title: NGS mouse spleen and liver

status: Public on Dec 03 2006

city: Madison

first: Todd

last: Richmond

state: WI

address: One Science Court

department: Bioinformatics

institute: NimbleGen Systems Inc.

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

overall_design: Refer to individual Series


title: The effect of paternal haploinsufficiency for Dnmt3L

status: Public on Mar 29 2007

city: Forest Hill

first: Russell

middle: Leigh

last: McInnes

state: Vic

address: 347 Burwood Hwy

department: LSCA

country: Australia

institute: Agilent Technologies

type: Genome variation profiling by genome tiling array

summary:
There is increasing evidence that epigenetic information can be inherited across generations in mammals, despite extensive reprogramming both in the gametes and the early developing embryo. One corollary to this is that disruption of the establishment of epigenetic state in the gametes of a parent, as a result of heterozygosity for mutations in genes involved in reprogramming, could affect the phenotype of offspring that do not inherit the mutant allele. Here we show that such effects do occur following paternal inheritance in the mouse. We detect changes to transcription and chromosome ploidy in adult animals. Paternal effects of this type have not been reported previously in mammals and suggest that the untransmitted genotype of male parents can influence the phenotype of their offspring.
Keywords: Offspring of Dnmt3L+/- sires compared to offspring of Dnmt3L+/+ sires

first: Suyinn

last: Chong

first: Nikki

last: Vickaryous

first: Alyson

last: Ashe

first: Natasha

last: Zamudio

first: Neil

last: Youngson

first: Emma

last: Whitelaw

first: Tomas

last: Stopka

first: Arthur

last: Skoultchi

first: Jacqui

last: Matthews

first: Hamish

middle: S

last: Scott

first: David

last: deKretser

first: Moira

last: Obryan

first: Marnie

last: Blewitt

first: Sarah

last: Hemley


status: Public on Aug 18 2009

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: To identify microRNAs impacting estrogen receptor ERα expression in breast cancer, we have screened ER-positive breast cancer cells with a library of pre-miRs, and systematically monitored the ERα expression by protein lysate microarrays. There was a significant enrichment of the in silico predicted ERα targeting microRNAs among the hits. The most potent pre-miRs miR-18a/b, miR-193b, miR-206, and miR-302c, were confirmed to directly target ERα and to repress estrogen-responsive genes. The effect of miRNA overexpression on gene expression profile  of MCF-7 cells was studied. Furthermore, miR-18a and miR-18b showed increased expression in ERα-negative as compared to ERα-positive clinical tumors. In summary, we present systematic and direct functional and correlative clinical evidence on microRNAs inhibiting ERα signaling in breast cancer.

overall_design: MCF-7 cells (300 000 per well on 6-well plates) were transfected with an siRNA for ERα or with Ambion pre-miR™ constructs for miR-18a, miR-193b, miR-206, miR-302c, or pre-miR negative control #1 (scrambled pre-miR) at 20 nM, and incubated for 24h.

first: Suvi-Katri

last: Leivonen

first: Rami

last: Mäkelä

first: Päivi

last: Östling

first: Saija

last: Haapa-Paananen

first: Kristine

last: Kleivi

first: Espen

last: Enerly

first: Anna

last: Aakula

first: Kirsi

last: Hellström

first: Niko

last: Sahlberg

first: Vessela

middle: N

last: Kristensen

first: Anne-Lise

last: Børresen-Dale

first: Petri

last: Saviranta

first: Merja

last: Perälä

first: Olli

last: Kallioniemi


title: Expression of cyclophilin B is associated with malignant progression and regulation of genes

status: Public on Apr 03 2009

city: Chicago

first: Feng

last: Fang

state: IL

address: 303 E Superior St Lurie 4-225

department: Department of Pathology

country: USA

institute: Northwestern University

summary: Microarray was conducted on Illumina Human Ref-6 Version 2 Expression Chip (Illumina, San Diego, CA).  Three independent cultures were used for RNA isolation with RNeasy plus mini kit (Qiagen, Valencia, CA). RNA quality was checked by Agilent Bioanalyzer (Agilent, Santa Clara, CA). An Ambion labeling kit was used for labeling cDNA followed by hybridization to Illumina chips. ChIP scan data was extracted by Illumina Beadstudio and subsequently analyzed using Bioconductor lumi package.

overall_design: T47D cells (si-Luc and si-CypB cells) were cultured in the growth medium for three days followed by 24 hours arrest prior to PRL treatment (100 ng/ml) for 2 hours.

first: Ayanna

middle: J

last: Flegler

first: Pan

last: Du

first: Simon

last: Lin

first: Charles

last: Clevenger


title: Comparative gene expression analysis in fruits of a tomato introgression line performing reduced ascorbic acid content

status: Public on May 30 2012

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

country: Italy

institute: University of Naples Federico II

summary: Ascorbic acid (AsA), important for plant cell protection against oxidative stresses, is useful for human health. Among vegetables, tomato is the most important specie due to its significant consumption at worldwide level. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood.  We used an introgression line (IL 10-1) containing a QTL inducing a reduced AsA accumulation in the fruit and carried out a comparative transcriptomic analysis in fruit tissues using a parental cultivar (M82) with normal fruit AsA levels as a reference. We identified 233 differentially expressed genes, indicating that AsA accumulation in IL 10-1 reflects modification in the peroxisomal metabolism and reduced glutathione biosynthesis. Evidences coming from the experiment suggest that the lower AsA accumulation in IL10-1 fruit is mainly achieved by increasing ROS generation through a NAD+-dependent isocitrate dehydrogenase  and promoting an increase in aminoacid catabolism, which is driven by a stress response and may lead to lower glutathione pool.

overall_design: Comparative microarray analysis between a tomato introgression line (IL10-1) expressing lower level of fruit ascorbic acid and its parental cultivar M82 (reference) was performed. In particular, samples were generated by pooling red-ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Three plant replica were used for each line (IL10-1 and M82) and the experiment was replicated over two consecutive years.