title: Metastasis in triple negative breast cancer is dependent on ΔNp63/CXCL2/CCL22-mediated recruitment of myeloid-derived suppressor cells

status: Public on Dec 26 2018

city: Philadelphia

first: Rumela

last: Chakrabarti

state: PA

address: 380 S University Ave, 411 Hill Pavilion

department: Department of Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

summary: Gene expression analysis of the knockdown of ΔNP63 in two different human breast cancer cell lines using RNA-Seq

overall_design: RNA was collected and analyzed for biological replicates of each condition (shΔNP63 vs Vector) from two different human breast cancer cell lines (HCC1806 and SUM1315)

first: Sushil

first: David

last: Wilkes

first: Nina

last: Samuel

first: Anupma

last: Nayak

first: Kevin

last: Alicea-Torres

first: Christian

last: Gluck

first: Satrajit

last: Sinha

first: Dmitry

last: Gabrilovich


title: Colonic miR-31 is a molecular stratifier and prognostic determinant of Crohn’s disease

status: Public on Oct 01 2018

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 5022 Genetic Medicine Building

department: Department of Genetics

country: USA

institute: The University of North Carolina at Chapel Hill

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Association between colonic level of microRNA 31 and subtypes of adult and pediatric Crohn's disease [pediatric]

summary: The course of Crohn's disease (CD) is heterogeneous, confounding effective personalized therapy. A previous analysis of differences in gene expression between patients with versus without CD groups revealed 2 subsets of patients with CD -- a group characterized by genes more highly expressed in the colon (colon-like CD) and a group with increased expression of ileum marker genes (ileum-like CD). We compared differences in microRNAs between these groups. We performed genome-wide microRNA profile analyses of colon tissues from 18 adults with CD and 12 adults without CD (controls). We performed principal component analyses to associate levels of microRNAs with CD subtypes. Colonic epithelial cells and lamina propria immune cells were isolated from intestinal tissues and levels of microRNA 31 (miR-31) were measured by real-time quantitative PCR. We validated the differential expression of miR-31 between the subtypes by measuring miR-31 levels in an independent cohort of 32 adult patients with CD and 23 controls. We generated epithelial colonoid cultures from controls and patients with CD, and measured levels of miR-31 in crypts. We performed genome-wide microRNA profile analyses of formalin-fixed paraffin-embedded colon and ileum biopsies from 76 treatment-naive pediatric patients with CD and 51 controls (234 samples) and collected data on disease features and outcomes. In comparing miRNA expression profiles between 9 patients with colon-like CD and 9 patients with ileum-like CD, we identified 19 miRNAs with significant differences in levels. We observed a 13.5-fold difference in level of miR-31-5p between tissues from patients with colon-like vs. ileum-like CD (Padj = 1.43 x 10-18). Principal component analysis found miR-31 to be the top contributor to the variance observed. Levels of miR-31 were increased 60-fold in tissues from patients with ileum-like CD compared with controls (Padj = 2.59 × 10-51). We validated the differential expression of miR-31 between the subtypes in the independent set of tissues. Colonoids derived from patients with CD had significantly higher levels of miR-31 than colonoids derived from control tissues (day 2 P=.041 and day 6 P=.0095). Levels of miR-31 were significantly increased in colon tissues from pediatric patients with CD compared with controls (~7.8-fold, P=4.64 ×10-7) and in ileum tissues from patients with CD patients vs. controls (~1.5-fold, P=9.97 × 10-7). A high level of miR-31 in index biopsies from pediatric patients with only inflammation and no other complications at time of diagnosis associated with development of fibrostenotic ileal CD. We identified differences in miR-31 levels in colon tissues from adult and pediatric patients with CD compared with controls, and in patients with ileum-like CD compared with colon-like CD. Further studies are needed to determine the mechanisms by which miR-31 might contribute to pathogenesis of this subtype of CD, or affect response to therapy.

overall_design:
234 small RNA-seq samples from Crohn's disease and non-IBD control FFPE tissue, 124 of which are from ascending colon biopsies at the time of surgery, and 110 from the terminal ileum at the time of surgery.
Raw data not available due to patient privacy concerns.

first: Benjamin

middle: P

last: Keith

first: Terrence

middle: S

first: Praveen

last: Sethupathy

first: Shehzad

middle: Z

last: Sheikh


title: The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [RNA-Seq Tumor]

status: Public on May 31 2018

city: Boston

first: Cigall

last: Kadoch

state: MA

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

type: Expression profiling by high throughput sequencing

summary: Synovial sarcoma (SS) is defined by the hallmark SS18-SSX fusion oncoprotein, which renders BAF complexes aberrant in two manners: gain of SSX to the SS18 subunit and concomitant loss of BAF47 subunit assembly. Here we demonstrate that SS18-SSX globally hijacks BAF complexes on chromatin to activate a SS transcriptional signature we define using primary tumors and cell lines. Specifically, SS18-SSX retargets BAF complexes from enhancers to broad polycomb domains to oppose PRC2-mediated repression and activate bivalent genes. Upon suppression of SS18-SSX, reassembly of BAF47 restores enhancer activation, but is not required for proliferative arrest. These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.

overall_design: RNA was harvested from patient samples of synovial sarocoma (SS) and sequenced for further analysis.

first: John

last: Pulice


title: Colonic miR-31 is a molecular stratifier and prognostic determinant of Crohn’s disease [adult]

summary: The clinical course of Crohn's disease (CD) is highly heterogeneous, confounding effective personalized therapy. There is a critical need to better understand the cellular mechanisms responsible for the variability in disease presentation and response to therapeutic modalities. We carried out whole transcriptome profiling in colon tissue from adult CD patients and controls and found that CD patients segregate into the same two molecular subtypes based on mRNA, long non-coding RNA, or microRNA profiles. MicroRNA-31 (miR-31) in colonic epithelium was identified as a primary contributor to this molecular stratification. We further performed small RNA-seq on formalin-fixed paraffin embedded colon and ileum biopsies obtained at the time of diagnosis from 130 treatment-naïve pediatric CD patients and controls. Colonic expression of miR-31 in pediatric patients was identified as predictive of either medically refractory rectal CD or fibrostenotic ileal CD. Our study reveals miRNAs as important molecular stratifiers and prognostic determinants of CD subtypes.

overall_design: 30 small RNA-seq samples from Crohn's disease and non-IBD control fresh tissue ascending colon biopsies.


title: The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [RNA-Seq Cell]

overall_design: Naïve synovial sarcoma cell lines (Aska,Yamato, HSSY2, YaFuSS, SYO1, Fuji) were grown in culture and RNA was harvested in biological duplicate for sequencing. Synovial sarcoma cell lines (Aska, HSSY2, SYO1) were lentivirally infected with either an shControl or a shSSX vector, selected for 48 hours with puromycin, then grown for either 1 day (3 days post-infection) or 5 days (7 days post-infection), at which point RNA was harvested from independent biological duplicate for sequencing. CRL7250 fibroblast cell line was lentivirally infected with either a V5-SS18 or V5-SS18-SSX expressing vector, selected for 48 hours with puromycin, then grown for 5 days, at which point RNA was harvested from independent biological duplicate for sequencing.


title: The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
Synovial sarcoma cell lines (Aska) were lentivirally infected with either an shControl or a shSSX vector, selected for 48 hours with puromycin, then grown for 5 days, at which point cells were harvested for ATAC-seq preparation. CRL7250 fibroblast cell line was lentivirally infected with either a V5-SS18 or V5-SS18-SSX expressing vector, selected for 48 hours with puromycin, then grown for 5 days, at which point cells were harvested for ATAC-seq preparation.

The processed data was generated on merged biological duplicate experiments and linked to the corresponding *rep1 sample records.


title: The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma


title: The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [ChIP-Seq]

overall_design: Synovial sarcoma cell lines (Aska, HSSY2, SYO1) were lentivirally infected with either an shControl or a shSSX vector, selected for 48 hours with puromycin, then grown for 5 days, at which point cells were harvested for ChIP-seq preparation. CRL7250 fibroblast cell line was lentivirally infected with either a V5-SS18 or V5-SS18-SSX expressing vector, selected for 48 hours with puromycin, then grown for 5 days, at which point cells were harvested for ChIP-seq preparation.


title: Histone demethylase JMJD1A coordinates acute and chronic adaptation to cold stress via thermogenic phospho-switch

status: Public on Feb 16 2018

city: Tokyo

first: Juro

last: Sakai

address: 4-6-1, Komaba, Meguro-ku

department: Division of Metabolic Medicine

country: Japan

institute: Research Center for Advanced Science and Technology, The University of Tokyo


title: Protointrons in Saccharomyces sp.

status: Public on Jan 01 2018

city: Santa Cruz

first: Jason

last: Talkish

state: CA

address: 1156 High St.

department: Molecular, Cellular, and Developmental Biology

institute: University of California, Santa Cruz

summary: We sequenced non-ribosomal RNA from a upf1 deletion mutant of S. cerevisiae, and from wild type S. mikatae and S. bayanus, and identified a new class of yeast introns.

sample_organism:
Saccharomyces bayanus
Saccharomyces cerevisiae
Saccharomyces mikatae

overall_design: Yeast non-ribosomal RNAs were isolated from vegetatively growing cells or cells treated with rapamycin for 60 minutes to mimick starvation, RNA was sequenced, and splice junctions were identified and validated.

first: Haller

last: Igel

first: Rhonda

middle: J

last: Perriman

first: Lily

last: Shiue

first: Sol

last: Katzman

first: Elizabeth

middle: M

last: Munding

first: Robert

last: Shelansky

first: John Paul

last: Donohue

first: Manuel

last: Ares Jr.


title: Genome-wide analysis of JMJD1A and PPARγ binding in immortalized, differentiated preadipocytes derived from inguinal subcutaneous white adipose tissue.

summary: In acute cold stress in mammals, JMJD1A, an H3K9 demethylase, up-regulates thermogenic gene expressions through β-adrenergic signaling in brown adipose tissue (BAT). Aside BAT-driven thermogenesis, mammals also have another mechanism to cope with  long-term cold stress by inducing the browning of subcutaneous white adipose tissue (scWAT). Here, we show that this occurs through a two-step process that requires both β-adrenergic dependent phosphorylation of S265 and demethylation of H3K9me2 by JMJD1A. The histone demethylation independent acute Ucp1 induction in BAT and demethylation dependent chronic Ucp1 expression in beige-scWAT provide complementary molecular mechanisms to ensure an ordered transition between acute and chronic adaptation to cold stress. JMJD1A mediates two major signaling pathways, namlely β-adrenergic receptor and PPARγ activation, via PRDM16-PPARγ-P-JMJD1A complex for beige adipogenesis.

overall_design: Preadipocytes derived from inguinal subcutaneous white adipose tissue were immortalized. Preadipocytes were differentiated for ChIP-seq analysis of JMJD1A and PPARγ using Illumina HiSeq 2500.


title: TSA-Seq Mapping of Nuclear Genome Organization

status: Public on Apr 25 2018

city: Urbana

first: Andrew

last: Belmont

state: IL

address: 601 S Goodwin Ave, CLSL B509

institute: University of Illinois at Urbana-Champaign

type: Genome binding/occupancy profiling by genome tiling array


title: RNA-sequence analysis of immortalized, differentiated preadipocytes derived from inguinal subcutaneous white adipose tissue.

summary: In acute cold stress in mammals, JMJD1A, an H3K9 demethylase, up-regulates thermogenic gene expressions through β-adrenergic signaling in brown adipose tissue (BAT). Aside BAT-driven thermogenesis, mammals also have another mechanism to cope with long-term cold stress by inducing the browning of subcutaneous white adipose tissue (scWAT). Here, we show that this occurs through a two-step process that requires both β-adrenergic dependent phosphorylation of S265 and demethylation of H3K9me2 by JMJD1A. The histone demethylation independent acute Ucp1 induction in BAT and demethylation dependent chronic Ucp1 expression in beige-scWAT provide complementary molecular mechanisms to ensure an ordered transition between acute and chronic adaptation to cold stress. JMJD1A mediates two major signaling pathways, namlely β-adrenergic receptor and PPARγ activation, via PRDM16-PPARγ-P-JMJD1A complex for beige adipogenesis.

overall_design: Preadipocytes derived from inguinal subcutaneous white adipose tissue were immortalized. Mouse Jmjd1a was knocked-down by shRNA and wild-type and mutant versions of hJMJD1A were retrovirally expressed in preadipocytes. Preadipocytes were differentiated for RNA extraction and RNA-sequence analysis using Illumina HiSeq 2500.


title: Expression data from embryonic day 17 (E17) enteric neural crest-dervied cells (ENCDC) and non-ENCDC

status: Public on Oct 09 2018

middle: O.

last: Heuckeroth

address: 3615 Civic Center Blvd, Abramson Research Center, 1116i

department: Pediatrics

institute: The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania

summary:
During the later stages of enteric nervous system (ENS) development, enteric neural crest derived cells (ENCDC) that have colonized the bowel must complete differentiating and mature into neurons and glia. This process is controlled by a complex array of intrinsic and extrinsic factors.
We used microarrays to dermine which genes were differntially expressed in ENCDC versus other cells in the developing bowel. We identified many geness enriched in ENCDC with potential roles in the later stages of ENS development

overall_design: We performed FACS of E17.5 bowel cells from Wnt1-Cre; R26R-EYFP mice to isolate EYFP-positive ENCDC and EYFP-negative non-ENCDC.  Microarray analysis was used to compare gene expression in these cell populations to identify ENCDC enriched genes with potential roles in late ENS development

first: Marina

last: Avetisyan

first: Silvia

last: Huerta Lopez

first: Christina

last: Wright

middle: O


title: ARA1 regulates not only L-arabinose but also D-galactose catabolism in Trichoderma reesei

status: Public on Nov 02 2017

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: Trichoderma reesei is used to produce saccharifying enzyme cocktails for biofuels. There is limited understanding of the transcription factors (TFs) that regulate the release and catabolism of L-arabinose and D-galactose, as the main TF XYR1 is only partially involved. The T. reesei ortholog of ARA1 from Pyricularia oryzae that regulates L-arabinose release and catabolism, was deleted and characterized by growth profiling and transcriptomics along with a xyr1 mutant and xyr1/ara1 double mutant. Our results show that, in addition to the L-arabinose-related role, T. reesei ARA1 is essential for D-galactose release and catabolism, while XYR1 is not involved in this process.

overall_design: In this study, we aim to identify the target genes of the arabinanolytic transcription factor ARA1 in the Ascomycetes Trichoderma reesei while growing on the monosaccharides L-arabinose and D-galactose through transcriptome analysis. We compare the  transcriptomes of the reference strain QM9414 with three deletion strains: hemicellulytic regulator XYR1, ARA1 and the double deletion XYR1ARA1 after 2h of growth in the different carbon sources.

first: Tiziano

last: Benocci

first: Maria

middle: V

last: Aguilar-Pontes

first: Roland

last: Kun

first: Bernhard

last: Seiboth

first: Paul

last: Daly


title: Transcriptome analysis of splenic monocytes from Foxp3DTR and WT mice post-MI versus sham operated animals

status: Public on Aug 19 2017

city: Udine

first: Simone

last: Scalabrin

state: UD

address: via Jacopo Linussio 51

country: Italy

institute: IGA Technology Services

summary: Objective: To study the impact of endogenous CD4+ Foxp3+ T-cells on splenic monocyte differentiation after MI.

overall_design: Methods and Results: Sorting of splenic monocytes on day 5 after MI followed by transcriptome analysis by means of RNA sequencing revealed that depletions of CD4+ Foxp3+ T-cells imposed a pro-inflammatory bias on splenic Ly6Chigh monocytes. In contrast, as compared to sham surgery there is minimal regulation of transcriptional activity in splenic monocytes in the presence of endogenous CD4+ Foxp3+ T-cells in response to myocardial infarction.

first: Nadine

last: Gladow

first: Ulrich

last: Hofmann


title: Sensing self and nonself circular RNAs

status: Public on Jun 29 2017

city: Stanford

first: Howard

middle: Y

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Dermatology

institute: Stanford University

summary: Circular RNAs (circRNAs) are single-stranded RNAs that are joined head to tail. Initially discovered as pathogen genomes such as hepatitis D virus (HDV) and plant viroids, circRNAs are recently recognized as a pervasive class of noncoding RNAs in eukaryotic cells, generated through back splicing. circRNAs have been postulated to function in cell-to-cell information transfer or memory due to their extraordinary stability. Whether and how circRNAs trigger immune recognition is not known. Here we show that exogenous circular RNAs potently stimulate immune signaling, and mammalian cells sense self vs. nonself circRNAs via circRNA biogenesis. Transfection of purified in vitro spliced circRNA into mammalian cells led to potent induction of innate immunity genes. The nucleic acid sensor RIG-I is necessary and sufficient to sense foreign circRNA, and RIG-I and foreign circRNA co-aggregate in cytoplasmic foci. CircRNA activation of innate immunity is independent of 5’ triphosphate, double-stranded RNA structure, or primary sequence of the foreign circRNA. Instead, self-nonself discrimination depends on the intron that programs the circRNA.  Use of a human intron to express a foreign circRNA sequence abrogates immune activation, and the mature human circRNA is associated with diverse RNA binding proteins reflecting its endogenous splicing and biogenesis. These results reveal innate immune sensing of circRNA, a prevalent class of host and pathogen RNAs, and highlight introns—the predominant output of mammalian transcription—as unexpected arbiters of self-nonself identity in the RNA world.

overall_design: 3 samples of RNA from Hela cells with mock or exogenous RNA transfected, 2 biological replicates each

first: Y

middle: G

last: Chen


title: Ribosomal profiling in Cystic Fibrosis Bronchial Epithelial cells

status: Public on May 18 2017

city: Hamburg

first: Robert

last: Rauscher

address: Martin-Luther-King-Platz 6

department: Biochemistry

country: Germany

institute: University Hamburg

summary: We performed ribosome profiling in Cystic Fibrosis Bronchial Epithelial cells which data set is used to calcualte codon-specific ribosome occupancy using the approach described by Lareau et al. eLife 2014.

overall_design: Ribosome profiling of cells at steady state. 3 biological replicates.

first: Sebastian

last: Kirchner

first: Zoya

last: Ignatova


title: Effect of selective glucocorticoid receptor modulation (SGRM) on gene expression in human prostate cancer cell lines

status: Public on Aug 18 2017

city: Chicago

first: WEN-CHING

last: CHAN

department: Biological Sciences Division

institute: The University of Chicago

summary: Human prostate cancer cell lines treated with androgen receptor (AR) agonists/antagonists and concurrent glucocorticoid receptor (GR) agonist/antagonists

overall_design: Human prostate cancer cell lines in charcoal-stripped FCS-containing media were treated for 3 days with AR agonists (R1881 1nM) +/-antagonist (enzalutamide 10uM) and then pulsed with 2 or 6 hour treatment with GR agonist (Dex 100nM)  +/- antagonist (SGRM, 335 1uM and 297 1uM) after which RNA was collected and sequenced

first: Russell

last: Szmulewitz

first: Suzanne

middle: D

last: Conzen

first: Donald

last: Vander Griend


title: Single-cell 5-formylcytosine Landscapes of Mammalian Early Embryos at Single-base Resolution

status: Public on Mar 29 2017

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

country: China

institute: Liangzhu Laboratory

type: Methylation profiling by high throughput sequencing

summary: Active DNA demethylation in mammals involves Ten-eleven translocation (TET) family proteins-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC, an oxidized derivative of 5mC) at the single-cell level remains unexplored. Here we present “CLEVER-seq”, which is a single-cell, single-base resolution 5fC sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing. CLEVER-seq of mouse early embryos reveals the highly patterned genomic distribution and parental specific dynamics of 5fC during mouse early pre-implantation development and synergistic 5fC production in paternal and maternal genomes. Integrated analysis demonstrates that promoter 5fC production precedes the expression upregulation of a clear set of developmentally and metabolically critical genes. Collectively, our work reveals the dynamics of active DNA demethylation during early mouse pre-implantation development and provides an important resource for further functional studies of epigenetic reprogramming in single cells. For the untreated control samples, the accession number of raw data is under GSE263008 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE263008).

overall_design: We developed a novel single-cell 5fC sequencing technique, termed “CLEVER-seq” (chemical labeling enabled C-to-T conversion sequencing), to map the genome-wide base resolution 5fC landscapes in mouse early embryos at single-cell level. We applied CLEVER-seq to mESCs (2i), mouse sperm, metaphase II oocytes, zygotes, 2-cell embryos, 4-cell embryos, inner cell mass (ICM) and trophectoderm (TE). The male and female pronuclei within each individual PN3-PN4 stage zygote were physically isolated by micromanipulation; the individual blasotomeres of 2-cell and 4-cell embryos were also separated. In addition to mESCs (2i), we also performed CLEVER-seq to mESCs (serum), mEpiSCs, and hESCs. In total, we sequenced more than 1,500 GB data for 139 single cells, and identified 3,216-41,347 5fCpG sites from these samples.

first: Chenxu

last: Zhu

first: Yun

last: Gao

first: Bo

last: Xia

first: Fuchou

last: Tang

first: Chengqi

last: Yi


title: TSA-Seq Mapping of Nuclear Genome Organization [seq]

first: Andrew

last: Belmont

summary: We describe TSA-Seq, a new mapping method able to estimate mean chromosomal distances from nuclear speckles genome-wide and predict several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling.  Ensemble-averaged results reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity.  This gradient represents a convolution of multiple, spatially separated nuclear domains, including two types of transcription ?hot-zones?.  Transcription hot-zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers.

overall_design: We used TSA-Seq to study genome organization relative to nuclear speckles and the nuclear lamina. For nuclear speckles, we performed TSA-Seq using two different antibodies against the protein SON and an antibody against a phosphorylated epitope of the protein SC35. We also performed TSA-Seq using an antibody against RNA Pol II as a general marker for active nuclear domains to compare with the speckle TSA-Seq chromosome patterns. For the nuclear lamina, we performed TSA-Seq using antibodies against lamin B and Lamin A/C. For each TSA-Seq experiment, a no primary control experiment was done in parallel, where the same TSA-Seq procedure is performed but with no added primary antibody.

first: Yu

first: Liguo

last: Zhang


title: Characterization of spleen Z cells from naïve NOD-SCID mouse

status: Public on May 02 2017

city: Tainan

first: Nan-Shan

last: Chang

address: 1 University Road

department: Molecular Medicine

country: Taiwan

institute: National Cheng Kung University

summary:
Eight NOD-SCID mice of 6-8 weeks old were sacrificed, and spleen cells harvested. Z cells were isolated using a red fluorescent TMR-Zfra peptide in cell sorting (Oncotarget. 2015 Feb 28;6(6):3737-51). Two cell populations were isolated, which are Z(-) and Z(+) cells, or designated as ZM for negative cells and ZP for positive cells. Mouse OneArray chips (Phalanx Biotech, Inc) were used for gene expression profiling.
The goal of this research is to determine the specific gene expression profile in newly isolated spleen Z cells.

overall_design: 8 spleen cells were sorted and isolated as Z(-) and Z(+).

middle: A

first: Chen

last: Lu


title: Identification of MEIOC targets in mouse postnatal testis

status: Public on Mar 22 2017

city: Cincinnati

first: Maria

middle: M.

last: Mikedis

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: MEIOC targets in mouse P15 testis

overall_design: RIP-seq of MEIOC targets in mouse P15 testis

first: M

first: D

middle: C

last: Page


title: Expression data of noncoding RNAs in response to genotoxic agents (UV and MMS) in HeLa cells

status: Public on Feb 15 2017

city: Changsha

first: Zheng

last: Zhou

address: Lushan Road (S), Yuelu District

institute: Hunan University

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

summary: DNA damage response and repair are key biological pathways to prevent genome instability caused by inefficient repair induced permanent mutations. Such changes may cause alterations to the normal cell cycle, the induction of apoptosis and the initiation and promotion of cancer development. Recently, the roles of ncRNAs functioning in the DNA damage response and DNA repair have gain more attention. To find out key ncRNAs involved in DNA damage response or repair pathways, we detected the transcription levels of ncRNAs in HeLa cells following ultraviolet (UV) light or methyl methanesulfonate (MMS) treatments by microarrays. This identified a variety of ncRNAs respond to UV or MMS-induced DNA damage. Therefore, further investigation on the ncRNAs in response to these genotoxic agents would help to provide a deeper understanding of the mechanism of ncRNAs functioning in the DNA damage response and repair pathways and new strategies of treatment of cancer by co-ordinately targeting ncRNA repair factors.

overall_design: HeLa cells were exposed to 5J/m^2, 10J/m^2 of UVC light and 0.005% MMS. Untreated cells were used as a control. Total RNA was extracted after cells recovery for 12 hours and then subjected to microarray analysis.

first: Runsheng

last: Chen

first: Dan

last: Wang

first: Dandan

last: He

first: Yunfei


title: Identification of YTHDC2 targets in mouse postnatal testis

summary: YTHDC2 targets in mouse P20 testis

overall_design: RIP-seq of YTHDC2 targets in mouse P20 testis


title: Identification of the mouse embryonic germ cell Meioc-/- transcriptome

summary: Meioc-/- transcriptome in E14.5 embryonic germ cells from mouse

overall_design: RNA-seq of wild-type, Meioc +/- heterozygote, Meioc-/- fetal ovaries from mouse

first: Y

middle: Q

last: Soh


title: ChIP-seq of naive and primed ES cells

status: Public on Jul 15 2016

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: We show by ChIP-seq that some transposable elements are differentially bound by KAP1 and enriched for H3K9me3 in Naive vs Primed states.

overall_design: ChIP-seq

first: Marc

last: Friedli

first: Julien

last: Pontis

last: Duc

first: Evarist

last: Planet


title: Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains

status: Public on Oct 17 2016

city: Tel Aviv

first: Irit

last: Gat-Viks

department: Cell Research and Immunology

country: Israel

institute: Tel-Aviv University

summary: A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions. We then leveraged a reference collection of metabolic biotransformation pathways to map potential relations between drugs and their underlying expression quantitative trait loci (eQTLs). By applying this approach on proximal eQTLs, including eQTLs acting on the overall expression of genes and on the expression of particular transcript isoforms, we were able to construct the organization of hepatic eQTL-drug connectivity across the CC population. The analysis revealed a substantial impact of genetic variation acting on drug biotransformation, allowed mapping of potential joint genetic effects in the context of individual drugs, and demonstrated crosstalk between drug metabolism and lipid metabolism. Our findings provide a resource for investigating drug disposition in the CC strains, and offer a new paradigm for integrating biotransformation reactions to corresponding variations in DNA sequences.

overall_design: This dataset includes RNA-Seq data of mRNA that were extracted from the liver of 55 male mice. The 55 mice belong to 29 different collaborative cross strains. The number of individual mice per strains is 3 for 3 strains, 2 for 16 strains, and 1 for 8 strains. All the mice are naïve without any special treatment.

first: Aharon

last: Nachshon

first: Hanifa

last: Abu-Toamih Atamni

first: Yael

last: Steuerman

first: Roa'a

last: Majed Shiekh Yosief

first: Alexandra

last: Dorman

first: Richard

last: Mott

first: Juliane

last: Dohm

first: Hans

last: Lehrach

last: Sultan

first: Ron

last: Shamir

first: Sascha

last: Sauer

first: Heinz

last: Himmelbauer

first: Fuad

last: Iraqi


title: Transcriptome response after addition of individual agonists of TLR4 (MPLA) and NOD2 (MDP) receptors to THP-1 cells or its combination

status: Public on Apr 05 2016

city: Moscow

first: Amir

last: Tukhvatulin

address: Gamaleya str, 18

department: Medical microbiology

country: Russia

institute: N.F. Gamaleya Research Center for Epidemiology and Microbiology

summary:
Using microarray analysis, we explored the differences in gene expression profiles between individual and combined stimulation of Toll-like receptor 4 (TLR4) and Nucleotide oligomerization domain (NOD)-like receptor (NOD2) in THP-1 cells.  Analysis was performed 3 hours post addition of TLR4 agonist MPLA and the NOD2 agonist MDP to THP-1 cells.
The results provide the detailed molecular profile of the the genetic response to individual and combined stimulation of TLR4 and NOD2 receptors

overall_design: THP-1 cells (Invivogen) were seeded in 3-cm culture dishes at 1x10^6 cells per dish in RPMI medium. Next day, cells were treated with MDP (20μg/ml) and MPLA (1μg/ml) individually or in combination or left untreated.

middle: I

first: Natalia

last: Tukhvatulina

first: Denis

last: Logunov


title: Profiling circulating microRNA expression in experimental sepsis by cecal ligation and puncture

status: Public on May 15 2015

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

institute: Kaohsiung Chang Gung Memorial Hospital

summary:
To profile the expression of circulating microRNAs (miRNAs) of mice in experimental sepsis by cecal ligation and puncture (CLP), the whole blood samples were obtained from C57BL/6 mice at 4, 8, and 24 h following CLP for miRNA expression analysis using a miRNA array (The Mouse & Rat miRNA OneArray® v3).
Briefly, mice were anesthetized with a combination of ketamine and xylazine as the anesthetic/analgesic agents and a midline abdominal incision was made. The cecum was mobilized, ligated in the middle of cecum below the ileocecal valve, punctured once with a 21 G needle, and a little stool was squeeze out of the cecum to induce polymicrobial peritonitis. The abdominal wall was closed in two layers. Sham-operated mice underwent the same procedure, including opening the peritoneum and exposing the bowel, but without ligation and needle perforation of the cecum.

overall_design: the whole blood samples were obtained from C57BL/6 mice at 4, 8, and 24 h following CLP for miRNA expression analysis using a miRNA array (The miRNA OneArray® v3).

first: Shao-Chun

last: Wu

first: Johnson

last: Yang

first: Cheng-Shyuan

last: Rau


title: Skeletal muscle gene expression changes with exercise mode, duration and intensity: STRRIDE study

status: Public on May 14 2015

city: Washington

first: Monica

last: Hubal

state: DC

address: 111 Michigan Ave NW

department: Integrative Systems Biology

institute: Children's National Medical Center

summary: Skeletal muscle adapts to exercise training of various modes, intensities and durations with a programmed gene expression response. This study dissects the independent and combined effects of exercise mode, intensity and duration to identify which exercise has the most positive effects on skeletal muscle health. Full details on exercise groups can be found in: Kraus et al Med Sci Sports Exerc. 2001 Oct;33(10):1774-84 and Bateman et al Am J Cardiol. 2011 Sep 15;108(6):838-44.

overall_design: This study uses a middle aged group of subjects that have 3+ markers of metabolic syndrome. One group remains an inactive control, while 5 groups undergo 9 mo supervised exercise training. Exercise groups are as follows: Inactive control (group B); Mild aerobic exercise - low amount/mod intensity (group A); Moderate aerobic exercise - low amt/vig intensity (group D); High aerobic exercise - high amt/vig intensity (group C); resistance training only (group F); and mod aerobic + resistance training (group E). Each group has 10 subjects (5 men and 5 women), however 3 subjects failed array QC, leaving 8 subjects in group E and 9 subjects in group F. Data were all analyzed pre to post training in a RM ANCOVA, covaried for age and sex or regression to determine genotype/phenotype interactions.

first: William

middle: E

last: Kraus


title: Molecular Criteria for Defining the Naive Human Pluripotent State

status: Public on Jul 18 2016

first: Joseph

last: Ecker

summary: Naive human pluripotent cells have been isolated in culture, but it remains unclear to what extent they resemble pluripotent cells in vivo. Here we present three lines of evidence indicating that naive pluripotent stem cells generated by small molecules share defining molecular signatures with the human preimplantation embryo. First, a comprehensive analysis of the transposcriptome reveals that naive human cells display a unique transposon expression profile of cleavage stage embryos. Second, induction of naive pluripotency is accompanied by a genome-wide depletion in DNA methylation that is reversible upon differentiation except at imprinted regions. Third, allele-specific analysis demonstrates that female naive cells exhibit an X chromosome signature of the human preimplantation embryo. However, when introduced into mouse embryos the naive cells failed to efficiently generate interspecies chimeras. Our work provides a set of molecular benchmarks for evaluating the developmental identity of distinct human pluripotent states captured in vitro.

overall_design: Please refer to individual Series. This SuperSeries is composed of the SubSeries listed below.

first: Thorold

middle: W

last: Theunissen

first: Marc

last: Friedli

first: Yupeng

last: He

first: Evarist

last: Planet

first: Ryan

last: Oneil

first: Styliani

last: Markoulaki

first: Haoyi

last: Wang

first: Julien

last: Pontis

first: Alexandra

last: Iouranova

first: Michaël

last: Imbeault

last: Duc

first: Malkiel

last: Cohen

first: Katherine

last: Wert

first: Rosa

last: Castanon

first: Zhuzhu

last: Zhang

first: Dorothea

last: Maetzel

first: Yanmei

last: Huang

last: Nery

first: Jesse

last: Drotar

first: Tenzin

last: Lungjangwa

first: Didier

last: Trono

first: Rudolf

last: Jaenisch


title: Identification of gene expression changes in rabbit uterus during embryo implantation

status: Public on Dec 18 2015

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: Embryo implantation in the rabbit is unique in that a typical fusion type of implantation is employed, in which trophoblast cells adhere and fuse to the apical surface of uterine epithelial cells. In the present study, we analyzed global gene expression changes in the rabbit uterus during embryo implantation by using RNA-seq.

overall_design: To systematically identify differentially expressed genes at the implantation site compared to the inter-implantation site.


title: Gene Expression Data for male C57BL/6, Mdr2-KO and Mdr2-KO/IL6-KO at the age of 14 months

status: Public on May 01 2015

city: Jerusalem

first: Jonathan

middle: Hillel

last: Axelrod

department: Gene Therapy

institute: Hadassah Medical School

summary:
Chronic inflammation is a common underlying condition associated with tumor development, accounting for approximately 20% of human cancers. This association is especially apparent in Hepatocellular carcinoma (HCC), which often develops on the background of chronic hepatitis and hepatic fibrosis, slowly unfolding on a background of chronic inflammation. HCC is one of the most common tumors worldwide, exhibiting a very poor prognosis and high mortality rate with limited available therapeutic tools. The etiology of liver cancer is well known, however there is still a lack of precise knowledge about pathogenesis of HCC. IL-6 have been shown to be of importance for liver protection and prevention of liver injury in animal models of acute sclerosing cholangitis and correlate with increased HCC in human patients. Using a murine model of chronic cholangitis based on the ablation of the Mdr2 gene, this study has examined the role of IL-6  signaling in chronic hepatitis and in the subsequent development of liver cancer.    The main observations of this study are that IL-6 signaling in male Mdr2-KO mice protects from the development of liver injury and fibrosis, but simultaneously promotes tumor initiation.  Thus, IL-6 deficiency in male Mdr2-KO mice dissociates the tight correlation between liver fibrosis and the development of inflammation-associated HCC.
To reveal the affected molecular pathways that lead to increased cholestasis and bile acid–induced liver injury, but reduced tumorigenesis in the male IL-6 deficient Mdr2-KO/IL6-KO mice, we performed gene array analysis and identified distinct classes of differentially-expressed genes in these mice.

overall_design: We performed genome-scale gene expression profiling by Affymetrix analysis on tumor-free livers samples from Mdr2-KO, Mdr2-KO/IL6-KO, and wild type C57BL/6 mice at the age of 14 months.

first: Anat

last: Shriki


title: Gene Expression Data for C57BL/6, Mdr2-KO and Mdr2-KO/IL6-KO mice at the age of 14 months

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

overall_design: Refer to individual Series


title: Identification of the embryonic germ cell Meioc-/- transcriptome, MEIOC targets in postnatal testis, and YTHDC2 targets in postnatal testis in mouse

first: Maria

last: Mikedis

overall_design:
RNA-seq of wildtype, Meioc +/- heterozygote, Meioc-/- fetal ovary; RIP-seq of MEIOC and YTHDC2 targets in postnatal testis in mouse.

This SuperSeries is composed of the SubSeries listed below.

first: Ying

last: Soh

first: David

last: Page


title: Gene Expression Data for female C57BL/6, Mdr2-KO and Mdr2-KO/IL6-KO at the age of 14 months

summary:
Chronic inflammation is a common underlying condition associated with tumor development, accounting for approximately 20% of human cancers. This association is especially apparent in Hepatocellular carcinoma (HCC), which often develops on the background of chronic hepatitis and hepatic fibrosis, slowly unfolding on a background of chronic inflammation. HCC is one of the most common tumors worldwide, exhibiting a very poor prognosis and high mortality rate with limited available therapeutic tools. The etiology of liver cancer is well known, however there is still a lack of precise knowledge about pathogenesis of HCC. IL-6 have been shown to be of importance for liver protection and prevention of liver injury in animal models of acute sclerosing cholangitis and correlate with increased HCC in human patients. Using a murine model of chronic cholangitis based on the ablation of the Mdr2 gene, this study has examined the role of IL-6  signaling in chronic hepatitis and in the subsequent development of liver cancer.    The main observations of this study are that IL-6 signaling in female Mdr2-KO mice protects from the development of liver injury and fibrosis, but simultaneously rduced tumor initiation.
To reveal the affected molecular pathways that lead to increased cholestasis and bile acid–induced liver injury, and increased tumorigenesis in the female IL-6 deficient Mdr2-KO/IL6-KO mice, we performed gene array analysis and identified distinct classes of differentially-expressed genes in these mice.


title: Systematic Identification of Defined Conditions for Induction and Maintenance of Naive Human Pluripotency

status: Public on Jul 16 2014

city: Cambridge

address: 9 Cambridge Center

department: Biology

institute: MIT/Whitehead Institute


title: Changes in membrane lipid composition during Iron depletion and starvation in Chlamydomonas reinhardtii

status: Public on Feb 20 2014

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

summary: C. reinhardtii cells exposed to abiotic stresses (e.g. iron-, nitrogen-, zinc- or phosphorus-deficiency) accumulate TAGs which are stored in lipid droplets. Here, we report that iron starvation leads to formation of lipids bodies and accumulation of TAGs. This occurs between 12 and 24 h of iron-starvation. C. reinhardtii cells deprived for iron have more saturated FA, due to the loss of functional FA desaturases, which are diiron enzymes. The abundance of a plastid ACP-acyl desaturase (FAB2) is significantly decreased to the same degree as observed for ferredoxin, which is a substrate of the desaturases. The increase in saturated FA (C16:0 and C18:0) is concomitant with the decrease in saturated FA (C16:4, C18:3 or C18:4). This pattern was observed for MGDG, DGTS or DGDG. When we monitored the absolute levels of glycerolipids, MGDG content dropped significantly after only 2 h of iron-starvation. On the other hand, DGTS and DGDG contents gradually decrease until a minimum is reached after 24-48 h of iron-deprivation. RNA-Seq analysis of iron-starved C. reinhardtii cells revealed significant changes in many transcripts coding for enzymes involved in FA metabolism. The mRNA abundances of genes coding for components involved in TAG accumulation (DGAT or MLDP) are increased. A more dramatic increase at the transcript level has been observed for many lipases, suggesting that a major remodeling of lipid membranes occurs during iron-starvation in C. reinhardtii.

overall_design: Sampling of Chlamydomonas CC-4532 (2137) cells cultivated photoheterotrophically (TAP) under iron-starvation condition (0 uM Fe-EDTA). Samples were collected from biological duplicates after washing in TAP medium lacking Fe at 0, 0.5, 1, 2, 4, 8, 12, 24 and 48 hours.

first: Eugen

last: Urzica

first: Astrid

last: Vieler

first: Anne

last: Hong-Hermesdorf

first: M

last: Casero

first: Sean

last: Gallaher

first: Janette

last: Kropat

first: Matteo

last: Pellegrini

first: Christoph

last: Benning

middle: S


title: Determination of Sigma 54 reglons in Bacillus thuringiensis HD73 strain

status: Public on Jun 29 2013

city: Beijing

first: Fuping

last: Song

address: No 2 West Yuan-Ming-Yang Road

institute: Instititue of plant protection, CAAS

summary: To determine Sigma 54 (SigL) reglons in Bacillus thuringiensis HD73 strain, A sigLmutant, HD(ΔsigL::kan), was constructed with insertion of kanamycin resistance gene cassete. We have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between mutant and wild-type strains.

overall_design: 2 ml samples were separately harvested from B. thuringiensis HD73 and HD(ΔsigL::kan) strains grown in Schaeffer’s sporulation medium (SSM) at stages T7 of stationary phase (7 hours after the end of the exponential phase). Three independent repeats were performed for each stain.

first: Qi

last: Peng


title: Systematic Identification of Defined Conditions for Induction and Maintenance of Naive Human Pluripotency [ChIP-Seq]

first: Rudolf

last: Jaenisch

summary: Embryonic stem cells (ESCs) of mice and humans have distinct molecular and biological characteristics, raising the question whether an earlier ‘naive’ state of pluripotency may exist in humans. Here we took a systematic approach to identify small molecules that support autonomous self-renewal of naive human ESCs based on maintenance of endogenous OCT4 distal enhancer activity, a molecular signature of ground state pluripotency. Iterative chemical screening identified a combination of five kinase inhibitors that induces and maintains OCT4 distal enhancer activity when applied directly to conventional human ESCs. These inhibitors generate a homogeneous population of human pluripotent stem cells in which transcription factors associated with the ground state of pluripotency are highly upregulated. Comparison with previously reported naive human ESCs indicates that our kinase inhibitor cocktail captures a novel pluripotent state in humans that closely resembles mouse ESCs.

overall_design: ChIP-seq data from human embryonic stem cells in naive and primed conditions were generated by deep sequencing using Illumina Hi-Seq 2000.

first: Thorold

last: Theunissen

first: Jessica

last: Reddy

first: Zi

middle: P

last: Fan


title: Brisbane Systems Genetics Study – DNA methylation data

status: Public on May 06 2014

city: St Lucia

first: Allan

middle: F

last: McRae

state: QLD

address: QBI Building (#79)

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

type: Methylation profiling by genome tiling array

summary: DNA methylation data on 614 individuals from 117 families consisting of combinations of MZ and DZ twin pairs, their siblings and their parents.

overall_design: Genomic DNA was extracted from peripheral blood lymphocytes. DNA concentrations were determined by NanoDrop quantification to include 500ng before bisulfite conversion using the EZ-96 DNA Methylation Kit

first: Grant

last: Montgomery

first: Peter

middle: M

last: Visscher


title: A biogenesis step upstream of Microprocessor controls miR-17~92 expression

status: Public on May 11 2015

city: Boston

first: Peng

last: Du

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

summary: The precise control of miR-17~92 microRNA (miRNA) is essential for normal development and overexpression of certain miRNAs from this cluster is oncogenic. Here we find the relative expression of the six miRNAs processed from the primary (pri-miR-17~92) transcript is dynamically regulated during embryonic stem cell differentiation. We identify a new miRNA biogenesis intermediate, termed ‘progenitor-miRNA’ (pro-miRNA), that is an efficient substrate for Microprocessor. An autoinhibitory 5’ RNA fragment is cleaved to generate pro-miRNA and selectively license Microprocessor-mediated production of pre-miR-17, -18a, -19a, 20a, and -19b. Using genetic, biochemical, and structural methods we define two complementary cis-regulatory repression domains required for the formation of this inhibitory RNA conformation. We find the endonuclease CPSF3 (CPSF73), and the Spliceosome-associated ISY1 are required for pro-miRNA biogenesis and expression of all miRNAs within the cluster except miR-92. Thus, developmentally regulated generation of pro-miRNA explains the posttranscriptional control of miR-17~92 expression in development.

overall_design: Illumina RNAseq in WT, dgcr8-/- and dicer-/- mESCs and small RNA seq in WT mESCs

first: Richard

last: Gregory


title: Hydrogen modulates signal transduction through manipulating oxidized phospholipid mediators

status: Public on Oct 17 2014

city: Kawasaki-city

first: Shigeo

last: Ohta

state: Kanagawa

address: 1-394, Kosugi-machi, Nakahara-ku

department: Department of Biochemistry and Cell Biology

institute: Institute of Development and Aging Sciences, Graduate School of Medicine, Nippon Medical School

summary: We have previously demonstrated that molecular hydrogen (H2) neutralizes hydroxyl radical (•OH) in cultured-cells and protects cells and tissues against oxidative stress.  Growing evidence has confirmed that H2-consumption exhibits preventive and therapeutic effects in patients with various diseases as well as model animals. Moreover, a small amount of H2 modulates signal transduction for regulating the expression of various genes; however, the primary target of H2 for exhibiting a variety of phenotypes was completely unknown. Here we show that H2 at low amounts manipulates oxidized phospholipid mediators to modulate Ca2+-signal transduction and gene expression.

overall_design: Gene expression  was measured at 4 hours after exposure to phospholipid, PAPC or oxidized PAPC that had been air-oxidized for 3 days with 0, 1.3 or 5% H2. Three independent experiments were performed for each experiment.

first: Katsuya

last: Iuchi

first: Akemi

last: Imoto

first: Naomi

last: Kamimura

first: Kiyomi

last: Nishimaki

first: Harumi

last: Ichimiya

first: Takashi

last: Yokota


title: Genome-wide signatures of differential DNA methylation and gene expression in pediatric ALL

status: Public on Sep 18 2013

city: Uppsala

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

country: Sweden

institute: Uppsala University


title: Expression profiling of glioma initiating cells (GICs) in the sphere and differentiation conditions

status: Public on Jan 26 2013

city: kumamoto

first: norie

last: araki

department: tumor genetics and biology

institute: kumamoto university

summary:
Glioma initiating cells (GICs) are considered responsible for the therapeutic resistance and recurrence of malignant glioma. To clarify the molecular mechanism of GIC maintenance/differentiation, we established GIC clones from GBM patient tumors having the potential to differentiate into malignant gliomas in mouse intracranial xenograft, and established an in vitro glioma induction system by using serum stimulation.
Upon the serum stimulation, the GIC spheres showed increased cellular proliferation, motility, filopodia/lameripodia formation and adhesion to the culture dishes. Simultaneously, the NSC marker proteins such as CD133 and Sox2 were down-regulated, and the astrocyte/glioma marker GFAP and the malignancy marker CD44 dramatically up-regulated. To identify genes/proteins whose expression changes dynamically during the differentiation of GICs into glioma cells, these GICs were subjected to DNA microarray/iTRAQ based integrated proteomics.

overall_design: Within 4 hours of tumor removal from GBM patients, tissues were subjected to GIC preparation. After successive cloning, total RNA from GIC clones (GIC03A and GIC03U) on day 2 or 7 of subculture in NSC medium with or without 10% FCS was subjected to the analysis with Affymetrix microarrays. Simultaneously, the proteins extracted from the same set of cells were subjected to LC-shot gun analyses using the 8-plex iTRAQ method. We sought to obtain the information of the common molecules that were up- or down-regulated during the GSC differentiation process, and functional targets for the early onset of GIC-associated glioma.

first: Norie

last: Araki

first: Akiko

middle: N

last: Niibori

first: Uichi

last: Midorikawa


title: Expression levels of xenobiotic transporters in kideny of Abcb4-null mice

status: Public on Jun 21 2011

city: Kyoto

first: Akio

last: Koizumi

address: Yoshida Konoe, Sakyo

department: Graduate School of Medicine

institute: Kyoto University

summary: The renal clearance of perfluorooctanoic acid (PFOA) increased in Abcb4 null mice compared with wild type mice, especially in male Abcb4 null mice. We evaluated the expression changes of transporters in kidney of male Abcb4 null mice by using microarray to reveal the candidate transporters of PFOA.

overall_design: Male of Abcb4-null mice and wild-type mice (3 mice of 8 weeks old in each group) were sacrificed, collected their kidneys. Six independent experiments were performed.


title: Molecular and Genetic Crosstalks Between mTOR and ERRα are Key Determinants of Rapamycin-induced Non-Alcoholic Fatty Liver.

status: Public on Apr 03 2013

city: Montréal

first: Vincent

last: Giguère

state: Québec

address: 1160 Pine Avenue West, room 710A

department: Biochemistry, Medicine and Oncology

country: Canada

institute: McGill University

summary: mTOR and ERRα are key regulators of common metabolic processes. However, the extent of functional overlap between these two factors has not been investigated. ChIP-sequencing analyses on mouse liver reveal mTOR recruitment to regulatory regions of genes on a genome-wide scale including enrichment at genes shared with ERRα that are involved in the TCA cycle and lipogenesis pathway. A total of 9469 and 23226 peaks were identified for mTOR and ERRα ChIP-seq datasets, respectively.

overall_design: mTOR and ERRα mouse liver ChIP-seq datasets obtained from pooling 8 individual ChIPs from a chromatin pool of 26 livers.

first: Cédric

last: Chaveroux

first: Lillian

middle: J

last: Eichner

first: Catherine

last: Dufour

first: Aymen

last: Shatnawi

first: Arkady

last: Khoutorsky

first: Guillaume

last: Bourque

first: Nahum

last: Sonenberg


title: Differential H3K4 methylation identifies developmentally poised hematopoietic genes

status: Public on Apr 29 2008

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

summary:
We assess the concordance of histone H3 lysine 4 dimethylation (H3K4me2) and trimethylation (H3K4me3) on a genome-wide scale in erythroid development by analyzing pluripotent,  multipotential and unipotent cell types. Although H3K4me2 and H3K4me3 are concordant at most genes, multipotential hematopoietic cells have a subset of genes that are differentially methylated (H3K4me2+/me3-). These genes are transcriptionally silent, highly enriched in lineage-specific hematopoietic genes, and uniquely susceptible to differentiation-induced H3K4 demethylation.  Self-renewing embryonic stem cells, which restrict H3K4 methylation to genes that contain CpG islands (CGIs), lack H3K4me2+/me3- genes. These data reveal distinct epigenetic regulation of CGI and non-CGI genes during development and indicate an interactive relationship between DNA sequence and differential H3K4 methylation in lineage-specific differentiation.
Keywords: comparison of different cell lines

overall_design: Multipotential and erythroid-differentiated hematopoietic cells were compared. Expression was measured using Affymetrix microarrays. H3K4me2 and H3K4me3 enrichment was assessed using Agilent tiling arrays.

first: Keith

last: Orford

middle: V


title: Bdellovibrio bacteriovorus attack phase and post-infection cells

status: Public on Dec 09 2009

city: Nottingham

first: Carey

last: Lambert

state: Notts

address: Queen's Medical Centre

department: Genetics

country: United Kingdom

institute: Nottingham University

summary:
Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes.  We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent “HI” manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack.
Keywords: Transcriptional analysis

overall_design: 3 replicates of attack phase cells and 3 replicates of 30 minutes post-infection cells were analysed on individual arrays. Replicate 3 was normalized separately.

first: Chien-Yi

last: Chang

first: Liz

last: Sockett


title: 5'-monophosphate-dependent small RNA sequencing from ego-1(om84) and control adult C. elegans hermaphrodites

status: Public on Jun 01 2011

city: Stanford

first: Jay

last: Maniar

address: 300 Pasteur Dr L302

institute: Stanford University

summary: Cellular RdRPs play a critical role in the development of many organisms.  Using high-throughput small RNA and messenger RNA sequencing we found that the Caenorhabditis elegans RdRP, EGO-1, is required to produce small RNAs antisense to a number of germline-expressed genes through several developmental stages.  We found that these genes fall into distinct classes including genes required for kinetochore and nuclear pore assembly, as well as the production of histone-modifying and centromeric proteins.  We also found several RNAi-related genes to be targets of EGO-1.  Finally, we show a strong correlation between the loss of small RNAs and the rise of mRNA levels in ego-1 mutant animals.

first: Andrew

middle: Z

last: Fire


title: Comparison of rat mammary carcinomas induced by pre- and postpubertal irradiation

status: Public on Jan 19 2011

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

institute: National Institutes for Quantum and Radiological Science and Technology

summary: Childhood exposure to carcinogens renders a higher risk of breast cancer. The molecular mechanisms underlying cancer development after such exposure are not, however, well understood. Here we examined how the mechanism of cancer development relates to the age at exposure to ionizing radiation (IR) or the carcinogen 1-methyl-1-nitrosourea (MNU). Pre- and postpubertal (3- and 7-week-old, respectively) female Sprague-Dawley rats were whole-body gamma-irradiated (2 Gy), injected intraperitoneally with MNU (20 mg/kg) or left untreated and were autopsied at 50 weeks of age. Mammary carcinomas were examined for estrogen receptor (ER) alpha, progesterone receptor (PR) and ErbB ligand expression and for expression microarrays. Early histological changes of the ovaries were also evaluated. The incidence of mammary cancer was higher after postpubertal, rather than prepubertal, IR exposure; the inverse was true for MNU. Most cancers were positive for both ER alpha and PR except for the prepubertal IR group. Interestingly, cancers of the prepubertal IR group expressed a different set of ErbB ligands from those of the other groups and did not overexpress Areg, which encodes an estrogen-regulated ErbB ligand, or other developmentally related genes including those for hormonally regulated mammary gland development. Prepubertal IR exposure resulted in ovarian dysfunction as revealed by a reduced follicular pool. Evidence thus suggests that mammary carcinogenesis induced by prepubertal IR exposure is independent of ovarian hormones but requires certain ErbB ligands; induction by postpubertal exposure depends on ovarian hormones and different ErbB ligands. In contrast, MNU-induced carcinogenesis was less influenced by the age at exposure.

overall_design: The gene expression of Sprague-Dawley rat mammary carcinomas induced by irradiation at 3 weeks of age (IR-3W; n = 4) or 7 weeks of age (IR-7W; n = 6) was compared with that of age-matched normal mammary gland tissues (n = 3).

first: Mayumi

last: Nishimura

first: Daisuke

last: Iizuka

first: Yukiko

first: Yasushi

last: Ohmachi

first: Yoshiya

last: Shimada


title: Circulating miRNA expression after subcutaneous injection of Gram negative and positive bacteria in the mice

status: Public on Jan 01 2014

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

institute: Kaohsiung Chang Gung Memorial Hospital

summary: To explore the circulating miRNA expression after subcutaneous injection of Gram negative and positive bacteria in the mice

overall_design: The recombinant specific Gram negative pathogens Escherichia coli (xen14) and Gram positive pathogens Staphyllococcus aureus (xen29) were purchased from the Caliper (Caliper, Princeton, NJ, USA). 1×108 Escherichia coli or Staphyllococcus aureus pathogen in 100 μl PBS was injected subcutaneously with Fr. 25 needle into the back of the mice to cause bacterial infection of the mice. An extra group of animals was inoculated with PBS to serve as a negative control. The mice had access to food and water ad libitum both before and after bacteria injection. The mice were killed at the indicated time points (4, 8, and 24 h) after the bacteria injection, and whole blood was drawn.

first: Shao-Chun

last: Wu

first: Johnson

last: Yang

first: Cheng-Shyuan

last: Rau


title: EGO-1, an essential C. elegans RdRP, modulates gene expression through the mRNA-templated production of short antisense effector RNAs