title: mRNA profile of dG9a-depleted early embryo in Drosophila melanogaster

city: matsugasakihashigami tyo

last: Shimaji

department: Applied biology

institute: Kyoto Institute of Technology

summary: Immunocytochemical studies revealed that dG9a moves into nucleus after cycle 8 and appears to regulate gene expression by di-methylating H3K9 from cycle 8 to cycle 11. To determine which genes are regulated by dG9a during cycles 8-11, we examined mRNA levels by performing RNA-sequence analysis using early embryos (0-2 h after egg laying) of dG9a null mutant and wild type as a control

overall_design: mRNA profiles of about 0-2h-old embryos of wild type (CantonS) and dG9a-depleted (dG9aRG5) strain

first: Yasuyuki

last: Ohkawa

first: Tetsuya

last: Sato

first: Mikita

last: Suyama

first: Masamitsu

last: Yamaguchi


title: Gene expression analysis of mouse intestinal cells that lack Cdk8

status: Public on Jul 31 2015

city: South San Francisco

first: Florian

last: Gnad

address: 1 DNA Way

country: USA

institute: Genentech

type: Expression profiling by high throughput sequencing

summary: RNAseq is performed (50bp single end reads) on parental young adult mouse intestinal cells (YAMC) or two clones in which Cdk8 allele is ablated using CRISPR

overall_design: Examination of transcriptomic changes after knockout of Cdk8 using CRISPR. Two clones of Cdk8 knockouts are compared to parental YAMC cells

first: Ron

last: Firestein

first: Mark

last: McCleland


title: Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus
synthetic construct

overall_design: Refer to individual Series


title: Identification of the miRNA targetome in hippocampal neurons using RIP-seq

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: We established a neuron-specific Argonaute2:GFP-RNA immunoprecipitation followed by high throughput sequencing (AGO2-RIP-seq) to analyse the regulatory role of miRNAs in mouse hippocampal neurons. Using this technique, we identified more than two thousand miRNA target genes in hippocampal neurons, regulating essential neuronal features such as axon guidance and transcription. Furthermore, we found that stable inhibition of the highly expressed miR-124 in hippocampal neurons led to significant changes in the AGO2 binding of target mRNAs, resulting in subsequent upregulation of numerous miRNA target genes. Our data suggest that target redundancies are common among microRNA families. Together, these findings greatly enhance our understanding of the mechanisms and dynamics through which miRNAs regulate their target genes in neurons.

overall_design:
Analysis of the miRNA targetome in hippocampal neurons after inhibition of 2 different miRNAs.

AAV5 injections into the hippocampus of adult C57BL/6 mice producing either of the following under a synapsin promoter: GFP only (Samples beginning with 'GFP124…' or 'GFP125…'), GFP-miR124sp (Samples beginning with 'miR124…'), GFP-miR125sp (Samples beginning with 'miR125…'), GFP-AGO2-miR292sponge (samples ending with '…292'), GFP-AGO2-miR124sponge (samples ending with '…124'), GFP-AGO2-miR125sponge (samples ending with '…125'). All other samples were sham-injected.

first: Josephine

last: Malmevik

first: Rebecca

last: Petri

first: Thies

last: Klüssendorf

first: Pina

last: Knauff

first: Malin

last: Åkerblom

first: Jenny

last: Johanssion

first: Shamit

last: Soneji

first: Johan

last: Jakobsson


title: Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

city: Heidelberg

first: Ana

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: Heterogeneous pools of adult neural stem cells (NSCs) contribute to brain maintenance and regeneration after injury. The balance of NSC activation and quiescence, as well as the induction of lineage-specific transcription factors, may contribute to diversity of neuronal and glial fates. To identify molecular hallmarks governing these characteristics, we performed single-cell sequencing of an unbiased pool of adult subventricular zone NSCs. This analysis identified a discrete, dormant NSC subpopulation that already expresses distinct combinations of lineage-specific transcription factors during homeostasis. Dormant NSCs enter a primed-quiescent state before activation, which is accompanied by downregulation of glycolytic metabolism, Notch, and BMP signaling and a concomitant upregulation of lineage-specific transcription factors and protein synthesis. In response to brain ischemia, interferon gamma signaling induces dormant NSC subpopulations to enter the primed-quiescent state. This study unveils general principles underlying NSC activation and lineage priming and opens potential avenues for regenerative medicine in the brain.

overall_design:
Single cell RNAseq of cells isolated from their in vivo niche in the subventricular zone, Striatum and Cortex during homeostasis as well as following ischemic injury.
In total 272 single cells. (<WT>: homeostasis samples; <Ischemic_injured> and <Ischemic_injured_and_Interferon_gamma_knockout>: samples following ischemic injuried).

first: Enric

last: Llorens-Bobadilla

first: Sheng

last: Zhao


title: A novel analytical brain block tool to enable functional annotation of discriminatory transcript biomarkers among discrete regions of the fronto-limbic circuit in primate brain

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

summary: We describe a novel method for obtaining discrete regions from the fronto-limbic circuits of a 4 year old and a 5 year old, male, intact, frozen non-human primate (NHP) brain, from which we use transcriptional profiling and a new algorithm to identify region-exclusive RNA signatures for Area 25 (NFκB and dopamine receptor signaling), the anterior cingulate cortex (LXR/RXR signaling), the amygdala (semaphorin signaling), and the hippocampus (Caþþ and retinoic acid signaling).

overall_design: Profiling of 4 discrete brain regions in 2 individual non-human primate subjects.

middle: L

first: Harvey

middle: B

last: Pollard


title: Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage [RNA-seq]

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: MyoD and NeuroD2 are master regulators of myogenesis and neurogenesis and bind to a "shared" E-box sequence (CAGCTG) and a "private" sequence (CAGGTG or CAGATG, respectively). To determine whether private-site recognition is sufficient to confer lineage-specification, we generated a MyoD-mutant with the DNA binding specificity of NeuroD2. Our results demonstrate that redirecting MyoD binding from MyoD-private sites to NeuroD2-private sites, despite preserved binding to the MyoD/NeuroD2-shared sites, is sufficient to change MyoD from a master regulator of myogenesis to a master regulator of neurogenesis.

overall_design: RNA-seq profiling of mouse P19 cells transfected with MyoD, NeuroD2 and chimera mutants. The chimeric mutants are MyoD with the bHLH domain replaced with the NeuroD2 bHLH domain.

first: Abraham

last: Fong

first: Zizhen

last: Yao

first: Jun

middle: W

last: Zhong


title: Identification and characterization of wilt and salt stress-responsive microRNAs from chickpea by high-throughput sequencing.

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

country: India

institute: Delhi University

summary:
Purpose: To identify Fusarium wilt and salt-responsive miRNAs at genome wide level in Chickpea.
Results: A total of 12,135,571 unique reads were obtained. In addition to 122 conserved miRNAs belonging to 25 different families, 59 novel miRNAs along with their star sequences were identified. Four legume specific miRNAs, miR5213, miR5232, miR2111 and miR2118 were found in all the libraries. The Poly (A) tailing assay based qRT-PCR was used to validate eleven conserved and five novel miRNAs. miR530 was highly up regulated in response to fungal infection and targets zinc knuckle and microtubule-associated proteins. Many miRNAs responded in a similar fashion under both biotic and abiotic stresses indicating a cross talk between the pathways involved in regulating these stresses. The potential target genes for the conserved and novel miRNAs were predicted based on sequence homology. miR166 targets a HD-ZIPIII transcription factor and was validated by 5’ RLM-RACE.
Conclusions: The present study has led to identification of several conserved and novel miRNAs in chickpea associated with gene regulation in reference to wilt and salt stress conditions. This study will help in better understanding of how chickpea functions in response to stresses.

overall_design: Total three small RNA libraries from chickpea were prepared and sequenced independently  [Control (C), Wilt stress (WS), Salt stress (SS)] on Illumina GAIIx.

first: Deshika

last: Kohli

first: Amit

last: Deokar

first: Ankur

middle: R

last: Bhardwaj

first: Manu

last: Agarwal

first: Surekha

last: Katiyar-Agarwal

first: Ramamurthy

last: Srinivasan

first: Pradeep

middle: K

last: Jain


title: Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage

type: Genome binding/occupancy profiling by high throughput sequencing


title: Aldehyde dehydrogenase activity is necessary for beta cell development and functionality in mice

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

institute: TU Dresden

summary:
Aims/hypothesis Pancreatic beta cells maintain glucose
homeostasis and beta cell dysfunction is a major risk factor
in developing diabetes. Therefore, understanding the developmental
regulatory networks that define a fully functional beta
cell is important for elucidating the genetic origins of the disease.
Aldehyde dehydrogenase activity has been associated
with stem/progenitor cells and we have previously shown that
Aldh1b1 is specifically expressed in pancreas progenitor
pools. Here we address the hypothesis that Aldh1b1 may regulate
the timing of the appearance and eventual functionality
of beta cells.
Methods We generated an Aldh1b1-knockout mouse line
(Aldh1b1tm1lacZ) and used this to study pancreatic development,
beta cell functionality and glucose homeostasis in the
absence of Aldh1b1 function.
Results Differentiation in the developing pancreas of
Aldh1b1tm1lacZ null mice was accelerated. Transcriptome
analyses of newborn and adult islets showed misregulation of
key beta cell transcription factors and genes crucial for beta cell
function. Functional analyses showed that glucose-stimulated
insulin secretion was severely compromised in islets isolated
from null mice. Several key features of beta cell functionality
were affected, including control of oxidative stress, glucose
sensing, stimulus-coupling secretion and secretory granule
biogenesis. As a result of beta cell dysfunction, homozygous
mice developed glucose intolerance and age-dependent
hyperglycaemia.
Conclusions/interpretation These findings show that
Aldh1b1 influences the timing of the transition from the pancreas
endocrine progenitor to the committed beta cell and
demonstrate that changes in the timing of this transition lead
to beta cell dysfunction and thus constitute a diabetes risk
factor later in life.

overall_design: Islets were isolated from postnatal day one and 8 week old Aldh1b1 null and wt mice. For each P1 samples islets from three mice were combined. Each week 8 sample came from a single mouse. Three samples were analysed per genotype and time point

first: Vivian

last: Anastasiou

first: Elpiniki

last: Ninou

first: Dimitra

last: Alexopoulou

first: Julia

last: Stertmann

first: Andreas

last: Müller

last: Dahl

first: Michele

last: Solimena

first: Stephan

last: Speier

first: Ioannis

last: Serafimidis


title: Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage [ChIP-seq]

first: Stephen

last: Tapscott

overall_design: ChIP-seq profiling of MyoD, NeuroD2 and chimera mutants in mouse P19 cells transfected with these genes. The chimeric mutants are MyoD with the bHLH domain replaced with the NeuroD2 bHLH domain.

first: Abraham

last: Fong

first: Zizhen

last: Yao

first: Jun

last: Zhong


title: Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRα+ Cells

city: Reno

first: Seungil

last: Ro

state: NV

address: 1664 North Virginia St

department: Physiology and Cell Biology

institute: University of Nevada School of Medicine

summary: Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRα+ cells (PαC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies.

overall_design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..

first: Chanjae

last: Park

first: Jared

last: Townsend

first: Doug

last: Redelman

first: Tsai-wei

last: Shen

first: Kenton

middle: M

last: Sanders


title: PIWI-interacting RNAs are dysregulated in renal cell carcinoma and associated with tumor metastasis and cancer specific survival

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Piwi-interacting RNAs (piRNAs) are a distinct group of small non-coding RNAs (sncRNAs) that silence transposable genetic elements to protect genome integrity. Due to their limited expression in gonads and sequence diversity, piRNAs remain the most mysterious class of small RNAs. Studies have shown piRNAs are present in somatic cells and dysregulated in gastric, breast and liver cancers. By deep sequencing 24 frozen benign kidney and clear cell renal cell carcinoma (ccRCC) specimens and using the publically available piRNA database, we found 26,991 piRNAs present in human kidney tissue. Among 920 piRNAs that at least had two copies in one specimen, 19 were differentially expressed in benign kidney and ccRCC tissues, and 46 were associated with metastasis. Among the metastasis-related piRNAs, we found 3 piRNAs, piR- 32051, piR-39894 and piR-43607, to be derived from the same piRNA cluster at chromosome 17. We confirmed the 3 selected piRNAs not to be miRNAs or miRNA-like sncRNAs. We further validated the aberrant expression of the 3 piRNAs in a 68-case formalin-fixed and paraffin-embedded (FFPE) ccRCC tissue cohort and showed the upregulation of the 3 piRNAs to be highly associated with ccRCC metastasis, late clinical stage and cancer-specific survival.

overall_design: ncRNA sequencing of 18 ccRCC samples and 6 normal renal tissues

first: Yuping

last: Li

first: Huiqing


title: Loss of Activating Transcription Factor 3 reveals a distinct gene expression program modulating cell organization during pancreatitis.

status: Public on Aug 01 2015

city: London

first: Christopher

last: Pin

state: Ontario

address: 800 Commissioners Rd. E

department: Physiology and Pharmacology/Peadiatrics

country: Canada

institute: The University of Western Ontario/CHRI

summary: Pancreatitis is triggered by environmental or cellular stress and is the leading contributor to pancreatic ductal adenocarcinoma.  Altered gene expression in response to acinar cell stress determines the severity and duration of pancreatitis.  However, it is unclear what factors contribute to this phenomenon.  Here, we define a novel role for Activating Transcription Factor 3 (ATF3) during pancreatic injury. ATF3, a key mediator in the unfolded protein response, is robustly expressed in acinar cells during pancreatitis. Targeted deletion of Atf3 altered the molecular response to injury, with Atf3-/- acinar cells maintaining cell organization in response to cerulein, a well-established inducer of pancreatitis. Characterization of the mechanism using chromatin immunoprecipitation followed by Next Generation sequencing (ChIP-seq) identified 11,771 enrichment spots for ATF3, with known transcriptional start sites for >3,000 genes within 5 kb of ATF3 enrichment.  Gene ontology analysis revealed a significant representation of ATF3 enrichment to genes affecting cell organization, including Mist1, a molecule required for establishing acinar cell organization. We confirmed a direct interaction of ATF3 to the Mist1 promoter during pancreatitis, and showed that ATF3 is required for altered Mist1 expression in response to injury.  Finally, we demonstrate that ATF3 repression of Mist1 involves HDAC5. These findings suggest that ATF3 is a key transcriptional regulator during pancreatitis and promotes loss of the mature acinar cell phenotype in response to pancreatic injury.

overall_design: Two samples were produced from male mice 4 hours after CIP initiation from intraparitoneal injections of cerulein, a ChIP sample using an ATF3 antibody and an IP control.


title: PATZ1 is a DNA damage responsive transcription factor that inhibits p53 function [with and without doxorubicin treatment]

status: Public on Jul 30 2015

city: Istanbul

first: Batu

last: Erman

address: Orhanli, Tuzla

department: Biological Sciences and Bioengineering Program

country: Turkey

institute: Sabanci University


title: Chlamydomonas diurnal transcriptome

city: St. Louis

first: James

last: Umen

state: MO

address: 975 N. Warson Rd.

institute: Donald Danforth Plant Science Center

summary: We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide periodic gene expression in Chlamydomonas.

overall_design: Synchronous phototrophic cultures of Chlamydomonas reinhardtii were prepared in controlled diurnal bioreactor growth conditions and sampled in two 24-hour replicate time courses at 1-hour and 0.5-hour intervals for Illumina paired-end RNA-Seq. More than ~3 million paired end reads were obtained for each sample.

last: Zones

first: Ian

last: Blaby

first: Sabeeha

middle: S

last: Merchant

middle: G


title: Interactions of melanoma cells with distal keratinocytes trigger metastasis via Notch signaling inhibition of MITF

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary: The most critical stage in initiation of melanoma metastasis is the radial to vertical growth transition, yet the triggers of this transition remain elusive. We introduce a novel perspective, suggesting that the microenvironment drives melanoma metastasis independently of mutation acquisition. Here we examined the changes in microenvironment that occur during melanoma radial growth. We show that direct contact of melanoma cells with the remote epidermal layer triggers vertical invasion via Notch signaling activation, the latter serving to inhibit MITF function. Briefly, within the native Notch ligand-free microenvironment, MITF, the melanocyte lineage master regulator, binds and represses miR-222/221 promoter in an RBPJK-dependent manner. However, when radial growth brings melanoma cells into contact with distal differentiated keratinocytes that express Notch ligands, the activated Notch intracellular domain impairs MITF binding to miR-222/221 promoter. This de-repression of miR-222/221 expression triggers initiation of invasion. Our findings may direct novel prevention opportunities via targeting specific microenvironment.

overall_design: Two replicates of Notch-activated cells that were seeded on Delta-like-1 (DLL1) (2 ng/µl ) coated plates were compared to two replicates of cells without Notch activation. The goal of this experiment is to evaluate the changes of miRs expression in melanoma cells upon Notch signaling activation.


title: Prevalent p53 gain-of-function mutants co-opt epigenetic pathways to drive cancer growth

city: Philadelphia

first: Morgan

last: Sammons

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
We investigated the genomewide binding pattern of prevalent p53 gain-of-function (GOF) mutants by ChIP-seq, in a panel of breast cancer cell lines.
We assessed the genomewide changes of H3K4me3 upon GOF p53 knockdown in MDA-MB-468 breast cancer cells bearing the p53 R273H mutation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: This study uses ChIP-seq of H3K4me3 and histone H3 in wild-type or p53 R172H knock-in MEFs.  Additionally, this study examines the transcriptome of wild-type or p53 R172H knock-in MEFs using polyA+ RNA-seq.

first: Shelley

last: Berger


title: Intra-macrophage transcriptome of Salmonella enterica serovar Typhimurium 4/74 using strand-specific RNA-seq

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary:
Bacterial transcription is controlled by many transcription factors and promoters. Currently many promoters are mapped only in in vitro conditions. We use an intra-macrophage model to map the promoters and their expression in vivo.
InSPI2 is an in vitro growth condition mimicking intra-macrophage condition. We also characterize the transcriptome of Salmonella during growth in an in vitro intra-macrophage growth condition.

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

overall_design:
Transcriptome analysis of S.Typhimurium 4/74 within macrophages using RNA-seq in biological replicates. dRNA-seq also performed in biological replicates.
Transcriptome analysis of S.Typhimurium 4/74 during InSPI2 growth using strand specific RNA-seq.

first: Shabarinath

last: Srikumar

first: Carsten

last: Kröger

first: Magali

last: Hèbrard

first: Aoife

last: Colgan

first: Siân

middle: V

last: Owen

first: Sathesh

last: Sivasankaran

first: Andrew

middle: D

last: Cameron

first: Jay

middle: C

last: Hinton


title: Nucleosome mapping of Tetrahymena thermophila chromatin in vivo and in vitro

city: New York

first: Leslie

last: Beh

department: Biochemistry & Molecular Biophysics

institute: Columbia University

summary: A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from subsets of nucleosomes, rather than the whole array, being present in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes, and affects codon usage and amino acid composition in genes. We propose that these ‘seed’ nucleosomes may aid the AT-rich Tetrahymena genome – which is intrinsically unfavorable for nucleosome formation – in establishing nucleosome arrays in vivo in concert with trans-acting factors, while minimizing changes to the coding sequences they are embedded within.

overall_design: All data are from the macronuclear genome. Datasets: 1)  Log-phase cells, fixed chromatin, light MNase digest; 2) Log-phase cells, native chromatin, heavy MNase digest; 3) Starved cells, fixed chromatin, light MNase digest; 4) Starved cells, native chromatin, heavy MNase digest; 5) in vitro reconstituted chromatin, 50ul reaction, 4:10 histone:DNA ratio, light MNase digest; 6) in vitro reconstituted chromatin, 50ul reaction, 7:10 histone:DNA ratio, light MNase digest; 7) in vitro reconstituted chromatin, 150ul reaction, 4:10 histone:DNA ratio, light MNase digest; 8) in vitro reconstituted chromatin, 150ul reaction, 4:10 histone:DNA ratio, heavy MNase digest; Control dataset: 9): MNase-digested naked DNA

middle: Y

first: Noam

last: Kaplan

first: Manuel

last: Muller

first: Tom

last: Muir

first: Laura

middle: F

last: Landweber


title: Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptomewide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale coexpression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.

overall_design: Analysing long and short poly(A)-tail fractions from 4 paps1 mutant and 4 Ler samples.

first: Christian

last: Kappel

first: Gerda

last: Trost

first: Hjördis

last: Czesnick

first: Anna

last: Ramming

first: Son

last: Vi

first: Cláudia

last: Bispo

first: Jörg

last: Becker

first: Cornelia

last: de Moor


title: Identification and functional characterization of long noncoding RNAs in breast cancer

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: In this study, we have integrated RNA-seq data from subcellular fractionated RNA (i.e., cytoplasm, nucleoplasm, and chromatin-associated) with GRO-seq data using a novel bioinformatics pipeline. This has yielded a comprehensive catalog of polyadenylated lncRNAs in MCF-7 cells, about half of which have not been annotated previously and about a quarter of which are estrogen-regulated. Knockdown of selected lncRNAs, such as lncRNA152 and lncRNA67 followed by RNA-seq suggest that these lncRNAs regulate the expression of cell cycle genes.

overall_design: characterization of long noncoding RNAs

first: Miao

last: Sun

first: Shrikanth

last: Gadad

first: Dae

last: Kim

first: W


title: Transcriptomic analysis of Rongchang pig brains and livers

city: Chongqing

first: Ling

last: Gan

address: 160#Xue Yuan Road,RongchangCounty

department: 1The Department of Veterinary Medicine

country: China

institute: Southwest University

summary: Recent developments in high-throughput RNA sequencing (RNA-seq) technology have had a dramatic impact on our comprehension of the structure and expression profiles of the mammalian transcriptome. This study performed transcriptome analysis of Rongchang pig brains and livers using deep RNA-seq technology to offer insights into potential swine genetic improvements, in addition to examining the use of the Rongchang pig as a biomedical model.By sequencing the mRNA of two extreme tissues, brains and livers, a total of 8.6 Gb of sequencing was obtained, with 91% resulting in clean reads, with approximately 43 million reads from the brain and 44 million reads from the liver samples. This analysis revealed tissue specificity through the identification of 5,575 and 4,600 differentially expressed genes (DEGs) in brains and livers respectively. Functional analysis of the differentially expressed genes showed that the top ten functional pathways with highly enriched gene expression in brains were associated with nerves, while in livers the pathways were predominantly related to metabolism. Furthermore, 83 neuropeptide gene transcripts, 69 neuropeptide receptor gene transcripts, 10 pro-neuropeptide convertase gene transcripts, 12 insulin-like growth factors binding protein gene transcripts, and other neuropeptide related protein gene transcripts were identified, to reveal different expression profiles in brain and liver samples. In this study, major characteristics of the transcriptional profiles of Rongchang pig brains and livers were present. Overall, our data provides useful information for future research pertaining to swine livestock and biomedical research.

overall_design: Transcriptional profiles of Rongchang pig brains and livers were generated by deep sequencing, using Illumina Hiseq 2000.

first: Ningjia

last: He


title: Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain [miRNA-Seq]

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

institute: SUNY Upstate Medical Univ

summary: We performed a global analysis of extracellular miRNAs in the serum of human subjects diagnosed with Alcohol Use Disorder (AUD) to identify robust biomarkers of early brain damage or dysfunction. This was performed in a set of 20 AUD subjects and 10 age-matched controls. They were subjected to comprehensive medical, neuropsychological and neuroimaging tests, followed by comparison of miRNA levels found in peripheral blood serum. The levels of miRNAs were quantified using two independent high-throughput methods: Affymetrix microarray and Illumina next-generation RNA-sequencing. Cross-species validation was performed using rat drinking models and mouse neural stem cell culture models, with tissue specificity of the serum miRNAs examined using additional RNA-sequencing of serum and body tissues in untreated rats. This data series includes the human miRNA data obtained from RNA-sequencing only but is part of a larger superseries.

overall_design: A total of 30 miRNA 3.0 GeneChips and 27 RNA-sequencing libraries were run on the same RNA samples from human subjects.

first: Cherry

last: Ignacio

first: Steven

last: Hicks

first: Patrick

last: Burke

first: Lambert

last: Lewis

first: Zsuzsa

last: Szombathyne-Meszaros


title: Analysis of the microRNA expression profile in the mouse epididymis detected by next generation sequencing

status: Public on Jul 29 2015

city: Callaghan

first: Bettina

middle: P

last: Mihalas

state: NSW

address: Level 4 Life Science Building, University Drive

department: Life Sciences

country: Australia

institute: University of Newcastle

summary: The functional maturation of mammalian spermatozoa is accomplished as the cells descend through the highly specialized microenvironment of the epididymis. This dynamic environment is, in turn, created by the combined secretory and absorptive activity of the surrounding epithelium and displays an extraordinary level of regionalization. Although the regulatory network responsible for spatial coordination of epididymal function remains unclear, recent evidence has highlighted a novel role for the RNA interference pathway. Indeed, as noncanonical regulators of gene expression, small noncoding RNAs have emerged as key elements of the circuitry involved in regulating epididymal function and hence sperm maturation. Herein we have employed next generation sequencing technology to profile the genome-wide miRNA signatures of mouse epididymal cells and characterize segmental patterns of expression. An impressive profile of some 370 miRNAs were detected in the mouse epididymis, with a subset of these specifically identified within the epithelial cells that line the tubule (218).  A majority of the latter miRNAs (75%) were detected at equivalent levels along the entire length of the mouse epididymis. We did however identify a small cohort of miRNAs that displayed highly regionalized patterns of expression, including miR-204-5p and miR-196b-5p, which were down- and up-regulated by approximately 39- and 45-fold between the caput/caudal regions, respectively. In addition we identified 79 miRNAs (representing ~ 21% of all miRNAs) as displaying conserved expression within all regions of the mouse, rat and human epididymal tissue. These included 8/14 members of let-7 family of miRNAs that have been widely implicated in the control of androgen signaling and the repression of cell proliferation and oncogenic pathways.  Overall these data provide novel insights into the sophistication of the miRNA network that regulates the function of the male reproductive tract.

overall_design: Examination of the microRNA expression profile in the whole mouse epididymis and mouse epididymal epithelial cells using next generation sequencing in duplicate.

first: Brett

last: Nixon

first: Simone

middle: J

last: Stanger

first: Jackson

middle: N

last: Reilly

first: Amanda

last: Anderson

first: Matthew

last: Dun

first: Sonika

last: Tyagi

first: Janet

middle: E

last: Holt

first: Eileen

last: McLaughlin


title: Maternal Nurtritional Programming in the Ovine Mammary Gland

city: Dunedin

first: Peter

middle: Kenneth

last: Dearden

address: 710 Cumberland St

department: Department of Biochemistry

country: New Zealand

institute: University of Otago

summary: Developmental programming is the concept that environmental factors, particularly during foetal life, can alter development, metabolism and physiology of an organism and this can have consequences later in life. There is growing interest in developmental programming in livestock species, particularly effects of maternal pregnancy nutrition, which is easy to manipulate. Recent research, using a sheep model, has shown that milk production in ewe offspring may be susceptible to maternal nutritional programming, such that over nutrition (ad libitum) of the pregnant dam, compared with maintenance nutrition, may impair their first lactation performance and result in the weaning of lighter lambs. RNA-seq was performed to identify gene expression differences as a result of maternal nutrition in ewe offspring during their first parity.  Samples were collected in late pregnancy and during lactation, allowing us to examine gene expression changes during maturation of the ovine mammary gland.

overall_design: Three biological replicates were sequenced for each of the treatment conditions (maternal nutrition: sub-maintenance, maintenance, and ad libitum) and time points (late pregnancy and lactation).  Each biological replicate consisted of RNA from multiple individuals (late pregnancy n=3, lactation n=2).

first: Amy

last: Paten

first: Elizabeth

last: Duncan

first: Sam

last: Peterson

first: Paul

last: Kenyon

first: Sarah

last: Pain

first: Hugh

middle: T

last: Blair


title: Brg1 promotes both tumor suppressive and oncogenic activities at distinct stages of Pancreatic cancer formation

city: San Francisco

first: Shivani

last: Malik

address: 1450 3rd street

department: Hematology

institute: UCSF

summary: Pancreatic Ductal Adenocarcinoma (PDA) develops predominantly through pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasm (IPMN) precursor lesions. Pancreatic acinar cells are reprogrammed to a “ductal like” state during PanIN-PDA formation. Here, we demonstrate a parallel mechanism operative in mature duct cells where they undergo “ductal retrogression” to form IPMN-PDA. Brg1, a catalytic subunit of the SWI/SNF complexes, plays a critical antagonistic role in IPMN-PDA development. In mature duct cells Brg1 inhibits the dedifferentiation that precedes neoplastic transformation, thus attenuating tumor initiation. In contrast, Brg1 promotes tumorigenesis in full-blown PDA by supporting a mesenchymal-like transcriptional landscape. We have exploited this duality of Brg1 functions to develop a novel therapeutic approach using an epigenetic drug JQ1. In summary, this study demonstrates the context-dependent roles of Brg1 and points to potential therapeutic treatment options based on epigenetic regulation in PDA.

overall_design: Duct cells were isolated from mice of 3 different genotypes and duct cells from 3 mice of each genotype were sequenced. For the put back experiments, control retrovirus and that expressing Brg1 were transdcued in Brg1 null IPMN mouse cell line.

first: Matthias

last: Hebrok

first: Eric

last: Collisson


title: Global Identification of Protein PTMs in a Single-pass Database Search

city: Solna

first: Emma

last: Lundberg

address: Science for Life Laboratory, Tomtebodavägen 23A

institute: KTH Royal Institute of Technology

summary: Bottom-up proteomics database search algorithms used for peptide identification cannot comprehensively identify posttranslational modifications (PTMs) in a single-pass because of high false discovery rates (FDRs). A new approach to database searching enables Global PTM (G-PTM) identification by exclusively looking for curated PTMs, thereby avoiding the FDR penalty experienced during conventional variable modification searches. We identified nearly 2500 unique, high-confidence modified peptides comprising 31 different PTM types in single-pass database searches.

overall_design: Male C57BL/6J (B6) and CAST/EiJ (CAST) mice were purchased from The Jackson Laboratories (Bar Harbor, Maine) and housed in an environmentally controlled vivarium at the University of Wisconsin Biochemistry Department. Mice were provided standard rodent chow (Purina no. 5008) and water ad libitum, and maintained on a 12-hour light/dark cycle (6 AM – 6 PM). At 10 weeks of age, mice were sacrificed by CO2 asphyxiation. All animal procedures were preapproved by the University of Wisconsin Animal Care and Use Committee.

first: Michael

last: Shortreed

first: Craig

last: Wenger

first: Brian

middle: L

last: Frey

first: Gloria

last: Sheynkman

first: Mark

last: Scalf

last: Keller

first: Alan

last: Attie

first: Lloyd

last: Smith


title: Genome-wide maps of chromatin states during B-cell to Macrophage lineage switching

city: Barcelona

first: Chris

last: van Oevelen

state: Catalunya

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: Using homogenous populations of cells undergoing lineage switching we studied enhancer nucleation.

overall_design: Examination of 3 histone marks several time points after induction of transdifferentiation

first: Samuel

last: Collombet

first: Cyrille

last: Lepoivre

first: Lars

last: Bussmann

last: Kallin

first: Guillermo

last: Vicent

first: Miguel

last: Beato

first: Aimee

last: Badeaux

first: Yang

last: Shi

first: Denis

last: Thieffry

first: Constanze

last: Bonifer

first: Thomas

last: Graf


title: Nucleosome density map during B-cell to Macrophage lineage switching

summary: Using homogenous populations of cells undergoing lineage switching we studied enhancer nucleation related to nucleosme organization.

overall_design: Examination of nucleosome densities by using Mnase-seq at several time points after induction of lineage switching

first: Eric


title: Genome-wide maps of transcription factor and co-factor binding during B-cell to Macrophage lineage switching

summary: Using homogenous populations of cells undergoing cell switching we observed an interplay between lymphoid and myeloid transcription factors during lineage switching

overall_design: Examination of transcription factors genome-wide binding profiles several time points after induction of B-cell to macrophage lineage switching


title: Analysis of transcriptomes during cardioac reprogramming by RNA-deep Sequencing

status: Public on Jul 28 2015

city: Aurora,

first: Kunhua

last: Song

state: CO

institute: University of Colorado

summary: Fibroblasts can be reprogrammed into cardiomyocyte-like cells by overexpressing transcription factors, GATA4, Hand2, Mef2C and Tbx5 (GHMT). A83-01, an inhibitor of ALK4, ALK5 and ALK7 and two microRNA, miR-1 and miR-133 increase the efficiency of cardiac reprogramming. RNA_Seq was performed to anyalyze effects of these factors on gene expression.

overall_design: Total RNAs were prepared from mouse embryonic fibroblasts (MEFs); Reprogramming fibroblasts including MEFs transduced with retroviruses encoding GHMT, MEFs transduced with with retroviruses encoding GHMT plus miR-1 and miR-133 (GHMT2m), MEFs transduced with with retroviruses encoding GHMT2m treated with A83-01, at day 7 after viral transduction; and neonatal mouse cardiomyocytes (NMCMs).

first: Yuanbiao

last: Zhao


title: Dynamics of H3K4me2 during cardiac lineage reprogramming

city: Aurora

first: Rebecca

last: O'Rourke

address: 12801 East 17th Ave

institute: University of Denver

summary: During reprogramming of fibroblasts into cardiomyocyte-like cells by overexpression of transcription factors, GATA4, Hand2, Mef2C and Tbx5 (GHMT), H3K4Me2, an active histone code, shifts from fibroblast-exclusive peaks to cardiomyocyte-exclusive peaks. Important cardiac genes are gradually marked by this active histone marker.

overall_design: Mouse embryonic fibroblasts (MEFs) and neonatal mouse ventricular cardiomyocytes (NMVMs) represent fibroblasts and cardiomyocytes, respectively. Chromatins harvested from MEFs infected with retroviruses carrying GHMT  at day 3, day 5, day 7 post-viral infection were prepared for immunoprecipitation.


title: MBNL Sequestration by Toxic RNAs and RNA Mis-Processing in the Myotonic Dystrophy Brain

city: Gainesville

first: Maurice

last: Swanson

state: Florida

address: 2033,Mowry Road

department: Molecular genetics and microbiology

institute: University of Florida

summary: For some neurological disorders, disease is primarily RNA-mediated due to expression of non-coding microsatellite expansion RNAs (RNAexp). Toxicity is thought to result from enhanced binding of proteins to these expansions and depletion from their normal cellular targets. However, experimental evidence for this sequestration model is lacking. Here, we use HITS-CLIP and pre-mRNA processing analysis of human control versus myotonic dystrophy (DM) brains to provide compelling evidence for this RNA toxicity model. MBNL2 binds directly to DM repeat expansions in the brain resulting in depletion from its normal RNA targets with downstream effects on alternative splicing and polyadenylation. Similar RNA processing defects were detected in Mbnl compound knockout mice, highlighted by dysregulation of Mapt splicing and fetal tau isoform expression in adults. These results demonstrate that MBNL proteins are directly sequestered by RNAexp in the DM brain and introduce a powerful experimental tool to evaluate RNA-mediated toxicity in other expansion diseases.

overall_design:
HITS-CLIP analysis was performed to identify RNA binding sites of MBNL2 in control, DM type 1 (DM1), and DM type 2 (DM2) autopsy-derived brain (n=3).  Two regions of the brain selected for the study included the frontal cortex and hippocampus. Libraries were sequenced and wiggle files were generated for each biological replicate as well as three pooled biological replicates (3BRs) per group (control, DM1, and DM2).  In addition, differential CLIP analysis (dCLIP) was performed to normalize binding data between groups and identify statistically significant changes in binding.  The dCLIP analysis generated bedgraph files representing normalized binding profiles of MBNL2 in each group (control, DM1, and DM2) for visualization and comparative analysis.
PolyA-seq was performed on control, DM1, and DM2 autopsy-derived brain samples (hippocampus and frontal cortex, n=3) as well as wild-type (WT) and Mbnl1; Mbnl2 conditional double knockout (Mbnl1-/-; Mbnl2c/c; Nestin-Cre+/- or DKO) brain (n=3).  Libraries were sequenced and the resultant files were processed and aligned to the reference genomes (hg19 and mm10).  Further computational processing was performed to remove internal oligo(dT) mis-priming events, identify valid polyA sites, and trim to the exact polyA sites.  BedGraph files were generated for each group in human (control, DM1, and DM2) and mouse (WT and Mbnl DKO) for comparative visualization.

first: Marianne

last: Goodwin

first: Apoorva

last: Mohan

first: Ranjan

last: Batra


title: Transcriptomic analysis of  fungus Penicillium oxalicum and its laeA deletion strains in 24h and 60h

status: Public on Jul 27 2015

city: Jinan

first: Yanan

last: Li

address: Shanda south road 27

institute: Shandong University

summary: The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), and laeA knockout strain (ΔlaeA) in different development phase. The deletion of laeA downregulated genes involved in oxidation- reduction process, alkaloid metabolic process, and transmembrane transport. We find the expression levels of seven secondary metabolism gene clusters (totally 28 clusters) were silenced inΔlaeA. This study provides the information that laeA function are required in conidiation and hydrolase activity of P. oxalicum.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and laeA knockout mutant strains in 24h and 60h in modified Czapek culture medium with 2% glucose as carbon resource. qRT–PCR validation was performed using SYBR Green assays.

first: Yuqi

last: Qin


title: LIN28A modulates splicing and gene expression programs in breast cancer cells

city: RTP

first: Trevor

last: Archer

address: 111 TW Alexander

institute: NIH

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

overall_design: Refer to individual Series


title: LIN28A modulates splicing and gene expression programs in breast cancer cells [RIP-Seq]

summary:
The goals of this study were to identify LIN28 downstream gene targets in breast cancer cells. We use a subclone of the MCF-7 breast cancer cell line, MCF-7M as our model system.
Methods: mRNA-protein complexes (mRNP) lysates were prepared from MCF-7M cells and incubated with Protein-A Sepharose beads (Sigma-Aldrich) and either LIN28 (Abcam) or control normal rabbit serum IgG antibodies. LIN28 interacting mRNAs were identified by whole genome sequencing.
Results: Using an optimized data analysis workflow, we mapped approximately 13 million sequence reads for LIN28-IP and CTL- IP (IgG), respectively to the to the human genome (build h19).
Conclusions: mRNA were significantly bound by LIN28 if LIN28 RIP had 2.5 fold increase in normalized reads compared to IgG. We found that LIN28 was predominantly bound at coding exons and 3'UTRs, 38% & 45% respectively, in the 843 mRNAs within MCF-7M genome.

overall_design: LIN28 mRNA enriched regions identified from LIN28/RNA complexes prepared from MCF-7M cells.


title: LIN28A modulates splicing and gene expression programs in breast cancer cells [RNA-Seq]

summary:
The goals of this study were to identify LIN28 downstream gene targets in breast cancer cells. We use a subclone of the MCF-7 breast cancer cell line, MCF-7M as our model system.
Methods: mRNA profiles from MCF-7M breast cancer cells treated with siRNA against non-targeting control (NT), LIN28, hnRNP A1, LIN28 and hnRNPA1 (LIN28A1) for 72 hrs were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped over 200 million sequence reads per sample to the human genome (build h19). Each of the four groups had two biological replicates. We developed a custom method to identify alternative splicing events and identified 111 genes with significant (FDR<0.05) differential splicing for LIN28 depleted cells compared to non-targeting siRNA control, as well as 249 and 182 genes for hnRNP A1 and LIN28A1 respectively. RNA-seq data were validated with by qRT–PCR analysis of a subset of genes.
Conclusions: Results reveal that LIN28 regulates alternative splicing and steady state mRNA expression of genes implicated in aspects of breast cancer biology. Notably, cells lacking LIN28 undergo significant isoform switching of the ENAH gene, resulting in a decrease in the expression of ENAH exon 11a isoform. Expression of ENAH isoform 11a has been shown to be elevated in breast cancers that express HER2.

overall_design: mRNA profiles of MCF-7M cells treated with siRNA for NT control, LIN28, hnRNP A1, and LIN28 plus hnRNP A1 (A1) (LIN28A1) were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000


title: RNA-SEQ of Satb1-knockdown in dopaminergic neurons from the mouse mid-brain

first: William

last: Shin

address: 1130 St Nicholas Ave

department: Systems Biology

summary: RNA-SEQ profiling of mouse dopaminergic neurons from the mouse mid-brain, with AAV1 injections using a Satb1 shRNA-EGFP construct or a scrambed shRNA-EGFP construct

overall_design: Murine midbrain dopaminergic neurons with Satb1 shRNA treatment or scrambled control

first: Lars

last: Brichta


title: Reporter Gene Silencing in Targeted Mouse Mutants is Associated with Promoter CpG Island Methylation

city: Oakland

first: David

middle: B

last: West

state: California

address: 5700 Martin Luther King Jr way

institute: CHORI

type: Methylation profiling by high throughput sequencing

summary: We report the generation and analysis of high-throughput DNA methylation profiles at nucleotide resolution in a subset of targeted gene trap mouse mutants. Using high-throughput sequencing of bisulfite treated DNA, we generated DNA methylation percentage for CpG islands, and LacZ (reporter) gene in mice with the apparent silencing of the targeted gene promoter reflected by reduced reporter mRNA level. These results were contrasted with findings for a set of mutants with no silencing or CpG methylation following targeted mutagenesis using the same gene trap vector. Our findings supports the hypothesis that presence of the exogenous DNA in the targeting vector may influence the expression of genes in close proximity or may lead to promoter silencing of the target where the promoter is marked by CpG methylation.

overall_design:
Examination of CpG methylation profiles in Knock-out and wild type mice

We evaluated targeted gene promoter silencing in a group of six mutants carrying the tm1a Knockout Mouse Project allele containing both a LacZ reporter gene driven by the native promoter and a neo selection cassette. Methylation of the promoter CpG islands and LacZ coding sequence were evaluated by sequencing of bisulfite-treated DNA. CpG Islands (samples labeled as CpG) and trans gene (samples labeled as LacZ) were amplified after Bisulfite treatment. Please note that the same gDNA was used to amplify CpG Island (Gene_CpG_KO ) and LacZ (Gene_LacZ_KO) reporter for the same gene. PCR product of amplification was gel separated, isolated and pooled. After libraries were prepared and sequenced, the alignment was performed. CpG island and LacZ alignments were done separately resulting in three different Processed Data files per gene investigated: Gene_CpG_KO, Gene_LacZ_KO and Gene_CpG_WT. LacZ reference is included in the submission, but is also available for download from KOMP Phenotype website (www.kompphenotype.org).

Also please note that the libraries were prepared using Illumina TruSeq RNA Sample Prep Kit starting from adapter binding step as samples were double stranded Bisulfite treated DNA amplicons. So the library preparation was done as with RNASeq, but samples investigated were bisulfite treated.

first: Julia

last: Kirov

first: Michael

last: Adkisson

first: AJ

last: Nava

first: Andreana

last: Cipollone

first: Brandon

last: Willis

last: Engelhard

first: K

last: Lloyd

first: Pieter

last: de Jong


title: LEF-1 and TCF-1 orchestrate T follicular helper (Tfh) cell differentiation by regulating Tfh differentiation circuits upstream of Bcl6

city: La Jolla

first: Shane

last: Crotty

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology


title: Runx1 deficiency decreases ribosome biogenesis and confers stress resistance to hematopoietic stem and progenitor cells

city: Philadelphia

first: Long

last: Gao

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

institute: The Children’s Hospital of Philadelphia

summary: The transcription factor RUNX1 is frequently mutated in myelodysplastic syndrome and leukemia. RUNX1 mutations can be early events, creating pre-leukemic stem cells that expand in the bone marrow. Here we show that, counter-intuitively, Runx1 deficient hematopoietic stem and progenitor cells (HSPCs) have a slow growth, low biosynthetic, small cell phenotype and markedly reduced ribosome biogenesis (Ribi). The reduced Ribi involves decreased levels of rRNA and many mRNAs encoding ribosome proteins. Runx1 appears to directly regulate Ribi; Runx1 is enriched on the promoters of genes encoding ribosome proteins, and binds the ribosomal DNA repeats. Runx1 deficient HSPCs have lower p53 levels, reduced apoptosis, an attenuated unfolded protein response, and accordingly are resistant to genotoxic and endoplasmic reticulum stress. The low biosynthetic activity and corresponding stress resistance provides a selective advantage to Runx1 deficient HSPCs, allowing them to expand in the bone marrow and outcompete normal HSPCs.

overall_design: Comparison of the phenotypic and molecular properties of normal (Runx1f/f, or WT) versus Runx1 deficient (Mut) hematopoietic stem cells.

first: Xiongwei

last: Cai

first: Li

last: Teng

first: Jingping

last: Ge

first: Zaw

last: Oo

first: Ashish

middle: R

last: Kumar

first: D

last: Gilliland

first: Philip

last: Mason

first: Kai

last: Tan

first: Nancy

middle: A

last: Speck


title: Impact of Lef1 overexpression on follicular helper T (Tfh) differentiation

summary: Comparison of transcriptome between GFP-RV+ Th1 cells and Lef1-RV+ Th1 cells

overall_design: B6 mice received GFP-RV+ or Lef1-RV+ LCMV gp specific TCRtg Smarta cells and were infected with LCMV. On four days after infection, splenocytes were collected to sort CXCR5- Th1 cells per genotype. Contributor: LIAI RNAi Center (LIAI)


title: Graded Expression Changes Determine Phenotype Severity In Mouse Models of CRX-Associated Retinopathy

city: St. Louis

last: Ruzycki

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

summary:
Background: Mutations in the cone-rod-homeobox protein CRX are typically associated with dominant blinding retinopathies with variable age of onset and severity. Five well-characterized mouse models carrying different Crx mutations show a wide range of disease phenotypes. To determine if the phenotype variability correlates with distinct changes in CRX target gene expression, we perform RNA-seq analyses on three of these models and compare the results with published data.
Results: Despite dramatic phenotypic differences between the three models tested, graded expression changes in shared sets of genes are detected.  Phenotype severity correlates with the down-regulation of genes encoding key rod and cone phototransduction proteins. Interestingly, in increasingly severe mouse models, the transcription of many rod-enriched genes decreases decrementally, whereas that of cone-enriched genes increases incrementally. Unlike down-regulated genes, which show a high degree of CRX binding and dynamic epigenetic profiles in normal retinas, the up-regulated cone-enriched genes do not correlate with direct activity of CRX, but instead likely reflect a change in rod cell-fate integrity. Furthermore, these analyses describe the impact of minor gene expression changes on the phenotype, as two mutants showed marginally distinguishable expression patterns but huge phenotypic differences, including distinct mechanisms of retinal degeneration.
Conclusions: Our results implicate a threshold effect of gene expression level on photoreceptor function and survival, highlight the importance of CRX in photoreceptor subtype development and maintenance, and provide a molecular basis for phenotype variability in CRX-associated retinopathies.

overall_design: All genotypes were analyzed in triplicate.  Heterozygous and homozygous mutants were all sequenced at P10, the control for which is the P10 C57BL6/J data.  Heterozygous mutants were also analyzed at P21, the control for which is the P21 C57BL6/J data.

first: Nicholas

middle: M

last: Tran

first: Alexander

last: Kolesnikov

first: Vladimir

last: Kefalov

first: Shiming

last: Chen


title: Lineage-Specific Chromatin Signatures Reveal a Master Lipid Switch in Microalgae

city: Walnut Creek

first: Chia-Lin

last: Wei

address: 2800 Mitchell Drive

department: Genomic Technologies

institute: DOE Joint Genome Institute

summary: Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify master regulators of lipid accumulation and decipher the regulation of lipid biosynthetic pathway, we performed an integrative chromatin signature and transcriptomic analysis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor PSR1 as a pivotal master switch that triggers cytosolic lipid hyper-accumulation an order of magnitude higher than stress regimens have achieved. Dissection of the PSR1 target network corroborates its central role in coordinating multiple stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a central regulator of algal lipid metabolism will facilitate targeted engineering strategies in microalgae.

overall_design:
1. Genome-wide H3K4me3 time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen starvation) was performed to determine time point to capture maximal chromatin changes.

2. Genome-wide H3K4me3, H3K27ac, H3K9me3, H3K27me3, H3K36me3 and Pol II profiling were performed at 0 hr, 1 hr after nitrogen starvation and 1 hr after sulfur starvation to determine chromatin signatures. Genome-wide H3K4me2 profiling was performed at 0 hr before starvation.

3. Transcriptome time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen and sulfur starvation separately) for chromatin signature characterization and integrative analysis.

4. Genome-wide PSR1 binding profiling was performed with polyclonal antibody against PSR1 peptide A region and PSR1 peptide B region individually. (At 30 min and 1 hr after nitrogen starvation, and 1 hr, 2 hr and 6 hr after sulfur starvation.)

Please note that the following reference genome and gene models used in these experiments are linked below;
C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz
reference_gene_model.gtf.gz
These are based off Phytozome (http://www.phytozome.net/) which does not provide access to earlier version data.

first: Chew Yee

last: Ngan

first: Chee-Hong

last: Wong


title: RNA-SEQ profiling of mouse whole midbrain and dopaminergic neurons from the mouse mid-brain

city: New York

first: William

last: Shin

institute: Columbia University

overall_design: Murine whole midbrain and murine midbrain dopaminergic neurons

first: Lars

last: Brichta

first: Mariano

last: Alvarez

first: Jack

last: Zhang

first: Andrea

last: Califano

first: Serge

last: Przedborski

first: Paul

last: Greengard


title: Identification of Hnf6 binding sites in male and female mouse liver

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: ∼40,000 HNF6 binding sites were identified in mouse liver chromatin, including several thousand sites showing significant differences in level of HNF6 binding between male and female mouse liver. These sex-biased HNF6 binding sites showed strong enrichment for sex-biased DNase hypersensitive sites and for proximity to genes showing local sex-biased chromatin marks and a corresponding sex-biased expression. ~90% of genome-wide CUX2 binding sites identified previously in female mouse liver (Conforto TL, Zhang Y, Sherman J, Waxman DJ., Mol Cell Biol. 2012;32(22):4611-4627) were also bound by HNF6, giving evidence for genome-wide competition between HNF6 and CUX2 for chromatin binding in female mouse liver.  These HNF6/CUX2 common binding sites were enriched for genomic regions more accessible in male than in female mouse liver chromatin, and showed strongest enrichment for male-biased genes, suggesting HNF6 displacement by CUX2 as a mechanism to explain the observed CUX2 repression of male-biased genes in female liver. However, HNF6 binding was sex-independent at a majority of its binding sites, and peak regions of HNF6 binding were frequently associated with co-binding by multiple other liver transcription factors, consistent with HNF6 playing a global regulatory role in both male and female liver.

overall_design: Livers were excised from individual male and female mice, cross-linked and sonicated, then used to identify HNF6 binding sites by ChIP-Seq using antibody specific to HNF6 (sc-13050; Santa Cruz Biotechnology, Inc).

first: Tara

last: Conforto

first: George

last: Steinhardt IV


title: A Novel Neuron-specific Histone H4K20 Demethylase LSD1n Promotes Transcriptional Elongation and is Essential for Learning and Memory

first: Yuliang

last: Tan

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

summary: LSD1n regulates transcriptional elongation by removing H4K20 methylation.

overall_design: Identification of genome-wide binding sites of LSD1, and examination of the histone modifications upon LSD1n deletion in primary cortical neurons

first: Michael

middle: G

last: Rosenfeld

first: Jianxun

last: Wang


title: Alternative splicing fine-tunes transcriptome and translatome in photomorphogenic Arabidopsis

status: Public on Jul 26 2015

city: Taipei

first: Chiung-Swey

middle: Joanne

last: Chang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica


title: Genome-wide Identification of CCA1 Targets Uncovers an Expanded Clock Network in Arabidopsis

city: Raleigh

first: Colleen

last: Doherty

state: NC

address: 128 Polk Hall CB7622

department: Biochemistry

institute: North Carolina State University

summary: The plant circadian clock exerts a critical role in the regulation of multiple biological processes including responses to biotic and abiotic stresses. It is estimated that the clock regulates up to 80% of the transcriptome in Arabidopsis, thus understanding the molecular mechanisms that control this rhythmic transcriptome requires identification of the targets of each clock component. The Arabidopsis core clock is partially comprised of a transcriptional regulatory loop between the MYB domain containing transcription factors CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB EXPRESSION1 (TOC1). As a key component of the clock, CCA1 is able to initiate and set the phase of clock-controlled rhythms. CCA1 regulates the transcription of several genes by directly binding to the evening element (EE) motif primarily found in the promoters of evening expressed genes. Using a genome-wide approach we have identified direct targets of CCA1 in plants grown in constant (LL) and driven conditions (LD). These CCA1 targets are enriched for a myriad of biological processes and stress responses. While many of these target genes are evening phased and contain the EE in their promoter regions, a significant subset is morning phased and lack an EE. Furthermore, several CCA1 targets do not cycle in either LL or LD or both. Expression analysis in CCA1 overexpressing plants confirms CCA1 regulation of analyzed targets. Our results emphasize an expanded role for the circadian clock in regulation of key pathways in Arabidopsis, and provide a comprehensive and solid resource for future functional studies.

overall_design: ChIP-Seq of CCA1-GFP plants under control of the CCA1 promoter in continuous light and diel conditions


title: RNA-SEQ profiling of dopaminergic neurons from the mid-brain of mice that received intraperitoneal injections of MPTP

state: NY

summary: RNA-SEQ of dopaminergic neurons from the mid-brain of mice that received one daily intraperitoneal injection of MPTP-HCl (30 mg/kg free base per day) or saline for five consecutive days. Samples were taken 4 days.

overall_design: Murine midbrain dopaminergic neurons that were treated with MPTP-HCl


title: DNF7 is required for the persistence of rhizobia in the nitrogen fixation zone

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

summary: We compare the transcription profile Using Solid5500XL-S system between the  wild-type A17 and DNF7 null mutant Medicago truncatula genontype after 17 days of inoculation with S. meliloti WSM419.

overall_design: RnaSeq analysis were performed in A17 and 6V genotype

first: Beatrix

last: Horváth

first: Ágota

last: Domonkos

last: Kereszt

first: Edit

last: Ábrahám

first: Ferhan

last: Ayaydin

first: Károly

last: Bóka

first: Yuhui

last: Chen

first: Rujin

first: Jeremy

last: Murray

last: Udvardi

first: Éva

last: Kondorosi

first: Péter

last: Kaló


title: Alternative splicing fine-tunes transcriptome and translatome in photomorphogenic Arabidopsis [seq]

summary: Light is a pivotal signal for plants’ growth and survival.  The promptly responses are required and achieving by sophisticated transcriptomic adjustments, the promptly translation enhancement, and effective protein surveillance.  However, the global role of alternative splicing regulations in response to the light is unknown.  Through global surveys of alternative splicing profile and frequency calculation for individual events normalized to transcriptomic changes, we identify nearly half of transcript present at this stage are alternatively spliced.  Through the unbiased event comparison in D and L4h mRNA, we reveal a clear impact of splicing control on 2,961 genes during early photomorphogenesis.  Intron retention is the most frequently event under controls of light as discovered in other developmental tissues and stages of Arabidopsis.  Cryptic exon is the most abundant event preserved only in the dark-grown Arabidopsis.  Genes underlying the splicing and transcriptional control mostly not overlapped indicate the distinct impacts of two regulatory mechanisms.  Through confirmation with a homemade microarray for their responsiveness of light, we conclude 1,792 genes as biological validated candidates.  Through functional study for genes underlying light-mediated splicing controls, we explore new light-signaling components which mainly responsive in isoform abundance but steady state mRNA.  Among examination both positive (RPR39, KH-RBP, RRM and RRC1) and negative (PIF4, AMI1, DNAJ, UKL3, TF-IIs-like, and ubknown-Golgi protein) factors are controlled by splicing.  Through predictions for example isoform structures, PIF4-IR4, AMI1-IR7-IR8, and DNAJ-IR1 both possess PTC and possibly produce truncated coding protein.  PIF4-IR4 becomes best illustration for the dysfunction for the negative regulator by light.  Above PTC+ isoforms together with one third of retained introns translate that evident for NMD-insensitive retained introns and supplements for protein levels.  The event identities and cis-motif signatures associated with light regulations confirm a given uniqueness for the gene expression regulation during Arabidopsis photomorphogenesis.

overall_design: mRNA and polysome-associated mRNA of 4 days old Arabidopsis seedling grown under the dark or with 4 h light-treatment were isolated and the transcriptome and splicing events profiles were surveyed by mRNAseq.  Independent 3 biological replicates of dark and L4h mRNA were applied for two-color-microarray using custom designed alternative-splicing array from Agilent Technologies.

first: Shu-Hsing

last: Wu


title: Treatment of prostate cancer cells with S-adenosylmethionine leads to genomewide alterations of transcription profiles.

status: Public on Jul 25 2015

city: Goettingen

first: Andreas

last: Leha

address: Humboldtallee 32

department: Medical Statistics

institute: University Medical Center Goettingen

summary: The analysis investigates the impact of methyl donor S-adenosylmethionin on transcription and methylation profiles of prostate carcinoma cells.

overall_design: PC-3 cells (Prostatecarcinoma cells) were treated with 160 micromolar S-adenosylmethionine or vehicle

first: Thomas

last: Schmidt

last: Lingner

first: Gabriela

last: Salinas-Riester


title: Regulatory T cells from colonic lamina propria [RNA-Seq]

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: The colonic lamina propria contains a distinct population of Foxp3+ T regulatory cells (Tregs) that modulate responses to commensal microbes. Analysis of gene expression revealed that the transcriptome of colonic Tregs is distinct from splenic and other tissue Tregs. Rorγ and Helios in colonic Tregs mark distinct populations: Rorγ+Helios- or Rorγ-Helios+ Tregs. We uncovered an unanticipated role for Rorγ, a transcription factor generally considered to be antagonistic to Foxp3. Rorγ in colonic Tregs accounts for a small but specific part of the colon-specific Treg signature.

overall_design: Nrp1- Tregs were sorted from Foxp3-cre.Rorcfl/fl mice, which have a Treg-selective deletion of Rorc, or paired WT littermates. For low-input RNAseq, 1,000 TCRb+CD4+YFP(Foxp3)+Nrp1- cells were double-sorted into Trizol, RNA extracted and reverse-transcribed using ArrayScript (Ambion). To reduce variability at least three replicates were generated.

first: Esen

last: Sefik

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: A Molecular Portrait Of High-Grade Ductal Carcinoma In Situ (DCIS) [RNA-seq]

city: Smithville

first: C. Marcelo

last: Aldaz

address: POB 389

department: Molecular Carcinogenesis

institute: The University of TX M.D. Anderson Cancer Center

summary: DCIS is a non-invasive precursor lesion to invasive breast carcinoma. We still have no understanding on why only some DCIS lesions evolve to invasive cancer while others appear not to do so during the life span of the patient. Here, we performed full exome (tumor vs. matching normal), transcriptome and methylome analysis of 30 pure high-grade DCIS (HG-DCIS) and 10 normal breast epithelial samples. Sixty two percent of HG-DCIS cases displayed mutations affecting cancer driver genes or potential drivers. Mutations were observed affecting PIK3CA (21% of cases), TP53 (17%), GATA3 (7%), MLL3 (7%) and single cases of mutations affecting CDH1, MAP2K4, TBX3, NF1, ATM and ARID1A. Significantly, 83% of lesions displayed numerous large chromosomal copy number alterations, suggesting they might precede selection of cancer driver mutations. Integrated pathway-based modeling analysis of RNA-seq data allowed us to identify two DCIS subgroups (DCIS-C1 and DCIS-C2) based on their tumor intrinsic subtypes, proliferative, immune scores and in the activity of specific signaling pathways. The more aggressive DCIS-C1 (highly proliferative, basal-like or ERBB2+) displayed signatures characteristic of activated Treg cells (CD4+/CD25+/FOXP3+) and CTLA4+/CD86+ complexes indicative of a tumor-associated immune suppressive phenotype. Strikingly, all lesions showed evidence of TP53 pathway inactivation. Similarly ncRNA and methylation profiles reproduce changes observed post-invasion. Among the most significant findings we observed upregulation of lncRNA HOTAIR in DCIS-C1 lesions and hypermethylation of HOXA5 and specific SOX genes. We conclude that most HG-DCIS lesions, in spite of representing a pre-invasive stage of tumor progression, displayed molecular profiles indistinguishable from invasive breast cancer.

overall_design:
RNAs from 25 out of 30 (83%) pure HG-DCIS and 10 normal breast organoids (total 35 samples) were subjected to RNA-Seq analysis by using Illumina HiSeq2000 platform

Please note that description of samples employed for the NGS analyses including age, race, ER/PR immunohistochemistry results, ITIL/STIL scores and PAM50 classification is provided the 'Supplementary Data1_Samples data.xlsx' (available on Superseries record)

first: C

first: M

middle: C

last: Abba


title: Regulatory T cells from colonic lamina propria

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

overall_design: Refer to individual Series


title: A Molecular Portrait Of High-Grade Ductal Carcinoma In Situ (DCIS)

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

Description of samples employed for the subseries NGS analyses including age, race, ER/PR immunohistochemistry results, ITIL/STIL scores and PAM50 classification is provided in the 'Supplementary Data1_Samples data.xlsx'.


title: A Molecular Portrait Of High-Grade Ductal Carcinoma In Situ (DCIS) [RRBS-seq]

overall_design:
DNA from 24 out of 30 (80%) HG-DCIS samples and 5 normal breast organoids (total 29 samples) were subjected to reduced representation bisulfite sequencing analysis (RRBS) by using Illumina HiSeq2000 platform.

Please note that description of samples employed for the NGS analyses including age, race, ER/PR immunohistochemistry results, ITIL/STIL scores and PAM50 classification is provided the 'Supplementary Data1_Samples data.xlsx' (available on Superseries record)


title: Transciptional response to acute thermal stress in Chinook salmon

city: Davis

first: Bernie

last: May

state: CA - California

address: 1 Shields Avenue

department: Animal Science

institute: UC Davis

summary: Thermal stress is a serious and growing challenge facing Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and poses a threat to dwindling salmon populations. In order to better understand how acute thermal stress affects the biology of salmon, we performed a transcriptional analysis of gill tissue from unacclimated Chinook juveniles exposed to short periods at water temperatures ranging from ideal to potentially lethal. Reverse transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified.

overall_design: Fifty-five fish were randomly assigned to one of five treatment groups and were allowed to acclimate at 12 degrees C in the experimental chambers overnight. Treatments consisted of a three-hour water bath at 15 degrees C, 18 degrees C, 21 degrees C or 25 degrees C degrees, followed by one hour of recovery at 12 degrees C. The experimental chambers were moved to water baths held at a constant temperature, facilitating very rapid change in the temperature experienced by the fish. Controls were handled identically to the other four treatment groups, but remained at 12 degrees C. Three replicates were performed on consecutive days. RNA from the 11 individuals in each treatment group were proportionally pooled and used to create 15 illumina libraries.

first: Katharine

last: Tomalty

first: Melinda

last: Baerwald

first: Gonzalo

last: Rincon

first: Mariah

middle: H

last: Meek

first: Nann

last: Fangue


title: H3K4me3 Epigenomic Landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells

status: Public on Jul 24 2015

city: Beijing

first: Yusi

last: Fu

address: biopic,PKU

institute: PKU

summary: Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) is a powerful tool to dissect global epigenetic landscapes of cells. However, this method usually consumes millions of cells. Here we develop a robust technique for performing ChIP-Seq using as low as 1,000 cells. This method combines a semi-automatic nanoliter ChIP reaction with a carrier-based sequencing library preparation strategy without pre-amplifying the ChIP product. We used this method to investigate the pattern of trimethylation of histone 3 lysine 4 (H3K4me3) of mouse post-implantation epiblast cells at embryonic day 6.5 (E6.5) and showed that it is more similar to that of mouse Epi-Stem cells (mEpiSCs) than that of mouse Embryonic Stem cells (mESCs). Together with the high similarity between the transcriptomes of EpiSCs and E6.5 epiblast cells, this suggests that mEpiSCs is a reliable in vitro model for post-implantation epiblast cells in vivo.

overall_design: Use 1 million mEpiSCs and 1million mESCs as the positive control,  1000 mEpiSC and 1000 mESCs samples are used to validate the protocol.  1000 mEpiblasts have two biological replicates

first: Yanyi

last: Huang

first: Fuchou

last: Tang


title: RNA-SEQ profiling of dopaminergic neurons from the substantia nigra pars compacta and ventral tegmental area regions of the mouse mid-brain

first: William

last: Shin

overall_design: Murine midbrain dopaminergic neurons from the SNpc and VTA regions

first: Lars

last: Brichta

first: Mariano

last: Alvarez

first: Andrea

last: Califano

first: Serge

last: Przedborski

first: Paul

last: Greengard


title: Transcriptome analysis of early differentiating Tfh vs Th1 cells

first: Shane

last: Crotty

summary: Comparison of transcriptome between early Tfh vs. early Th1 cells

overall_design: Blimp-1-YFP LCMV gp specific TCRtg Smarta cells were transferred into B6 mice, which were then infected with LCMV Armstrong. On day 3 after infection, splenocytes were stained to sort Blimp-1-YFP+IL-2Ra+ Th1 cells or Blimp-1-YFP-IL-2Ra- Tfh cells for RNAseq analysis. Contributor: LIAI RNAi center (LIAI)


title: Genome-wide chromatin-immunoprecipitation studies of purified SAN cells reveals critical direct targets of ISL1 and suggests potential co-factor families for ISL1 action in SAN cells

status: Public on Jul 23 2015

city: Milan

first: Paola

last: Cattaneo

address: Via Fantoli 16/15

department: Institute of Genetic and Biomedical Research

country: Italy

institute: National Research Council of Italy

summary: Understanding factors that drive development and function of the sinoatrial node (SAN) is crucial to development of potential therapies for sinus arrhythmias, including potential generation of biological pacemakers. Here, we identify a key cell autonomous role for the LIM homeodomain transcription factor ISL1 for survival, proliferation and function of pacemaker cells throughout development. Chromatin immunoprecipitation assays performed utilizing antibody to ISL1 in chromatin extracts from FACS purified SAN cells demonstrated that ISL1 directly binds genomic regions within several genes critical for normal pacemaker function, including subunits of the L-type calcium channel, Ank2, and Tbx3. Other genes implicated in abnormal heart rhythm in humans were also direct downstream targets of ISL1 in SAN cells. Our studies represent the first in vivo ChIP-seq studies for SAN cells which provide a basis for further exploration of factors critical to SAN formation and function and highlight the potential for utilization of ISL1 in combination with other SAN transcription factors for generating pacemaker cells for therapy or drug screening purposes.

overall_design: ISL1 ChIP-seq profiling was performed in Hcn4-H2BGFP SAN cells purified from neonatal hearts.

first: Nathanael

last: Spann

first: Xingqun

last: Liang

first: Qingquan

last: Zhang

first: Xiaohui

last: Gong

first: Shaowei

last: Zhuang

first: Christopher

middle: K

last: Glass

first: Ju

last: Chen

first: Yunfu

last: Sun

first: Sylvia

last: Evans


title: Regulation of B cell early development by CNOT3

city: Kisarazu

first: Osamu

last: Ohara

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Technology Development

country: Japan

institute: Kazusa DNA Research Institute

summary: The CCR4-NOT complex, bearing poly(A) deadenylation activity, is a highly conserved regulator that is involved in biological control; however its action mechanisms and physiological targets remain unclear. Using genetic deletion of the CNOT3 subunit of this complex in early B cell progenitors, we show that CNOT3 plays a critical role in pro- to pre-B cell transition. CNOT3 participated in controlling germline transcription, compaction of the immunoglobulin heavy chain (Igh) locus, and Igh rearrangement, and in destabilizing tumor suppressor p53 mRNA. Moreover, by genetic ablation of p53 or introduction of pre-rearranged Igh transgene, the B cell developmental defect in the Cnot3 knockout background could be partly rescued, suggesting that CCR4-NOT complex exerts critical control in B cell differentiation processes by co-utilizing transcriptional and post-transcriptional mechanisms.

overall_design: Pro-B cells mRNA profiles of Mb1(cre/+) and Cnot3(fl/fl)Mb1(cre/+) mice were generated by deep sequencing using Illumina HiSeq 1500

first: Takehi

last: Inoue

first: Atsushi

last: Hijikata

first: Takaho

last: Endo

first: Yoko

last: Fukuda-Yuzawa

first: Taro

last: Fukao

first: Tomohiro

last: Kurosaki


title: Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

summary: CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in mutually exclusive manners in DNA binding and transcriptional regulation. Here we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells. In summary, we discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells

overall_design:
Genome-wide mapping of CTCF and BORIS occupancies in both germ and cancer cells.
ChIP-seq and expression profiling by high throughput sequencing

first: Victor

last: Lobanenkov


title: Genome-wide mRNA expression analyses revealed dysregulation of  genes important for SAN function in Hcn4-CreERT2;Isl1 mutants.

first: Paola

last: Cattaneo

summary: Understanding factors that drive development and function of the sinoatrial node (SAN) is crucial to development of potential therapies for sinus arrhythmias, including potential generation of biological pacemakers. Here, we identify a key cell autonomous role for the LIM homeodomain transcription factor ISL1 for survival, proliferation and function of pacemaker cells throughout development. Analysis of several Isl1 mutant mouse lines, including one in which Isl1 was specifically ablated in SAN (Hcn4- CreERT2;Isl1) revealed an early requirement for Isl1 within SAN for embryonic viability. RNA-seq analyses on FACS purified SAN cells revealed dysregulation of a number of genes critical for SAN function to be downstream of ISL1 in Hcn4-CreERT2;Isl1 mutants, including transcription factors and ion channels. Our studies demonstrated that ISL1 regulated approximately one third of genes that were significantly expressed in SAN, and highlight the potential for utilization of ISL1 in combination with other SAN transcription factors for generating pacemaker cells for therapy or drug screening purposes. Results also suggest Isl1 as a candidate gene for sick sinus syndrome.

overall_design: RNA-seq analyses were performed on samples from Hcn4-CreERT2;Isl1 mutant and control SANs

first: Xingqun

last: Liang

first: Alexander

last: Zambon


title: De Novo Transcriptomic Analysis of a High Lipid-producing Mutant in the Green Alga Dunaliella tertiolecta through RNA-Seq

city: Singapore

first: Lina

last: Yao

address: 5 Science Drive 2

department: Department of Microbiology and Immunology

country: Singapore

institute: National University of Singapore

summary:
Background: For many years, increasing demands for fossil fuels have met with limited supply. As a potential substitute and renewable source of biofuel feedstock, microalgae have received significant attention. However, few of the current algal species produce high lipid yields to be commercially viable. To discover more high yielding strains, next-generation sequencing technology is used to elucidate lipid synthetic pathways and energy metabolism involved in lipid yield. When subjected to manipulation by genetic and metabolic engineering, enhancement of such pathways may further enhance lipid yield.

Results: In this study, transcriptome profiling of a random insertional mutant with enhanced lipid production generated from a non-model marine microalga Dunaliella tertiolecta is presented. D9 mutant has a lipid yield that is 2-4 fold higher than that of wild type. Using novel Bag2D-workflow scripts developed and reported here, the non-redundant transcripts from de novo assembly were annotated based on the best hits in five model microalgae, namely Chlamydomonas reinhardtii, Coccomyxa subellipsoidea C-169, Ostreococcus lucimarinus, Volvox carteri, and Chlorella variabilis NC64A. The assembled contigs (~181 Mb) includes 481,381 transcripts, covering 10,185 genes. Pathway analysis showed that a pathway from inositol phosphate metabolism to fatty acid biosynthesis is the most significantly correlated with higher lipid yield in this mutant.

Conclusion: Herein, we described a pipeline to analyze RNA-Seq data without pre-existing transcriptomic information. The draft transcriptome of D. tertiolecta was constructed and annotated, which offered useful information for characterizing high lipid-producing mutants. D. tertiolecta mutant was generated with an enhanced photosynthetic efficiency and lipid production. RNA-Seq data of the mutant and wild type were compared, providing biological insights into the expression patterns of contigs associated with energy metabolism and carbon flow pathways. Comparison of D. tertiolecta genes with homologs of five other green algae can facilitate the annotation of D. tertiolecta, and lead to a more complete annotation of its sequence database, thus laying the groundwork for optimization of lipid production pathways based on genetic manipulation.

overall_design:
Examine two sets of RNA-Seq data from high lipid-producing mutant and wild-type sample

Dt_v1*: the FASTA and annotation files used for D9_1, WT_1 samples
Dt_v10*: the FASTA and annotation files used for D9_2, WT_2 samples
Dt_v10-hit*: the FASTA and annotation files only including the contigs that can be annotated in Dt_v10
Additional file 1.xls: processed data for sample 1,2
Additional file 4.xls: processed data for sample 3-6

first: Tin

middle: W

last: Tan

first: Yi-Kai

last: Ng

first: K

last: Ban

first: Hui

last: Shen

first: Huixin

last: Lin

first: Yuan

last: Lee


title: Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: Novel protein-coding genes, intra-species sequence variations, and trans-spliced RNA leaders

city: Shanghai

first: Kaile

last: Zhang

address: No. 600 Yishan Road

department: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

institute: Shanghai Jiao Tong University

summary: The appendicularian, Oikopleura dioica, is a marine or planktonic tunicate that has a swimming tadpole shape through its entire life. For several reasons, this animal possesses advantages as a model organisms: (1) It has a short life cycle (about 5 days at 20℃); (2) Its development is rapid and it completes organogenesis within 10 hour of post-fertilization to form functional body; (3) its morphogenesis and cell linages are well-described; (4) live imaging of embryos by introducing fluorescent protein mRNAs is feasible; (5) RNAi method is available for knockdown of zygotic mRNA as well as maternal mRNAs in the ovary and eggs. (6) It has a compact and sequenced genome of 70 Mb, the smallest ever found in chordate. The number of genes is estimated as approximately 18,000, indicating a high gene density (one gene per 5 kb in the genome). These features make O. dioica a useful organism to study development and genome plasticity in tunicate with short generation time, namely, rapidly evolving chordate lineage.

overall_design: Two stages: egg and larvae, two biological replicates

first: Kai

last: Wang

first: Tatsuya

last: Omotezako

first: Kanae

last: Kishi

first: Hiroki

last: Nishida

first: Takeshi

last: Onuma


title: 14-3-3ζ controls adipocyte progenitor cell cycle and differentiation via Gli3-dependent p27Kip expression

city: Montreal

first: Gareth

last: Lim

state: Quebec

address: R08.482- 900 rue St Denis

institute: CRCHUM

summary: 14-3-3 proteins facilitate cytoplasmic-nuclear shuttling of transcription factors.Adipocyte differentiation requires the function of critical transcription factors to drive the development of a mature adipocyte. The aim of the study was to investigate if 14-3-3ζ is required for the adipogenic transcriptional program.

overall_design: Examination of the transcriptome in siCon- and si14-3-3ζ-transfected 3T3-L1 cells undergoing differentiation at t=0, 24, and 48 hours.

first: James

middle: D

last: Johnson


title: Analysis of differences in the transcriptome of WAT from Wildtype and 14-3-3zeta knockout mice

summary: Due to inherent differences in adipcoyte size between wildtype and knockout animals, we sought to examine if the decrease in adipocyte size was due to differences in the transcriptome and more specifcially, adipogenic genes.

overall_design: Examination of the transcriptome in wildtype (WT) and knockout (KO) gonadal white adipose tissue from adult mice


title: MicroRNA-203 represses selection and expansion of oncogenic HRas transformed tumor initiating cells [seq]

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Colorado School of Medicine

summary: In many mouse models of skin cancer, only a few tumors typically form although many cells competent for tumorigenesis receive the same oncogenic mutations. These observations suggest a selection process for defining tumor initiating cells. Here we use quantitative mRNA- and miR-Seq to determine the impact of HRasG12V on the transcriptome of keratinocytes. We discover that microRNA-203 is downregulated by HRasG12V. Using a knockout mouse model, we demonstrate that loss of microRNA-203 promotes selection and expansion of tumor-initiating cells. Conversely, restoration of microRNA-203 with an inducible model potently inhibits proliferation of these cells. We comprehensively identify microRNA-203 targets required for HRas-initiated tumorigenesis. These targets include important effectors of the Ras pathway and essential genes required for cell division. Together, this study establishes a role for the loss of microRNA-203 in promoting selection and expansion of HRas mutated cells and identifies a mechanism through which microRNA-203 antagonizes HRas-mediated tumorigenesis.

overall_design: Identifying mRNA and microRNA networks regulated by oncogenic HRasG12V in primary keratinocytes through the use of 3Seq and small-RNA-Sequencing. Additionally we utilize ribosome-profiling, 3Seq, Microarray and Ago2-HITS-CLIP approaches to identify novel miR-203 target genes.

first: Rui

last: Yi


title: Genome-wide ChIP-seq binding profiles and linked gene expression arrays

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge


title: RGA binding sites in Arabidopsis thaliana seedlings

city: Heidelberg

first: Jan

last: Lohmann

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies Heidelberg

country: Germany

institute: University Heidelberg

summary: DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis.

overall_design: Provided are 3 biological replicates analysing RGA binding sites in Arabidopsis seedlings. ChIP-seq was performed on plants expressing RGA-GFP under the native RGA promoter and on non-transgenic control plants as reference

first: Nora

last: Marín-de la Rosa

first: Anne

last: Pfeiffer

first: Kristine

last: Hill

first: Antonella

last: Locascio

first: Rishikesh

middle: P

last: Bhalerao

first: Pal

last: Miskolczi

last: Grønlund

first: Aakriti

last: Wanchoo-Kohli

first: Stephen

last: Thomas

first: Malcolm

middle: J

last: Bennett

middle: U

first: Miguel

last: Blázquez

first: David

last: Alabadí


title: Chromatin marking is associated to transcriptional stability during fly development

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

summary: We have conducted ChIP-Seq and RNA-Seq analyses in order to perform a comparative study between wing imaginal discs and eye imaginal discs from Drosophila melanogaster.

overall_design: Examination of several histone modifications and gene expression quantification in wing/eye imaginal discs cells

first: Sílvia

last: Perez-Lluch

first: Hagen

last: Tilgner

first: Joao

last: Curado

first: Montse

last: Corominas

first: Roderic

last: Guigó


title: Transcriptional activation without chromatin marking in developmentally regulated genes

overall_design: Refer to individual Series