulfite sequencing for input DNA from less than 100 cells

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

summary: We improved the tagmentation-based whole genome bisulfite sequencing technology, enabling stable library construction with complexity from minimally 0.5ng of initial genomic DNA, which equals less than 100 cells. This new approach is highly attractive for the complete methylome analysis of very limited cell numbers, e.g., pre-implantation embryos, or tiny biopsy specimens.

overall_design: Applying this newly modified T-WGBS, we sequenced the methylome of a rice strain using libraries constructed from 10 ng, 1 ng and 0.5 ng of input genomic DNA. Two libraries were independently constructed and sequenced for each aliquot of input genomic DNA

first: Fei

last: Gao

first: Hanlin

last: Lu


title: Genome wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

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

overall_design: Refer to individual Series

first: Dennis

last: McCancer


title: Mechanisms of coral response to climate change

city: Pacific Grove

first: Stephen

last: Palumbi

address: 120 Ocean View Blvd

institute: Stanford University

summary: RNASeq data on corals transplanted reciprocally into two different thermal microhabitats on Ofu Island

overall_design: Six individual corals transplanted into two habitats


title: Midgut transcriptome response to a Cry toxin in the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae)

city: Guangzhou

first: Yanyuan

last: Lei

state: Guangdong

address: No. 7 Jinying Rd., Tianhe District

institute: Guangdong Academy Agricultural Sciences

summary: We investigate the functional complexity of the Plutella xylostella transcriptome in defending against a Bt toxin using Illumina sequencing technology. Over 2,900 differentially expressed unigenes were obtained in resistant P. xylostella comparison to their susceptible counterpart.

overall_design: All the P. xylostella were maintained on cabbage.The susceptible strain (MM) was cultured without exposure to any Bt toxins.Before the sample collected, Cry1Ac-resistant P. xylostella were treated with 750μg/mL Bt toxin Cry1Ac to eliminate the heterozygous individuals. Then the survivors were collected after 48 hours and designed as the resistant sample (MK and GK). Then fourth-instars larvae midgut tissues of MK,GK and MM were collected, respectively, The RNA was extracted and sequenced using Illunima HiSeq 2000.

first: Xun

last: Zhu

first: Wen

last: Xie

first: Xuguo

last: Zhou

first: Youjun


title: Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes

last: Cuvier


title: Mechanisms for thermal adaptation: Transcriptional response to heat stress among desert and montane populations of redband trout

city: Hagerman

first: Nathan

middle: Reed

last: Campbell

state: Idaho

address: 3059F National Fish Hatchery Rd

department: Genetics Lab

institute: Columbia River Inter-Tribal Fish Commission

summary: RNAseq used to examine gene expression in thermal challenged redband rainbow trout

overall_design: RNAseq data obtained from libraries prepared from Gill RNA

first: Shawn

last: Narum


title: Identification and Initial Functional Characterization of SENCR, a Long Non-Coding RNA Enriched in Human Vascular Cells

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

institute: aecom

summary: RNA sequencing (RNA-seq) analysis revealed 31 novel lncRNAs in HCASMC, including a vascular cell-enriched lncRNA called SENCR (for Smooth muscle and Endothelial cell long Non-Coding RNA). RT-PCR and hybridization studies show SENCR exists in two isoforms and is transcribed antisense from the 5’ end of the FLI1 gene. Knockdown of SENCR has no effect on FLI1 mRNA or protein expression. Biochemical fractionation and RNA fluorescence in situ hybridization (FISH) studies indicate SENCR is a cytoplasmic lncRNA. RNA-seq experiments in HCASMC where SENCR is attenuated disclose decreased expression of Myocardin and many SMC contractile genes; conversely a pro-migratory gene signature is increased. RT-PCR and Western blotting validated several differentially expressed genes following SENCR knockdown. Loss-of-function studies in scratch wound and Boyden chamber assays support SENCR as an inhibitor of vascular cell migration.

overall_design: Total RNAs of 3 replicates of normal human coronary artery smooth muscle cells (Mock1, Mock2 and Mock3) were sequenced and analyzed for identification of novel lncRNAs. One of identified novel lncRNAs from that experiment is SENCR. To study its function, SENCR knock-down experiment were performed and then RNA-seq profiles of 3 replicates of both SENCR-knockdown samples and corresponding controls were compared.

first: Joseph

middle: M

last: Miano

first: Mingyan

last: Lin


title: Epigenetic and genetic changes during mouse hematopoietic stem cell aging

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University


title: Comparative analysis of the small RNA transcriptome of four developmental stages of the Citrus red mite (Panonychus citri)

first: Bin

last: Liu

state: Beijing

address: Hai Dian

department: School of Life Sciences

institute: Tsinghua University

summary: Total RNAs from the Citrus red mite at the embryo, larva, nymph and adult stages were used to construct small RNA libraries for Solexa sequencing. Several categories of sRNAs were identified, including 594 known microRNAs (miRNAs) grouped into 206 families and 31 novel miRNAs. In addition, according to bioinformatics analysis and S-Poly(T) miRNA assays, the expression level of many miRNAs varied among the developmental stages. Furthermore, the prediction of miRNAs target genes and their functional annotation indicated that miRNAs are involved in the regulation of multiple pathways in the Citrus red mite.

overall_design: The total RNAs from embryo, larva, nymph and adult stages of Panonychus citri were used to construct small RNA libraries for Solexa sequencing. The data from Solexa sequencer (Illumina) was compared to identify small RNAs in different stages of Panonychus citri.

first: Wei

last: Dou

first: Tianbo

last: Ding

first: Rui

last: Zhong

first: Chongyu

last: Liao

first: Wenkai

last: Xia

first: Jinjun

last: Wang


title: Epigenetic and genetic changes during mouse hematopoietic stem cell aging [Bisulfite-Seq]

summary: To investigate the global DNA methylation changes in mouse hematopoietic stem cell aging, we performed whole-genome bisulfite sequencing (WGBS). We generated 1,494 million (4mo HSCs), and 1,493 million (24mo HSCs) raw reads; about 82.6% and 84.3%, respectively, were successfully aligned to either strand of the reference genome (mm9). Of all the cytosines present in the reference genome sequence, about 93% of Cs and 99% of CGs were covered in both datasets, with an average coverage of 46-fold (4mo) and 50-fold (24mo). In contrast to the age-associated hypomethylation observed in studies of somatic cells, mentioned above, HSCs showed an increase of methylation with age. The average methylation level over all 16 million covered CpGs increased from 83.5% in young (4mo) HSC to 84.6% in old (24mo) HSC. We observed a total of 448,166 differentially methylated CpGs (DMCs), defined as those having a 20% or more difference in methylation ratio, of which 38.5% (172,609) were hypomethylated (hypo-DMCs) and 61.5% (275,557) were hypermethylated (hyper-DMCs) with aging. For different genomic features, a slightly greater DNA methylation ratio increase was observed for the gene body, LINEs and SINEs, while CGIs and promoters showed balanced increases and decreases. Localization analysis of DMCs indicates that DNA encoding for ribosome RNA (rDNA) is primarily a hotspot for hypo-DMCs, while promoters without CpG islands, CpG island shores and LINE repetitive elements exhibit both hypo- and hyper-DMCs.

overall_design: Mouse hematopoietic stem cell DNA methylation profiles of 4 month and 24 month old WT mice were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000.

first: Deqiang

last: Sun

last: Li


title: Epigenetic and genetic changes during mouse hematopoietic stem cell aging [RNA-Seq]

summary: To investigate the global transcriptome changes in mouse hematopoietic stem cell aging, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified 4 month, and 24 month-old HSCs (SP-KSL-CD150+). With biological duplicates, more than 200 million reads in total for each age of HSC were obtained.   Comparison of the young and old HSC transcriptomes revealed that 1,337 genes that were up-regulated, and 1,297 genes were down-regulated with HSC aging. The most highly represented upstream regulator was growth factor TGFB1, accounting for ~ 19% of differential gene expression in young versus old HSC (p-value = 1.96E-33). Gene ontology (GO) analyses indicated that up-regulated genes in 24mo HSCs are highly enriched in Regulation of Cell Adhesion, Regulation of Cell Proliferation and Ribosome, while down-regulated genes are enriched in DNA Base Excision Repair, DNA replication and Cell Cycle. RNA-seq also allowed us to examine alternative isoforms with aging including alternative splicing, promoter usage and pre-mRNA abundance.

overall_design: Mouse hematopoietic stem cell mRNA profiles of 4 month and 24 month old WT mice were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000

first: Sun

last: Deqiang


title: Epigenetic changes underlying mouse hematopoietic stem cell aging

summary: We investigate the aging changes for Histone marks H3K4me3, H3K27me3 and H3K36me3 for mouse hematopoietic stem cells.

overall_design: Mouse hematopoietic stem cell histone methylation profiles of 4 month and 24month old WT mice were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000


title: High-throughput sequencing of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) targets

city: Pasadena

first: Frederick

last: Tan

address: 1200 E. California Blvd, M/C 114-96

department: Biology and Applied Physics

institute: California Institute of Technology

summary: We conducted RNA/RNA binding protein immunoprecipitation (RIP) followed by high throughput sequencing to identify mRNA targets of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) in mouse embryonic stem cells. We collected over 190 million sequencing reads and identified many highly enriched protein coding mRNAs. Gene ontology analysis of enriched genes reveals that transcription factors and intercellular signaling proteins account for a large fraction of the targets, many of which are important for pluripotency and differentiation.

overall_design: Identification of Brf1 and Brf2 mRNA targets

first: Michael

last: Elowitz


title: YY1 is indispensable for Lgr5+ intestinal stem cell renewal

status: Public on Apr 29 2014

city: Piscataway

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey


title: YY1 ChIP-seq in mouse intestine

summary: We mesured YY1 binding in isolated mouse crypt epihtelium using ChIP-seq

overall_design: Jejunal crypt epithelia were isolated and processed for ChIP using YY1 antibody Santa Cruz, SC-1703, lot E0511

first: Ansu

last: Perekatt

first: Mike


title: The Transcriptome of Utricle Hair Cell Regeneration in the Avian Inner Ear

city: London

last: Lovett

state: London

address: Dovehouse St

department: NHLI

institute: Imperial College

summary: A comprehensive transcriptome profile of chicken utricle hair cell across a 7 days regenerative time course.

overall_design: Compare gene expression changes in chicken utricle treated with streptomycin to the control. A total of 60 samples were collected from 11 different time points. Each time point contains at least 2 biological samples.

first: Yuan-Chieh

last: Ku


title: Micro-RNA sequencing from 78 adrenocortical carcinomas

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

summary: Micro-RNA sequencing of adrenocortical tumors and normal adrenal samples.

overall_design: miRNA sequencing of  45 adrenocortical carcinomas (ACC), 30 adrenocortical adenomas (ACA) and 3 normal adrenal samples.

first: Eric

last: Letouzé

first: Aurélien

last: de Reyniès

first: Olivia

last: Barreau

first: Windy

last: Luscap

first: Guillaume

last: Assié

first: Jérome

last: Bertherat


title: RNA-sequencing analysis of 5' capped RNAs identifies novel differentially expressed genes in sessile serrated colon polyps (SSPs)

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: RNA-sequencing of SSP RNA from patients with serrated polyposis syndrome identifies VSIG1 and MUC17 as potential diagnostic markers for SSPs

overall_design: 5' capped RNA from seven ascending SSPs, six patient matched uninvolved right colon and two normal right colon samples was used for RNA sequencing (15 samples total)

first: Curt

last: Hagedorn

first: Don

middle: A

last: Delker


title: Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system

status: Public on Apr 28 2014

city: Zürich

first: Seth

last: Barribeau

state: Canton of Zurich

address: Universitatstrasse 16

department: Institute of Integrative Biology

country: Switzerland

institute: ETH Zürich

summary: Expression of bumblebees (Bombus terrestris) from four colonies exposed to 3 different genotypes of the trypanosome parasite Crithidia bombi

overall_design: RNA from guts of exposed individuals. Sacrificed 18hr after exposure.

first: Paul

last: Schmid-Hempel


title: ChIP-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

institute: EPFL

summary: Hox genes are essential regulators of embryonic development. They are activated in a temporal sequence following their topological order within their genomic clusters. Subsequently, states of activity are fine-tuned and maintained to translate into domains of progressively overlapping gene products. While the mechanisms underlying such temporal and spatial progressions begin to be understood, many of their aspects remain unclear. We have systematically analyzed the 3D chromatin organization of Hox clusters in vivo, during their activation using high-resolution circular chromosome conformation capture (4C-seq). Initially, Hox clusters are organized as single 3D chromatin compartments decorated with bivalent chromatin marks. Their progressive transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch one after the other, from an inactive to an active 3D compartment. These local 3D dynamics occur within a larger constitutive framework of interactions within the surrounding Topological Associated Domains, which confirms previous results that regulation of this process in primarily cluster intrinsic. The local step-wise progression in time can be stopped and memorized at various body levels and hence it may accounts for the various chromatin architectures previously described at different anterior to posterior body levels for the same embryo at a later stage.

overall_design: ChIP-seq samples (H3K4me3 and H3K27me3) from mouse ES cells and mouse embryonic stage E8.5 pre-somitic mesoderm. Data based on 4 biological samples.

first: D

last: Noordermeer

first: M

last: Leleu

last: Duboule


title: Genome-wide transcriptional changes of ramie (Boehmeria nivea L．Gaud) in response to the infection of root-lesion nematode

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: The Root-lesion nematode (RLN) Pratylenchus coffeae is a major ramie pest causing severe fiber yield loss annual in China. The response mechanism of ramie to RLN-infection is poorly understood. Two RLN-infected plants (Inf1 and Inf2) and two control plants (CO1 and CO2) were individually used to sequence by Illumina pair-end sequencing. About 56.3, 51.7, 43.4 and 45.0 million sequencing reads were generated from the libraries of CO1, CO2, Inf1 and Inf2, respectively. De novo assembly for these 196 million reads yielded 50,486 unigenes with an average length of 853.3 bp. Based on sequence similarity search with known proteins, a total of 24,820 (49.2%) genes were annotated for their function. Comparison of gene expression level between CO and Inf ramie based on the normalized value of read counts per kilobase of exon model per million reads (RPKM) revealed that there were 777 differentially expressed genes (DEGs). Further, these functional category of DEGs were classified by assigning them to gene ontology (GO) and clusters of orthologous group (COG). Pathway enrichment analysis showed that three pathways (Phenylalanine metabolism, Carotenoid biosynthesis and Phenylpropanoid biosynthesis) were severely influenced by RLN-infection. The genome-wide expression profiling of ramie responding to RLN-infection was first characterized. A series of candidate genes and pathways that may contribute to defense response against RLN in ramie will be helpful for further improving the resistance to RLN-infection.

overall_design: A total of four samples, two replicates of control plant (CO1 and CO2) and two replicates of RLN-infected plants (Inf1 and Inf2) were used for RNA-seq.


title: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

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

overall_design: Refer to individual Series


title: Dicer knockout NSCLC RNAseq and miRseq

status: Public on Apr 25 2014

city: Cambridge

first: Sidi

last: Chen

state: MA

department: Biology

institute: MIT

summary: Dicer knockout NSCLC mRNAseq profiles the transcriptome, Dicer knockout NSCLC miRseq profiles the miRnome

overall_design: DicerHet and DicerKO NSCLC, 2 biological reps each genotype for mRNAseq, 1 biological rep each for miRseq

first: Phillip

last: Sharp


title: The DNA methylome of Epiblast Stem Cells and Embryonic Stem Cells is distinct and not fully reversible

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

institute: Radboud University Nijmegen, RIMLS

summary: Embryonic Stem Cells (ESCs) and Epiblast Stem Cells (EpiSCs) are the in vitro representants of naïve and primed pluripotency, respectively. It is currently unclear how their epigenome underpin the phenotypic and molecular characteristics of these states of pluripotency. Here, we performed the first qualitative and quantitative comparison of DNA methylation between ESCs and EpiSCs. The global level and genomic distribution of DNA methylation were very similar between the two cell types. However, the analysis of promoter methylation patterns in EpiSCs revealed several distinct features: (i) the repression of germline-related genes by DNA methylation, a process already ongoing in ESCs but far more pronounced in EpiSCs; (ii) the hypermethylation of promoters (especially CpG rich) in EpiSC compared to both ESCs and dissected epiblasts from E6.5 and E7.5 embryos; (iii) the inability of hypomethylated (Dnmt-deficient) ESCs to be converted into EpiSCs despite their ability to self-renew.  Altogether, our data show that DNA methylation is an important epigenetic regulator of gene expression in EpiSCs and suggest that it is essential for the obtention of EpiSCs.

overall_design: MethylCap-Seq (DNA methylation profiling) and RNA-Seq of 3 EpiStem Cells (EpiSCs) and 1 Embryonic Stem Cell line of which the data has been submitted to GEO before (part of GEO SuperSeries GSE23943 and GSE31343)

first: Anne-Clémence

last: Veillard

first: Andreia

last: Bernardo

first: Luc

last: Jouneau

first: Laloé

last: Denis

first: Laurent

last: Boulanger

first: Anita

last: Kaan

first: Vincent

last: Brochard

middle: G

last: Stunnenberg

first: Alice


title: Therapeutic Targeting of BET Bromodomain Proteins in Castration-Resistant Prostate Cancer

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan


title: Tissue-Resident Natural Killer (NK) Cells Are Cell Lineages Distinct From Thymic and Conventional Splenic NK Cells (part 2)

status: Public on Apr 26 2014

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Natural killer (NK) cells belong to the innate immune system where they can control virus infections and developing tumors by cytotoxicity and production of inflammatory cytokines. Most studies of mouse NK cells, however, have focused on conventional NK (cNK) cells found in the spleen. Recently, we described two populations of NK cells within the liver, tissue-resident NK (trNK) cells and those resembling splenic cNK cells. However, the lineage relationship of trNK to cNK cells was unclear because trNK cells display a phenotype associated with immature, developing cNK cells. Moreover, liver trNK cells could be related to thymic NK cells or alternatively, a lineage distinct from both cNK and thymic NK cells. Herein we used detailed transcriptomic, flow cytometric, and functional analysis of mice deficient in several transcription factors to determine that liver trNK cells form a distinct lineage from cNK and thymic NK cells, especially because they do not require NFIL3 (E4BP4), the previously described NK cellspecification factor. Analysis of other tissues indicate the presence of trNK cells in skin and uterus with different transcription factor requirements. Thus, there are at least four distinct lineages of NK cells: cNK, thymic, liver (and skin) trNK, and uterine trNK cells.

overall_design: Liver DX5-CD49+, liver DX5+CD49-, spleen DX5+ CD49- populations of NK cells were sorted with FACS pooling cells from individual mice to end up with ~100k cells for each samples. mRNA was derived from lysates using Invitrogen oligo-dT beads

first: Yulia

last: Ivanova


title: Tissue-Resident Natural Killer (NK) Cells Are Cell Lineages Distinct From Thymic and Conventional Splenic NK Cells (part 1)

overall_design: Liver NK 1.1+CD49+, liver NK 1.1+CD49-, spleen NK 1.1+ CD49- populations of NK cells were sorted with FACS pooling cells from individual mice to end up with ~100k cells for each samples. mRNA was derived from lysates using Invitrogen oligo-dT beads


title: Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: Phenotypic differences between closely related species are thought to arise primarily from changes in gene expression due to mutations in cis-regulatory sequences (enhancers). However, it has remained unclear how frequently mutations alter enhancer activity or create functional enhancers de novo. Here we use STARR-seq, a recently developed quantitative enhancer assay, to determine genome-wide enhancer activity profiles for five Drosophila species in the constant trans-regulatory environment of Drosophila melanogaster S2 cells. We find that the functions of a large fraction of D. melanogaster enhancers are conserved for their orthologous sequences owing to selection and stabilizing turnover of transcription factor motifs. Moreover, hundreds of enhancers have been gained since the D. melanogaster-Drosophila yakuba split about 11 million years ago without apparent adaptive selection and can contribute to changes in gene expression in vivo. Our finding that enhancer activity is often deeply conserved and frequently gained provides functional insights into regulatory evolution.

sample_organism:
Drosophila ananassae
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila yakuba
Drosophila willistoni

overall_design: STARR-seq was performed in S2 cells with paired-end sequencing in two replicates and respective inputs using genomic DNA from different Drosophila species. RNA-seq was performed in a non-stranded manner without replicates for two Drosophila species.

first: Cosmas

last: Arnold

last: Spies

first: Jessica

last: Matts

first: Yuliya

last: Sytnikova

first: Michaela

last: Pagani

first: Nelson

middle: C

last: Lau

first: Alexander

last: Stark


title: EDD: a program for detection of wide genomic enrichment domains robust against local variations

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo


title: 4C-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

first: Marion

last: LELEU

overall_design: Circular Chromosome Conformation Capture (4C-seq) samples from mouse ES cells and mouse embryonic samples at different stages of development. Data based on 41 biological samples.

first: D

last: Noordermeer

first: M

last: Leleu

last: Duboule


title: RNA-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

overall_design: RNA-seq from mouse ES cells and mouse embryonic stage E10.5 forebrain. Data based on 2 biological samples.


title: EDD: a program for detection of wide genomic enrichment domains robust against local variations [ChIP-Seq]

summary: Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome-wide. We disclose a novel algorithm, Enriched Domain Detector (EDD), for analysis of broad enrichment domains from ChIP-seq data. EDD enables discovery of genomic domains interacting with broadly distributed chromatin-associated proteins such as lamins. The main advantage of EDD over existing broad peak callers is sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations. EDD is downloadable from http://github.com/eivindgl/edd.

overall_design: LMNA ChIP-seq experiments in human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs).

first: Eivind

last: Lund

first: Anja

last: Oldenburg


title: EDD: a program for detection of wide genomic enrichment domains robust against local variations [RNA-Seq]

overall_design: RNA-seq experiments in human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs).


title: DNA methylation dynamics studies with MethylRO mouse

status: Public on Apr 24 2014

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi, Higashi

department: Faculty of Medical Sciences

country: Japan

institute: Kyushu University

summary: We have knocked-in mCherry-MBD-NLS probe, which recognizes methylated CpG, to ROSA26 locus and named this reporter MethylRO (methylation probe in ROSA26 locus). In this study, we showed that MethylRO can capture DNA methylation dynamics both in vitro and in vivo.

overall_design: The detection of DNA methylation

first: Jun

last: Ueda

first: Kazuo

last: Yamagata

first: Kazumitsu

last: Maehara


title: Controlling for gene expression changes in transcription factor protein networks.

city: Kansas City

first: Chris

middle: W

last: Seidel

department: Genomics

institute: Stowers Institute

summary: The development of affinity purification technologies together with mass spectrometric analyses of the purified protein mixtures (AP-MS) has been used both to identify new protein-protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactions, however, have not been systematically analyzed using these approaches. Here, we have investigated whether ectopic expression of an affinity tagged transcription factor as bait in AP-MS experiments perturbs gene expression in cells resulting in false positive identification of bait associated proteins when typical experimental controls are used. Using quantitative proteomics and RNA-Seq, we determined that the increase in the abundance of a set of proteins caused by overexpression of the transcription factor RelA is not sufficient for these proteins to then copurify non-specifically and be misidentified as bait associated proteins. Therefore typical controls should be sufficient and a number of different baits can be compared with a common set of controls. This is of practical interest when identifying bait interactors from a large number of different baits. As expected, we found several known RelA interactors enriched in our RelA purifications (NFêB1, NFêB2, Rel, RelB, IêBá, IêBâ and IêBå). We also found several proteins not previously described in association with RelA, including the small mitochondrial chaperone Tim13. Using a variety of biochemical approaches, we further investigated the nature of the association between Tim13 and NFêB family transcription factors. The work here therefore provides a conceptual and experimental framework for analyzing transcription faction protein interactions.

overall_design: Gene expression profiles were assayed in triplicate from HEK293 cells expressing either Halo-RelA, Halo-NFkB1, or Halo tag alone.

first: Charles

last: Banks

first: Zachary

last: Lee

first: Gina

last: Boanca

first: Mahadevan

last: Lakshminarasimhan

first: Brad

last: Groppe

first: Zhihui

last: Wen

first: Gaye

last: Hattem

first: Laurence

last: Florens

first: Michael

last: Washburn


title: Protein Kinase A Regulates Gene-Specific Translational Adaptation in Differentiating Yeast

first: Pavanapuresan

last: Vaidyanathan

address: 68-341, 31 Ames Street

institute: Massachusetts Institute of Technology

summary: Cellular differentiation is driven by coordinately regulated changes in gene expression. Translational control of gene expression is increasingly recognized as pervasive and quantitatively significant, but the mechanisms responsible for widespread changes in gene-specific translation activity are largely unknown. Here we investigate the mechanisms responsible for translational reprogramming during cellular adaptation to the absence of glucose, a stimulus that induces invasive filamentous differentiation in yeast. We show that gene-specific translation efficiencies are highly adapted to cellular conditions and that glucose withdrawal is accompanied by widespread translational reprogramming at the level of translation initiation. We demonstrate that transcripts from <5% of genes make up the majority of translating mRNA in both rapidly dividing and starved cells. Moreover, the identities of these highly translated genes are growth-state specific, and they are subject to condition-dependent translational privilege. By comparing glucose starvation to other growth-attenuating stresses, we distinguish a glucose-specific translational response that regulates ribosomal protein and mitochondrial protein-coding genes. This response is mediated through signaling by protein kinase A (PKA). These findings reveal a high degree of growth-state specialization of the translatome and identify PKA as an important regulator of gene-specific translation activity.

overall_design: Examine translational adaptation in yeast in response to glucose starvation

first: P

first: B

last: Zinshteyn

first: M

middle: K

last: Thompson

first: W

middle: V

last: Gilbert


title: Therapeutic Targeting of BET Bromodomain Proteins in Castration-Resistant Prostate Cancer (ChIP-Seq)

first: Marcin

last: Cieslik

summary: Men who develop metastatic castration-resistant prostate cancer (CRPC) invariably succumb to the disease.  The development and progression to CRPC following androgen ablation therapy is predominantly driven by unregulated androgen receptor (AR) signaling1-3.  Despite the success of recently approved therapies targeting AR signaling such as abiraterone4-6 and second generation anti-androgens MDV3100 (enzalutamide)7,8, durable responses are limited, presumably due to acquired resistance. Recently JQ1 and I-BET, two selective small molecule inhibitors that target the amino-terminal bromodomains of BRD4, have been shown to exhibit antiproliferative effects in a range of malignancies9-12.  Here we show that AR signaling-competent CRPC cell lines are preferentially sensitive to BET bromodomain inhibition. BRD4 physically interacts with the N-terminal domain of AR and can be disrupted by JQ111,13. Like the direct AR antagonist, MDV3100, JQ1 disrupted AR recruitment to target gene loci.  In contrast to MDV3100, JQ1 functions downstream of AR, and more potently abrogated BRD4 localization to AR target loci and AR mediated gene transcription including induction of TMPRSS2-ERG and its oncogenic activity.  In vivo, BET bromodomain inhibition was more efficacious than direct AR antagonism in CRPC xenograft models.  Taken together, these studies provide a novel epigenetic approach for the concerted blockade of oncogenic drivers in advanced prostate cancer.

overall_design: Examination of AR, BRD2, BRD3, BRD4, ERG, RNA Pol II and H3K27ac in prostate cancer cells with respect to BET inhibitors

first: Irfan

last: Asangani


title: Identification of potential miRNAs and their targets in Vriesea carinata (Poales, Bromeliaceae) [mRNA-seq]

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary: miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Bromeliaceae family is an example of a large and well described adaptive radiation of plant families in the Neotropics. This family is composed of terrestrial xerophytes and both facultative and obligatory epiphytes, occurring in a wide range of habitats. Bromeliads have different habits, varying from terrestrial to epiphytical, and are found from sea level to altitudes above 4,000 m, in both desert and humid regions, as well as in soils subject to regular floods and in places with very little or great luminosity. This huge habitat plasticity makes bromeliads an interesting model to study the expression of miRNAs in different natural conditions and the first step is to identify miRNAs and its targets. For this purpose, we used a high-throughput sequencing analysis (Solexa technology) of small RNAs (sRNAs) from the endemic South American species Vriesea carinata.

overall_design: RNA profiles in 1 leaf library of Vriesea carinata by deep sequencing (Illumina HiSeq2000)

first: Frank

middle: F

last: Guzman

first: Mauricio

last: Almerao

first: Rogério


title: Genome-wide mapping of Klf4 and Klf5 in pluripotent mouse embryonic stem cells (ESCs)

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

institute: Stem Cell and Brain Research Institute

summary: We identified the binding profile of Klf4 and Klf5, which are both transcription facyors involved in the maintenance of pluripotency of ESCs by inhibiting their differentiation either into endoderm or mesoderm respectively.

overall_design: Undifferentiated mouse ESCs were used to identify Klf4 and Klf5 bidning sites

first: Pierre

last: Savatier


title: Transcriptomics studies in Vriesea carinata


title: Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation.

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

summary: Autophagy as a conserved degradation and recycling machinery is important in normal development and physiology, and defects in this process are linked to many kinds of disease. Because too much or too little autophagy can be detrimental, the process must be tightly regulated both temporally and in magnitude. The transcriptional induction and repression of the autophagy-related (ATG) genes is one crucial aspect of this regulation, but the transcriptional regulators that modulate autophagy are not well characterized. In this study, we identified Pho23 as a master transcriptional repressor for autophagy, with transcriptome profiling revealing that ATG9 is one of the key target genes. Physiological studies with a PHO23 null mutant, or with strains expressing modulated levels of Atg9, demonstrate a critical role of this protein as a regulator of autophagosome formation frequency; Atg9 protein levels correlate with the number of autophagosomes generated upon autophagy induction, and the level of autophagy activity.

overall_design: WT yeast and pho23 deletion mutants were grown under nutrient rich or nitrogen starvation conditions; gene expression was quantified across these 4 samples.

first: Meiyan

last: Jin

first: Ding

last: He

first: Steven

last: Backues

first: Xu

last: Liu

first: John

last: Kim

first: Daniel

middle: J

last: Klionsky


title: A mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

overall_design: Refer to individual Series


title: Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells

city: Berkeley

first: Dirk

last: Hockemeyer

department: Molecular and Cellular Biology

institute: University of California Berkeley

summary: Genetically engineered human pluripotent stem cells (hPSCs) have been proposed as a source for transplantation therapies and are rapidly becoming valuable tools for human disease modeling. However, many of the potential applications are still limited by the lack of robust differentiation paradigms that allow for the isolation of defined functional tissues. These challenges could be overcome by the use of adult tissue stem cells derived from hPSCs, as their restricted potential could limit the differentiation towards other undesired linages, and allow in vitro expansion and long- term propagation of fully differentiated tissue. To isolate adult stem cells from hPSCs, we applied genome-editing to generate an LGR5-GFP reporter system and subsequently developed a differentiation protocol for human intestinal tissue comprising an adult stem cell niche and all major cell types of the adult intestine. This novel derivation protocol is highly robust and even permits the isolation of intestinal organoids without the LGR5 reporter. Transcriptional profiling, electron microscopy and functional analysis revealed that such human organoid cultures could be derived with high purity, and a composition and morphology similar to that of cultures obtained from human biopsies. Importantly, hPSC-derived organoids responded to the canonical signaling pathways that control self-renewal and differentiation in the adult human intestinal stem cell compartment. With our ability to genetically engineer hPSCs using site-specific nucleases, this adult stem cell system provides a novel platform by which to study human intestinal disease in vitro.

overall_design: RNA from primary organoid samples was isolated from organoid lines that were both cultured for 1-6 months and derived from duodenum, ileum, or rectum biopsies of human subjects as described previously (Sato et al., Gastroenterology 2011) grown in media called WENR+inhibitors. RNA was also isolated from various steps in the culturing and differentiation protocol.

first: Ryan

last: Forster

first: Kunitoshi

last: Chiba

first: Lorian

last: Schaeffer

first: Samuel

last: Regalado

first: Christine

last: Lai

first: Qing

last: Gao

first: Samira

last: Kiani

first: Henner

last: Farin

first: Hans

last: Clevers

first: Gregory

last: Cost

first: Andy

last: Chan

first: Edward

last: Rebar

first: Fyodor

last: Urnov

first: Philip

last: Gregory

first: Lior

last: Pachter

first: Rudolf

last: Jaenisch


title: A mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia [HTS]

first: Huimin

last: Geng

summary: The plasma cell transcription factor XBP1 is critical for terminal differentiation of B cells into plasma cells but has no known role at earlier stages of B-cell development. Here we show that XBP1 is not only important during early B-cell development and for survival of pre-B cells but also protects pre-B ALL cells. Among pre-B ALL subset, XBP1 was hypomethylated and highest expressed in the Ph+ ALL subset. Cre-mediated deletion of XBP1 in a mouse model of Ph+ ALL compromised proliferation and viability and prolonged survival of leukemia-bearing mice. Interestingly, XBP1 expression levels were positively transcriptionally regulated by STAT5 and negatively by BACH2 and BCL6. High XBP1 expression in high risk ALL patients at the time of diagnosis predicted poor outcome in two clinical trials. Clinically, small-molecule inhibition of IRE1-dependent XBP1-activation caused cell death of patient-derived pre-B ALL cells and affected leukemia-initiation in transplant recipient mice. Collectively, these studies identify XBP1 as an important survival factor and as a potential therapeutic target to overcome drug-resistance in pre-B ALL.

overall_design: Genome-wide profiling of mRNA levels in p210 transduced murine Xbp1 fl/+ pre-B cells with ERT2 (XE.1,2,3) and Cre- ERT2  (XC.1,2,3).

first: Behzad

last: Kharabi

first: Markus

last: Muschen


title: The miRNA profiling of goat CD49f-positive and negative testicular cells

city: Yangling

first: wu

last: jiang

state: Shaanxi

address: Taicheng road #3

department: College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology

institute: Northwest A&F University

summary:
Purpose: miRNAs, a member of the small RNA, play critical roles in the mammalian spermatogenesis. Spermatogonia was the foundation of spermatogenesis and valuable for the study of spermatogenesis. However, it is still not clear that the expression profiling of the miRNAs in spermatogonia of dairy goat.
Methods:  The CD49f was one of the surface markers for spermatogonia enrichment by MACS. Therefore, we used CD49f microbeads antibody to purify CD49f-positive and negative cells of dairy goat testicular cells by MACS (Magnetic Activated Cell Sorting), and then in-depth analyzed the miRNA expression in these cells using Illumina sequencing technology.
Results: The results of miRNAs expression profiling in purified CD49f-positive and negative testicular cells showed that 933 were miRNAs upregulated in CD49f-positive cells and 916 were miRNAs upregulated in CD49f-negative cells with a 2-fold increase, respectively; some spermatogonial stem cells(SSCs) specific miRNAs and marker genes in testis had a higher level expression in CD49f-positive testicular cells, such as miR-221, miR-23a, miR-29b, miR-24, miR-29a, miR-199b, miR-199a, miR-27a, miR-21.
Conclusions: our comparative miRNAome data provided some useful miRNAs profiling data of dairy goat spermatogonia cells and suggested CD49f could be used to enrich dairy goat spermatogonia-like cells, including SSCs.

overall_design: miRNA profiles of goat CD49f-positive and negative testicular cells were generated by deep sequencing, in triplicate, using Illumina GAIIx

first: Jiang

last: Wu

first: Mingzhi

last: Liao

first: Jinlian

last: Hua


title: mRNA expression in iPS cells generated by a synthetic self-replicative RNA

city: La Jolla

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary: We generated iPS cells with a synthetic self-replicative RNA that expresses four independent reprogramming factors (OCT4, KLF4, SOX2 and either c-MYC or GLIS1).  We performed whole genome RNA sequencing (RNA-seq) of iPS cell clones, parental BJ and HUES9 ES cell controls. All iPS cell clones analyzed by RNA-seq showed unsupervised hierarchical clustering and expression signatures characteristic of human HUES9 ES cells that were highly divergent from parental human fibroblasts.

overall_design: RNA-seq in two OKS-iM iPS clones (generated from OCT4, KLF4, SOX2 and cMYC expressing RNA replicon), two OKS-iG clones (generated from OCT4, KLF4, SOX2 and GLIS1 expressing RNA replicon), HUES9 and BJ cells.

first: Hairi

first: Naohisha

last: Yoshioka

first: Xiang-Dong

last: Fu

first: Steve

last: Dowdy


title: Absolute quantification of protein production reveals principles underlying protein synthesis rates

first: Gene-Wei

address: 1700 4th Street, BH404

summary: A quantitative view of cellular functions requires precise measures of the rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resultant E. coli dataset transforms our understanding of the extent to which protein synthesis is precisely controlled to optimize function and efficiency. For example, members of multi-protein complexes are made in precise proportion to their stoichiometry, whereas components of functional modules are produced differentially according to their hierarchical role. Estimates of absolute protein abundance also reveal principles used to optimize design. These include how the level of different types of transcription factors is optimized for rapid response, and how a metabolic pathway (methionine biosynthesis) balances production cost with activity requirements. More broadly, our studies reveal how general principles, important both for understanding natural systems and for synthesizing new ones, emerge from global quantitative analyses of protein synthesis.

overall_design: 4 samples of E. coli ribosome profiling and mRNA-seq, including biological replicates

first: David

last: Burkhardt

first: Carol

last: Gross

first: Jonathan

last: Weissman


title: The RUNX2 Cistrome in Osteoblasts: Characterization, Downregulation Following Differentiation and Relationship to Gene Expression [ChIP-Seq]

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

summary: RUNX2 is a transcription factor that is first expressed in early osteoblast-lineage cells and represents a primary determinant of osteoblastogenesis.  While numerous target genes are regulated by RUNX2, little is known of sites on the genome occupied by RUNX2 or of the gene networks that are controlled by these sites.  To explore this, we conducted a genome-wide analysis of the RUNX2 cistrome in both pre-osteoblastic MC3T3-E1 cells (POB) and their mature osteoblast progeny (OB), characterized the two cistromes and assessed their relationship to changes in gene expression.  We found that although RUNX2 was widely bound to the genome in POB cells, this binding profile was reduced upon differentiation to OBs.  Numerous sites were lost upon differentiation, new sites were also gained; many sites remained common to both cell states.  Additional features were identified as well including location relative to potential target genes, abundance with respect to single genes, the frequent presence of a consensus TGTGGT RUNX2 binding motif, co-occupancy by C/EBPβ and the presence of a typical epigenetic histone enhancer signature. This signature was changed quantitatively following differentiation. While RUNX2 binding sites were associated extensively with adjacent genes, the distal nature of the majority of these sites prevented assessment of whether they represented direct targets of RUNX2 action. Changes in gene expression, however, revealed an abundance of genes that contained RUNX2 binding sites and were regulated in concert.  These studies establish a basis for further analysis of the role of RUNX2 activity and its function during osteoblast lineage maturation.

overall_design: 2 transcription factors and 5 histone modifications were examined in undifferentiated MC3T3-E1 cells as well as post 15 day osteogenic differentiation MC3T3-E1 cells.  The samples were completed in biological replicate and examined separately.

first: Nancy

last: Benkusky

first: J

last: Pike


title: The RUNX2 Cistrome in Osteoblasts: Characterization, Downregulation Following Differentiation and Relationship to Gene Expression

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


title: Genome-scale analysis in blood progenitor and mast cells reveals how lineage-affiliated transcription factors control distinct regulatory programs [ChIP-Seq/RNA-Seq Experiments]

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

institute: Cambridge Institute for Medical Research

summary: Despite major advances in the generation of genome-wide binding maps, the mechanisms by which transcription factors (TFs) regulate cell type identity have remained largely obscure. Through comparative analysis of 10 key haematopoietic TFs in both mast cells and blood progenitors, we demonstrate that the largely cell-type specific binding profiles are not opportunistic, but instead contribute to cell-type specific transcriptional control, because (1) mathematical modelling of differential binding of shared TFs can explain differential gene expression, (2) cell-type specific binding is largely mediated through consensus binding sites, and (3) knock-down of blood stem cell regulators Gata2 and Erg in mast cells reveals mast cell specific genes as direct targets. Finally we show that the known mast cell regulators Mitf and c-Fos likely contribute to the global reorganisation of TF binding profiles. Taken together therefore, our study elucidates how key regulatory TFs contribute to transcriptional programmes in several distinct mammalian cell types.

overall_design: Comparison of HPC7 cell line (haematopoietic multipotent progenitor) and primary mast cells. 10 key haematopoietic transcription factors and mRNA expression were profiled in both cell types.

first: Fernando

last: Calero-Nieto

first: Nicola

last: Wilson

first: Rebecca

last: Hannah

first: Evangelia

last: Diamanti

first: Victoria

last: Moignard

first: Ana

middle: I

last: Leal-Cervantes

first: Isabel

last: Jimenez-Madrid

first: Lorenz

last: Wernisch

first: Berthold

last: Gottgens


title: Comparative transcriptomics of geographic strains of catfishes exposed to chronic high temperatures

status: Public on Apr 23 2014

city: Mississippi State

last: Arick II

state: MS

address: 650 Stone Blvd.

department: Institute for Genomics, Biocomputing & Biotechnology

institute: Mississippi State University

summary: This study examined differentially expressed (DE) gene transcripts and regulated pathways of two geographically distinct channel catfish (Ictalurus punctatus) strains and one hybrid catfish (I. punctatus x [blue catfish] I. furcatus) strain to test whether one particular catfish type handled thermal stress better. Following a six-week growth experiment, where fish were subjected to daily cycling temperatures of either 27-31°C or 32-36°C, mimicking pond fluctuations. We sequenced 18 cDNA libraries of liver samples to obtain 61 million reads per library. There were 5,443 DE transcripts and 41,689 regulated pathways. Northern channel catfish had the highest amount of DE transcripts (48.6%), 5 times that of southern channel catfish, and the greatest amount of transcripts with fold changes ≥ 2. The overall amount of temperature-induced DE transcripts between southern hybrid and southern channel catfish was fairly comparable in relation to that of northern channel catfish, however, there were more transcripts up- or downregulated with ≥ 2 fold changes in channel catfish strains compared to the southern hybrid catfish. Results from this study strongly suggest genetic differences between geographic catfish types affect physiological responses to thermal stress. Furthermore, a number of genes were linked to thermal stress tolerance, which may be beneficial for understanding geographic differences in thermal stress tolerance in ectotherms and for strain development of catfish.

sample_organism: Ictalurus punctatus x Ictalurus furcatus

overall_design: Hepatic mRNA profiles of three fingerling catfish types following a six week growth experiment of daily cycling temperatures of either 27-31°C or 32-36°C, mimicking pond fluctuations.

first: Heather

last: Stewart

first: Brian

last: Peterson

first: Kurt

last: Showmaker

first: Peter

last: Allen


title: Definition of the fibroblast SRF-mediated immediate-early transcriptional response

city: London

first: Francesco

last: Gualdrini

address: 44 Lincoln's Inn Fields

institute: Francis Crick Institute

summary: To control transcription, SRF recruits signal-regulated co-activators, the Ternary Complex Factors (TCFs) and the Myocardin-related Transcription Factors (MRTFs), which compete for a common site on its DNA-binding domain. The TCFs - SAP-1, Elk-1 and Net - are Ets proteins that link SRF activity to Ras-ERK signalling. In contrast, the two MRTFs, MRTF-A and MRTF-B, link SRF activity to Rho-actin signalling. In this novel signalling pathway, the actin-binding MRTF RPEL domain acts as a G-actin sensor, controlling MRTF nuclear accumulation in response to signal-induced depletion of the G-actin pool.    Previous studies have suggested that the Ras-ERK signalling and Rho-actin pathways control specific subsets of SRF target genes. We used ChIP-seq and RNA-seq to analyse the immediate-early transcriptional response in NIH3T3 fibroblasts, using pathway-specific inhibitors to identify the contributions of Ras-ERK and Rho-actin signalling

overall_design: Chromatin immunoprecipitation and sequencing (ChIP-seq) in NIH3T3 fibroblast after serum stimulation in presence or absence of LatrunculinB or U0126 drugs and using antibodies against SRF, MRTF-A, MRTF-B, SAP1, ELK1, NET, Pol II, PolII S5P, PolII S2P and total H3. Validation by ChIP-PCR. Strand specific total-RNA-seq following DSN normalisation and validation by qRT-PCR from NIH3T3 stimulated by serum or Cytochalasin D in presence or absence of LatrunculinB and/or U0126 drugs.

first: Cyril

last: Esnault

first: Aengus

first: Phil

last: East

first: Stuart

last: Horswell

first: Nik

last: Matthews

first: Richard

last: Treisman