title: Dnmt3a haploinsufficiency transforms Flt3-ITD myeloproliferative disease into a rapid, spontaneous, and fully-penetrant acute myeloid leukemia (Bulk RNA-Seq)

status: Public on Mar 27 2016

first: Nathan

last: Salomonis

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Cytogenetically normal acute myeloid leukemia (CN-AML) represents nearly 50% of human acute myeloid leukemia (AML) cases with a 5-year overall survival of approximately 30%. In CN-AML with poorer prognosis, mutations in the de novo DNA methyltransferase (DNMT3A) and the FMS-like tyrosine kinase 3 (Flt3) commonly co-occur (1-3). We demonstrate that mice with Flt3-internal-tandem duplication (Flt3ITD) and inducible deletion of Dnmt3a spontaneously develop a rapidly-lethal, completely-penetrant, and transplantable AML of normal karyotype. These murine AML retain a single Dnmt3a floxed allele, revealing the oncogenic potential of Dnmt3a haploinsufficiency. FLT3-ITD/DNMT3A-mutant primary human and murine AML demonstrate a similar pattern of global DNA methylation. In the murine model, rescuing DNMT3A expression was accompanied by DNA re-methylation and loss of clonogenic potential, suggesting that Dnmt3a-mutant oncogenic effects are reversible.  Differentially methylated genomic regions were associated with changes in the expression of nearby genes. Moreover, dissection of the cellular architecture of the AML model using single-cell RNA-Seq, flow cytometry and colony assays identified clonogenic subpopulations that differentially express genes that are sensitive to the methylation of nearby genomic loci and varied in response to Dnmt3a levels. Thus, Dnmt3a haploinsufficiency transforms Flt3ITD myeloproliferative disease by modulating methylation-sensitive gene expression within a clonogenic AML subpopulation.

overall_design: To identify the gene expression changes associated with Dnmt3a loss of function in human and murine Flt3-ITD and Dnmt3a-mutant AML (Bulk RNA-Seq).

first: Sara

last: Meyer

first: Tingting

last: Qin

first: David

last: Muench

first: Kohei

last: Masuda

first: Meenakshi

last: Venkatasubramanian

first: Emily

last: Orr

first: Elisabeth

last: Paietta

first: Martin

last: Tallman

first: Hugo

last: Fernandez

first: Ari

last: Melnick

first: Michelle

last: Beau

first: Scott

last: Kogan

first: Maria

last: Figueroa

first: H

last: Grimes


title: Expression of MERTK based on Multiple Sclerosis (MS) risk haplotype

status: Public on Feb 06 2016

city: Parkville

first: Andrew

middle: David

last: Fox

state: VIC

address: 30 Royal Parade

department: MS Division

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

type: Expression profiling by high throughput sequencing

summary: Whole transcriptome RNA-seq analysis to measure group-wise RNA expression level of the MERTK gene in 3 healthy controls (known to be homozygous non-risk haplotype at MERTK gene locus) and to compare this to the group-wise RNA expression level of the MERTK gene in 5 Multiple Sclerosis-affected (MS-affected) individuals (known to be homozygous for the MS risk haplotype at the MERTK gene locus).

overall_design: We sequenced the whole transcriptome of 3 healthy control samples which were all homozygous for the MS non-risk haplotype at the MERTK gene. We also did the same RNA-seq protocol on 5 MS-affected subjects that were all homozygous for the Risk haplotype at the MERTK gene. All 8 samples were sequenced evenly across 3 lanes of an Illumina HiSeq NGS machine to remove any batch-type effects that could be caused by sequencing e.g. all cases in one lane and all controls in another lane.

first: Michele

middle: D

last: Binder

first: Daniel

last: Merlo

first: Laura

middle: J

last: Johnson

first: Lauren

last: Giuffrida

first: Sarah

middle: E

last: Calvert

first: Rainer

last: Akkermann

first: Gerry

middle: Z

last: Ma

first: Ashwyn

middle: A

last: Perera

first: Melissa

middle: M

last: Gresle

first: Louise

last: Laverick

first: Grace

last: Foo

first: Marzena

last: Fabis-Pedrini

first: Timothy

last: Spelman

first: Margaret

last: Jordan

first: Alan

middle: G

last: Baxter

first: Simon

last: Foote

first: Helmut

last: Butzkueven

first: Trevor

last: Kilpatrick

first: Judith

last: Field


title: Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes

status: Public on Feb 10 2016

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

country: USA

institute: University of Vermont

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: 3D Chromosome Regulatory Landscape of Human Pluripotent Cells [RNA-Seq]

status: Public on Nov 22 2015

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The control of cell identity is orchestrated by transcriptional and chromatin regulators in the context of specific chromosome structures. With the recent isolation of human naive embryonic stem cells (ESCs) representative of the ground state of pluripotency, it is possible to deduce this regulatory landscape in one of the earliest stages of human development. Here we generate cohesin ChIA-PET chromatin interaction data in naive and primed human ESCs and use it to reconstruct and compare the 3D regulatory landscapes of these two stages of early human development. The results reveal shared and stage-specific regulatory landscapes of topological domains and their subdomains, which consist of CTCF-CTCF/cohesin loops and enhancer-promoter/cohesin loops. The enhancer-promoter loop data reveal that genes with key roles in pluripotency are nearly always regulated by one or more super-enhancers, and show that these genes tend to occur in insulated neighborhoods. Our results reveal the key features of the 3D regulatory landscape of early human cells that form the foundation for embryonic development.

overall_design: Polyadenylated RNA-seq from naive and primed human embroynic stem cells.

first: Xiong

last: Ji


title: Ctr9, a key subunit of PAFc, affects global estrogen signaling and drives ERalpha-positive breast tumorigenesis

status: Public on Sep 25 2015

city: Madison

first: Hao

last: Zeng

state: WI

address: 1111 Highland Ave

department: Department of Oncology

institute: University of Wisconsin Madison

summary: The human RNA polymerase II-associated factor complex (hPAFc) and its individual subunits have been implicated in human diseases including cancer. However, its involvement in breast cancer cells awaits investigation. Using data mining and human breast cancer tissue microarrays, we found that Ctr9, the key scaffold subunit in hPAFc, is highly expressed in ERα+ luminal breast cancer and the high expression of Ctr9 correlates with poor prognosis. Knockdown of Ctr9 in ERα+ breast cancer cells almost completely erased estrogen regulated transcriptional response. At the molecular level, Ctr9 enhances ERα protein stability, promotes recruitment of ERα and RNAPII and stimulates transcription elongation and transcription-coupled histone modifications. Knockdown of Ctr9, but not other hPAFc subunits, alters the morphology, proliferative capacity and tamoxifen-sensitivity of ERα+ breast cancer cells. Together, our study reveals that Ctr9, a key subunit of hPAFc, is a central regulator of estrogen signaling that drives ERα+ breast tumorigenesis, rendering it a potential target for the treatment of ERα+ breast cancer.

overall_design: To globally identify Ctr9 regulated genes, MCF7-tet-on-shCtr9 cells were cultured in DMEM supplemented with 10% FBS in the absence or presence of 500 ng/ml Dox for 4 days, followed by continuing cultured in stripped medium in the absence or presence of 500 ng/ml Dox for another 3 days. Cells were then treated with DMSO or 10 nM E2 for 4 hours prior to cell collection. Total RNA was extracted using a Qiagen RNeasy Plus Kit according to manufacturer protocol, and three independent experiments were performed. Purified total RNA was submitted to the University of Wisconsin Madison Biotechnology Center for RNA quality analysis, reverse transcription, labeling, and hybridization to the Affymetrix human transcriptome array 2.0 containing >6.0 million distinct probes covering 44,699 protein coding genes and 22,829 non-protein coding genes. Data analysis and visualization were performed using the Affymetrix Transcriptome Analysis Console (TAC) Software.

first: Wei

last: Xu


title: The metabolome regulates the epigenetic landscape during naïve to primed human embryonic stem cell transition

status: Public on Nov 17 2015

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed mRNA-seq and small RNA-seq on the newly derived ELF human naïve pluripotent stem cell line and compared with the existing H1 human primed line. Expression analysis revealed that mitochondria oxidative phosphorylation and fatty acid beta-oxidaton is up-regulated in naive state while fatty acid synthesis is up-regulated in primed state. Small RNA-seq revealed consistent expression changes in microRNAs that target key fatty acid beta-oxidation and synthesis genes. Integration with metabolomics data revealed consistent changes in the expression of NNMT (higher in naive state) and IDO1 (higher in primed state) and in the concentration of corresponding metabolic substrates and products. As a regulator of S-Adenosyl methionine (SAM) level, NNMT is proposed as a candidate regulator of epigenetic states. ChIP-seq analysis releaved that naive lines have lower H3K27me3 marks in developmental genes. Inhibition of STAT3, a known regulator of NNMT, reduces NNMT expression level and decreases overall H3K27me3 marks around transcriptional start sites. In particular, STAT3 inhibitor treatment increased H3K27me3 marks in 313 genes that also have higher H3K27me3 marks in primed state than naive state. These 313 genes are enriched with developmental functions, and include several WNT pathway genes. In summary, integrative analysis of RNA-seq, ChIP-seq and metabolomics data revealed key metabolic differences between naive and primed pluripotency and identified NNMT as a key regulator of epigeneitc state.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
2 biological replicates for ELF RNA-seq; 2 biological replicates for ELF small RNA-seq; one sample for ELF H3K27me3 ChIP-seq and one sample as input; one sample for ELF treated with STAT3 inhibitor for 6 hours and one sample as input.

UPDATE: We performed RNA-seq on two additional human naïve embronic stem cell lines (H1 4iLIF and Lis1), as well as mouse in vivo preimplantation inner cell mass and postimplantation epiblast. These RNA-seq samples are included in the naïve vs. primed comparisons in the study; 2 biological replicates of H1 4iLIF; 2 biological replicates of Lis1; 3 biological replicates of mouse preimplantation inner cell mass; 2 biological replicates of mouse postimplantation epiblast.

first: Henrik

last: Sperber

first: Julie

last: Mathieu

first: Yuliang

last: Wang


title: DNA methylome analysis in infants from The Gambia / Aflatoxin / Seasonality study

status: Public on Apr 18 2015

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary:
Genome wide DNA methylation profiling in infant's blood from a mother/child cohort in The Gambia. The main variables of the analyses were the intra-uterine exposure to aflatoxin B1 (AFB1) and the season of conception.
The Illumina Infinium HumanMethylation 450k Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in whole peripheral blood obtained at 3-6 months of age. A total of 124 samples were analysed, including 3 technical replicates.

overall_design: Bisulphite converted DNA from the 124 samples were hybridised to the Illumina Infinium HumanMethylation 450k Beadchip

first: Matt

last: Silver


title: Expression profiling of wheat heads from spring wheat Chinese Spring (CS) and CS-7EL (CS with additional chromosome arm 7EL from Thinopyrum elongatum), after inoculation with either water (mock inoculation) or Fusarium graminearum

status: Public on Sep 14 2015

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

summary: The ditelocentric addition line CS-7EL of the spring wheat (Triticum aestivum) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS-7EL), which confers high resistance to fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into commercial wheat varieties.  The objectives of this study were to identify candidate genes expressed from the 7EL chromosome of CS-7EL, to develop 7EL-specific molecular markers, and to validate their usefulness to characterize recombination between one of the group 7 chromosomes of wheat and Th. elongatum. High-throughput sequencing of Fusarium graminearum-infected and control CS and CS-7EL cDNA libraries was performed using RNA-Seq. A stepwise bioinformatics strategy was applied to assemble the sequences obtained from RNA-Seq and to create a conservative list of candidate genes expressed from the foreign chromosome 7EL. PCR primer pairs were designed and tested for 135 candidate genes. A total of 48 expressed molecular markers specific for the chromosome 7EL were successfully developed. Screening of progenies from two BC1F2 families from the cross CS-7E(7D)×2*CSph1b showed that these markers are useful to characterize recombination events between the chromosomes 7D from wheat and 7E from Th. elongatum.

overall_design: Expression profiling of inoculated rachis from CS and CS-7EL heads sampled at 4 days after inoculation. Inoculation of all developed spikelets on each head at mid-anthesis was done with either water or F. graminearum strain DAOM 180378. Three biological replicates were done for each treatment, and 10 to 12 heads were inoculated per biological replicate.

first: Margaret

last: Balcerzak

first: Lulu

last: Gou

first: Jiro

last: Hattori

first: George

last: Fedak

first: Nicholas

last: Tinker

first: Andrew

last: Sharpe


title: Skeletal muscle profiling in HMDP (high-fat/high-sucrose diet)

status: Public on Jan 13 2015

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Identify genes in the skeletal muscle whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP).  The HMDP comprises classical inbred and recombinant inbred wild type mice.  The neqc-normalized values of genes were used for genome wide association.  These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness.

overall_design: GWAS for expression of skeletal muscle in inbred strains fed chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks

first: Aldons

last: Lusis

first: Brian

last: Parks

first: Frode

last: Norheim


title: Sharp changes in gene expression levels along germinal layers distinguish the development of gyrencephaly

status: Public on May 21 2015

city: San Juan de Alicante

first: Victor

last: Borrell

state: Alicante

address: Av Ramon y Cajal s/n

department: Institute of Neuroscience

country: Spain

institute: CSIC

summary: Gyrencephalic species develop folds in the cerebral cortex in a stereotypic manner, but the genetic mechanisms underlying this unique patterning process are unknown. We present a large-scale transcriptomic analysis of individual germinal layers in the developing cortex of the gyrencephalic ferret, comparing between regions prospective of fold and fissure. We find unique transcriptional signatures in each germinal compartment, indicating that thousands of genes are differentially expressed between regions, including ~80% of genes mutated in human cortical malformations. Regional differences result from sharp changes in gene expression levels, which occur at multiple locations across the developing cortex of ferret and human, but not in the lissencephalic mouse. These complex expression patterns emerge sequentially during development and map the eventual location of specific folds and fissures. Our findings demonstrate that step-wise gene expression maps within germinal layers distinguish the development of gyrencephaly from lissencephaly, and may contribute to identify novel genes responsible for human malformations.

overall_design: Six samples were analyzed with 3 replicates of each of them. Comparisons were done taking different reference sample depending on the comparison ( Usually taking the SG as reference)

first: Camino

last: Romero

first: Carl

last: Bruder

first: Maria

last: Martínez-Martínez

first: Ugo

last: Tomasello

first: José

last: Sanz-Anquela

first: Víctor


title: DamID in HeLa-C cells

status: Public on Jun 24 2016

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: DamID with sPom121, Nup98 and control proteins (GFP and Cbx1)

overall_design: N-term tag sPom121, Nup98 or GFP and express in HeLa-C cells - conduct deep sequencing

first: Tobias

last: Franks

first: Martin

last: Hetzer


title: Genomic Run On (GRO): determination of the nascent transcriptional rates and mRNA levels in several yeast mutants.

status: Public on Dec 31 2015

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: In order to maintain the appropriate level of mRNA it is necessary coordinate simultaneously all the steps along the mRNA life cycle. It has been shown that several factors act in the regulation of gene expression as global coordinators. Thus, some kind of information is transferred from the nucleus to the cytoplasm, imprinted in the mRNA. In this way, it is conceivable the existence of mechanisms that ensure the balance between mRNA synthesis and degradation through the information flow from the cytoplasm to the nucleus and vice versa, as a crosstalk among both process to ensure the proper mRNA homeostasis in the cell. In this study, we have used null mutants related with transcription and mRNA degradation and we find that the lack of those factors impacts both over transcription and RNA stability at genome wide levels to compensate the impaired effect produce by the loss of each studied factor.

overall_design: This study focus on the transcriptional activity of RNA pol II in yeast genes. S. cerevisiae cells grown in YPD or YPGal to exponential phase were subjected to Genomic Run On.  Data were normalized by the ArrayStat software. Home-made macroarrays containing 6035 ORF were used.

last: Pérez-Ortín

first: Daniel

last: Medina

first: Mordechai

last: Choder

first: Sebastían

last: Chávez


title: RNA-seq in HepG2 and IMR90 cells

status: Public on Jun 22 2016

summary: Expression analysis in HepG2 and IMR90 cells in presence of Fluc siRNA or sPom121 or Nup98 siRNA

overall_design: Transfect siRNA - extract RNA 72 hrs post transfection


title: Liver Profiling In HMDP (high-fat/high-sucrose diet)

status: Public on Jan 08 2015

first: Calvin

last: Pan

summary: Identify genes in the liver whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP).  The HMDP comprises classical inbred and recombinant inbred wild type mice.  The RMA values of genes were used for genome wide association as described in Parks et al Cell Metabolism 2015.  These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness.

overall_design: GWAS for expression of liver in inbred strains fed chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks

first: Aldons

last: Lusis


title: Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes [ChIP-seq]

first: Jonathan

last: Gordon

summary: The molecular signature at histone H3K4 involved in epigenetic regulation of normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology.  This study examines the dynamic distribution of H3K4me3 and H3K4ac histone modification associated with active chromatin to provide an understanding of the changes in epigenetic regulation associated with the unique breast cancer subtypes.

overall_design: H3K4me3 and H3K4ac histone modification study in normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology

first: Terri

last: Messier

first: Joseph

last: Boyd

first: Gary

last: Stein


title: 3D Chromosome Regulatory Landscape of Human Pluripotent Cells

status: Public on Nov 21 2015

first: Richard

last: Young


title: Expression data in colon mucosa samples from individuals with ulcerative colitis and normal controls

status: Public on Jan 01 2015

city: Houston

first: R.

middle: Alan

last: Harris

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Genome wide expression profiling of ulcerative colitis, and normal colon mucosa samples. The GeneChip PrimeView Human Gene Expression Array was used to obtain expresion profiles across colon mucosa samples. Samples came from 5 ulcerative colitis affected, and 5 normal individuals.

overall_design: RNA from the 10 samples were hybridized to the GeneChip PrimeView Human Gene Expression Array

last: Kellermayer

first: R


title: DNA methylation in a validation cohort of colon mucosa samples from individuals with Crohns' disease or ulcerative colitis and normal controls

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 5 Crohn's disease affected, 5 ulcerative colitis affected, and 12 normal individuals. One ulcerative colitis sample was assayed before and after treatment with infliximab and mesalamine.

overall_design: Bisulfite converted DNA from the 23 samples were hybridized to the  Illumina Infinium HumanMethylation450 BeadChip v1.1


title: Transcript Profiling of Scarlet Runner Bean Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq

status: Public on May 10 2014

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: We used laser capture microdissection (LCM) to capture globular scarlet runner bean embryo propers and suspensors, and profiled the transcriptomes of these two embryo regions using next-generation sequencing. Our long-term goal is to understand the region-specific differentiation processes that occur during early embryo development and how genes are activated specifically in the suspensor and embryo proper.

overall_design: Illumina sequencing of transcripts from laser-captured embryo proper and suspensor regions of scarlet runner bean globular stage embryos. Two biological replicates were collected for each embryo region.

first: Robert

middle: B

first: Xiaomeng

last: Wu

first: Min

last: chen

first: Jungim

last: Hur


title: Transcript Profiling of Phaseolus coccineus and Phaseolus vulgaris Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq

sample_organism:
Phaseolus vulgaris
Phaseolus coccineus

platform_organism:
Phaseolus vulgaris
Phaseolus coccineus


title: MicroRNA targetome analysis during HCMV infection

status: Public on Dec 03 2014

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: To elucidate miRNA-mediated temporal crosstalk during productive infection, we identified genome-wide miRNA target sites using Argonaute-crosslinking and immunoprecipitation followed by high-throughput sequencing (AGO-CLIPseq) in human cytomegalovirus (HCMV)-infected cells and evaluated the targeting efficacy by applying our new AGO-CLIPseq enrichment (ACE)-scoring algorithm.

overall_design: To uncover the miRNA targetome in uninfected or infected human foreskin fibroblasts with HCMV (24, 48 and 72 post-infection hour) were subjected to take AGO-CLIPseq as well as mRNAseq/smallRNAseq.

first: Sungchul

last: Kim

first: Kwangseog

last: Ahn


title: AMPK governs lineage specification through Tfeb-dependent regulation of lysosomes

status: Public on Mar 09 2016

first: April

last: Williams

summary: Faithful execution of developmental programs relies on the acquisition of unique cell identities from pluripotent progenitors, a process governed by combinatorial inputs from numerous signaling cascades that ultimately dictate lineage-specific transcriptional outputs. Despite growing evidence that metabolism is integrated with many molecular networks, how pathways that control energy homeostasis may affect cell fate decisions is largely unknown. Here, we show that AMPK, a central metabolic regulator, plays critical roles in lineage specification. Although AMPK-deficient embryonic stem cells (ESCs) were normal in the pluripotent state, these cells displayed profound defects upon differentiation, failing to generate chimeric embryos and preferentially adopting an ectodermal fate at the expense of the endoderm during embryoid body (EB) formation. AMPK-/- EBs exhibited reduced levels of Tfeb, a master transcriptional regulator of lysosomes, leading to diminished endolysosomal function. Remarkably, genetic loss of Tfeb also yielded endodermal defects, while AMPK-null ESCs over-expressing this transcription factor normalized their differential potential, revealing an intimate connection between Tfeb/lysosomes and germ layer specification. The compromised endolysosomal system resulting from AMPK or Tfeb inactivation blunted Wnt signaling, while up-regulating this pathway restored expression of endodermal markers. Collectively, these results uncover the AMPK pathway as a novel regulator of cell fate determination during differentiation.

overall_design: 2 WT and 2 AMPK DKO ESC lines were differentiated into embryoid bodies (EBs) for various lengths of time (2, 4, 8, and 12 days) in high and low glucose conditions. Both ESC and EB samples were profiled by mRNA-seq to examine how global gene expression changes associated with ESC differentiation are affected by AMPK deletion.

first: Nathan

middle: P

first: Anwesh

last: Kamireddy

first: Jeanine

middle: L

last: Van Nostrand

first: Lillian

last: Eichner

first: Maxim

middle: N

last: Shokhirev

first: Yelena

last: Dayn

first: Reuben

last: Shaw


title: DNA methylation in a discovery cohort of colon mucosa samples from individuals with Crohns' disease or ulcerative colitis and normal controls

status: Public on Jun 01 2013

first: R.

summary: Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 10 Crohn's disease affected, 4 ulcerative colitis affected, and 10 normal individuals. One ulcerative colitis sample was assayed before and after treatment with 6-mercaptopurine and mesalamine.

overall_design: Bisulfite converted DNA from the 25 samples were hybridized to the  Illumina Infinium HumanMethylation450 BeadChip v1.1

first: Richard

first: R


title: Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis

status: Public on Feb 01 2013

city: Albany

first: Yu

last: Zhang

address: 800 Buchanan Street

department: Plant and Microbial Biology

institute: UC Berkeley

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

overall_design: Refer to individual Series


title: DNA methylation in Crohns' disease and ulcerative colitis

status: Public on Dec 19 2012

last: Harris


title: Gene expression changes induced by overexpression of EVI1 in Lin- hematopoietic cells [Lin]

status: Public on Jan 09 2013

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

summary: The transcription factor Evi1 is essential for the formation and maintenance of hematopoietic stem cells, and induces clonal dominance with malignant progression upon constitutive activation by chromosomal rearrangements or transgene integration events. To understand the immediate and adaptive response of primary murine hematopoietic cells to the transcriptional upregulation of Evi1, we developed an inducible lentiviral vector system with a robust expression switch. We found that Evi1 delays differentiation and promotes survival in myeloid culture conditions, orchestrating a battery of genes involved in stemness (Aldh1a1, Ly6a [Sca1], Abca1, Epcam, among others). Importantly, Evi1 suppresses Cyclins and Cyclin-dependent kinases (Cdk), while it upregulates Cdk inhibitors, inducing quiescence in various proliferation-inducing cytokine conditions and operating in a strictly dose-dependent manner. Hematopoietic cells with persisting Evi1-induction tend to adopt a relatively low expression level. We thus classify Evi1 as a dormancy-inducing oncogene, likely requiring epigenetic and genetic compensation for cell expansion and malignant progression.

overall_design: Lin- Rosa26rtTA cells were isolated, transduced in S3F11 cytokines, induced the next day with DOX [1 μg/ml] and  20 hours later sorted for negative/low or highly EGFP expressing cells, from which total RNA was extraced and subjected to Microarray Analysis

first: Olga

last: Kustikova


title: Transcript Profiling of Common Bean Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq

first: Bob

last: Goldberg

summary: We used laser capture microdissection (LCM) to capture globular stage common bean embryo proper and suspensor, and profiled the transcriptome of these two embryo regions using next-generation sequencing. Our long-term goal is to understand the region-specific differentiation processes that occur during early embryo development and how genes are activated specifically in the suspensor and embryo proper.

overall_design: Illumina sequencing of transcripts from laser-captured embryo proper and suspensor regions of common bean globular stage embryo. Two biological replicates were collected for each embryo region.

first: Robert

first: Xiaomeng

last: Wu

first: Min

last: Chen

first: Jungim


title: Histone H3 K36me3 in wildtype, isw1 and chd1 yeast strains

status: Public on Jul 25 2012

city: Kansas City

first: Michaela

last: Smolle

state: Missouri

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip assays to measure the occupancy of histone H3 K36me3 over the yeast genome in  wildtype, isw1 and chd1 yeast strains. ChIPs were done with K36me3 antibody (Ab 9050) in G1 arrested yeast cells.

overall_design: Two color experiment. Biological replicates=3 per IP per cell type.

first: Madelaine

last: Gogol

first: Hua

last: Li

first: Jerry

last: Workman


title: DNA extracted from saliva for methylation studies of psychiatric traits

status: Public on Sep 24 2014

city: Atlanta

first: Alicia

last: Smith

address: 101 Woodruff Circle

institute: Emory University

summary: DNA methylation has become increasingly recognized in the etiology of psychiatric disorders. Because brain tissue is not accessible in living humans, epigenetic studies are most often conducted in blood. Saliva is often collected for genotyping studies but is rarely used to examine DNA methylation because the proportion of epithelial cells and leukocytes varies extensively between individuals.  The goal of this study was to evaluate whether saliva DNA is informative for studies of psychiatric disorders.   Saliva and blood methylation was clearly distinguishable though there was positive correlation overall. There was little correlation in CpG sites within relevant candidate genes.  Correlated CpG sites were more likely to occur in areas of low CpG density (i.e. CpG shores and open seas). There was more variability in CpG sites from saliva than blood, which may reflect its heterogeneity. Thus, this study provides a framework for using DNA methylation from saliva and suggests that DNA methylation of saliva may offer distinct opportunities for epidemiological and longitudinal studies of psychiatric traits.

overall_design: DNA methylation was assessed in saliva and blood samples from 64 adult African Americans. Both saliva and blood samples were collected from each participant. Saliva was stored in Oragene DNA sample collection kits (DNA Genotek), and blood was collected in EDTA vacuum tubes.  DNA was extracted using the Puregene Genomic DNA kit (Invitrogen). DNA methylation was interrogated for each sample using the HumanMethylation450 BeadChip (Illumina).  Analyses for tissue-specific DNA patterns were conducted using linear regression adjusted for appropriate covariates, including estimated cellular proportions.  The estimated proportion of epithelial cells in saliva DNA ranged from 3-99% (median 26%). In blood, the estimated proportion of lymphocytes ranged from 25-70% (median 48%) and neutrophils ranged from 42-84% (median 58%).  Methylation of 68.8% of all CpG sites differed relative to epithelial cell proportion (FDR<.05).  Our results provide a framework for methylation studies in DNA extracted from saliva and highlight the importance of controlling for the proportion of epithelial and leukocyte cells.  This presents an attractive opportunity for investigators that have already collected salivary DNA for genetic studies of psychiatric traits.

first: A

middle: K

first: V

last: Kilaru

first: T

last: Klengel

first: K

last: Mercer

first: B

last: Bradley

last: Conneely

last: Ressler

first: E

last: Binder


title: Gene expression changes induced by overexpression of EVI1 in Lin- hematopoietic cells

status: Public on Jan 08 2013

first: Adrian

last: Schwarzer


title: Molecular characterization of immortalization of human MSCs by a combination of p53 knockdown and TERT overexpression

status: Public on Apr 13 2011

city: Singapore

first: Tongming

last: Liu

address: 60 Biopolis street

department: Cancer stem group

country: Singapore

institute: Genome Institute of Singapore

summary: Gene expression profile of p53 knockdown MSCs or p53 knockdown+TERT MSCs was compared with that of control MSCs. Our data show p53 knockdown prolongs the lifespan of MSCs, and a combination of p53 knockdown and TERT overexpression is sufficient to immortalize MSCs. The results provide important information about the molecular basis underlying p53 knockdown in MSCs and immortalization-related genes of MSCs.

overall_design: Total RNA obtained from p53 knockdown MSCs or p53 knockdown+TERT MSCs from three patients were compared with control MSCs.

first: Tong

first: Eng

middle: H

last: Lee

first: Bing

last: Lim


title: Gene expression in adipose tissue of intrauterine growth restricted (IUGR) and Macrosomic animals that developed in a crowded uterine horn

status: Public on Apr 25 2012

city: Columbia

first: Julia

last: Taylor

state: MO

address: 114 Lefevre Hall

department: Biological Sciences

institute: University of Missouri

summary:
Animals that are growth restricted in utero may show rapid postnatal growth that ultimately results in adult obesity.  Macrosomic animals at birth typically remain large and are also obese as adults.  Our goal was to examine the differences between animals that reach obesity in different ways.  We also aimed to examine gene expression in animals that start out lean and stay lean compared to those that start out lean and become fat.
We used microarrays to detail gene expression in adipose tissue.

overall_design: 3 samples each from IUGR animals with rapid postnatal growth (IH), IUGR animals with slower postnatal growth (IL), and macromsomic animals (M).

first: Benjamin

last: Coe

first: Toshi

last: Shioda

first: Frederick

middle: S

last: vom Saal


title: Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

first: Michaela

last: Smolle

platform_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C


title: Long non-coding RNA HOTAIR is an independent prognostic marker of metastasis in estrogen receptor positive primary breast cancer

status: Public on Nov 29 2013

city: Odense C

first: Kristina

last: Sørensen

address: Srd. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

summary: Expression of HOX transcript antisense intergenic RNA (HOTAIR)—a long intergenic non-coding RNA (lincRNA)—has been examined in a variety of human cancers, and overexpression of HOTAIR is correlated with poor survival among breast, colon, and liver cancer patients. In this retrospective study, we examine HOTAIR expression in 164 primary breast tumors, from patients who do not receive adjuvant treatment, in a design that is paired with respect to the traditional prognostic markers. We show that HOTAIR expression differs between patients with or without a metastatic endpoint, respectively. Survival analysis shows that high HOTAIR expression in primary tumors is significantly associated with worse prognosis independent of prognostic markers. This association is even stronger when looking only at estrogen receptor (ER)-positive tumor samples. In ER-negative tumor samples, it is not possible to detect a prognostic value of HOTAIR expression. These results are successfully validated in an independent dataset with similar associations.  Furthermore, we find that high HOTAIR expression is associated with strong positive expression of multiple neighboring HOXC genes of the HOXC locus on chromosome 12q13.13 and have both negative and positive correlation with other genes located on different chromosomes. Independent datasets verify these significant correlations and thus indicate that HOTAIR might regulate additional genes than those previously reported.  In conclusion, our findings suggest that HOTAIR expression may serve as an independent biomarker for the prediction of the risk of metastasis in ER-positive breast cancer patients.

overall_design: 164 breast cancer samples

first: Mads

last: Thomassen

first: Qihua

last: Tan

first: Martin

last: Bak

first: Søren

last: Cold

first: Mark

last: Burton

middle: J

last: Larsen

first: Torben

last: Kruse


title: Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]

first: Yu

last: Zhang

summary: Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.

overall_design: Four biological replicates data of PIF3-binding sites were collected by comparing the parallel ChIP samples from transgenic seedlings overexpressing Myc-epitope-tagged PIF3 (35S:PIF3-5xMyc, P3M) in pif3-3 null mutant background and the wild-type (WT) control.

first: Oleg

last: Mayba

first: Peter

last: Quail


title: Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes—GMUCT 2.0

status: Public on Mar 08 2014

city: Philadelphia,

first: Nathan

middle: Daniel

last: Berkowitz

state: Pennsylvania

address: 433 S University Ave.

department: Biology

institute: University of Pennsylvania

summary: The advent of high-throughput sequencing has led to an explosion of studies into the diversity, expression, processing, and lifespan of RNAs.  Recently, three different high-throughput sequencing-based methods have been developed to specifically study RNAs that are in the process of being degraded.  All three methods—genome-wide mapping of uncapped and cleaved transcripts (GMUCT), parallel analysis of RNA ends (PARE), and degradome sequencing—take advantage of the fact that Illumina sequencing libraries use T4 RNA ligase 1 to ligate an adapter to the 5’ end of RNAs that have a free 5’-monophosphate.  This condition for T4 RNA ligase 1 substrates means that mature mRNAs are not substrates of the enzyme because they have a 5’-cap.  As a result, these sequencing libraries are specifically made up of clones of decapped or degrading mRNAs and the 3’ fragment of cleaved miRNA and siRNA targets.  In this paper, we present a massively streamlined protocol for GMUCT that takes 2-3 days and can be initiated with as little as 5 µg of starting total RNA and involves only one gel size-selection step.  We show that the results are similar to libraries made using the previous GMUCT protocol and PARE.

sample_organism:
Arabidopsis thaliana
Homo sapiens

platform_organism:
Arabidopsis thaliana
Homo sapiens

overall_design: GMUCT libraries were made from flower buds of the Arabidopsis thaliana accession Columbia (Col-0) and three human cell lines—the cervical cancer cell line HeLa, human embryonic kidney 293 T (HEK293T) cell line, and the human chronic myelogenous leukaemia cell line K562—two replicates of each.  Matched mRNA-seq libraries were made for each Col-0 GMUCT replicate. These libraries were sequenced on the Illumina HiSeq 2000 and the reads were trimmed to remove the adapter sequences (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCA). The abundance of each unique read was determined, and unique reads were mapped to the Arabidopsis and human genomes, respectively.

first: M

middle: R

last: Willmann

first: N

middle: D

first: B

last: Gregory


title: Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [RNA-Seq]

overall_design: Transcriptomic profiles of the wild-type (WT), pif3 monogenic mutant, pif1pif4pif5 (pif145) triple mutant, and pif1pif3pif4pif5 (pifq) quadruple mutant were collected from biological triplicates using 3’-end-captured directional RNA-seq analysis.


title: Expression data from bone marrow CD34+ cells of MDS patients and healthy controls

status: Public on Mar 13 2010

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

country: United Kingdom

institute: University of Oxford

summary: In order to gain insight into the molecular pathogenesis of the myelodysplastic syndromes (MDS), we performed global gene expression profiling and pathway analysis on the hematopoietic stem cells (HSC) of 183 MDS patients as compared with the HSC of 17 healthy controls. The most significantly deregulated pathways in MDS include interferon signaling, thrombopoietin signaling and the Wnt pathway. Among the most significantly deregulated gene pathways in early MDS are immunodeficiency, apoptosis and chemokine signaling, whereas advanced MDS is characterized by deregulation of DNA damage response and checkpoint pathways. We have identified distinct gene expression profiles and deregulated gene pathways in patients with del(5q), trisomy 8 or –7/del(7q). Patients with trisomy 8 are characterized by deregulation of pathways involved in the immune response, patients with –7/del(7q) by pathways involved in cell survival, whilst patients with del(5q) show deregulation of integrin signaling and cell cycle regulation pathways. This is the first study to determine deregulated gene pathways and ontology groups in the HSC of a large group of MDS patients. The deregulated pathways identified are likely to be critical to the MDS HSC phenotype and give new insights into the molecular pathogenesis of this disorder thereby providing new targets for therapeutic intervention.

overall_design: 183 patients with MDS patients and 17 healthy controls were included in the study. Bone marrow samples were obtained and CD34+ cells isolated from MDS patients and healthy controls. Samples were hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays

first: Jacqueline

last: Boultwood

first: James

last: Wainscoat


title: Dnmt3a haploinsufficiency transforms Flt3-ITD myeloproliferative disease into a rapid, spontaneous, and fully-penetrant acute myeloid leukemia

status: Public on Mar 27 2016

city: Cincinnati

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital