title: Broad H3K4me3 Reveals Increased Transcription Elongation and Enhancer Activity at Tumor Suppressors

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

summary: Tumor suppressors are mostly defined by inactivating somatic mutations in tumors, yet little is known about their epigenetic features in normal cells. Here, through integrative analysis of 1,134 genome-wide epigenetic profiles and mutations from >8,200 tumor-normal pairs, we discovered broad H3K4me3 (wider than 4 kb) as the first epigenetic signature for tumor suppressors in normal cells. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity together leading to exceptionally high gene expression, and is distinct from other broad epigenetic features, such as super enhancers. Broad H3K4me3 conserved across normal cells represents core tumor suppressors, such as P53 and PTEN, whereas cell-type-specific broad H3K4me3 may indicate cell-identity genes and cell-type-specific tumor suppressors. Furthermore, widespread shortening of broad H3K4me3 in cancers is strongly associated with repression of tumor suppressors. Together, the broad H3K4me3 epigenetic signature we reported here may provide a new direction for the discovery and characterization of novel tumor suppressors.

overall_design: H3K4me3 ChIP-Seq was conducted in 1) liver tumor and matched tissue, 2) lung tumor and matched tissue, 3) cell line A549 grown under normal and flavopiridol treatment conditions.

first: Wei

first: Qianben

last: Wang


title: Chicken gut DM asymmetry

status: Public on Jul 21 2015

city: Ithaca

first: Natasza

middle: A

last: Kurpios

state: NY

address: C4-161 Vet Med Center

department: College of Veterinary Medicine

country: USA

institute: Cornell University

summary:
HH stage 21 chicken dorsal mesentery is laser microdissected into four morphological compartments, and subject to global expression analyses on Affymetrix Chicken 3' microarray
Goal is to identify genes expressed in each of left epitelium, left mesenchyme, right mesenchyme, right epithelium; genes on the left may be direct or indirect transcriptional targets of Pitx2.

overall_design: Three biological experiments were performed, among which 1939 laser cut sections were collected for RNA analyses. Transcript targets from a single biological experiment were pooled and hybridized to a single chip. Thus, the experiment was run in biologcal triplicate with no technical replicates. Three biological replicates with four cell compartments each gives a total of 12 samples in the collection.

first: David

middle: W

last: Gludish


title: High-throughput sequencing of DNA G-quadruplex structures in the human genome

status: Public on Jul 19 2015

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

summary: Nucleic acid secondary structures play a critical role in the regulation of biological processes. Genome-wide detection of DNA and RNA secondary structures is essential to identify pathways that are regulated by nucleic acid folding. There are no methods to interrogate DNA secondary structure formation on a genome-wide scale. We present G4-Seq, a method that applies the concept of polymerase interference at G-quadruplex (G4) DNA secondary structures to a human genome scale by massively parallel array-sequencing. Our approach generated a high-resolution map of more than 700,000 distinct G4s in the human genome, including non-canonical structural variants with bulges or extended loops, which are difficult to predict by classical approaches. This experimental map reveals many previously uncharacterized G4 structures in functional genomic regions, of which we highlight those associated with cancer, that include oncogenes, tumor suppressors and somatic copy-number alterations.

overall_design: 4 library samples, 150 base pairs custom protocol (G4-Seq) sequenced as two-times single-end reads on HiSeq 2500: 2 replicates for Na+ (Read-1) and K+ (Read-2); 2 replicates for Na+ (Read-1) and PDS+Na+ (Read-2).

first: Vicki

middle: S

last: Chambers

first: Jonathan

middle: M

last: Boutell

first: Marco

last: Di Antonio

first: Geoff

middle: P

last: Smith

first: Shanakr

last: Balasubramanian


title: Gene differential expressions between cell subpopulations with high invasiveness (invaded) and low invasiveness (non-invaded) in human lung cancer H460 cell line

status: Public on Jul 15 2015

city: Los Angeles

first: Xufeng

last: Chen

state: CA

address: 10833 Le Conte Ave.

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

summary: Cell populations with different invasiveness were isolated and collected with cell culture inserts of Boyden-type cell invasion chambers coated with 1xBME (base membrane extract). Cells that invaded to bottom chamber were collected  as cell population with high-invasiveness , and cells that remained in the insert chamber were collected as cell population with low-invasiveness. The selection with Boyden-type cell invasion chambers was repeated six times, and cells with high invasiveness were terms as H-INV subline, and cells with low invasiveness were termed as L-INV subline. Microarray analysis was performed with Illumina HumanHT-12 v4 Expression BeadChips

overall_design: The transcriptional profile of invaded cell subpopulations  (H-INV, n=3) was compared to non-invaded cell subpopulations (L-INV, n=3), 968 genes were found to be differentially expressed compared with fold changes more than 2 and FDR <0.05.

first: Shenglin

last: Ma

first: Binghui

last: Shen

first: Chao

last: Guo


title: The E3 ubiquitin ligase DDB1 controls homeostasis of hematopoietic stem and progenitor cells

status: Public on Jul 10 2015

city: Omaha

first: Shannon

last: buckley

state: Nebraska

address: 985805 Nebraska Medical Center

department: Genetics, Cell Biology, and Anatomy

institute: Unviversity of Nebraska Med Center

summary:
Hematopoietic stem cells (HSC) are regulated to keep the balance between self-renewal and differentiation. However, little is known about post-translational regulations in HSCs. In this study, we characterize the role of DDB1, a component of the Cul4A-DDB1 E3 ubiquitin ligase complex, in HSCs and progenitors by using conditional DDB1 knockout models. We show that the maintenance and differentiation of both adult and fetal HSCs and progenitor cells is dependent on DDB1 function. Deletion of DDB1 alters cell cycle progression and induces apoptosis. Furthermore, deletion of DDB1 in developing thymocytes had no effects on T cell differentiation, whereas DDB1-deficient peripheral T cells were not able to enter cell cycle when stimulated in vitro. In addition, DDB1 is essential for T cell leukemia initiation. Our results reveal that DDB1 is required for adult and fetal hematopoiesis as it controls progenitor and stem cell homeostasis.
Transcriptional consequences of inactivating DDB1 in fetal LSK cells.

overall_design: Four samples were analyzed: wild-type (WT) control and DDB1-deficient (DDB1) Lin-ckit+Sca1+ (LSK) cells sorted from fetal livers E16.5 of DDB1 flox/flox, VavCre+ and control mice.

first: Jie

last: Gao

last: Buckley

first: Guangchun

last: Song

first: Charles

middle: G

last: Mullighan

first: Yong

last: Cang

first: Stephen

last: Goff

first: Iannis

last: Aifantis


title: Comparative expression analysis of roots of two soybean cultivars with contrasting drought-tolerant phenotype under well-watered and dehydration conditions.

status: Public on Jul 02 2015

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

institute: texas tech university

summary: To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used.

overall_design: The Williams 82 and DT2008 soybean plants were grown for 14 days in the vermiculite soil under greenhouse conditions. The whole plants of 14-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 10 h. All roots of independent 14-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.

first: Chien

middle: V

last: Ha

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Lam-Son

last: Tran


title: Response of HK-2 cells to stimulation with IL6 and TNF-alpha (72 hours)

status: Public on Jul 01 2015

city: Stanford

first: Zach

middle: Klapholz

last: O'Brown

address: 279 Campus Drive West

department: Developmental Biology

institute: Stanford

summary: Abstract:  Human kidney function declines with age, accompanied by stereotyped changes in gene expression and histopathology, but the mechanisms underlying these changes are largely unknown. We compared age-associated changes in global gene expression patterns in the human kidney with genome-wide maps of transcription factor occupancy in human cell lines to identify potential regulators of gene expression changes in the aging kidney. The strongest associations involved three inflammation-associated transcription factors: NFκB, STAT1 and STAT3. We found that the activity of these transcription factors increases with age in epithelial compartments of the renal cortex. Stimulation of renal tubular epithelial cells with the inflammatory cytokines IL-6 (a STAT3 activator), IFN-γ (a STAT1 activator), or TNFα (an NFκB activator) recapitulated age-associated gene expression changes. We found that common DNA variants in the two genes that encode the subunits of the canonical NFκB transcription factor (RELA and NFKB1) showed significant associations with kidney function and chronic kidney disease in gene association studies, providing the first evidence for a direct link between genetic variation in NFκB and individual differences in age-related phenotypes in the kidney. Our results point to chronic inflammation, mediated by NFκB, STAT1 and STAT3, as a dominant mechanism influencing gene expression changes during kidney aging.

overall_design: Biological triplicate experiments were performed for each cytokine treatment condition or control treatment.

middle: K


title: Response of HK-2 cells to stimulation with IFN, IL6 and TNF-alpha in different combinations

overall_design: Biological duplicate or triplicate experiments were profiled for each cytokine treatment or control condition


title: Response of HK-2 cells to STAT3 activation by interleukin-6 and inhibition with S3I-201

overall_design: Duplicate or triplicate experiments (biological replicates) were performed for each condition


title: Transcription factor Bcl11b controls identity and function of mature innate lymphoid cells type II

status: Public on Jul 28 2015

city: albany

first: dorina

last: avram

address: 47 new scotland ave

department: center for immunology and microbial disease

institute: albany medical college

type: Expression profiling by high throughput sequencing

summary: Type-2 innate lymphoid cells (ILC2s) promote anti-helminth responses and contribute to allergies. Though Bcl11b has been previously considered a T-lineage identity transcription factor (TF) that restrains the innate-cell genetic programs, we report here that Bcl11b is highly expressed in mature ILC2s and acts upstream of the key ILC2 TFs Gfi1, Gata-3, and of IL-33 receptor IL1rl1 (T1ST2). Additionally, Bcl11b-/- ILC2s de-repressed Rorγt, Ahr and IL-23 receptor, normally expressed in type-3 ILCs (ILC3s). Consequently, Bcl11b-/- ILC2s lost ILC2 functions and gained ILC3 functions, expanding in response to the protease allergen papain, however producing IL-17 and IL-22, and not IL-5 and IL-13, causing lung neutrophilia rather than eosinophilia, and diminished mucus production. Our results broaden Bcl11b's role from a T-cell only TF, and establishes that Bcl11b sustains mature ILC2 genetic and functional programs and lineage fidelity through positive regulation of essential ILC2 TFs and negative regulation of pivotal ILC3 TFs.

overall_design: RNA-seq analysis on sorted ILC2s from the mLNs of Bcl11bF/F Cre-ERT2 and wildtype mice at steady state following tamoxifen mediated deletion of Bcl11b

first: Danielle

last: Califano

first: Dorina

last: Avram


title: Global identification of genes specific for rice meiosis

city: Yangzhou

first: Bingwei

last: Zhang

state: JiangSu

address: 48 Wenhui East Road

department: Agricultural college

country: China

institute: Yangzhou University

summary: The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homolog of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and to identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq, bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast.

overall_design: We sequenced the transcriptome of young panicles of Osam1 mutant and wild-type rice.

first: BingWei

first: Meng

last: Xu

first: ShiQuan

last: Bian

first: LiLi

last: Hou

first: Ding

last: Tang

first: YaFei

last: Li

first: MingHong

last: Gu

first: ZhuKuan

last: Cheng

first: HengXiu

last: Yu


title: miRNA and mRNA profiling of tumor-educated macrophages (miRNA 2)

city: Goettingen

first: Annalen

last: Bleckmann

address: Robert-Koch-Straße 40

department: Hematology/Oncology

country: Germany

institute: University Medical Center Goettingen

summary: We profiled miRNA and mRNA expression of in vitro tumor-educated macrophages (TEM) by indirectly co-culturing with estrogen-receptor-positive (ER+) MCF-7 breast cancer cells.

overall_design: 3 biological replicates of untreated and co-cultured macrophages, parallel analysis of miRNA and mRNA expression

first: Florian

last: Klemm


title: miRNA and mRNA profiling of tumor-educated macrophages (mRNA)


title: miRNA and mRNA profiling of tumor-educated macrophages (miRNA 1)

overall_design: 2 biological replicates of untreated and co-cultured macrophages, parallel analysis of miRNA and mRNA expression


title: Perturbed neonatal size is associated with differential DNA methylation and gene expression in human placentas

status: Public on Jun 30 2015

city: Cold Spring Harbor

first: Wen-Wei

last: Liao

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

type: Methylation profiling by high throughput sequencing

summary: Fetal growth in utero is affected by both inherent genetic programming in combination with environmental factors, such as maternal health and nutrition. Epidemiologic data in growth-altered fetuses, either growth-restricted (IUGR) or large for gestational age (LGA), demonstrate compelling evidence that these fetuses are at increased risk for cardiovascular and metabolic disease in adulthood. In this study, we used RRBS to examine genome wide DNA methylation variation in placental samples from offspring born IUGR, LGA, and appropriate for gestational age (AGA). We identified almost 200 differentially methylated genes among these groups. Among these genes, the differentially methylated regions were disproportionately located in transcription-regulatory regions such as promoters. Our results suggest that the gene expression and methylation state of the human placenta are related and sensitive to the intrauterine environment.

overall_design: We profiled DNA methylation for 17 human placentas, in which 5 were from LGA, 6 from IUGR and 6 from AGA placentas as controls

first: Pao-Yang

last: Chen

first: Alison

last: Chu

first: Liudmilla

last: Rubbi

first: Carla

last: Janzen

first: Fei-Man

last: Hsu

first: Amit

last: Ganguly

first: Shanthie

last: Thamotharan

first: Matteo

last: Pellegrini

first: Sherin

middle: U

last: Devaskar


title: miRNA and mRNA profiling of tumor-educated macrophages

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

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

overall_design: Refer to individual Series


title: Transcriptional programs that regulate brain cortical development

status: Public on Jun 27 2015

city: London

first: Justyna

last: Nitarska

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

institute: University College London

summary: Dynamic changes of histone epigenetic modifications and chromatin structure represent an universal mechanism by which cells adapt their transcriptional response to rapidly changing environmental conditions.  During neuronal development, extensive chromatin remodelling takes place allowing the transition of pluripotent cells into differentiated neurons. Here we investigate the transcriptional programs that are differentially regulated during cortical development in vivo.

overall_design: Gene expression analysis was performed in the mouse embryonic cortex at three developmental stages: E12.5, E15.5 and E18.5 using total RNA obtained from four embryos for each time point.

first: Richard

last: Mitter

first: Antonella

last: Riccio


title: Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome

status: Public on Jun 29 2015

city: Heidelberg

first: Bastian

last: Linder

address: Meyerhofstraße 1

department: Genome Biology Unit

institute: European Molecular Biology Laboratory (EMBL)

summary: N6-methyladenosine (m6A) is the most abundant modified base in eukaryotic mRNA and has been linked to diverse effects on mRNA fate and function.  Current m6A mapping approaches rely on immunoprecipitation of m6A-containing RNA fragments to identify regions of transcripts that contain m6A.  This approach localizes m6A residues to 100-200 nt-long regions of transcripts.  The precise position of m6A in mRNAs cannot be identified on a transcriptome-wide level because there are no chemical methods to distinguish between m6A and adenosine.  Here we show that anti-m6A antibodies can induce specific mutational signatures at m6A residues after ultraviolet light-induced antibody-RNA crosslinking and reverse transcription.  Similarly, we find these antibodies induce mutational signatures at N6, 2’-O-dimethyladenosine (m6Am), a nucleotide found at the first encoded position of certain mRNAs.  Using these mutational signatures, we map m6A and m6Am at single-nucleotide resolution in human and mouse mRNA and identify snoRNAs as a novel class of m6A-containing ncRNAs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: UV-crosslinking and immunoprecipitation with m6A-specific antibodies was used to map m6A and m6Am in cellular RNA with single nucleotide resolution.

first: Anya

last: Grozhik

first: Anthony

middle: O

last: Olarerin-George

first: Cem

last: Meydan

first: Christopher

last: Mason

first: Samie

middle: R

last: Jaffrey


title: Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation

status: Public on Jul 23 2015

city: Rehovot

first: kfir

middle: baruch

last: Umansky

state: Rehovot

address: POB 25

country: Israel

institute: Weizmann Institute

type: Genome binding/occupancy profiling by high throughput sequencing


title: Extensive transcriptome changes during vegetative bud dormancy in Populus

status: Public on Jun 26 2015

city: Corvallis

first: Glenn

last: Howe

state: OR

address: 321 Richardson Hall

department: Forest Ecosystems and Society

institute: Oregon State University

summary:
We investigated differential gene expression patterns in Populus vegetative buds between paradormant, endodormant, and ecodormant dormancy states.
Our primary objectives were to (1) identify which individual genes, biological processes, molecular functions, and regulatory pathways were differentially expressed among dormancy states, (2) classify the differentially expressed genes into contrasting gene expression patterns, and (3) identify cis-acting elements associated with each gene expression group.
For more details consult Howe et al. (Frontiers in Plant Science, 2015, pending).

overall_design:
Nimblegen whole genome microarrays (n=10 arrays) were hybridized with total RNA isolated from axillary buds collected on five dates between August and March.
On each date, RNA was isolated from two P. trichocarpa trees (clone Nisqually-1) growing in the field.  After cDNA synthesis and labeling, the samples were sent to NimbleGen for fragmentation, hybridization, and detection.
The Nimblegen microarray was designed for the Populus v1.0 genome assembly, but for data analysis, the 60-mer probes were reassigned to the Populus v3.0 gene models.

middle: T

first: David

last: Horvath

first: Palitha

last: Dharmawardhana

first: Henry

middle: D

last: Priest

first: Todd

middle: C

last: Mockler

first: Steven

middle: H

last: Strauss


title: Response of HK-2 cells to stimulation with IL6 and TNF-alpha (90 minutes)

first: Zach

last: O'Brown


title: Differentiating human embryonic stem cells into corneal epithelial-like cells

status: Public on Jun 24 2015

city: Qingdao

first: zhenyu

last: wang

address: No. 5. Yanerdao Road

institute: Shandong Eye Institute

summary: Transplantation of ex vivo expanded limbal stem cells (LSC) is the main treatment for limbal stem cell deficiency though the clinical problem of donor tissues shortage. Recently, as the development of tissue engineering, embryonic stem cells (ESC) derived corneal epithelial-like cells (ESC-CEC) has become a new direction to this issue.Our group successfully induced ESC into corneal epithelial-like cells, and in the present study we explored various aspects of physiological properties of ESC-CEC.

overall_design:
The experiment included three samples: hES, the human embryonic stem cell line H1, RA_SB, the corneal epithelial-like cells derived from hES by differentiation with RA and SB, epithelial_cell, the primary human limbal stem cells from cadaver eyes.
hES, the human embryonic stem cell line H1,
RA_SB, the corneal epithelial-like cells derived from hES by differentiation with RA and SB,
epithelial_cell, the primary human limbal stem cells from cadaver eyes.

first: Qingjun

last: Zhou

first: Haoyun

last: Duan

first: Yao

last: Wang

first: Zhenyu

first: Muchen

last: Dong

first: Weiyun

last: Shi


title: Escherichia coli DH5α: Control vs dr1558 expression

city: chongup

first: sun

middle: wook

last: Jeong

state: Chonbuk

address: Sinjeongdong 1266

department: Radiation biotechnology

country: South Korea

institute: Korea atomic energy research institute

summary:
Transcriptional profiling of E. coli cells comparing control harboring the empty vector pRadGro (Ec-pR) with E. coli expressing the Deinococcus radiodurans response regulator DR1558 (Ec-1558)
Expression of DR1558 conferred to multi-stress tolerance to E. coli.

overall_design: Cells grown to exponential phase (OD600 = 0.8) were harvested. Biological replicates, 3. Escherchia coli K12 oligonucleotide 3X15 K microarray (MYcroarray Inc. USA)

first: Deepti

last: Appukuttan

first: Sangyong

last: Lim


title: An interactive database for the assessment of histone antibody specificity

status: Public on Jun 21 2015

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: Commercially available histone antibodies were analyzed using peptide microarrays to assess specificity. For two H3K27me3 antibodies from different vendors, we performed ChIP-seq in WT and EED-null murine ES cells to assess specificity. Cell lines were generated from e3.5 blastocysts of EED fl/fl animals and transfected with plasmid CAG-CRE-ERT2. Null cells were generated by single cell clones from tamoxifen-treated parent cell line.

overall_design:
Analysis of the specificity of two H3K27me3 antibodies using WT and EED (Embryonic Ectoderm Develepment)-null (mutants lacking H3K27me3) ES cells. The goal was to compare WT and KO for each antibody with the expectation that if the antibodies were specific, there would remain few peaks and little signal in the knockout. We sequenced 2 replicates of each condition (3 for WT input) and after comparing replicates, we merged data, called peaks, and calculated signal in bins centered on the wild type H3K27me3 peaks. As little to no signal remained either by direct comparison of peaks or looking at 'metagenes' of the peaks, we concluded that the antibodies were specific.

Antibodies:
Abcam H3K27me3 (ab6002, lot# GR130002-1)
Upstate H3K27me3 (07-449, lot# 2455635)


title: Expression data in HeLa cells treated with CENP-E siRNA or Eg5 siRNA in the presence of BubR1 siRNA

status: Public on Jun 25 2015

city: Fujisawa

first: Akihiro

last: Ohashi

address: 26-1 Muraoka-Higashi 2-chome

department: Oncology Drug Discovery Unit

country: Japan

institute: Takeda Pharmaceutical Company Ltd.

summary:
The molecular mechanism responsible for cell fate after mitotic slippage is unclear. We investigate the postmitotic effects of different mitotic aberrations, misaligned chromosomes produced by CENP-E siRNA (siCENP-E), and monopolar spindles resulting from Eg5 siRNA (siEg5).
To determine which signaling pathways contribute to the postmitotic effect of siCENP-E in the presence of siBubR1 (siCENP-E+siBubR1) compared with siEg5+siBubR1, we performed a comprehensive gene expression analysis by microarray comparisons.
SUBMITTER_CITATION: Expression data of HeLa cells treated with CENP-E siRNA or Eg5 siRNA in the presence of BubR1 siRNA, Yusuke Nakayama, Akihiro Ohashi, Genomics Data, Volume 6, December 2015, Pages 44-45, doi:10.1016/j.gdata.2015.08.002

overall_design: HeLa cells were treated with siNS (non-silencing) +siBubR1, siCENP-E+siBubR1, or siEg5+siBubR1. The siNS cells were used as a control. Each siRNA treatment was duplicated. Three days after the siRNA treatments, the siRNA-transfected HeLa cells were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yusuke

last: Nakayama


title: The P. aeruginosa PA14 transcriptome recorded under 14 different experimental conditions

status: Public on Jun 16 2015

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

summary: We analyzed the transcriptional profile of P.aeruginosa PA14 grown under 14 different environmental conditions. These included conditions of growth within biofilms, at various temperatures, osmolarities and phosphate concentrations, under anaerobic conditions, attached to a surface and conditions encountered within the eukaryotic host. We found that >30% of the PA14 genome was differentially regulated at least under one of the 14 environmental conditions (referred to as the adaptive transcriptome). Most of the genes were also differentially regulated upon sigma factor hyper expression and/or inactivation (GEO accession number GSE54999) and many of those belonged to primary alternative sigma factor regulons.

overall_design:
The samples of P. aeruginosa PA14 wild type strain were cultivated under 14 different experimental conditions and were analyzed by RNA-seq. For each condition, at least two biological replicates were generated
Please note that PA14 is our standard lab strain used for all generated data in this records. There is no mutation introduced for any of those experiments, and thus, the descriptions only highlight the growth conditions.

first: Sebastian

last: Schulz

first: Susanne

last: Häussler


title: Tumor exosome integrins determine organotropic metastasis

status: Public on Jun 17 2015

city: New York

first: David

last: Lyden

department: Departments of Pediatrics, Cell & Developmental Biology

institute: Weill Medical College of Cornell University

summary: Stephen Paget first proposed, in 1889, that organ distribution of metastases is a non-random event, yet metastatic organotropism remains one of the greatest mysteries in cancer biology. Here, we demonstrate that exosomes released by lung-, liver- and brain-tropic tumor cells fuse preferentially with resident cells at their predicted destination, such as fibroblasts and epithelial cells in the lung, Kupffer cells in the liver, and endothelial cells in the brain. We found that exosome homing to organ-specific cell types prepares the pre-metastatic niche and that treatment with exosomes derived from lung tropic models can redirect metastasis to the lung. Proteomic profiling of exosomes revealed distinct integrin expression patterns associated with each organ-specific metastasis. Whereas exosomal integrins α6β4 and α6β1 were associated with lung metastasis, exosomal integrins αvβ5 and αvβ3 were linked with liver and brain metastases, respectively. Targeting α6β4 and αvβ5 integrins decreased exosome uptake and metastasis in the lung and liver, respectively. Importantly, we demonstrate that exosome uptake activates a cell-specific subset of S100 family genes, known to support cell migration and niche formation. Finally, our clinical data indicate that integrin-expression profiles in circulating plasma exosomes from cancer patients could be used to predict organ-specific metastasis.

overall_design: Education of human von Kupffer cells in vitro with human pancreatic cancer exosomes

first: Ayuko

last: Hoshino

first: Bruno

last: Costa-Silva

first: Tang-Long

last: Shen

first: Goncalo

last: Rodrigues

first: Ayako

last: Hashimoto

first: Milica

last: Tesic Mark

first: Henrik

last: Molina

first: Shinji

last: Kosaka

first: Angela

last: Di Giannatale

first: Sophia

last: Ceder

first: Swarnima

last: Singh

first: Caitlin

last: Williams

first: Yonathan

last: Ararso

first: Tuo

last: Zhang

first: Elin

last: Kure

first: Kavita

last: Mallya

first: Surinder

last: Batra

first: Rajesekhar

last: Vinagolu

first: Oystein

last: Fodstad

first: Volkmar

last: Muller

first: Klaus

last: Pantel

first: Mina

middle: J

last: Bissell

first: Cyrus

last: Ghajar

first: Benjamin

middle: A

last: Garcia

first: Yibin

last: Kang

first: Irina

last: Matei

first: Hector

last: Peinado

first: Jacqueline

last: Bromberg


title: Nitrosative stress response in uropathogenic Escherichia coli (UPEC)

status: Public on Jun 15 2015

city: Richardson

first: Stephen

last: Spiro

address: 800 W Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

summary: A strain of UPEC CFT073 lacking the three known NO detoxifiaction mechanisms, Hmp, FlRd and Nrf is used to study the global effect of NO on the pathogen

overall_design: Cultures were anaerobically grown in triplicates under two conditions: Without nitrosative stress or with nitrosative stress, induced by anaerobic growth on nitrate. RNA was extracted from the samples and following rRNA depletion, samples were analyzed by RNA-seq for genome wide transcriptional differences.

first: Heer

last: Mehta

first: Yuxuan

last: Liu

first: Michael


title: A mex3 homolog is required for differentiation during planarian stem cell lineage development

city: Portland

first: Bret

last: Pearson

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: Neoblasts are adult stem cells (ASCs) in planarians which sustain cell replacement during homeostasis and regeneration of any missing tissue.  While numerous studies have examined genes underlying neoblast pluripotency, molecular pathways driving the postmitotic fate remain poorly defined.   Here we used transcriptional profiling of irradiation-sensitive and -insensitive cell populations and RNA interference (RNAi) functional screening to uncover markers and regulators of postmitotic progeny.  We identified 32 new markers, which distinguish two epithelial progenitor populations, and a planarian homolog to the MEX3 RNA-binding protein (Smed-mex3-1) as a key regulator of lineage progression.  mex3-1 is required for generating progenitors of epithelial, neural, eye, pharyngeal, and protonephridial lineages, and restricting expansion of the stem cell compartment.  We also demonstrate the utility of using mex3-1(RNAi) animals to identify additional progenitor markers.  These results show that mex3-1 promotes differentiation in multiple, if not all, lineages, and maintains the balance between ASC self-renewal and commitment.

overall_design: Sorted and irradiated animals were collected as previously described (Labbe, et al., 2012) and RNAi conditions were triplicated, RNA was purified independently, then each replicate was pooled in equal amounts for sequencing at the timepoint:  1 feed day 12 for control RNAi and mex3-1 RNAi.

first: Shu-Jun

last: Zhu

first: Stephanie

middle: E

last: Hallows

first: Ko

middle: W

last: Currie

first: ChangJiang

last: Xu


title: Splenic gene expression profile of mice immunized with an anti-Fasciola hepatica vaccine candidate: insights into the immunological mechanisms leading to protection

status: Public on Jun 06 2015

city: Salamanca

first: Jose

last: Rojas-Caraballo

state: Salamanca

address: C/Licenciado Mendez Nieto s/n

department: Molecular Parasitology and Immunology

country: Spain

institute: University of Salamanca

summary: Fasciolosis remains an important food-borne tremaode disease causing high morbidity around the world and affecting grazing animals and humans. A deeper understanding concerning the molecular mechanisms by which Fasciola hepatica infection occurs as well as the molecular basis involved in acquiring protection is extremely important in designing and selecting new vaccine candidates. The present study gives a first report of microarray-based technology for describing changes in splenic gene expression profile for mice immunised with a highly effective, protection-inducing,multi-epitope, subunit-based, chemically-synthesised vaccine candidate. Female CD1 mice were immunised with synthetic peptides containing B- and T-cell epitopes as novel vaccine candidates and challenged with Fasciola hepatica metacercariae.  Spleen RNA from mice immunised with the highest protection-inducing synthetic peptides was isolated, amplified and labelled using Affymetrix standardised protocols. The Ingenuity Pathway Analysis tool was used to annotate bio-functions and constructing and visualising molecular interaction networks. Immunising mice with a combination of three peptides containing T-cell epitopes induced high protection against experimental challenge according to survival rates and hepatic damage scores. It also induced differential expression of 820 genes; 168 being up-regulated and 652 down-regulated. Functional study revealed changes in pathways related to nitric oxide and reactive oxygen species production, IL-12 signalling and production in macrophages and IL-8 signalling with up-regulation of S100A8, MMP9 and CXCR2 genes. The data obtained in the present study provided us with a more comprehensive overview concerning the possible molecular pathways implied in inducing protection against Fasciola hepatica in a murine model

overall_design: Three mice were used as healthy controls and remained untreated along the experiment. Three mice were subcutaneously immunised with our vaccine candidate on day 0, and two booster doses were applied on days 14 and 28, respectively. Two-weeks after the last immunisation, all of the mice used in the present study (including controls) were humanely euthanised by intraperitoneal injection of pentobarbital (60mg/Kg) and necropsied for spleen recovery and RNA isolation using standardised protocols. Splenic gene expression profile was compared between healthy and immunised groups.

first: Julio

last: Lopez-Aban

first: Darwin

last: Moreno-Perez

first: Belen

last: Vicente

first: Pedro

last: Fernandez-Soto

first: Esther

last: del Olmo

first: Manuel

last: Patarroyo

first: Antonio

last: Muro


title: Myc-driven medulloblastoma cells treated with Panobinostat (LBH589)

status: Public on Jun 02 2015

city: La Jolla

first: Kun-Wei

address: 10901 N Torrey Pines Rd

institute: Sanford-Burnham Medical Research Institute

summary:
Mouse MycT58A/DNp53 (MP) medulloblastoma cells were treated with DMSO or HDAC inhibitor (HDACi) panobinostat for 6 or 12 hours in vitro.
Gene expression profiling was performed to compare cells treated with panobinostat and DMSO.

overall_design: Using the mouse model for MYC-driven Group 3 medulloblastoma, we tried to understand the mechanism of HDACi-induced cytotoxicity by comparing the gene expression profiles of cells treated with panobinostat (LBH-589) to cells treated with DMSO control.

first: Robert

last: Wechsler-Reya


title: MicroRNAome of Spodoptera frugiperda cells (Sf9) and its alteration following baculovirus infection

status: Public on Jun 11 2015

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) as small non-coding RNAs play important roles in many biological processes such as development, cell signalling and immune response. Studies also suggest that miRNAs are important in host–virus interactions where the host limits virus infection by differentially expressing miRNAs that target essential viral genes. Here, we identified conserved and new miRNAs from Spodoptera frugiperda cells (Sf9) using a combination of deep sequencing and bioinformatics as well as experimental approaches. S. frugiperda miRNAs share common features of miRNAs in other organisms, such as uracil (U) at the 59 end of miRNA. The 59 ends of the miRNAs were more conserved than the 39 ends, revealing evolutionary protection of the seed region in miRNAs. The predominant miRNAs were found to be conserved among arthropods. The majority of homologous miRNAs were found in Bombyx mori, with 76 of the 90 identified miRNAs. We found that seed shifting and arm switching have happened in this insect’s miRNAs. Expression levels of the majority of miRNAs changed following baculovirus infection. Results revealed that baculovirus infection mainly led to an overall suppression of cellular miRNAs. We found four different genes being regulated by sfr-miR-184 at the post-transcriptional level. The data presented here further support conservation of miRNAs in insects and other organisms. In addition, the results reveal a differential expression of host miRNAs upon baculovirus infection, suggesting their potential roles in host–virus interactions. Seed shifting and arm switching happened during evolution of miRNAs in different insects and caused miRNA diversification, which led to changes in the target repository of miRNAs.

overall_design: Identification of miRNA and other small non coding RNA in NPV infected Sf9 cells

first: Sassan

last: Asgari


title: Elucidating the etiology and molecular pathogenicity of infectious diarrhea by high throughput RNA sequencing

status: Public on Jun 04 2015

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

summary: Diarrhea remains a major cause of death in children. Current diagnostic methods largely rely on stool culture and suffer from low sensitivity and inadequate specificity, often leading to inappropriate treatment. The objective of the present study was to use RNA sequencing (RNAseq) analysis to determine blood transcriptional profiles specific for several common pathogenic bacteria and viruses that cause diarrhea in children. We collected whole blood samples from children in Mexico having diarrhea associated with a single pathogen and without systemic complications. Our RNAseq data suggested that the blood signatures can differentiate children with diarrhea from healthy children either with or without bacterial colonization. Moreover, we detected different expression profiles from bacterial and viral infection, demonstrating for the first time the use of RNAseq to identify the etiology of infectious diarrhea.

overall_design: 255 whole blood samples from 246 children including children with diarrhea caused by rotavirus (n=60 total; 5 repeated; 55 unique), E.coli (n=55), Salmonella (n=36), Shigella (n=37), adenovirus (n=8), norovirus (n=7), and control children (n=52 total; 4 repeated; 48 unique).

first: Prasong

last: Khaenam

first: Mussaret

last: Zaidi

first: Teresa

last: Estrada-Gracia

first: Dimitry

last: Popov

first: Kimberly

last: O'Brien

first: Quynh-Anh

last: Nguyen

first: Vivian

last: Gersuk

first: James

last: Eddy

first: Peter

middle: S

last: Linsley


title: DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma.

status: Public on Jun 03 2015

city: Esplugues de Llobregat

first: Cinzia

last: Lavarino

state: Barcelona

address: Santa Rosa 39-57

department: Oncology

institute: Hospital Sant Joan de Déu

type: Methylation profiling by genome tiling array


title: Differential mRNA expression profile regulated by HNF4α in Hep3B cells

status: Public on Jun 01 2015

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

summary:
A previous study from this laboratory demonstrated that up-regulating HNF4a could reverse the malignant phenotypes of HCC by inducing redifferentiation of HCC cells to hepatocytes. To study the mechanisms of the hepatic differentiation effect by HNF4α, we used the cDNA microarray to detect differential gene expression profiles of Hep3B infected with AdHNF4α and AdGFP.
Expression profile analysis revealed that HNF4α positively regulated 1218 mRNAs and negatively regulated 1411 mRNAs for more than 2 times. The pathway analysis for the differential genes showed that the genes were involved in Complement and coagulation cascades, metabolism, Type II diabetes mellitus, Pathways in cancer etc.

overall_design: Hepatoma cell lines Hep3B cells were seeded onto culture dishes  and infected with AdHNF4α and AdGFP (as a control) at MOI 100. After Hep3B was infected by AdHNF4α or AdGFP for 72 hours, the cells were collected for cDNA Microarray analysis.

first: Chuan

last: Yin

first: Junliang

last: Hou

first: Xin

last: Zhang

first: Weifen

last: Xie


title: DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [gene expression]

summary:
DNA methylation changes in neuroblastoma, a clinically-heterogeneous pediatric tumor, have been described essentially in promoter regions. We analyzed the DNA methylome of neuroblastoma using high-density microarrays and observed differential methylation not only in promoters but also in intragenic and intergenic regions at both CpG and non-CpG sites. These epigenetic changes showed a non-random distribution relative functional chromatin domains, and targeted development and cancer-related genes, relevant for neuroblastoma pathogenesis. CCND1, a gene overexpressed in neuroblastoma, showed hypomethylation of gene-body and upstream regulatory regions. Furthermore, tumors with diverse clinical-risk showed clear differences affecting CpG and, remarkably, non-CpG sites. Non-CpG methylation was present in clinically-favorable tumors and affected genes such as ALK, where non-CpG methylation correlated with low gene expression. Finally, we identified CpG and non-CpG methylation signatures which correlated with patient’s age at time-points relevant for neuroblastoma clinical behavior, and targeted genes related to neural development and neural crest regulatory network
We report on the first DNA methylomes of neuroblastoma tumors using high-density microarrays. DNA methylation changes in this pediatric tumor affected both CpG and non-CpG sites associated with developmental and cancer-related genes such as CCND1 and ALK. Our study also provides new insights into the molecular basis of the heterogeneous clinical behavior of neuroblastoma.

overall_design: RNA from 20 neuroblastoma tumor and 4 non patological tissues (2 fetal brain and 2 adrenal gland) samples  were hybridised to the Affymetrix Human Genome U219- 24array plate.


title: DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [methylation]

overall_design: Bisulphite converted DNA from the 35 neuroblastomas tumor, 2 ganglioneuromas and 4 non patological tissues ( 2 fetal brain and 2 adrenal gland) samples  were hybridised to the Illumina Infinium HumanMethylation450K BeadChip


title: Transcriptome analysis of Sch9-depedent thermotolerance mechanism reveals a dual functional heat shock transcription factor, Hsf1, in Cryptococcus neoformans [HSF1 overexpression]

city: Seoul

first: Dong-Hoon

last: Yang

address: Yonsei-ro 50

institute: Yonsei University

summary: Thermotolerance is a crucial virulence attribute for Cryptococcus neoformans, which causes fatal fungal meningitis in humans. A protein kinase, Sch9, suppresses the thermotolerance of C. neoformans but its regulatory mechanism remains unknown. Here we elucidated the Sch9-dependent and -independent signaling networks for modulating the thermotolerance of C. neoformans through a genome-wide transcriptome analysis and reverse genetics approaches. We found that more than 1,800 genes were under transcriptional control during temperature upshift. Genes encoding for molecular chaperones and heat shock proteins were mainly upregulated, while those for translation, transcription, and sterol biosynthesis were highly suppressed. In this process Sch9 was found to regulate basal or induced expression levels of some temperature-responsive genes. Interestingly we found that Sch9 was involved in transcriptional regulation of the Ire1 kinase, which is a key sensor for the unfolded protein response pathway, and was found to be involved in ER stress response. Most notably, our data demonstrated that expression of HSF1, encoding a heat shock transcription factor 1, was downregulated during temperature upshift and Sch9 suppresses its downregulation. In spite of such expression patterns, Hsf1 was essential for growth and its overexpression indeed promoted the thermotolerance of C. neoformans, suggesting dual roles of Hsf1 in thermotolerance. This idea was supported by additional transcriptome analysis with HSF1 overexpression strain, which revealed that Hsf1 served as both activator and repressor. Hsf1 promoted genes such as Hsp104 and Hsp70 (Ssa1 and Ssa2), both of which were found to be highly upregulated during temperature upshift and required for thermotolerance, while Hsf1 repressed genes involved in oxidative stress and thermotolerance.

overall_design: There are more than 95% of genome homology between JEC21 and H99. Therefore 6 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligo are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted  2 strains from H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A), PH3:HSF1), We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy3 as Sample dye and Cy5 as a control dye.

first: Kwang-Woo

last: Jung

first: Soohyun

last: Bang

first: Jang-Won

last: Lee

first: Min-Hee

last: Song

first: Anna

last: Floyd

first: Richard

last: Festa

first: Giuseppe

last: Ianiri

first: Alex

last: Idnurm

first: Dennis

last: Thiele

first: Joseph

last: Heitman

first: Yong-Sun

last: Bahn


title: Effect of miR-650 overexpression on gene expression profile of human monocyte-derived dendritic cells

status: Public on May 27 2015

city: Tuebingen

first: Tica

last: Pichulik

address: Auf der Morgenstelle 15

institute: University of Tuebingen

summary: Transcriptional profiling of human monocyte-derived dendritic cells, comparing cells transfected for 24h with Pre-miR-650 or nonsense control.

overall_design: 2 condition experiment: nonsense control versus miR-650 mimic - 3 biological replicates for each condition and control

first: Alison

last: Simmons


title: Transcriptome analysis of Sch9-depedent thermotolerance mechanism reveals a dual functional heat shock transcription factor, Hsf1, in Cryptococcus neoformans [mutants]

overall_design: There are more than 95% of genome homology between JEC21 and H99. Therefore 36 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligo are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted  4 strains from H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A), sch9delta, iredelta, hxldelta), We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy3 as Sample dye and Cy5 as a control dye.


title: Wide-spread disruption of transcription termination in HSV-1 infection:  Next generation sequencing of total and newly transcribed (4sU-RNA) RNA

status: Public on May 26 2015

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. Newly transcribed RNA was purified following the protocol described in Raedle et al. JoVE 2013.

overall_design: Newly transcribed RNA was labelled in one hour intervals during the first eight hours of HSV-1 infection. All nine 4sU-RNA samples as well as total cellular RNA of every second hour of infection were sent for sequencing. Two independent biological replicates were analysed.

first: Andrzej

last: Rutkowski

first: Florian

last: Erhard

first: Anne

last: L'Hernault

first: Thomas

last: Bonfert

first: Markus

last: Schilhabel

first: Colin

last: Crump

first: Philip

last: Rosenstiel

first: Stacey

last: Efstathiou

first: Ralf

last: Zimmer

first: Lars

last: Dölken


title: Transcriptome analysis of Sch9-depedent thermotolerance mechanism reveals a dual functional heat shock transcription factor, Hsf1, in Cryptococcus neoformans

first: Dong-Hoon

last: Yang

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

overall_design: Refer to individual Series


title: Arsenic-Associated Differential DNA Methylation in Human Uroepithelial Cells

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary: There is strong epidemiologic evidence supporting that exposure to inorganic arsenic (iAs) exposure is responsible for a myriad of adverse health effects, including carcinogenesis of the bladder. This research aimed to identify novel epigenetic biomarkers of iAs exposure in target cells within a human population. Here we assessed genome-wide, gene-specific promoter DNA methylation levels assessed in exfoliated human bladder uroepithelial cells (BECs) in relationship to BEC iAs, monomethylated As (MMAs), dimethylated As (DMAs), and total As (tAs) concentrations from 46 individuals with varying levels of As exposure in Chihuahua, Mexico. These analyses identified genes with increased methylation associated with BEC iAs(III+V), MMAs(III+V), and tAs(III+V).  These genes were enriched for signaling related to metabolic disease and cancer.

overall_design: Individuals participating in the present study (n=46) represent a subcohort of a larger study (n=374) among residents of Chihuahua, Mexico, recruited between 2008 and 2013. Study participants were required to be at least 18 years of age and have at least 5 years of uninterrupted residency in the study area. Urine samples were collected and uroepithelial cell isolation occurred immediately. Exfoliated bladder uroepithelial cells (BECs) were isolated from freshly collected urine. As species in BECs were measured using hydride generation (HG) with preconcentration by cryotrapping (CT) and inductively coupled plasma-mass spectrometry (ICP-MS) (HG-CT-ICP-MS). DNA was extracted from the exfoliated BECs of 46 subjects using the QIAamp DNA Blood Mini Kit (Qiagen, Valenica, CA) according to manufacturer’s instruction. CpG-methylated DNA was isolated using the MethylMinerTM Methylated DNA Enrichment Kit (Invitrogen/Life Technologies, Grand Island, NY), amplified, and hybridized to Affymetrix Human Promoter 1.0R arrays.

first: Julia

last: Rager


title: Comparison of gene expresson between larger sized tetraploid and smaller sized diploid HCA2

status: Public on May 22 2015

city: Minato-ku

first: Yoshikazu

last: Johmura

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

institute: University of Tokyo

summary: In order to determine the factors that regulate senescence induction, we tried to identfy genes that are predominantly expressed in large sized senescent cells with tetraploid DNA.

overall_design: We sorted large or small sized HCA2 cells treated wth IR (10Gy) according to size and structure (FSC and SSC) by FACScan and analyzed global gene expression patterns.

first: Makoto

last: Nakanishi


title: Genome wide binding sites of NsrR in uropathogenic E.coli CFT073

first: Stephen

last: Spiro

summary: We applied ChIP-seq to identify genome wide binding targets of NsrR in E.coli CFT073. NsrR is a nitric oxide sensitive regulator of transcription.  Genome wide binding targets of NsrR have been identified in E.coli K12 using ChIP-chip. The genome of CFT073 is about 0.6Mb larger than that of K12. In this study,  we identify the novel NsrR binding sites in CFT073.

overall_design: The nsrR gene was modified by the addition of DNA sequences encoding a C-terminal 3X-Flag tag, and the tagged gene was integrated into the chromosome. NsrR bound DNA was isolated by chromatin immunoprecipitation and  it was sequenced using Miseq platform.

first: Yuxuan

last: Liu

first: Michael

last: Zhang


title: Expression data from HeLa cells treated with RZ2

status: Public on May 19 2015

city: Barcelona

first: Oscar

last: Reina Garcia

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

summary:
The newly sinthesized compound RZ2 induces cell death to human cancer cells. To obtain insights into its mechanism of action, the effects on autophagy and apoptosis were examined.
Global perturbations in genome-wide RNA expression of HeLa cells treated with RZ2 were measured by gene expression microarray.

overall_design: Confluent cultures of HeLa cells were treated with 5 μM RZ2 or the vehicle (DMSO) for 24 hours, followed by RNA preparation and hybridization to a GeneChip PrimeView Human Gene Expression Array (Affymetrix)

first: Rubí

last: Zamudio-Vázquez

first: Saška

last: Ivanova


title: Development of gene expression for an INH-responsive transcriptional regulator InbR

status: Public on May 30 2015

city: wuhan

first: yang

last: min

state: Hubei

address: No. 1, Shizishan Road/Street, Hongshan District

institute: Huazhong Agricultural University

summary: To further determine the gene expression profile of InbR, encoded by Rv0275c in Mycobacterium tuberculosis, whole genome microarray analysises were applied to inbR-overexpressing strain and wild type Mycobacterium bovis BCG. Comparison of the gene expression pattern of logarithmic growth phase wild-type M. bovis BCG and that of the inbR-overexpression strain revealed a total of 142 genes that were significantly up-regulated (2-fold to 187-fold, p < 0.05) and 200 that were down-regulated (2-fold to 113-fold, p < 0.05). Strikingly, most of the genes in the regulon were predicted to function as molecular chaperones, heat shock proteins, or transcription factors.

sample_organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

overall_design: Microarrays used in this study consisted of 15744 60-mer probes, which were synthesized in situ by Agilent Technologies. The probes were designed based on the genome sequences of M. bovis BCG Pasteur_1173P2_uid58781 (GenBank accession numbers: NC_008769) and covered 3934 ORFs. Each probe was repeated thrice on the array. The Inb-overexpression M. bovis BCG strain, M. bovis BCG wild-type strain, and INH-treated strain (M. bovis BCG wild-type strain grown on exponential phase OD600 ≈ 0.8 and treated with 0.5 μg/mL INH for 24 h) grown on exponential phase OD600 ≈ 1.2 were harvested. Total RNA was extracted and purified using RNeasy mini kit (Cat. #74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions. RNA integrity was determined by utilizing RNA integrity number (RIN) generated using an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat. #5190-2305, Agilent technologies) following the manufacturer’s instructions. Labeled cRNA were purified using the RNeasy mini kit.   Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit of Agilent technologies (Cat. #5188-5242) according to the manufacturer’s instructions. After 17 h of hybridization with 15744 60-mer probes, slides were washed in staining dishes (Cat. # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat. # 5188-5327, Agilent Technologies) following the manufacturer’s instructions. Slides were scanned using an Agilent Microarray Scanner (Cat. # G2565CA) with default settings; Dye channel: Green; Scan resolution = 5 μm; and PMT = 100% and 10%, 16 bit. Data were extracted with Feature Extraction software (ver. 10.7, Agilent Technologies). Raw data were normalized using the Quantile algorithm in the Gene Spring Software (ver. 11.0, Agilent Technologies). Normalized microarray expression data deemed significant (P ≤ 0.05) from the InbR-overexpression M. bovis BCG or BCG exposed to INH were selected, and the genes with fold change > 2.0 were selected for further analysis.

first: Min

first: Chun-Hui

last: Gao

first: Jialing

last: Hu

first: Lei

last: Zhao

first: Qiaoyun

last: Huang

first: Zheng-Guo

last: He


title: Genome-wide DNA-binding profile of the Vibrio cholerae histone-like nucleoid structuring protein (H-NS)

status: Public on May 13 2015

city: Atlanta

first: Julio

middle: C.

last: Ayala

state: Georgia

address: 1600 Clifton Rd NE Rm 3-642

department: Division of STD Prevention

institute: Centers for Disease Control and Prevention

summary: The cholera disease bacterium V. cholerae, can adopt planktonic or biofilm lifestyles depending on the intracellular concentration of the second messenger cyclic diguanylic acid (c-di-GMP). Biofilm formation protects Vibrios from stressful conditions and facilitates disease transmission by enhancing infectivity. The histone-like nucleoid structuring protein (H-NS) is a global regulator of genes associated with pathogenicity and responses to environmental stresses. H-NS represses the transcription of genes vpsT, vpsA and vpsL, which are required for the biosynthesis of the biofilm exopolysacchide matrix. Here we demonstrate that the c-di-GMP-binding protein VpsT disrupts H-NS nucleoprotein complexes at the vpsA and vpsL promoters and that this effect is enhanced by c-di-GMP. We used ChIP coupled with Next Generation Sequencing (ChIP-Seq) and transcriptome analysis (RNA-Seq) to identify additional loci repressed by H-NS affecting biofilm formation. This study showed that H-NS directly represses the transcription of genes encoding proteins present in the biofilm matrix such as the rbmA-F cluster, hemolysin and chitinase. Similar to vpsA and vpsL, the promoter region of vpsU, rbmA and rbmF exhibited overlapping H-NS and VpsT binding motifs. Deletion of vpsT increased H-NS occupancy at the vpsU, vpsA, vpsL, rbmA and rbmF promoters. Conversely, artificially increasing the c-di-GMP pool diminished H-NS occupancy at the above promoters. Deletion of vpsT did not affect H-NS occupancy at its own promoter. However, deletion of genes encoding the regulators AphA and VpsR significantly increased H-NS occupancy at the vpsT promoter. In sum, our study shows that c-di-GMP enhances biofilm formation by acting through VpsT to activate an H-NS anti-repression cascade.

overall_design: The Binding profile of V. cholerae H-NS to the genome was determined by ChIP followed by Next Generation Sequencing (ChIP-Seq) using the Illumina HiSeq2000 platform. V. cholerae C7258 cells expressing H-NS-FLAG fusion protein from the hns transcription and translation signals were collected from LB cultures grown to mid-exponential phase (OD600 0.5). An anti-FLAG Immunoprecipitation (IP) and an Input samples were used for the analysis.

first: Hongxia

last: Wang

first: Anisia

last: Silva

first: Jorge

last: Benitez


title: Integrated copy number and expression analysis identifies profiles of whole-arm chromosomal alterations and subgroups with favorable outcome in ovarian clear cell carcinomas

status: Public on May 11 2015

city: Tokyo

first: Yuriko

last: Uehara

institute: Tokyo University

summary: Ovarian clear cell carcinoma (CCC) is generally associated with chemoresistance and poor clinical outcome, even with early diagnosis; whereas high-grade serous carcinomas (SCs) and endometrioid carcinomas (ECs) are commonly chemosensitive at advanced stages. Although an integrated genomic analysis of SC has been performed, conclusive views on copy number and expression profiles for CCC are still limited. In this study, we performed single nucleotide polymorphism arrays in 57 (31 CCCs, 14 SCs, and 12 ECs) and expression microarrays in 55 epithelial ovarian cancers (25 CCCs, 16 SCs, and 14 ECs), and then evaluated PIK3CA mutations and ARID1A expression in CCCs. SNP array analysis classified 13% of CCCs into a cluster with high frequency and focal range of copy number alterations (CNAs), significantly lower than for SCs (93%, P < 0.01) and ECs (50%, P = 0.017). The ratio of whole-arm to all CNAs was higher in CCCs (46.9%) than SCs (21.7%) (P < 0.0001). SCs with loss of heterozygosity (LOH) of BRCA1 (85%) also had LOH of NF1 and TP53, and LOH of BRCA2 (62%) coexisted with LOH of RB1 and TP53. Microarray analysis classified CCCs into three clusters. One cluster (CCC-2, n = 10) showed more favorable prognosis than the others (CCC-1and CCC-3) (P = 0.041). Coexistent alterations of PIK3CA and ARID1A were more common in CCC-1 and CCC-3 (7/11, 64%) than in CCC-2 (0/10, 0%) (P < 0.01). Being in cluster CCC-2 was an independent favorable prognostic factor in CCC. In conclusion, CCC was characterized by a high ratio of whole-arm CNAs; whereas CNAs in SC were mainly focal, but preferentially caused LOH of well-known tumor suppressor genes. As such, expression profiles might be useful for sub-classification of CCC, and might provide useful information on prognosis.

overall_design: Gene expression in 55 epithelial ovarian cancers (25 CCCs, 16 SCs, and 14 ECs) was analyzed by Affymetrix U133plus2 array.

first: Katsutoshi

last: Oda

first: Yuji

last: Ikeda

first: Takahiro

last: Koso

first: Shingo

last: Tsuji

first: Shogo

last: Yamamoto

first: Kayo

last: Asada

first: Kenbun

last: Sone

first: Reiko

last: Kurikawa

first: Chinami

last: Makii

first: Otoe

last: Hagiwara

first: Michihiro

last: Tanikawa

first: Daichi

last: Maeda

first: Kosei

last: Hasegawa

first: Shunsuke

last: Nakagawa

first: Osamu

last: Wada-Hiraike

first: Kei

last: Kawana

first: Masashi

last: Fukayama

first: Keiichi

last: Fujiwara

first: Tetsu

last: Yano

first: Yutaka

last: Osuga

first: Tomoyuki

last: Fujii

first: Hiroyuki

last: Aburatani


title: Transcriptional Profiling of the Immune Response to Marburg Infection

city: Boston

first: Ignacio S.

last: Caballero

state: MA

address: 620 Albany St., NEIDL 401V

department: NEIDL/Microbiology

institute: Boston University School of Medicine

summary: Marburg virus is a genetically simple RNA virus that causes a severe hemorrhagic fever upon infection in humans and non-human primates. The mechanism of how this pathogenesis comes about is not well understood, but it is well accepted that pathogenesis is significantly driven by a hyperactive immune response. To better understand the overall response to Marburg virus challenge, we undertook a transcriptomic analysis of immune cells circulating in the blood following aerosol exposure of cynomolgus macaques to a lethal dose of Marburg virus. Using two-color microarrays, we analyzed the transcriptome of peripheral blood mononuclear cells that were collected throughout the course of infection from 1 to 9 days postexposure, representing the full course of the infection. The host response to aerosolized Marburg was evident at 1 day post-exposure. The response followed a 3-phase response that was led by a robust innate immune response. Analysis of cytokine transcripts that were overexpressed during infection indicated that previously unanalyzed cytokines are likely induced in response to exposure to Marburg virus, and further suggested that the immune response may favor a Th2 response that would hamper the development of an effective antiviral immune response.  Late infection events included the upregulation of coagulation associated factors. These findings suggest new avenues for investigating the pathogenesis of Marburg virus infection and provide rich dataset of factors expressed throughout the course of infection that can be investigated as markers of infection and targets for therapy.

sample_organism:
Macaca fascicularis
Homo sapiens

overall_design: RNA was isolated from a total of 30 PBMC samples from 15 cynomologus macaques infected with Marburg Virus. Samples were obtained at sequential timepoints post-infection, and included a pre-infection specimen from each animal. These samples were then processed and hybridized onto the Agilent 2-color arrays.

first: John

last: Connor

first: Shikha

last: Malhotra

first: Ignacio

first: Sara

last: Garamszegi

first: Judy

middle: Y

last: Yen

first: Kenny

last: Lin

first: Lisa

last: Hensley

first: Arthur

last: Goff


title: cDNA microarray analysis of sulforaphane effect on mouse acute lung injury caused by hyperoxia

city: Research Triangle Park

first: Dr. Steven

last: Kleeberger

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Protective roles of Nrf2, a key transcription factor for antioxidant and defense genes, have been determined in oxidative lung injury, and health benefits of Nrf2 agonists including sulforaphane have been demonstrated. The current study was designed to investigate the effect of sulforaphane on model acute lung injury and sulforaphane-mediated transcriptome changes in mouse lungs. Adult mice genetically deficient in Nrf2 (Nrf2-/-) and wild-type controls (Nrf2+/+, ICR) received oral sulforaphane (9 mmol/daily) or vehicle before (-5, -3, -1 days) hyperoxia or air exposure (3 days), and lung injury and gene expression changes were assessed. Sulforaphane significantly reduced hyperoxia-induced airway injury, inflammation, and mucus hypersecretion in Nrf2+/+ mice while relatively marginal treatment effect was found in Nrf2-/- mice. Sulforaphane significantly altered expression of lung genes associated with oxidative phosphorylation and mitochondrial dysfunction (Atp2a2, Cox7a1, Ndufa1) basally and cell function/cycle and protein metabolism (Actr1a, Wasf2, Ccne1, Gtpbp4) after hyperoxia in Nrf2+/+ mice. Nrf2-dependently modulated lung genes by sulforaphane and hyperoxia were associated with tissue development and hereditary disorders (Slc25a3, Pccb, Psmc3ip). Results demonstrate preventive roles of sulforaphane against oxidant lung injury in mice, and reveal potential downstream mechanisms. Our observations also suggest Nrf2-independent mechanisms of sulforaphane in prevention of acute lung injury.

overall_design: Nrf 2 knockout and wild-type mice were dosed with 9 uM R-Sulforaphane before their continuous exposure to air (21% O2) or hyperoxia (100% O2) for 3 days in a whole-body inhalation chamber

first: Steven


title: Deep, strand-specific, non-polyA-selected RNA sequencing of biological replicate Plasmodium falciparum blood stage time-courses

status: Public on May 08 2015

city: Cambridge

first: Kate

middle: Mariel

last: Broadbent

address: FAS Center for Systems Biology Northwest Building, room 469 52 Oxford Street

department: Systems Biology

institute: Harvard University

summary: The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive immune escape, invasion of human liver and blood cells, and transmission through the female Anopholes mosquito. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. However, there is mounting evidence across a broad range of species that intergenic long non-coding RNA (lncRNA) and antisense RNA can regulate chromatin state and gene expression. To pursue such functional roles for lncRNAs in P. falciparum, we performed deep, strand-specific RNA sequencing of fifteen non-polyA-selected blood stage samples, and assembled and characterized the properties of 660 intergenic lncRNAs, 474 antisense RNAs, and 1381 circular RNAs (circRNAs). We further validated the non-canonical splice junctions of seven P. falciparum circRNAs, an emerging class of non-coding RNA with regulatory potential and unexplored functional significance in P. falciparum. Our comprehensive analysis of P. falciparum lncRNAs indicates a functional role for these transcripts; P. falciparum intergenic lncRNAs and antisense RNAs are developmentally regulated in a similar periodic fashion to annotated transcripts, and sense-antisense pair expression is significantly anti-correlated. Notable outliers include intergenic lncRNAs that strongly peak in expression during parasite invasion, such as the telomere-associated lncRNA-TARE family, antisense transcripts that drop in expression during parasite invasion, and a highly correlated, multi-exonic, antisense counterpart to P. falciparum Gametocyte Developmental Protein 1 (PfGDV1). Taken together, our results present over two thousand P. falciparum intergenic lncRNA, antisense, and circRNA candidates and highlight promising P. falciparum lncRNAs for future investigation.

overall_design: We harvested fifteen blood stage samples from two biological replicate time-courses. The first time-course comprised of eleven samples that finely map temporal changes during P. falciparum blood stage development. We harvested samples over 56 hours, at roughly 4-hour time intervals, from a tightly synchronized P. falciparum 3D7 parasite population. As the asexual blood stage is an approximately 48-hour cycle, this time-course allowed us to profile gene expression during RBC rupture and parasite invasion. The second time-course comprised of four samples harvested in synchronous P. falciparum 3D7 parasites approximately four hours before and after the ring to trophozoite and trophozoite to schizont morphological stage transitions, which occur during the blood stage at 24 hours post invasion (hpi) and 36 hpi, respectively.

first: Jill

first: Ulf

last: Ribacke

first: Dyann

last: Wirth

middle: L

last: Rinn

first: Pardis

last: Sabeti


title: Gene expression data from ependymal tumor samples

status: Public on May 21 2015

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

summary: Ependymal tumors across age groups have been classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patient outcome. We aimed at establishing a reliable molecular classification using DNA methylation fingerprints and gene expression data of the tumors on a large cohort of 500 tumors. Nine robust molecular subgroups, three in each anatomic compartment of the central nervous system (CNS), were identified.

overall_design: Total RNA from 209 ependymal tumor samples were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays.

first: Kristian

last: Pajtler

first: Hendrik

last: Witt

first: Martin

last: Sill

first: Andrey

last: Korshunov

first: Stefan

middle: M

last: Pfister


title: Expression data from endothelial progenitor cells (EPCs)

status: Public on May 06 2015

city: shanghai

first: Li

middle: xi

last: zhe

address: xinsongjianglu 650

department: cadiovascular surgery

institute: Shanghai general hospital

summary:
Endothelial progenitor cells (EPCs) are a group of cells which can differentiate to mature endothelial cells in a certain culture condition, and were first isolated from adult human peripheral blood by Asahara et al. in 1997. EPCs have a critical role in the restoration of injured vessel endothelium and the neovascularization in the area of ischemia injury. Recently, the role of androgens in the proliferation, differentiation and adhesion of EPCs is more and more focused. Dihydrotestosterone (DHT) is a kind of unmetabolizable androgen.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of regulated genes in DHT-treated EPCs.

overall_design: EPCs were isolated from mouse bone marrow. Male C57BL/6 mice (8 weeks age) mice were sacrificed by cervical dislocation. For microarray analysis, the cells were grown in culture medium supplemented with 10nmol/L DHT, which was changed on day 2. On day 7, cells was collected for RNA extraction and subsequent experiments.

first: Xizhe

last: Li

first: Junjie

last: Yang


title: QKI5-regulated miRNAs

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5

department: Department of Biochemistry and Molecular Biology Institute of Basic Medical Sciences

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

summary: microRNAs (miRNAs) accomplish a remarkable variety of biological functions. Their expression is tightly controlled, and the final production of a miRNA is dependent on the cooperation of multiple mechanisms and their net effect. Here we show that miR-124-1 is transcriptionally activated during erythroid differentiation by GATA-1, however its post-transcriptional processing is attenuated. We found that QKI5 binds to a distal QKI response element (QRE) embedded in the primary transcript of miR-124-1 (pri-124-1) and modulates Microprocessor function by direct association with DGCR8. Strikingly, Microprocessor recruitment to pri-124-1 is disrupted upon RNAi-mediated depletion of QKI5, consistent with the decrease in mature miR-124. Moreover, addition of QKI5 increases the conversion efficiency of pri-124-1 in cell-free extracts. For erythropoiesis, the decreased QKI5 leads to attenuated Microprocessor-mediated processing of pri-124-1, which confers the exquisite miRNA abundance necessary for development. This regulation also gives rise to a unique miRNA signature required for normal erythropoiesis. Thus, this QKI5-regulated miRNA processing may represent a common paradigm for erythroid development, and specifically, it may serve as a post-transcriptional fault security to prevent misexpression of certain miRNAs, that is essential for the establishment of particular gene expression patterns during development.

overall_design: Two samples are analyzed: K562 cells transduced with GFP lentivirus; and K562 cells transduced with QKI5-overexpressing lentivirus.

first: Wei

last: Song

first: Hongmei

last: Zhao

first: Yuxia

first: Lei

last: Dong

first: Yong

last: Zhu

first: Xiaoxia

last: Ren

first: Shuailai

last: Wu

first: Fei

last: Miao

first: Yanni

last: Ma

first: Junwu

last: Zhang

first: Jingyi

last: Hui

first: Linfang

last: Wang


title: Transcriptional response of P. aeruginosa PA3 to bacteriophage PaP3 infection

city: ChongQing

first: Xia

address: Shapingba

institute: Third military medical school

summary: Explore the genome-scale phage–host interactions across different developmental infection stages

platform_organism:
Bruynoghevirus PaP3
Pseudomonas aeruginosa PAO1

overall_design: Samples were taken from the PA3 Lysates infected with phage Pap3 at six internal time (0,5,10,20,30,80min). Three independent experiments were performed at each time.

first: Yinling

last: Tan


title: The microbial functional structure along the latitudinal gradient from the north to the south in China mainland as characterized by GeoChip

status: Public on May 23 2015

city: Changsha

first: Jing

last: Cong

address: Yuelushan

institute: Central South University

summary: Understanding and quantifying the effects of environmental factors influencing the variation of abundance and diversity of microbial communities was a key theme of ecology. For microbial communities, there were two factors proposed in explaining the variation in current theory, which were contemporary environmental heterogeneity and historical events. Here, we report a study to profile soil microbial structure, which infers functional roles of microbial communities, along the latitudinal gradient from the north to the south in China mainland, aiming to explore potential microbial responses to external condition, especially for global climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 5.0, we showed that microbial communities were distinct for most but not all of the sites. Using substantial statistical analyses, exploring the dominant factor in influencing the soil microbial communities along the latitudinal gradient. Substantial variations were apparent in nutrient cycling genes, but they were in line with the functional roles of these genes.

platform_organism: Bacteria Archaea Eukaryota

overall_design: 300 samples were collected from 30 sites along the latitudinal gradient, with 10 replicates in every site

first: Yu

middle: G


title: Gene expressions specifically induced by the presence of SFB

status: Public on May 01 2015

city: hangzhou

first: chen

last: bo

state: zhejiang

address: 79 Qingchun Road

department: The First Affiliated Hospital, School of Medicine

institute: zhejiang university

summary: To investigate SFB-host interactions and the host response to SFB, we compared gene expression profiles in terminal ileal mucosa collected from 5 SFB-positive and 5-negative age-matched patients identified from SFB PCR. We observed that 472 genes were different between the two groups (P < 0.05). Among them, 290 genes were up-regulated and 182 were down-regulated. GO biological pathway analysis of up-regulated genes revealed positive regulation of T-cell differentiation and activation pathways were enhanced (P < 0.001), suggesting that SFB colonization stimulated the human immune system, specifically T-cell maturation. Indeed, enhanced expression of Cd3e, Ifng, IL10, Foxp3 was observed in terminal ileal mucosa of 5 SFB-positive patients.

overall_design: To find immune-related genes significantly expressed (p < 0.05) between SFB-positive and -negative

first: Chen

last: Bo

first: Li

last: Jia

first: Mizu

last: Jiang

first: Wang

last: Xin

first: Chalie

last: Xiang


title: Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (ChIP-chip)

status: Public on Apr 27 2015

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: Physiologically relevant concentrations of retinoic acid are added to Mouse ES cells and a time course (0-72 hours) is examined with tiling array ChIP-chip and RNA-seq to characterize the early dynamics of expression of coding and non-coding RNAs and epigenetics in and around the Hox clusters.

overall_design: Expression, epigenetics, and RARs are examined at various timepoints (0-24hrs) after retinoic acid induced neuronal differentiation

first: Bony

last: De Kumar

first: Mark

last: Parrish

first: Brian

last: Slaughter

first: Jay

last: Unruh

first: Christopher

last: Seidel

first: Ariel

last: Paulson

first: Hua

last: Li

first: Karin

last: Zueckert-Gaudenz

first: William

last: McDowell

last: Fleharty

first: Youngwook

last: Ahn

first: Chengqi

last: Lin

first: Edwin

last: Smith

first: Ali

last: Shilatifard

first: Robb

last: Krumlauf


title: Comparative genome-wide analysis of human BM IL3Rα-high precursors show a more MΦ-, DC- and OC committed gene expression profile, as compared to IL3Rα-low precursors

status: Public on Apr 28 2015

city: Amsterdam

first: yanling

last: xiao

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: To clarify the lineage relationship between IL3Rαhigh- and IL3Rαlow precursor cells and to find potential molecules involved in their differentiation, we compared the IL3Rαhigh- and IL3Rαlow precursor populations from three independent donors by mRNA deep sequencing and used the Ingenuity Pathway Analysis (IPA)- and Multi-experimental Viewer (MeV) to analyze the differentially expressed genes (p<0.001). Analysis of the protein coding genes showed that the samples from IL3Rαhigh precursor cells clustered together, as did the IL3Rαlow samples. This indicated that the gene expression patterns of these cells are likely to be conserved. Further analysis revealed a list of (649) differentially expressed molecules between the two populations.  Among these, most notably, genes involved in the differentiation of cell in general, amongst which differentiation of MΦ, OC and antigen presenting cells appeared to be activation increased.

overall_design: Examination of two hematopoietic precursor populations in human BM

first: Yanling

last: Xiao

first: Sebastiaan

last: Zijl


title: Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters.

first: Madelaine

last: Gogol

summary: Physiologically relevant concentrations of retinoic acid are added to Mouse ES cells and a time course (0-72 hours) is examined with expression tiling arrays and RNA-seq to characterize the early dynamics of expression of coding and non-coding RNAs in and around the Hox clusters.

overall_design: Gene expression is examined at various timepoints (0-72 hrs) after retinoic acid induced neuronal differentiation

first: Bony

last: De Kumar

last: Parrish


title: Differential gene expression between infected and non-infected dendritic cells with HIV-1

status: Public on Apr 24 2015

city: Madrid

first: Esther

last: Calonge

address: Ctra Pozuelo-Majadahonda Km 2

department: Centro Nacional Microbiologia

institute: Instituto Salud Carlos III

summary: The whole genome microarray shows differences in ISGs and chemokine gene expression

overall_design: Productive infection of dendritic cells was carried out with Vpx+ virus. Control of infection was carried out with defective RT HIV-1

first: Jose

last: Alcami


title: Methylation Changes in Arabidopsis seed development

status: Public on Apr 22 2015

city: Los Angeles

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: There are four major seed developmental phases in Arabidopsis seed development: morphogenesis, maturation, dormancy and germination. What methylation changes occurring in the different phases, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of four major seed developmental phases of Arabidopsis using Illumina sequencing: global stage (glob) and linear cotyledon stage (lcot) for morphogenesis phase; mature green stage (mg) and post mature green stage (pmg) for maturation phase; dry seed (dry) for dormancy phase; leaves (leaf) from 4 week plant for vegetative tissues.

overall_design: Illumina sequencing of bisulfite-converted genomic DNA from six seed developmental stages in Arabidopsis: global stage (glob), linear cotyledon stage (lcot), mature green stage (mg), post mature green stage (pmg), dry seed (dry) and leaves (leaf) from 4 week plant.

first: Robert

middle: B

first: Jer-Young

first: Min

last: Chen


title: Expression analysis of M.tb H37Rv after treatment with DTT (reduced) for 3 hrs

city: Chandigarh

first: Ashwani

last: Kumar

state: Chandigarh

address: Sec 39A

department: Molecular Microbiology

country: India

institute: CSIR-Institute of Microbial Technology

summary: Effect of Thiol reductive stress (DTT 1mM) on M.tb Rv was studied.

overall_design: DTT reduced at 1 mM concentration was added to log pahse culture of M.tb H37Rv. After Three hours RNA was isolated and  hybridization was done on  HRI-UMNDJ Mycobacterium tuberculosis 4.8K CAG_Mtb microarrays.

first: Abhisek

last: Trivedi

first: Parminder

last: Singh Mavi

first: Deepak

last: Bhatt


title: Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (tiling)

type: Expression profiling by genome tiling array

summary: Physiologically relevant concentrations of retinoic acid are added to Mouse ES cells and a time course (0-72 hours) is examined with expression tiling arrays to characterize the early dynamics of expression of coding and non-coding RNAs in and around the Hox clusters.

first: Mark

first: Brian

last: Slaughter

first: Jay

last: Unruh

first: Christopher

last: Seidel

first: Ariel

last: Paulson

first: Hua

last: Li

first: Karin

last: Zueckert-Gaudenz

first: William

last: McDowell

last: Fleharty

first: Youngwook

last: Ahn

first: Chengqi

last: Lin

first: Edwin

last: Smith

first: Ali


title: Gene expression profile of phenylpropanoid pathway in black and red rice pericarps.

status: Public on Apr 18 2015

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: We analyzed expression change of the genes which involved in anthocyanin and pro-anthocyanin biosynthesis to search an origin of black rice.

overall_design: The submitted samples were transcriptome data in black and red rice pericarps. Rice pericarps were harvested in 7 and 14 days after heading, respectively.

first: Taichi

last: Oguchi


title: Calibrating ChIP-seq with nucleosomal internal standards to measure histone modification density genome-wide

status: Public on May 07 2015

city: Chicago

first: Alexander

last: Ruthenburg

state: Illinois

address: 920 E 58th St

department: Molecular Genetics and Cell Biology

institute: The University of Chicago

summary: Despite serving as a central experimental technique in epigenetics research, chromatin immunoprecipitation (ChIP) suffers from several serious drawbacks: it is a relative measurement untethered to any external scale that obviates fair comparison amongst experiments; it employs antibody reagents that have differing affinity and specificity for target epitopes, which are in turn variable in abundance; and it is frequently not reproducible. To address these problems, we developed internal standard calibrated ChIP (ICeChIP), a method of spiking a native chromatin sample with nucleosomes reconstituted from recombinant and semisynthetic histones on barcoded DNA prior to immunoprecipitation. ICeChIP measures local histone modification densities on a biologically meaningful scale, enabling unbiased trans-experimental comparisons and revealing a correlation between the apparent symmetry of H3K4me3 in promoter nucleosomes and gene expression.  Direct in situ assessment of immunoprecipitation accommodates for a number of experimental pitfalls, and provides a critical examination of untested assumptions inherent in conventional ChIP.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus
synthetic construct

overall_design: Examination of spiked-in semi-synthetic nucleosomes in ICeChIP-seq experiments performed for HEK293, mESC E14 and DM S2 cell line

first: Adrian

middle: T

last: Grzybowski

first: Zhonglei

last: Chen


title: NBAT1 overexpression effect on breast cancer cell line MDA-MB-231

status: Public on Apr 21 2015

city: Guangzhou

first: Pengnan

last: Hu

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

summary: Analysis of MDA-MB-231 breast cancer cells overexpressing lncRNA neuroblastoma associated transcript 1 (NBAT1). Results provide insight into the function of NBAT1 in breast cancer.

overall_design: NBAT1 overexpressed in breast cancer cells MDA-MB-231 compared to control (empty vector alone). Three replicates of each treatment were analyzed.


title: Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study

status: Public on Apr 17 2015

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

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

overall_design: Refer to individual Series


title: Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study [gastric tumors]

summary: Gastric cancer, a leading cause of cancer related deaths, is a heterogeneous disease, with little consensus on molecular subclasses and their clinical relevance. We describe four molecular subtypes linked with distinct patterns of molecular alterations, disease progression and prognosis viz. a) Microsatellite Instable: hypermutated intestinal subtype tumors occurring in antrum, best overall prognosis, lower frequency of recurrence (22%), with liver metastasis in 23% of recurred cases b) Mesenchymal-like: diffuse tumors with worst prognosis, a tendency to occur at an earlier age and highest recurrence (63%) with peritoneal seeding in 64% of recurred cases, low frequency of molecular alterations c) TP53-inactive with TP53 loss, presence of focal amplifications and chromosomal instability d) TP53-active marked by EBV infection and PIK3CA mutations. The key molecular mechanisms and associated survival patterns are validated in multiple independent cohorts, to provide a consistent and unified framework for further preclinical and clinical research.

overall_design: ACRG Gastric cohort: microarray profiles from 300 gastric tumors from gastric cancer patients.

first: Razvan

last: Cristescu

first: Jeeyun

last: Lee

first: Kyoung-Mee

last: Kim

first: Jason

middle: C

last: Ting

first: Swee

last: Wong

first: Jiangang

last: Liu

first: Yong

last: Yue

first: Jian

last: Wang

first: Kun

last: Yu

first: Xiang

last: Ye

first: In-Gu

last: Do

first: Shawn

first: Lara

last: Gong

first: Jake

last: Fu

last: Jin

first: Min

last: Choi

first: Tae

last: Sohn

first: Joon

middle: H

first: Jae

last: Bae

first: Seung

first: Se

last: Park

first: Patrick

last: Tan

first: Chen

last: Ronghua

first: James

last: Hardwick

first: Won

middle: K

last: Kang

first: Mark

last: Ayers

first: Dai

last: Hongyue

first: Christoph

last: Reinhard

first: Amit

last: Aggarwal

first: Sung

first: Andrey

last: Loboda


title: Methylation Profile of postmature-green-stage seed and dry seed from Arabidopsis ddcc mutant

first: Bob

last: Goldberg

summary: The role of non-CG methylation in seed development and dormancy remains unknown. There are four genes in charge of non-CG methylation in Arabidopsis: drm1, drm2, cmt2 and cmt3. The majority of non-CG methylation in vegetative tissues, leaf, is gone in homozygous ddcc mutant line (Hume et al., 2014). To uncover the possible role of non-CG DNA methylation in seed development and dormancy, we characterized the methylome of ddcc mutant in Arabidopsis postmature-green-stage seed and dry seed using Illumina sequencing. Meanwhile, vegetative tissue, leaves from 3 week plant with ddcc mutant and from wild-type, and postmature-green-stage seed and dry seed from wild-type plant were used as control.

overall_design: Illumina sequencing of bisulfite-converted genomic DNA from postmature-green-stage seed, dry seed, and 3-week-plant leaves of ddcc mutant and wild-type.

first: Robert

first: Jer-Young

last: Lin

last: Chen


title: A novel BRAT1–BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis [RNA-Seq]

status: Public on Apr 14 2015

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: To identify BRAT1 target loci at the whole-genome level, we performed RNA deep sequencing and examined the transcript levels of transposable elements and genes in the wild type, brat1, nrpe1, and brat1nrpe1.

overall_design: Compare the mRNA profiles of 10-day old seedlings materials of mutants (brat1, nrpe1, and brat1nrpe1) to wild type by Illumina suquencing.

first: Xinjian

last: He

first: Cuijun

last: Zhang

first: Huanwei

last: Huang


title: Expression data from liver samples of Pemt-/- and Pemt+/+ mice under high fat-high-sucrose (HFHS) diet

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

institute: Okayama University

summary: We used microarrays to detail the global programme of gene expression in the liver of Pemt-/- and Pemt+/+ under HFHS diets.

overall_design: Liver sample of Pemt-/- and Pemt+/+ mice under HFHS for 1, 2, 3, 4 weeks were used for RNA extraction and hybridization on Affymetrix microarrays. Genes in liver of Pemt-/- mice, successively suppressed compared with Pemt+/+ mice, were obtained.

first: Atsuko

last: Nakatsuka


title: A novel BRAT1–BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis [BS-Seq]

summary: Active DNA demethylation is an important epigenetic phenomenon in many eukaryotes. In Arabidopsis thaliana, ROS1, a 5-methylcytosine DNA glycosylase, is responsible for active DNA demethylation via a base excision repair process. Here, we found that Bromodomain and ATPase domain-containing protein 1 (BRAT1) associates with BRP1 (BRAT1 Partner 1) and forms a tight BRAT1–BRP1 complex required for DNA demethylation. To identify hypermethylated loci at the whole-genome level in brat1, brp1, and ros1, we performed whole-genome bisulfite sequencing.

overall_design: Compare the DNA methylation profiles of 10-day old seedlings materials of mutants (brat1, brp1, and ros1) to wild type by whole-genome bisulfite sequencing.


title: Expression data from MAP3K11/GDF15 axis is a critical driver of cancer cachexia

status: Public on Apr 23 2015

city: Cambridge

first: Lorena

last: Lerner

address: 650 E. Kendall Street

institute: AVEO Oncology

summary: MAP3K11 overexpression in tumors leads to weight loss in the host

overall_design: We assessed the ability of potential tumor maintenance genes to drive tumor growth in vivo using a directed complementation (DC) approach. This assay involves testing the ability of an introduced gene to maintain tumor growth when expression of an inducible driving oncogene is turned off.  In this case, we tested the ability of MAP3K7/TAK1 or MAP3K11/MLK3 to form tumors in vivo in a genetically engineered model originally driven by a doxycycline-inducible HER2(V659E) oncogene.  In this system, the expression and activity of HER2 was suppressed by doxycycline withdrawal and followed by the introduction of one of 13 genes (ErbB3, FAK1, FGFR2aIIIb, FGFR2aIIIc, FGFR3, HER2, MAP3K11, PIP5K1B, RONd160, RON+MSP, RSK2, MAP3K7, TNK2)

first: Rick

last: Nicoletti


title: Epigenome analysis of liver tissues from Pemt-/- and Pemt+/+ under high fat-high sucrose (HFHS) diet

summary: Genome wide DNA methylation profiling of  liver tissues from Pemt-/- and Pemt+/+ under HFHS diets.

overall_design: Pemt-/- and Pemt+/+ mice were fed HFHS from 5 to 25 weeks of age and liver tissues were obtained at 25 weeks. Bisulphite converted DNAs were enriched with EpiXplore Methylation DNA Enrichment Kit (Clontech). Genomic DNA libraries was prepared by TruSeq ChIP Sample Preparation Kit.


title: A novel BRAT1-BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis