title: Genome-wide identiﬁcation of circular RNAs in Arabidopsis thaliana

status: Public on Sep 01 2016

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: To exlore more circRNAs involved in Arabidopsis thaliana, we deeply sequenced 14 samples including whole plants from four developmental stages (rosette leaves > 1 mm in length; rosette growth complete; 50% of flowers to be produced have opened; first silique shattered), aerial part of plants from four stress treatments (control, drought, salinity and heat), five organs (roots, stems, leaves, flowers and siliques) and a mixed sample from whole plants across the lifespan (cotyledons emergence, rosette leaves﹥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and paired-end (PE) sequenced by Illumina HiSeq 2500 (read length, PE125, the mixed sample) and Illumina Hiseq X Ten (read length, PE150, 13 independent samples) platforms. We obtained 181.97 Gb raw data (151.37 Gb from 13 samples and 30.6 Gb from a mixed sample) and identified 5861 circRNAs with expression quantity. We annotated the parent genes of these circRNAs and predicted their target sites of microRNAs.

overall_design: A genome-wide identiﬁcation and analysis of circRNAs in Arabidopsis thaliana were performed using the Illumina HiSeq 2500 and Illumina Hiseq X Ten platforms.

first: Gang

last: Chen

first: Jiawen

last: Cui

first: Zhaogeng

last: Lu


title: Comparative Physiological and Transcriptome Profiling of Grapevine Rootstocks Identified Their Physiological Adaptations and Gene Regulation  Networks behind Drought Tolerance

status: Public on Oct 25 2016

city: tokat

first: Kubilay

last: Yıldırım

address: tasliciftlik kampusu

country: Turkey

institute: gaziosmanpasa university

summary: Since the roots of grapevine rootstocks have a direct contact with drying soil and has an important role in abiotic stimuli, any plasticity on the architecture of the rootstocks would enable grapevine varieties to a better respond to drought stress. However, genomics evidences behind the physiological responses of rootstocks under prolonged drought stress are poorly documented in the literature. In the current study, eight widely used hybrid grapevine rootstocks in viticulture were firstly grafted with sultana seedless and subjected to drought stress to test their physiological and biochemical responses. The results of experiment indicated that the roots of V.rupestris X V.berlandieri (110 R, 1103P, 140 Ru) rootstocks possessed much higher water content as well as non-structural carbohydrate and nitrogen concentrations compared to V.riparia X V.berlandieri (SO4, 5BB, 420A, 8B) and V.vinifera X V.berlandieri (41B) hybrids under drought. V.rupestris X V.berlandieri hybrids were also performed much higher root elongation performance under drought compared to other rootstock hybrids. Three rootstock varieties (110R, 5BB and 41B) having different pedigrees and root architectural responses to drought were also investigated at transcriptome level to find out gene regulation network behind differential physiological responses to drought. Transcriptome analysis revealed 2795, 1196 and 1612 differentially expressed transcripts for the roots of 110R, 5BB and 41B, respectively.  The highest expression increases in 110R compared to other rootstocks were recorded for the transcripts functional in carbohydrate (SWEET14, CWINV) and nitrate/peptide (NRT1/ PTR FAMILY) transportation as well as osmoregulation (dehydrins, osmotins, LEAs and proline-glycine rich proteins) during drought. Higher induction of these genes in the roots of tolerant 110R genotype indicated importance of efficient uptake of carbohydrate and nitrogen source released from canopy under drought and preservation of water with osmotic regulation on the root elongation and drought tolerance of grapevines. Expression increases in several other pathogenesis related proteins, regulation of cell wall modification enzymes and activity of several secondary metabolites have been also associated to altered root architecture and drought tolerance in the grapevine rootstocks for the first time with the current study.

sample_organism: Vitis cinerea var. helleri x Vitis rupestris

sample_organism: Vitis cinerea var. helleri x Vitis vinifera

sample_organism: Vitis cinerea var. helleri x Vitis riparia

overall_design: Total RNA used in microarray experiment was isolated from the roots of grafted 110R, 5BB and 41B rootstocks.  Total RNA used in the microarray experiment was isolated from the roots of plants grown under well watered and drought treated conditions.  RNA isolation was made according to Lithium chloride precipitation method described in Chang et al. (1993). Roots of two replications were used in RNA isolation (biological replicates) for the plants and each isolated RNAs loaded onto one Affymetrix vitis Geneome arrays (technical replicates). Totally, 12 GeneChips (three different root tissue  × 2 different water availibility × 2 biological replicates) were used for transcriptional analysis.

last: YILDIRIM

first: Adem

last: Yağcı

first: Seda

last: Sucu


title: Pluripotent Reprogramming of Human AML Resets Leukemic Behavior and Models Therapeutic Targeting of Subclones

status: Public on Nov 14 2016

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary:
Understanding the contribution of abnormal genetic and epigenetic programs to acute myeloid leukemia (AML) is necessary for the integrated design of targeted therapies. To investigate this, we determined the effect of epigenetic reprogramming on leukemic behavior by generating induced pluripotent stem cells (iPSCs) from AML patient samples harboring MLL rearrangements. AML-derived iPSCs (AML-iPSCs) retained leukemic mutations, but reset leukemic DNA methylation/gene expression patterns and lacked leukemic potential. However, when differentiated into hematopoietic cells, AML-iPSCs reacquired the ability to give rise to leukemia in vivo and reestablished leukemic methylation/gene expression patterns, including an aberrant MLL signature, indicating that epigenetic reprogramming was insufficient to eliminate leukemic behavior. In one case, we identified distinct AML-iPSC KRAS mutant and wildtype subclones that demonstrated differential growth properties and therapeutic susceptibilities, predicting KRAS wildtype clonal relapse due to increased cytarabine resistance. Increased cytarabine resistance was further observed in a cohort of KRAS wildtype MLL-rearranged AML samples, demonstrating the utility of AML-iPSCs in predicting subclonal relapse and facilitating clonal targeting in AML.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Mouse embryonic heart transcriptomic response to Ddc (Ddc_exon1a isoform) ablation

status: Public on Oct 05 2016

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

summary: Analysis of gene expression in mouse E15.5 embryonic heart tissue, either wildtype, Ddc-/+ (maternal transmission of Ddc^Gt(OST129277)Lex knockout allele), Ddc+/- (paternal transmission), or Ddc-/-.

overall_design:
A single experiment involving 12 samples: 3x wildtype, 4x Ddc-/+ (MatKO), 4x Ddc+/- (PatKO), 1x Ddc-/- (KO)
----------------------------------------------------------
NIHR BRC Genomics Facility at Guy's Hospital

first: Adam

last: Prickett

first: Rebecca

last: Oakey

first: Scott

last: Baldwin


title: Low H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas

status: Public on Nov 23 2016

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

institute: University of Michigan

summary: A subgroup of  Posterior fossa ependymomas show reduced H3K27me3, global DNA hypomethylation, are more invasive, exhibit poor prognosis and epigenetically deregulated genes converge on radial glial factors, suggesting developing cerebellar radial glia as candidate cells-of-origin.

overall_design: RNA-sequencingwas performed  in 15 posterior fossa (PF) ependymoma samples. 11 samples show low H3K27me3 and designated PF_H3K27me3-ve; 4 samples show high H3K27me3 and designated PF_H3K27me3+ve

first: Marcin

last: Cieslik


title: A resource for systems analysis of transcriptional modules involved in drought response in rice

status: Public on Jul 20 2016

city: Fayetteville

first: Chirag

last: Gupta

state: AR

address: 115 Plant Sciences Building

department: Crop Soil and Environmental Sciences

institute: University of Arkansas

summary:
The severity of impact of drought on crops is contingent on the developmental stage of the plant, with the most sensitive stage being the reproductive stage. Hence, gene expression profiling has been used to understanding drought response and resistance mechanism in rice.
Here we present drought transcriptomes of rice in three developmental stages and gain insights into the processes and regulatory mechanisms involved in common and stage specific drought responses.

overall_design: Total RNA was isolated from the rice seedlings, vegetative (V4) and reproductive (R4) tissues of both control and stress treated plants for hybridization on Affymetrix microarrays. Two independent replicates for seedling and reproductive stages, and three replicates for vegetative stages were generated, for both control and stress samples. For drought treatments, plants were gradually subjected to field drought conditions in order to reach 50% field capacity (FC) by regulating water supply, whereas control plants were maintained at 100% FC.

first: Andy

last: Pereira


title: Transcriptomics of single-cell and bulk sorted and micro-dissected mouse bone marrow, fetal liver and small intestine crypt cells

status: Public on Nov 01 2016

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

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


title: Characterization of the small RNAs of Volvox carteri associated with an Argonaute protein

status: Public on Jul 01 2016

city: Munich

first: Anne

last: Dueck

state: Bavaria

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: TUM

summary: The green alga Volvox carteri is a model organism for the development of multicellularity. It has a spherical shape with a complete division of labor between around 2000 somatic cells and 16 reproductive cells. When comparing Volvox with its unicellular relative Chlamydomonas rheinhardtii, one striking observation is the similarity in the protein coding genes [1]. Additionally, Baulcombe and colleagues showed that Chlamydomonas contains functional RNAi and miRNA machineries [2].   We deep sequenced small RNAs associated with one Argonaute protein of the female Volvox strain Vol6 during its vegetative growth phase. Using these data, we established a miRNA identification pipeline that takes into account plant miRNA feature in general and also uses parameters employed in finding miRNAs in Chlamydomonas. Other small RNAs that are functionally incorporated into Ago are characterized.    1. Prochnik, S.E., et al., Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science, 2010. 329(5988): p. 223-6.  2. Molnar, A., et al., miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature, 2007. 447(7148): p. 1126-9.

overall_design: Examination of small RNAs bound to an Argonaute protein of Volvox carteri

first: Maurits

last: Evers

first: Stefan

middle: R

last: Henz

first: Norbert

last: Eichner

first: Katharina

last: Unger

first: Eugene

last: Berezikov

first: Stephan

last: Wenzl

first: Detlef

last: Weigel

first: Gunter

last: Meister


title: Low H3K27me3  define poorly prognostic pediatric posterior fossa ependymomas

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A subgroup of  Posterior fossa ependymomas show reduced H3K27me3 are more invasive, exhibit poor prognosis and epigenetically deregulated genes converge on radial glial factors, suggesting developing cerebellar radial glia as candidate cells-of-origin.

overall_design: H3K27me3 ChIP sequencing was performed on 3 posterior fossa (PF) and 3 supratentorial (ST) ependymoma samples. 3 PF ependmoma samples showed low H3K27me3 and designated PF_H3K27me3-ve; all 3 ST ependymoma samples show high H3K27me3 and desginated ST_H3K27me3+ve


title: DNA methylation anaylsis of placenta samples exposed to variable levels of arsenic during pregnancy

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

institute: Rollins School of Public Health at Emory University

type: Methylation profiling by genome tiling array

summary:
Genome-wide profiling of placental DNA methylation in relation to arsenic exposure. The Illumina 450k methylation array was used to profile 343 samples for which 3 different measurements of arsenic exposure were available during gestation.
These samples have been collected from the New Hampshire Birth Cohort Study (NHBCS).

overall_design: Bisulfite converted DNA was hybridized to the 450k platform and processed at the University of Minnesota Genomic Core

middle: J

first: Margaret

last: Karagas


title: DNA methylation profiling of promoter DNA associated to the T2D patients in Taiwan

status: Public on May 26 2016

city: Taichung

first: Yng-Tay

last: Chen

address: No 2 Yude road

department: Department of medical research

country: Taiwan

institute: China Medical University Hospital

summary: The GeneChip® Human Promoter 1.0R Array is designed for chromatin immunoprecipitation (ChIP) experiments. Sequences used in the design of the Human Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker.

overall_design: In total 40 samples, 30 T2D patients and 10 healthy control were selected for human DNA promoter methylation status was tested.

first: Fuu-Jen

last: Tsai


title: Novel Regions of Variable DNA Methylation in Human Placenta associated with Newborn Neurobehavioral Traits

status: Public on Jun 01 2016

summary:
Genome-wide profiling of placental DNA methylation in relation to neurobehavioral development. The Illumina 450k methylation array was used to profile 335 samples.
These samples have been collected from the Rhode Island Child Health Study (RICHS).

overall_design: Illumina analysis performed on 335 human placentas

first: Alison

middle: G

last: Paquette

first: Andres

middle: E

last: Houseman

first: Benjamin

middle: B

last: Green

first: Corina

last: Lesseur

first: David

middle: A

last: Armstrong

first: Barry

last: Lester


title: Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons

status: Public on Jun 30 2016

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: PIWI-interacting RNAs (piRNAs) mediate transposable element (TE) silencing at the transcriptional or post-transcriptional level in animal gonads. In the Drosophila ovary, Piwi–piRNA complexes (Piwi–piRISCs) repress TE transcription by modifying the chromatin state, such as H3K9me3 marks. Here, we demonstrate that Piwi physically interacts with linker histone H1. Depletion of Piwi decreases H1 density on target loci, leading to TE derepression. Loss of H1 results in gain of chromatin accessibility at target loci without affecting H3K9me3 and heterochromatin protein 1a (HP1a) density at the same loci. Piwi-mediated TE silencing also requires HP1a by regulating chromatin accessibility through its association with target loci. Thus, Piwi–piRISCs require both H1 and HP1a to repress TEs, and the silencing is correlated with the state of chromatin formation rather than H3K9me3 marks. These findings suggest that Piwi–piRISCs regulate the interaction of chromatin components with target loci to maintain silencing of the TE state through the modulation of chromatin accessibility.

overall_design: RNA levels, H1 and H3K9me3 occupancy, chromatin accessibility, and Piwi-associated small RNA levels in ovarian somatic cells (OSC) depleted of piRNA pathway components and H1.

middle: W

first: Kuniaki

last: Saito

first: Haruhiko

last: Siomi


title: Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures. [SNP]

status: Public on May 13 2016

city: Ann Abor

first: Maureen

last: Sartor

address: 100 Washtenaw Ave.

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Purpose: There is substantial heterogeneity within the human papillomavirus (HPV) positive head and neck cancer (HNC) tumors that predispose them to different outcomes, however this subgroup is poorly characterized due to various historical reasons.  Experimental Design: we perform unsupervised gene expression clustering on well-annotated HPV(+) HNC samples from two cohorts ( 84 total primary tumors), as well as 18 HPV(-) HNCs, to discover subtypes, and begin to characterize the differences between the subtypes in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number variations and mutation frequencies. Results: We identified two distinctive HPV(+) subtypes by unsupervised clustering. Membership in the HPV(+) subtypes correlates with genic viral integration status, E2/E4/E5 expression levels and the ratio of spliced to full length HPV oncogene E6. The subtypes also show differences in copy number alterations, in particular the loss of chr16q and gain of chr3q, PIK3CA mutation, and in the expression of genes involved in several biological processes related to cancer, including immune response, oxidation-reduction process, and keratinocyte and mesenchymal differentiation. Conclusion: Our characterization of two subtypes of HPV(+) tumors provides valuable molecular level information in relation to the alternative paths to tumor development and to that of HPV(-) HNCs. Together, these results will shed light on stratifications of the HPV(+) HNCs and will help to guide personalized care for HPV(+) HNC patients.

overall_design: 36 head and neck primary tumors (18 HPV+ and 18 HPV-) and their matched blood samples were collected and genotyped by Illumina OmniExpress SNP array. RNA-seq was also performed on the same set of tumor samples.

first: Sartor

last: Maureen

first: Rozek

last: Laura

first: Zhang

last: Yanxiao

first: Arthur

last: Anna

first: Carey

last: Tom

first: Chepeha

last: Douglas

first: Hall

last: Pelle

first: Koneva

last: Lada

first: Virani

last: Alisha

last: Shama

first: Warden

last: Charles


title: Characterization of the small RNAs of Volvox carteri

first: Anne

last: Dueck

summary:
The green alga Volvox carteri is a model organism for the development of multicellularity. It has a spherical shape with a complete division of labor between around 2000 somatic cells and 16 reproductive cells. When comparing Volvox with its unicellular relative Chlamydomonas rheinhardtii, one striking observation is the similarity in the protein coding genes [1]. Additionally, Baulcombe and colleagues showed that Chlamydomonas contains functional RNAi and miRNA machineries [2].
We deep sequenced small RNAs of the female Volvox strain HK10 in different life stages (asexual reproduction to sexual reproduction), each time dividing the samples into somatic cells and reproductive cells. This allowed for the observation not only of differences in individual life stages, but also for monitoring sRNA content in the two cell types.
We show that Volvox expresses miRNAs and that they are 2’-O-methylated at the 3’ end. The expression profiles of several miRNAs were validated by Northern blotting showing a differential expression both between cell types and between life stages. Intriguingly, most miRNAs do not seem to be conserved between Volvox and Chlamydomonas, raising the interesting question if this changed miRNome leads to differently targeted mRNAs thus resulting in cell differentiation. Since only little is known about the transcriptome of Volvox, we performed RNASeq in order to analyze potential miRNA targets.
In conclusion, most miRNA in Volvox are not conserved in Chlamydomonas although the two species are evolutionary close together. This suggests that dramatic changes in the miRNA expression might be one of the driving forces for the development of multicellularity.
1. Prochnik, S.E., et al., Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science, 2010. 329(5988): p. 223-6.
2. Molnar, A., et al., miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature, 2007. 447(7148): p. 1126-9.

overall_design: Examination of small RNAs of Volvox carteri during different stages of its life cycle

first: Maurits

last: Evers

first: Stefan

last: Henz

first: Norbert

last: Eichner

first: Katharina

last: Unger

first: Eugene

last: Berezikov

first: Stephan

last: Wenzl

first: Detlef

last: Weigel

first: Gunter

last: Meister


title: Analysis of Hybrid Incompatability between C nigoni and C briggsae by mRNA sequencing

status: Public on May 11 2016

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

summary: Two introgression strains (ZZY10307 and ZZY10330) of C. briggsae onto the X chromosome of C. nigoni results in male sterility. In order to determine the cause, we sequenced the mRNAs from young adult males from these two strains, and compared to fertile males of the two parent species (AF16 and JU1421). Two wild-type female samples were also included as platform QC.

sample_organism:
Caenorhabditis briggsae
Caenorhabditis nigoni

overall_design: mRNA profiles of young adult male worms from sterile hybrid strains (ZZY10307 and ZZY10330) and normal fertile parental strains (JU1421 and AF16) were generated by deep sequencing, in triplicate, using Illumina MiSeq V2 kit in 2*150 pair-end format.

first: Xiaoliang

last: Ren

first: Zhongying

last: Zhao


title: Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures. [RNA-Seq]

first: Maureen

last: Sartor

first: Sartor

last: Maureen

first: Rozek

last: Laura

first: Zhang

last: Yanxiao

first: Arthur

last: Anna

first: Carey

last: Tom

first: Chepeha

last: Douglas

last: Pelle


title: Two mutually exclusive local chromatin states drive efficient V(D)J recombination

status: Public on Apr 12 2016

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: V(D)J recombination is the first determinant of antigen receptor diversity. Understanding how recombination is regulated requires a comprehensive, unbiased readout of V gene usage. We have developed VDJ-seq, a DNA-based next-generation- sequencing technique that quantitatively profiles recombination products. We reveal a 200-fold range of recombination efficiency among recombining V genes in the primary mouse Igh repertoire. We used machine learning to integrate these data with local chromatin profiles to identify combinatorial patterns of epigenetic features that associate with active VH gene recombination. These features localise downstream of V genes and are excised by recombination, revealing a new class of cis-regulatory element that governs recombination, distinct from expression. We detect two mutually exclusive chromatin signatures at these elements, characterised by CTCF/RAD21 and PAX5/IRF4, that segregate with the evolutionary history of associated VH genes. Thus local chromatin signatures downstream of V genes provide an essential layer of regulation that determines recombination efficiency.

overall_design: Two nuclear RNA-seq replicate samples, two H3K4me3 ChIP-seq replicate samples and one input sample from flow sorted ex vivo Rag1-/- progenitor B cells and two VDJ-seq sample replicates from flow-sorted WT pro-B cells

first: Daniel

last: Bolland

first: Louise

last: Matheson

first: Anne

last: Corcoran


title: Global analysis of non-co-linear transcripts in human embryonic stem cells

status: Public on Feb 16 2016

city: Taipei

first: Trees-Juen

last: Chuang

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

department: Genomic Research Center

institute: Academic Sinica

summary: We investigate different types of non-co-linear RNA, for example, circular, trans-splicing and gene fusion.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Human (H9) and Rhesus macaque (O6) RNA-seqs; HeLa nanopore-seqs


title: Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures.


title: Progranulin Deficiency Promotes Circuit-Specific Synaptic Pruning by Microglia via Complement Activation

status: Public on Mar 31 2016

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Microglia repair injury and maintain homeostasis in the brain, but whether aberrant microglial activation can contribute to neurodegeneration remains unclear. Here, we use transcriptome profiling to demonstrate that deficiency in frontotemporal dementia (FTD) gene progranulin (Grn) leads to an age-dependent, progressive up-regulation of lysosomal and innate immunity genes, increased complement production, and synaptic pruning activity in microglia. During aging, Grn-/- mice show profound accumulation of microglia and preferential elimination of inhibitory synapses in the ventral thalamus, which contribute to hyperexcitability in the thalamocortical circuits and obsessive-compulsive disorder (OCD)-like grooming behaviors. Remarkably, blocking complement activation by deleting C1qa gene significantly reduces synaptic pruning by Grn-/- microglia, and mitigates neurodegeneration, behavioral phenotypes and premature mortality in Grn-/- mice. These results uncover a previously unrecognized role of progranulin in suppressing microglia activation during aging, and support the idea that blocking complement activation is a promising therapeutic target for neurodegeneration caused by progranulin deficiency.

overall_design:
Gene expression study in multiple brain regions from a mouse model of progranulin deficiency
Please note that 9 outlier samples were excluded from data analysis. Therefore, there are 326 raw data columns (i.e. 163 samples) in the non_normalized data matrix while 154 samples are represented here.

For arrays from Agilent platform, there are 16 samples/experiments were carried out, and 1 sample was excluded from analysis, therefore 15 samples are represented in the records.

first: Hansen

last: Lui

first: Jiasheng

last: Zhang

first: Stefanie

last: Makinson

first: Michelle

middle: K

last: Cahill

first: Hsin-Yi

last: Huang

first: Yulei

last: Shang

first: Kevin

last: Kelley

first: Michael

middle: C

last: Oldham

first: Lauren

middle: H

last: Martens

first: Fuying

last: Gao

first: Steven

last: Sloan

first: Eileen

last: Bigio

first: Ian

last: Mackenzie

first: William

last: Seeley

first: Anna

last: Karydas

first: Bruce

middle: L

last: Miller

first: Barbara

last: Borroni

first: Roberta

last: Ghidoni

first: Robert

middle: V

last: Farese Jr

first: Jeanne

middle: T

last: Paz

first: Ben

last: Barres

first: Eric


title: Novel transcripts associated with lymph node metastasis in triple negative breast cancer [discovery cohort]

status: Public on Dec 02 2015

city: New Lambton Heights

first: Kelly

last: Kiejda

state: NSW

address: HMRI

country: Australia

institute: University of Newcastle

summary: Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype with the worst prognosis. It is characterised by the absence of hormone receptors for estrogen, progesterone, and human epidermal growth factor 2, and as a consequence there are no targeted endocrine treatments available. TNBC patients are more likely to develop metastases and disease relapse than patients with other breast cancer subtypes. The identification of biomarkers that can be used to predict which patient is likely to develop metastatic disease remains a priority since this is the major cause of cancer-related death in these women.

overall_design: A total of 33 grade 3 invasive ductal carcinomas were used in this study, from which we were able to compare 17 matched normal adjacent tissues from the tumour specimens and 15 lymph node metastases.  Gene expression microarray analysis was used to reveal which transcripts were differentially expressed between patients with lymph node involvement and those who only presented with a primary tumour.

first: Andrea

last: Mathe

last: Avery-Kiejda

first: Michelle

last: Wong-Brown

first: Brianna

last: Morten

first: John

middle: F

last: Forbes

first: Stephen

last: Braye

first: Rodney

last: Scott


title: Dependency of ISG expression on IFNAR1 and Tyk2

status: Public on Nov 20 2015

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We analyze the expression profile of ISGs in the context of IFNAR1-KO primary murine B cells and macrophages. These analses were used to define ISG gene sets that are under tonic control. Furthermore, these analyses enabled the definition of ISGs that are dependent on Tyk2 signaling.

overall_design: Male C57BL/6 IFNAR1-KO mice were injected subcutaneously with 10,000U IFNa for 2hrs. Splenic B cells and peritoneal macrophages were sorted by FACS directly into TriZol and gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.

first: Sara

last: Mostafavi

first: Hideyuki

last: Yoshida

first: Devapregasan

last: Moodley

first: Andrew

last: Rhoads

first: Adriana

last: Ortiz-Lopez

first: Liang

last: Yang

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Comparative Morphophysiological Analyses and Molecular Profiling Reveal ‘Pi-Efficient Strategies’ of a Traditional Rice Genotypefor Low Phosphorus Tolerance in Traditional indica Rice

status: Public on Jan 29 2016

city: New Delhi

first: JITENDER

last: GIRI

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: NIPGR

summary: Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice cultivars are naturally compatible to low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes - Dular (low Pi tolerant) and PB1 (low Pi sensitive) - have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes raised under Pi deficient and sufficient conditions revealed the potential low Pi tolerance mechanisms of traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) are highly induced in traditional rice genotype, Dular. Higher reserve of phospholipid and greater accumulation of galactolipids under low Pi in Dular indicated its better internal Pi utilization. Furthermore, Dular also maintained better root growth than PB1 under low Pi resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.

overall_design: 15-days-old Root and shoot tissue of rice seedlings (variety: Dular and PB1) grown under Phosphorus deficient conditions were compared with corresponding Phosphorus sufficient conditions

first: Poonam

last: Mehra;

first: Bipin

last: Pandey

first: Jitender

last: Giri


title: Novel transcripts associated with lymph node metastasis in triple negative breast cancer

status: Public on Dec 01 2015

first: Kelly

last: Kiejda

overall_design: Refer to individual Series


title: Gene expression profiles in NORAD knockout and PUMILIO overexpressing cells

status: Public on Dec 03 2015

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: UT Southwestern Medical Center Dallas

summary:
Purpose: PUMILIO proteins are known to repress target genes by specifically binding to PUMILIO response elements (PREs) in target mRNAs.  NORAD is a noncoding RNA that negatively regulates PUMILIO activity. The goal of this study was to determine the gene expression changes that result from knockout of NORAD or overexpression of PUMILIO and to test whether NORAD knockout causes PUMILIO hyperactivity.
Methods: RNA-seq libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat Sample Preparation kit (Illumina) and sequenced using the 100 bp paired-end protocol on an Illumina HiSeq 2000.  For comparing NORAD+/+ and NORAD-/- HCT116 cells, 3 biological replicates per genotype were sequenced.  For PUM overexpression experiments, 3 replicates of GFP-expressing HCT116 cells (negative control) and 2 independent PUM1- or PUM2-overexpressing clones (2 replicates each) were sequenced.
Results: Gene expression profiles show that PUMILIO target genes are downregulated in both NORAD knockout cells and PUMILIO overexpressing cells.
Conclusions: These data indicate that NORAD sequesters PUMILIO, preventing excessive repression of PUMILIO target genes that are important for maintaining genomic stability.

overall_design: Gene expression profiles of genetically modified HCT116 cells were determined by RNA-seq.

first: Sungyul

last: Lee

first: Florian

last: Kopp

first: Tsung-Cheng

last: Chang

first: Beibei

last: Chen

first: Yang

last: Xie


title: Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica

status: Public on Nov 19 2015

city: Toledo

first: Javier

last: Cabrera

address: Avda. Carlos III s/n

country: Spain

institute: UCLM

summary: Root-knot nematodes (RKNs) induce inside the vascular cylinder the giant cells (GCs) imbibed into a gall. Gene-repression in early developing GCs could be facilitated by small RNAs (sRNA) as miRNAs. 24nt-sRNAs, rasiRNAs and 21-22nt-sRNAs can also mediate epigenetic mechanisms. Three sRNA libraries from 3dpi galls and three from uninfected root segments were sequenced following Illumina-Solexa technology.

first: Carolina

last: Escobar


title: Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver [RNASeq]

status: Public on Nov 10 2015

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

institute: University Of Queensland

summary: Diurnal oscillations of gene expression are a hallmark of rhythmic physiology across most living organisms. Such oscillations are controlled by the interplay between the circadian clock and feeding rhythms. While rhythmic mRNA accumulation has been extensively studied, comparatively less is known about their transcription and translation. Here, we quantified simultaneously temporal transcription, accumulation, and translation of mouse liver mRNAs under physiological light-dark conditions and ad libitum or night-restricted feeding in wild-type and Bmal1 deficient animals. We found that rhythmic transcription predominantly drives rhythmic mRNA accumulation and translation for a majority of genes. Comparison of wild-type and Bmal1 KO mice shows that circadian clock and feeding rhythms have broad impact on rhythmic genes expression, Bmal1 deletion having surprisingly more impact at the post-transcriptional level. Translation efficiency is differentially regulated during the diurnal cycle for genes with 5’-TOP sequences and for genes involved in mitochondrial activity and harboring a TISU motif. The increased translation efficiency of 5’-TOP and TISU genes is mainly driven by feeding rhythms but Bmal1 deletion impacts also amplitude and phase of translation, including TISU genes. Together this study emphasizes the complex interconnections between circadian and feeding rhythms at several steps ultimately determining rhythmic gene expression and translation.

overall_design: RNA-Seq from total RNA of mouse liver during the dirunal cycle. Time-series mRNA profiles of wild type (WT) and Bmal -/- mice  under ad libitum and night restriced feeding regimen were generated by deep sequencing.

last: Atger

first: Cédric

last: Gobet

first: Julien

last: Marquis

first: Eva

last: Martin

first: Benjamin

last: Weger

first: Grégory

last: Lefebvre

first: Patrick

last: Descombes

first: Felix

last: Naef


title: Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver [Ribosome Profiling]

overall_design: RIbosome profiling from total RNA of mouse liver during the dirunal cycle. Time-series ribosome density of wild type (WT) and Bmal -/- mice under ad libitum and night restriced feeding regimen were generated by deep sequencing.


title: Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

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


title: Time-resolved genome-wide pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) via RNA-Seq

status: Public on Sep 22 2015

city: Jeonju

first: Seunghwan

last: Kim

address: Nongsaengmyeong-ro

department: Genomics Division

country: South Korea

institute: National Academy of Agricultural Science

summary: Host-pathogen interactions, in particular during the early stages of infection, are important for the fate of both the invading pathogen and host. In pathogens, these interactions activate diverse pathogenic signals to cause disease in the host and evade the inevitably activated immune responses of the infected host. In this study, we used in vitro assay system and RNA-seq to analyze the time-resolved genome-wide gene expressions of Xanthomonas oryzae pv. oryzae (Xoo) evoked by the interactions with rice leaf extracts. RNA-seq analysis was carried out with samples of 7 different time points within 1 h. The RNA-seq data were verified by qRT-PCR. The in vitro system successfully initiated the pathogenic signals in Xoo cell culture. Many pathogenicity-related genes were expressed within 15 min. The hrpG gene was transcribed at maximum level within 10 min, and hrpX gene expression reached maximum level in 15 min. Chemotaxis and flagellar biosynthesis-related genes and cyclic-di-GMP synthesizing genes having GGDEF motif, were down-regulated until 10 min and after then up-regulated. Genes related to iron uptake and two component systems of phoB-phoR, phoP-phoQ, and pmrA-pmrB were up-regulated before 5 min. Data of multiple time points enabled non-linear regression fit of the time-resolved expression data, with which we newly developed the continuous time-resolved heat map to help the comparison of gene expression profiles. Essentiality of the transcriptionally up-regulated genes was also analyzed by the pathogenicity assay using the Xoo knockout strains, which showed not necessarily all the up-regulated genes were required for pathogenicity.

sample_organism: Xanthomonas oryzae pv. oryzae KACC 10331

overall_design: the time-dependent, 0, 5, 10, 15, 30, 45, and 60 min, transcriptome analysis of genome-wide Xanthomonas oryzae pv. oryzae genes from the pathogenic interactions with RLX via RNA-Seq

first: Lin-Woo

last: Kang


title: ImmGen Cytokines: Interferons

status: Public on Nov 24 2015

first: CBDM

last: Lab


title: Expression data from Arabidopsis during de-etiolation

status: Public on Aug 06 2015

city: La Jolla

first: Jesse

middle: Daniel

last: Woodson

address: 10010 N. Torrey Pines Rd.

department: Plant Biology

institute: The Salk Institute

summary:
Arabidopsis fc2-1 mutants fail to properly de-etiolate after a prolonged period in the dark. Our goal was to monitor whole genome expression during the first 2 hours of de-etiolation to determine the cuase of this growth arrest.
In comparison with other mutants that also affect de-etiolation, we identified a subset of genes specifically regulated by FC2 function during de-etiolation.

overall_design: Seedlings were grown in the dark for 4 days and then exposed to white light for 30 or 120 minutes to initiate de-etiolation and photomorphogenesis

first: Joanne

last: Chory


title: Somatic Primary piRNA Biogenesis Driven by Cis-Acting RNA Elements and Trans- Acting Yb

status: Public on Jun 05 2015

first: Yuka

last: Iwasaki

summary: Primary piRNAs in Drosophila ovarian somatic cells arise from piRNA cluster transcripts and the 3′ UTRs of a subset of mRNAs, including Traffic jam (Tj) mRNA. However, it is unclear how these RNAs are determined as primary piRNA sources. Here, we identify a cis-acting 100-nt fragment in the Tj 3′ UTR that is sufficient for producing artificial piRNAs from unintegrated DNA. These artificial piRNAs were effective in endogenous gene transcriptional silencing. Yb, a core component of primary piRNA biogenesis center Yb bodies, directly bound the Tj-cis-element. Disruption of this interaction markedly reduced piRNA production. Thus, Yb is the trans-acting partner of the Tj-cis-element. Yb-CLIP revealed that Yb-binding correlated with somatic piRNA production but Tj-cis-element downstream sequences produced few artificial piRNAs. Thus, Yb determines primary piRNA sources by two modes of action; primary binding to cis-elements to specify substrates, and secondary binding to downstream regions to increase diversity in piRNA populations.

overall_design: HITS-CLIP of Yb in OSCs (Ovarian Somatic Cells) depleted for tj cis-element, and small RNA sequencing of Piwi-piRNAs in OSCs depleted for tj cis-element.

first: Hirotsugu

last: Ishizu

first: Mikiko

last: Siomi


title: Krimper enforces an antisense bias on piRNA pools by binding AGO3 in the Drosophila germline

status: Public on May 28 2015

summary: Piwi-interacting RNAs (piRNAs) suppress transposon activity in animal germ cells. In the Drosophila ovary, primary Aubergine (Aub)-bound antisense piRNAs initiate the ping-pong cycle to produce secondary AGO3-bound sense piRNAs. This increases the number of secondary Aub-bound antisense piRNAs that can act to destroy transposon mRNAs. Here we show that Krimper (Krimp), a Tudor-domain protein, directly interacts with piRNA-free AGO3 to promote symmetrical dimethylarginine (sDMA) modification, ensuring sense piRNA-loading onto sDMA-modified AGO3. In aub mutant ovaries, AGO3 associates with ping-pong signature piRNAs, suggesting AGO3’s compatibility with primary piRNA loading. Krimp sequesters ectopically expressed AGO3 within Krimp bodies in cultured ovarian somatic cells (OSCs), in which only the primary piRNA pathway operates. Upon krimp-RNAi in OSCs, AGO3 loads with piRNAs, further showing the capacity of AGO3 for primary piRNA loading. We propose that Krimp enforces an antisense bias on piRNA pools by binding AGO3 and blocking its access to primary piRNAs.

overall_design: In order to investigate function of Krimp in piRNA pathway, sequencing of Piwi subfamily protein associated small RNAs was performed using adult Drosophila ovaries and Ovarian Somatic Cells (OSCs) depleted for Krimp or Aub.

first: Kaoru

last: Sato

first: Haruhiko


title: Abrogation of WNT signaling by dominant-negative TCF4

status: Public on Apr 01 2015

city: Amsterdam

first: Jarom

last: Heijmans

address: Meibergdreef 69-71

department: Tytgat Institute for liver and intestinal research

institute: Academic Medical Center

summary: To assess cellular changes upon abrogation of the WNT-signaling pathway, we induced expression of a dominant-negative T-cell factor 4 (TCF4). This showed a remarkable overlap with activation of the unfolded protein response (UTR) in the same colon cancer cell line.

overall_design: 500,000 cells were plated in a 10 cm2 plate, and the following day, treated for 20 hrs with doxycycline (Dox) or vehicle. Three independent biological replicates per treatment.


status: Public on Aug 24 2015

first: Marcelo

last: Rivas

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: University of California San Diego

summary:
The relationship between gene network structure and expression variation among individuals and species:
Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species, using the mammalian limb as a model system. We first built interaction networks for key genes regulating early (outgrowth; E9.5-11) and late (expansion and elongation; E11-13) limb development in mouse. This resulted in an Early (ESN) and Late (LSN) Stage Network. Computational perturbations of these networks suggest that the ESN is more robust. We then quantified levels of the same key genes among mouse individuals, and found that they vary less at earlier limb stages and that variation in gene expression is heritable. Finally, we quantified variation in gene expression levels among four mammals with divergent limbs (bat, opossum, mouse and pig), and found that levels vary less among species at earlier limb stages. We also found that variation in gene expression levels among individuals and species are correlated for earlier and later limb development. In conclusion, results are consistent with the robustness of the ESN buffering among-individual variation in gene expression levels early in mammalian limb development, and constraining the evolution of early limb development among mammalian species.

Transcriptomic insights into the genetic basis of mammalian limb diversity:
From bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species. We assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species. Taken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses.

sample_organism:
Sus scrofa
Mus musculus
Monodelphis domestica
Carollia perspicillata

overall_design:
Bat, mouse, opossum, and pig  mRNA profiles at early and late developmental stages on each species fore and hind-limbs. Various replicates of each library were generated by single-end sequencing using Illumina HiSeq 2500.

Please note that the De novo transcriptome assembly for bat (Trinity.fasta) was generated from pooled RNA-seq data of fore and hind-limbs at various embryonic developmental stages;
Beginning stage (Wanek stage 2: 3 FL and 3 HL samples), early-stage (Wanek stage 3/4: 2 FL and 2 HL samples), and late_stage (Wanke stage 6: 2 FL and 2 HL samples).

Gene expression libraries (RNA-seq) were created at ridge, bud, and paddle developmental stages among fore and hind-limbs of bat, mouse, opossum, and pig. Various replicates of each condition were generated by single-end sequencing using Illumina HiSeq 2500. The ridge, bud, and paddle stages were defined based on morphology and correspond to the following embryonic developmental stages: W2, W3, and W6, respectively, on mouse; 13, 14, and 15, respectively, on bat; 27/30 (fore/hindlimb), 31, and 32, respectively, on opossum; and 20, 22, and 26, respectively, on pig.

first: Karen

last: Sears

first: Jennifer

last: Maier

last: Rivas-Astroza

first: Rachel

last: Poe

first: Sheng

last: Zhong

first: Kari

last: Kosog

first: Jonathan

middle: D

last: Marcot

first: Richard

last: Behringer

first: Chris

last: Cretekos

first: John

last: Rasweiler IV

first: Zoi

last: Rapti

first: Jenny

last: Deng

first: Anna

last: Dowling

first: Paige

last: Oboikovitz

first: Xiaoyi

last: Cao


title: High throughput sequencing of Siwi and BmAGO3 associated piRNAs from Bombyx mori BmN4 cells

status: Public on Dec 31 2014

first: Yuka

last: Iwasaki

summary: In germ cells, piRNAs are amplified through the Ping-Pong cycle that depends on reciprocal Slicer-mediated target RNA cleavage by two PIWI members. A germ-specific DEAD-box protein Vasa is required for the process. However, Vasa’s function is poorly understood. Here, we show that target RNAs cleaved by a Bombyx mori (silkworm) PIWI, Siwi, remain to be bound with the protein upon cleavage, but are released in the presence of Vasa in B. mori (BmVasa) and ATP. Under normal conditions, BmVasa co-purifies with Siwi, but not with second B. mori PIWI BmAgo3. However, when BmVasa loses the ATP-binding and RNA-unwinding activities, BmVasa avidly associates with Siwi and BmAgo3, which contains transposon transcripts predominantly in sense orientation, the sources of BmAgo3-piRNAs. Without BmVasa, BmAgo3 is devoid of piRNAs. Thus, BmVasa actively releases target RNAs from Siwi, upon its cleavage, to urge BmAgo3-piRNA complex formation in the Ping-Pong cycle, enabling continuous supply of piRNAs in germ cells.

overall_design: small RNA libraries were prepared from Siwi, BmAGO3, and Flag-Siwi immuno-precipitate samples of BmN4 cells

first: Kazumichi

middle: M

last: Nishida

first: Haruhiko

last: Siomi

first: Mikiko


title: Pathological impact of hepatitis B virus surface proteins on the liver is associated with the host genetic background

status: Public on Jan 01 2015

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Development of cirrhosis and hepatocellular carcinoma is main dangerous consequences of Hepatitis B virus (HBV) infection. Although a lot of data accumulated about host's immune response against infected hepatocytes, less is known about direct pathogenic effects of HBV proteins. Here we have investigated pathological outcomes of HBV envelope polypeptides expression in the liver of transgenic mice. Expression of HBV proteins induced endoplasmic reticulum (ER) stress response in hepatocytes. ER stress response included activation of PKR-like ER-localized eukaryotic initiation factor 2α (eIF2α) kinase (PERK) and eIF2α phosphorylation. In young transgenic mice on BALB/c genetic background eIF2α phosphorylation resulted in activation of GADD153/CHOP-dependent apoptosis that led to stronger liver injury and fibrosis compared to transgenic mice on C57BL/6 genetic background. Hepatic stellate cells represented the main collagen-producing cells in the liver of HBV transgenic mice. Further, key regulator of hepatocytes proliferation transcription factor c-Jun was up-regulated and this up-regulation was accompanied by c-Jun N-terminal kinases (JNK) activation in the liver of HBV transgenic mice. Thus, HBV envelope polypeptides induced host genetic background-dependent liver injury and fibrosis, and, more important, stimulated c-Jun expression and activated PERK genetic background-independent creating conditions in the liver that promote cancer cell proliferation and tumour growth.

overall_design: Microarray experiments were performed as dual-color hybridizations. In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed.

first: Yuri

last: Churin

first: Martin

last: Roderfeld

first: Elke

last: Roeb


title: Transcriptome analysis of Osbhlh148 mutant plants under controlled drought stress and well-watered conditions at vegetative stage

status: Public on Jan 16 2015

city: Fayetteville

first: Andy

last: Pereira

address: 115 Plant Science Building,

department: Crop, Soil and Environmental Sciences (CSES)

institute: University of Arkansas,

summary: The members of bHLH transcription factor superfamily are known to play key role in plant development and abiotic stress response. Loss-of-function of OsbHLH148 gene resulted in increased sensitivity of rice plants to drought stress. To identify the targets of OsbHLH148 and dissect the drought stress response pathway regulated by it, we performed transcriptome profiling of Osbhlh148 mutant plants under drought stress as well as well-watered conditions by RNA-sequencing.

overall_design: OsbHLH148 loss-of-function rice plants (Oryza sativa ssp. japonica cv. Nipponbare) were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.

first: Ramegowda

last: Venkategowda

first: Subodh

last: Srivastava


title: Genome-wide identification of H2A.Z-interacting proteins by bPPI-seq

status: Public on Apr 20 2016

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

summary: Histone variant H2A.Z is a critical player in setting up the chromatin environment that mediates transcription and other activities on chromatin. However, how H2A.Z is incorporated to specific chromatin regions is not clear. To examine the potential role of sequence-specific transcription factors in targeting H2A.Z, we screened for genome-wide H2A.Z-interacting proteins in vivo using a novel technique called bait Protein-Protein Interaction-sequencing (bPPI-seq). Among the hundreds of H2A.Z-interacting proteins identified by bPPI-seq, we show that a zinc-finger transcription factor, Osr1 interacts with H2A.Z both in vitro and in vivo and co-localizes with H2A.Z on chromatin. Knockdown of Osr1 compromised H2A.Z deposition to hundreds of chromatin sites enriched with Osr1 binding motifs. Furthermore, Osr1 and H2A.Z co-regulate the expression of numerous target genes. These results indicate that Osr1 directly interacts with H2A.Z, mediates its incorporation to a large number of target sites and regulates gene expression. Our data indicate that bPPI-seq can be widely applied to identify unbiasedly interacting proteins under physiologic conditions.

overall_design:
Examination of the H2A.Z-interacting proteins by a novel bait Protein-Protein Interaction-sequencing method

GSM2628249-GSM2628254: ReMTH-VNC 1,2 and 3 (3 different reading frames) and pEco were co-transfected into GP2 293 cells using Lipofectamine 2000 (Invitrogen). Supernatants containing packaged viral particles were collected 48h after transfection. 30 ml viral particles were used to infect 50 million 3T3 Tet-on 3G stable cell line expressing GFPN-H2A.Z, GFPN-H2A or GFPN alone  to avoid multiple integrations. After 48 hours of infection, the cells were selected in DMEM containing 2μg/ml puromycin (Sigma) for 2 days and maintained in 1μg/ml puromycin for 3 days. Then equal number of cells infected with viruses for the 3 reading frames were pooled and induced by  2μg/ml Doxycycline for 48 hrs before sorting for green cells. GFP-positive cells were sorted with FACSAria (BD Biosciences).

first: Yi

last: Zhang

first: Wai

last: Ku

first: Shuai

last: Liu

first: Kairong

last: Cui

first: Wenfei

last: Jin

first: Qingsong

last: Tang

first: William

last: Lv

first: Bing

last: Ni


title: Plasma microRNA profile in chronic thromboembolic pulmonary hypertension patients and healthy controls

city: Beijing

first: Lijuan

last: Guo

address: 2 Yinghua Dongjie, Hepingli Beijing

country: China

institute: intensive care unit

summary:
We aimed to identify the ebbrantly hypothesized that circulating miRNA profile might reflect the miRNAs involved in the pathogenesis of CTEPH more comprehensively, thus could be used as
candidate biomarker and shed light on the recognition of CTEPH pathogenesis.

overall_design: In this presented study, 10 CTEPH patients without any drug treatment for pulmonary hypertension except anticoagulation before blood collection and 10 healthy controls paired in age and gender were enrolled. The exclusion criteria included malignancies, other cardiovascular diseases, and patients who had ever received any treatment for pulmonary hypertension except for anticoagulation.

first: Chen

last: Wang

first: Jun


title: MDA-231-Gem cells and MDA-231 cells

status: Public on Nov 11 2014

city: Shanghai

first: XIN

last: HU

state: Shanghai

address: 270 Dong An Road, Build 7, RM303

department: Department of Breast Surgery

institute: Fudan Unversity Shanghai Cancer Center

type:
Expression profiling by array
Non-coding RNA profiling by array


title: microRNA Expression profiles of MDA-231-Gem cells and MDA-231 cells

summary:
Gemcitabine was approved to be sufficient effects on most solid tumors, including breast cancer and others. There has been little study of how the evolution of chemoresistance in cancer affects other aspects of disease pathogenesis.
The primary aim of this study was to explore the molecules involved in gemcitabine resistance and its underlying regulatory mechanisms in breast cancer.

overall_design: MDA-231-Gem and MDA-231 cells were collected at logarithmic growth phase for microRNA extraction and hybridization on Agilent microarrays. We sought to explore the diffierential microRNAs expression between MDA-231-Gem and MDA-231 cells, in order to explore the underlying mechanisms accounting for the resistance to gemcitabine in breast cancer.

first: Fu-Gui

last: Ye

first: Xin

last: Hu


title: Induction of ER stress in the colon cancer cell line LS174 with SubAB

status: Public on Feb 24 2013

first: Jarom

last: Heijmans

summary: To assess the effect of activation of the unfolded protein response (UPR) in colon cancer cell lines, we treated cells with the AB5 subtilase cytotoxin (SubAB). This proteolytically cleaves the 78-kDa glucose-regulated protein (GRP78; also known as HSPA5 or BiP) inside the endoplasmic reticulum. We find that the WNT signaling pathway is highly affected upon treatment with SubAB.

overall_design: 500,000 cells were plated in a 10 cm2 plate, and the following day, treated for 20 hrs with SubAB or the control (SubAA272B), and then harvested. Three independent biological replicates per treatment.

first: Gijs

middle: R

last: van den Brink


title: mRNA Expression profiles of MDA-231-Gem cells and MDA-231 cells

overall_design: MDA-231-Gem and MDA-231 cells were collected at logarithmic growth phase for RNA extraction and hybridization on Affymetrix microarrays. We sought to explore the diffierential genes expression between MDA-231-Gem and MDA-231 cells, in order to explore the underlying mechanisms accounting for the resistance to gemcitabine in breast cancer.


title: Expression profile and RNA Polymerase II occupancy of transposable elements among knock down of the piRNA pathway components in OSCs

status: Public on Aug 01 2013

city: Tokyo

first: Yuka

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

institute: Keio University School of Medicine

summary:
The Piwi–piRNA complex (Piwi–piRISC) in Drosophila ovarian somatic cells represses transposons transcriptionally to maintain genome integrity; however, the underlying mechanisms remain obscure.
We performed mRNA-seq analysis from OSCs transfected with siRNAs against CG3893, the known piRNA pathway genes, Piwi, Maelstrom, HP1a and Armitage, and the control (EGFP), and PolII ChIP-seqanalysis from OSCs transfected with siRNAs against CG3893, Piwi, Mael and the control (EGFP).  This result indicates that CG3893 is a novel factor for primary piRNA pathway in OSCs.

overall_design:
RNA levels in wild-type (EGFP control knock-down) ovarian somatic cells (OSC) and RNAi knock-downs of Piwi, Armi, Mael, CG3893, and HP1a.
RNA Polymerase II occupancy in wild-type (EGFP control knock-down) ovarian somatic cells (OSC) and RNAi knock-downs of Piwi, Mael, and CG3893.

first: Hitoshi

last: Ohtani

first: Kuniaki

last: Saito

first: Haruhiko

last: Siomi


title: HITS-CLIP analysis of Yb binding sites in Drosophila ovary cell line

status: Public on Jun 24 2014

summary: piRNAs direct Piwi to repress transposons to maintain genome integrity in Drosophila ovarian somatic cells. piRNA maturation and association with Piwi occur at perinuclear Yb bodies, the centers of piRNA biogenesis. Here, we show that piRNA intermediates arising from the piRNA cluster flamenco (flam) concentrate into perinuclear foci adjacent to Yb bodies, termed Flam bodies. Although flam expression is not required for Yb body formation, Yb, the core component of Yb bodies, is required for Flam body formation. Abolishment of the RNA-binding activity of Yb disrupts both Yb bodies and Flam bodies. Loss of Zucchini, an endoribonuclease necessary for piRNA maturation, enlarges Flam bodies, which now superimpose with Yb bodies. Yb directly binds flam, but not neighboring protein-coding gene, transcripts. Thus, Yb integrates piRNA processing factors and piRNA intermediates into Yb bodies and Flam bodies, respectively, through direct binding to enhance piRNA biogenesis and formation of piRNA-inducing silencing complexes.

overall_design: HITS-CLIP was performed using OSC (Ovarian Somatic Cells). The antibody for Drosophila Yb, which was generated in this study, was used. Obtained CLIP tags were analyzed using illumina HiSeq200.

first: Hirotsugu

last: Ishizu

first: Yukiko

last: Murota

first: Mikiko


title: Screen mRNAs specifically regulated by mTORC1 in colon epithelial cells from mice with dextran sulfate sodium (DSS)-induced experimental colitis

status: Public on Nov 05 2015

city: guangzhou

first: zhipeng

last: zou

state: guangdong

address: tonghe road

department: Cell Biology

institute: southern medical university

summary: To screen mRNAs specifically regulated by mTORC1, a global mRNA expression profile in colon epithelial cells (CECs) from mice with or without CECs-specific TSC1 knockout (KO)  was developed using microarray.

overall_design: Wile-type or CECs-specific TSC1 KO mice with experimental colitis were sacrificed, with CECs harvested and subjected to total RNA extraction.

first: Xiaochun

last: Bai

first: Zhipeng

last: Zou


title: Gene Expression analysis of castration-resistant prostate cancer bone metastases

status: Public on Jun 02 2011

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

country: Sweden

institute: Umeå University

summary: Analysis of bone metastases tissue from castration-resistant prostate cancer patients at the RNA level in relation to expression of constitutively active androgen receptor variants termed AR-V7 and AR-V567es.

overall_design: Total RNA obtained from frozen bone metastases samples were analyzed using a gene expression array and further to reveal differences in-between sample groups according to expression of AR-V7 and AR-V567es mRNA levels. Samples were defined to have high (AR-V high) or low (others) expression of those variants, respectively, for definition and more information please see Hörnberg et al PLoS One April 2011 Vol 6 Issue 4 , link and PMID below.

first: E

last: Hörnberg

last: Ylitalo

first: S

last: Crnalic

first: H

last: Antti

first: P

last: Stattin

first: A

last: Widmark

last: Bergh


title: Study of mating type genes and their roles in mating interactions of the basidiomycete Schizophyllum commune

status: Public on Jun 15 2012

city: Jena

first: Erika

last: Kothe

address: Neugasse 25

department: Microbial Communication, Institute of Microbiology

institute: Friedrich-Schiller-University

summary: Transcriptome changes associated with mating interactions were performed in order to identify signaling components and targets of pheromone response. Two monokaryons  (S. commune 12-43 and  4-39), a dikaryon (W22 x 12-43), both semi-compatible mating interactions (Aon: W22 x 4-39; Bon, flat: W21 x 4-39), and different S. commune pheromone receptor recipient strains (Vbar2f, Vbar2t) were analyzed for that purpose. In addition, a S. commune strain showing the thin-phenotype (W22-thin) was investigated to figure out the role of Thn1 in mating.

overall_design: With microarray analysis mRNA expression in different mating interactions of the basidiomycete S. commune was analyzed. Genes which show regulation in the comparison of the two monokaryons 12-43 and 4-39 has been eliminated from other comparisons as strain specific differences. Two biological or technical replicate samples were analyzed for each condition.

first: Susann

last: Erdmann

first: Daniela

last: Freihorst


title: Mesenchymal stem cells reduce inflammation while enhancing bacterial clearance and improving survival in sepsis.

status: Public on Dec 31 2012

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

country: Canada

institute: Saint Michaels Hospital

summary:
Expression data from Total RNA extracted from murine spleen, liver, lungs, kidneys and hearts. Sepsis was induced in C57Bl/6J mice by cecal ligation and puncture (CLP), followed 6 hours later by an intravenous injection of Mesenchymal Stem Cell (MSC) or saline.  Twenty-eight hours after CLP, plasma, bronchoalveolar lavage (BAL) fluid and tissues were collected for analyses.  Total RNA was extracted using Trizol (as per manufactures' instruction) followed by clean-up procedure using Qiagen RNA easy Prep (as per manufactures instructions)
In the following study we hypothesized that mesenchymal stem cells (MSCs), which have documented immunomodulatory properties, would reduce sepsis-associated inflammation and organ injury in a clinically relevant model of sepsis.

overall_design: To identify the molecular changes associated with decreased inflammation in CLP-injured mice treated with MSCs, we analyzed the gene expression profiles from spleens, liver, lungs, kidneys and heart collected at 28 hours from 4 animals per group:  sham/saline, CLP/saline, and CLP/MSCs.

first: Shirley

last: Mei

first: Jack

middle: J

last: Haitsma

last: Dos Santos

first: Yupu

last: Deng

first: Patrick

last: Lai

first: Arthur

middle: S

last: Slutsky

first: W

last: Liles

first: Duncan

last: Stewart


title: Mesenchymal Stem Cells Reduce Inflammation while Enhancing Bacterial Clearance and Improving Survival in Sepsis

status: Public on Nov 22 2010

summary:
Expression data from Total RNA extracted from murine spleen. Sepsis was induced in C57Bl/6J mice by cecal ligation and puncture (CLP), followed 6 hours later by an intravenous injection of Mesenchymal Stem Cell (MSC) or saline.  Twenty-eight hours after CLP, plasma, bronchoalveolar lavage (BAL) fluid and tissues were collected for analyses.  Total RNA was extracted using Trizol (as per manufactures' instruction) followed by clean-up procedure using Qiagen RNA easy Prep (as per manufactures instructions)
In the following study we hypothesized that mesenchymal stem cells (MSCs), which have documented immunomodulatory properties, would reduce sepsis-associated inflammation and organ injury in a clinically relevant model of sepsis.

overall_design: To identify the molecular changes associated with decreased inflammation in CLP-injured mice treated with MSCs, we analyzed the gene expression profiles from spleens collected at 28 hours from 4 animals per group:  sham/saline, CLP/saline, and CLP/MSCs.


title: Characterization of lactic acid and acetic acid mutants in batch fermentation

status: Public on Mar 01 2012

city: Hanover

first: Lee

last: Lynd

state: NH

address: 8000 Cummings Hall

department: Thayer School of Engineering

institute: Dartmouth College

summary: Four C. thermocellum DSM-1313 derived strains were assessed using metabolite and DNA microarray tools in order to better understand carbon and electron flow within this organism. C. thermocellum is able to ferment cellulose into its fermentation end products L-lactate, acetate, formate, hydrogen gas, and ethanol, with the latter being the desired end product to be used as biorenewable fuel. In addition to the parent strain (genotype: hpt spo0A), strains with either or both of the genes encoding lactate dehydrogenase (ldh) and phosphate acetyltransferase (pta) deleted were studied. The strains used are a parent strain (M1726: genotype: hpt spo0A), and strains with either the gene encoding lactate dehydrogenase (M1629: hpt spo0A ldh) or phosphate acetyltransferase (M1630: hpt spo0A pta) deleted, or with both genes deleted (M1725: hpt spo0A ldh pta). Controlled batch fermentations using cellobiose as sole carbon source were grown for each strain, and samples in mid-exponential phase and at the time of carbon depletion were examined by DNA microarray.

overall_design: Four strains were grown each as three independent biological replicates (fresh batch of media was made before each run). Per fermentation, two samples were taken for DNA microarray analysis as was determined by the optical density: mid-exponential was defined as O.D. 0.4 (measured by Dasgip probe); point of carbon depletion was defined by both the maximum O.D. reached and observation that no base was added to the fermentation to control pH. In total, 4 strains x 3 fermentation x 2 time points per fermentor = 24 arrays. Parent strain was used as reference strain.

first: Douwe

last: van der Veen

first: Steven

last: Brown

first: Courtney

last: Johnson


status: Public on Jul 06 2010

city: Tsu

first: Naohito

last: Aoki

address: 1577 Kurimamachiya-cho

department: Graduate School of Bioresources

institute: Mie University

summary: miRNA profiles of adipocyte-derived microvesicles (ADMs) on the Day 2-4 and Day 8-10 were compared.

overall_design: ADMs were prepared from the 48h-conditioned medium of 3T3-L1 adipocytes (Day 2-4 and Day 8-10) followed by RNA isolation.


title: ImmGen Microarray Phase 1

status: Public on May 02 2009

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: Gene-expression microarray datasets generated as part of the Immunological Genome Project (ImmGen). Primary cells from multiple immune lineages are isolated ex-vivo, primarily from young adult B6 male mice, and double-sorted to >99% purity. RNA is extracted from cells in a centralized manner, amplified and hybridized to Affymetrix 1.0 ST MuGene arrays. Protocols are rigorously standardized for all sorting and RNA preparation. Data is released monthly in batches of cell populations.

overall_design: This Series record provides access to Immunological Genome Project data submitted to GEO.


title: Small RNA and gene expression profile in the adult testes of the common marmoset

status: Public on Jun 01 2014

first: Yuka

last: Iwasaki

department: Department of Molecular Biology

summary: Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis was piRNAs, while 353 novel miRNAs but few endo-siRNAs were also identified. MARWI, a marmoset homolog of mouse MIWI and a very abundant PIWI in adult testes, associates with piRNAs that show characteristics of mouse pachytene piRNAs. As in other mammals, most marmoset piRNAs are derived from conserved clustered regions in the genome, which are annotated as intergenic regions. However, some of these piRNA cluster regions contain antisense-orientated pseudogenes, suggesting regulation of parental functional protein-coding genes. More piRNAs map to transposable element (TE) subfamilies when they have copies in piRNA clusters. In addition, the strand-bias observed for piRNAs mapped to each TE subfamily correlates with the polarity of copies inserted in clusters. These findings suggest that pachytene piRNA clusters determine the abundance and strand-bias of TE-derived piRNAs, and also regulate protein-coding genes via pseudogene-derived piRNAs.

overall_design: small RNA levels in the adult marmoset testis, and MARWI-IP small RNA levels and  RNA levels from the adult marmoset testis with two replicates.

first: Takamasa

last: Hirano

first: Haruhiko

last: Siomi