title: Tamoxifen induction of Cre recombinase does not cause long lasting or sexually divergent responses in the CNS epigenome or transcriptome: implications for the design of aging studies (RNA-Seq).

status: Public on Aug 13 2019

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: The systemic delivery of tamoxifen (Tam) to activate inducible CreERT2-loxP transgenic mouse systems is now widely used in neuroscience studies. This critical technological advancement allows temporal control of DNA-cre recombination, avoidance of embryonically lethal phenotypes, and minimization of residual cell labeling encountered in constitutively active drivers. Despite its advantages, the use of Tam has the potential to cause long-lasting, uncharacterized side effects on the transcriptome and epigenome in the CNS, given its mixed estrogen receptor (ER) agonist/antagonist actions. With the welcome focus on including both sexes in biomedical studies and efforts to understand sex differences, Tam administration could also cause sexually divergent responses that would confound studies. To examine these issues, epigenetic and transcriptomic profiles were compared in C57BL/6J female and male hippocampus, cortex, and retina 1 month after a five- day Tam treatment typical for cre induction, or vehicle control (sunflower seed oil). Cytosine methylation and hydroxymethylation levels, in both CG and non-CG contexts, were unchanged as determined by oxidative bisulfite sequencing. Long-lasting Tam transcriptomic effects were also not evident/minimal. Furthermore, there is no evidence of sexually divergent responses with Tam administration and Tam did not alter sex differences evident in controls. Combined with recently reported data that Tam alone does not cause long-lasting changes in behavior and neurogenesis, our findings provide confidence that Tam can be used as a cre-recombinase inducer without introducing significant confounds in transcriptomic and epigenomic neuroscience studies, particularly those focused on genomic and transcriptomic aspects of the aging brain.

overall_design: Examination of the effect of tamoxifen administration on RNA Expression in the retina, cortex, and hippocampus of mouse by RNA-Seq

first: Ana

last: Chucair-Elliott

first: Sarah

last: Ocanas

last: Stanford

first: Niran

last: Hadad

first: Benjamin

last: Wronowski

first: Laura

last: Otalora

first: Willard

last: Freeman


title: Transcriptomic analysis of OsRUS1 overexpression rice lines with rapid and dynamic leaf rolling morphology

status: Public on Mar 27 2019

city: Guangzhou

first: Xuewen

last: Hou

state: Guangdong

address: NO 483 Wushan Road, Tianhe District

department: Department of Plant Sciences, College of Life Sciences

country: China

institute: South China Agricultural University

type: Expression profiling by high throughput sequencing

summary: OsRUS1-GFP overexpression (OsRUS1-OX) transgenic rice lines were generated using ZH-11 wildtype. Under well-watered conditions, the leaves of OsRUS1-OX transgenic rice lines could roll in about four minutes under sunlight, and the rolled leaves of OsRUS1-OX transgenic rice lines could expand in about seven minutes if the sunlight was shaded, while the leaves of wildtype ZH-11 expanded all the times at the same conditions. The mechanism behind the light-responded rapid and dynamic leaf rolling phenotype of OsRUS1-OX transgenic rice lines is unknown. Therefore, in order to understand this mechanism the RNA-Seq approach was used to explore the expressed genes difference between OsRUS1-OX and ZH-11.

overall_design: When ZH-11 and OsRUS1-OX plants were at the heading stage, the flag leaves were collected on a sunny summer day (11:00 am, WT with expanded leaves, OsRUS1-OX with rolled leaves) with triplicate. mRNA profiles of above samples were generated by deep sequencing using Illumina Hiseq platform.

first: Ning

last: Yu


title: mTORC1 dependent lipid signalling drives acute proteolytic rewiring of mitochondria by YME1L

status: Public on Aug 28 2019

city: Cologne

first: Thomas

last: MacVicar

address: Joseph-Stelzmann Str 9B

country: Germany

institute: Max Planck Institute for Biology of Ageing

summary: Metabolic reprogramming of mitochondria occurs during development, cell differentiation and in disease and is coupled to changes in mitochondrial mass and shape. Here, we demonstrate that the i-AAA protease YME1L rewires the proteome of pre-existing mitochondria in response to hypoxia or nutrient starvation. Inhibition of mTORC1 induces a lipid signalling cascade via the phosphatidic acid phosphatase LIPIN1, which decreases phosphatidylethanolamine levels in mitochondrial membranes and promotes proteolysis. YME1L degrades mitochondrial protein translocases, lipid transfer proteins and metabolic enzymes to acutely limit mitochondrial biogenesis and support cell growth. YME1L-mediated mitochondrial reshaping ensures spheroid and xenograft growth of pancreatic ductal adenocarcinoma (PDAC) cells. Similar mitochondrial proteome changes occur in tumour tissues of PDAC patients, suggesting that YME1L is relevant to the pathophysiology of specific solid tumours. Our results identify the mTORC1-LIPIN1-YME1L axis as a novel post-translational regulator of mitochondrial proteostasis at the interface of metabolism and mitochondrial dynamics.

overall_design: Transcript profiles of WT mouse embryonic fibroblasts (MEF) incubated in normoxia (21% O2) or hypoxia (0.5 % O2) for 16 h. The dataset includes biological triplicates for each condition (6 samples in total)

last: Langer

first: Janine

last: Altmüller

first: Franziska

last: Metge


title: Trancriptomic analysis of flower bud dormancy in sweet cherry

status: Public on Dec 16 2019

city: Villenave d'Ornon

first: Benedicte

last: Wenden

address: 71 avenue Edouard Bourlaux

country: France

institute: INRA

summary:
Bud dormancy is a crucial stage in perennial trees and allows survival over winter and optimal subsequent flowering and fruit production. Environmental conditions, and in particular temperature, have been shown to influence bud dormancy. Recent work highlighted some physiological and molecular events happening during bud dormancy in trees. However, we still lack a global understanding of transcriptional changes happening during bud dormancy.
We conducted a fine tune temporal transcriptomic analysis of sweet cherry (Prunus avium L.) flower buds from bud organogenesis until the end of bud dormancy using next-generation sequencing.
We observe that buds in organogenesis, paradormancy, endodormancy and ecodormancy are characterised by distinct transcriptional states, and associated with different pathways. We further identified that endodormancy can be separated in two phases based on its transcriptomic state: early and late endodormancy. We also found that transcriptional profiles of just 7 genes are enough to predict the main cherry tree flower buds dormancy stages.
Our results indicate that transcriptional changes happening during dormancy are robust and conserved between different sweet cherry cultivars. Our work also sets the stage for the development of a fast and cost effective diagnostic tool to molecularly define the flower bud stage in cherry trees.

overall_design: Branches and flower buds were collected from four different sweet cherry cultivars with contrasted flowering dates: ‘Cristobalina’, ‘Garnet’ and ‘Regina’ which display extra-early, early and late flowering dates, respectively. Ten or eleven dates spanning the entire period from flower bud organogenesis (July 2015) to bud break (March 2016) were chosen for RNA sequencing. For each date, flower buds were sampled from different trees, each tree corresponding to a biological replicate.

first: Noémie

last: Vimont

first: Sandra

last: Cortijo

first: Bénédicte

first: Philip

middle: A

last: Wigge

first: Varodom

last: Charoensawan


title: Stranded RNA-seq were performed on total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina) for 3 brain , 8 IDHwt and 5 IDHmut glioma samples.

status: Public on Sep 09 2019

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

summary: Aberrant DNA methylation is a well-defined feature of cancer cells that is commonly associated to transcriptional alteration. Nonetheless, a primary role of this defect in genome-wide cancer-associated gene misregulation is still being questioned.  Here, we used adult glioma, a widespread type of brain tumor, to evaluate the relative contribution of DNA methylation-dependent and -independent mechanisms on transcriptional alteration at CpG-island/promoter-associated genes in cancer cells.   By extensive molecular analyses conducted in both IDH wild-type (IDHwt) and IDH mutated (IDHmut) samples, we show that DNA hypermethylation affects only a minority of genes that show a loss or a gain of expression. In IDHwt samples, for instance, more than 75% of aberrantly repressed genes do not display DNA methylation defect at their CpG-island promoter. Rather, an alteration in the H3K27me3 signature is the predominant molecular defect at misregulated genes. We also observed that a bivalent chromatin signature in stem cell might not only predispose genes to hypermethylation, as widely documented, but more generally to all type of transcriptional alterations. In addition, we evidenced that transcriptional strength in healthy brain influences the choice between DNA methylation- or H3K27me3- associated silencing pathway at repressed genes in glioma. Combined our study supports a model whereby the altered developmental control of H3K27me3 dynamics, and more specifically defects in the interplay between polycomb protein complexes and brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells.  Together our study provides a comprehensive and revisited picture of epigenetic gene deregulations in cancer. Our observations are also of importance for the design of drugs that aims to target cancer epigenetic defects.

overall_design: Total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina) for 3 brain , 8 IDHwt and 5 IDHmut glioma samples.

first: Franck

last: Court

first: Philippe

last: Arnaud


title: Therapeutic effects of ASO-mediated reduction of Atxn1 in a SCA1 Mouse Mode: Proof of concept with distinct disease-associated transcriptome profiles in cerebellum and medulla

status: Public on May 31 2019

city: Minneapolis

first: Harry

middle: T

last: Orr

state: MN

address: 2101 6th Strreet SE

department: Laboratory Medicine and Pathology

country: USA

institute: University of Minnesota

summary: RNA-targeting approaches have improved disease symptoms in preclinical rodent models of several neurological diseases. Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited ataxia caused by expansion of a polyglutamine tract in the encoded protein Ataxin-1 (ATXN1). Despite advances in understanding this CAG repeat/polyglutamine expansion disease, there are still no therapies to alter its progressive fatal course. Here we investigate the therapeutic capability of an antisense oligonucleotide (ASO) targeting mouse Atxn1 in Atxn 1 154Q/2Q knockin mice that manifest motor deficits and premature lethality. Following a single ASO treatment at 5 weeks of age, mice demonstrated rescue of these disease-associated phenotypes. In addition, RNA-seq on vehicle-treated Atxn1 154Q/2Q and ASO-treated Atxn1 154Q/2Q mice were used to demonstrate molecular differences between SCA1 pathogenesis in the cerebellum that underlies ataxia with disease in the medulla associated with lethality. Together, these findings support the efficacy and therapeutic importance of directly targeting ATXN1 expression as a strategy to rescue both motor deficits and lethality seen in SCA1.

overall_design: Medulla and pons (18 and 28 week mice) and cerebella (18 week only) mRNA profiles of wild type (WT) and Atxn1[82Q] knockin mice  were generated by deep sequencing using Illumina HiSeq 2500. Atxn1[82Q] knockin mice mRNA profiles were assessed with and without treatment with an anti-sense oligonucleotide targeting Atxn1.

first: Christine

last: Henzler


title: Genomic copy number variation correlates with survival outcomes in glioblastoma patients

status: Public on Jan 18 2019

city: Atlanta

first: Zachary

last: Buchwald

state: GA

address: 1365 Clifton Rd # 1-A

institute: Emory University

summary: Allele-specific copy number analysis of tumors (ASCAT) assesses copy number variations (CNV) while accounting for aberrant cell fraction (ACF) and tumor ploidy. Here, we evaluate if ASCAT-assessed CNV are associated with survival outcomes in patients with WHO grade IV gliomas.  Methods:    We identified 56 patients with WHO grade IV gliomas. Tumor data analyzed by Affymetrix OncoScan FFPE Assay yielded the log ratio (R) and B-allele frequency (BAF). Input into ASCAT quantified CNV using the segmentation function to measure copy number inflection points throughout the genome. Actuarial overall survival (OS) and progression-free survival (PFS) assessed with Kaplan-Meier method and subgroups compared by the log-rank test. Results were validated on The Cancer Genome Atlas (TCGA) glioblastoma dataset.   Results:    Our cohort’s median age was 60.4 years (range: 26.1-86.3). Tumors were hyper-methylated at MGMT in 25 (44.6%) with IDH1 mutations in 6 (10.7%). Median follow-up time was 36.4 months, and median PFS and OS were 8 and 14.7 months, respectively.  PFS was longer for higher log R and BAF segment counts with hazard ratios (HR) of 0.32 and 0.49 respectively (p<0.001 and p=0.022). Patients with higher log R segment counts had significantly longer 12-month OS (81% vs 46.3%, p=0.0088). In the TCGA validation cohort, higher BAF segment counts had longer 12-month OS with a trend for log R (62.3% vs. 51.9%, p=0.0129 and 63.6% vs. 55.2%, p=0.0696 respectively).  Conclusions:   Our analysis demonstrated a longer PFS and OS for patients with increased genomic CNV. This may provide a novel method for assessing glioblastoma outcomes.

overall_design: After obtaining IRB approval, 56 patients treated at Emory University between 1/2009 and 8/2015 were evaluated and their charts were reviewed. Inclusion criteria included a pathologic diagnosis of a primary glioblastoma, no prior brain radiotherapy and an OncoScan analysis for the ASCAT inputs.  Treatment  At Emory University, all glioblastoma patients were discussed at a multi-disciplinary tumor board, including surgical oncology, neurosurgery, pathology, radiology, and medical and radiation oncology services. Decisions for therapeutic management were done in a joint manner.   Baseline characteristics recorded included age, gender, tumor location, performance status, MGMT methylation, 1p19q co-deletion and IDH1/2 mutation status. Radiation characteristics were also recorded, including radiation total dose, dose per fraction, and receipt of concurrent and adjuvant temozolomide.      SNP array  For the Emory Institutional dataset, Affymetrix OncoScan FFPE single nucleotide polymorphism (SNP) array was used for raw genomic data acquisition. Two data tracks are produced from SNP arrays: total signal intensity and allelic contrast. Log ratio (R) represents the total signal intensity, which reflects the total copy number on a logarithmic scale. The B allele frequency (BAF) represents the allelic contrast and demonstrates the relative presence at each SNP locus evaluated of the two alternative nucleotides. For the TCGA dataset, Affymetrix Genome-Wide Human SNP Array 6.0 was utilized for the raw genomic data.     ASCAT Analysis  Following acquisition of the raw genomic data from biopsy or resected tumor samples, we opened each microarray case in Affymetrix Chromosome Analysis Suite v3.0 and used the "Export Probe Level Data" function to create a text file with the microarray probe set name, log 2 ratio (log R) signal, and B-allele frequency (BAF) BAF signal suitable for processing with the ASCAT v2.4.4 library in R v3.4.1.   These data were input into the ASCAT algorithm. As a function of the SNP data, ASCAT models the allele-specific copy number and arrives at the solution that is closest to integer copies at all assessed loci. To do this accurately, the ASCAT algorithm accounts for important factors including polyploidy and aberrant cell fraction when calculating the CNV profile.8 Aneuploidy, a deviation from the normal chromosomal number, can confound copy number analysis. Non-aberrant cell admixture or aberrant cell fraction reflects the non-tumor component of the sample and can differ significantly between samples again confounding copy number studies. As an intermediate output of the ASCAT algorithm, we quantified the number of segments with changes in the log R and BAF. A segment is defined as a region of the genome with a fixed copy number. For a representative log R data sample, there were an average of 4,866,610 base pairs and 332 probes per segment with a range of 109,439 – 8,276,5227 base pairs and 7 – 5,997 probes. The total number of segments reflects the number of CNV inflection points or changes in copy number in the genome.      Statistical analysis  PFS was defined as months from diagnosis to progression, death or last follow-up, where those alive without progression were censored at last follow-up. Progression was defined radiographically based on the T1 post-contrast MRI. OS was defined as months from diagnosis to death or last follow-up, where those who survived were censored at last follow-up.  Genomic characteristics considered for analysis were ASCAT ploidy, ASCAT aberrant cell fraction, ASCAT log ratio segment count, and ASCAT BAF segment count.  These variables were analyzed as continuous variables, and as categorical variables dichotomized at their median values.  A cut point analysis was also performed to identify statistically significant cut points for each genomic variable and each endpoint using an outcome-oriented approach.15 All reported survival data used the optimal cut point.  The log-rank statistic was maximized, and the significance of each cut points was assessed.  Statistically significant cut points were considered for further analysis.    Descriptive statistics were reported for each variable.  PFS and OS curves were estimated using the Kaplan-Meier method, and compared using log-rank tests. Median follow-up is estimated using the reverse Kaplan-Meier approach, where the censoring indicator is switched such that deaths are now censored. Univariate Cox proportional hazards models were also fit, modeling PFS and OS as a function of age, gender, KPS, surgery type, the four genomic characteristics, IDH1 mutation (positive vs. negative), and MGMT (methylated vs. unmethylated). Multivariable Cox proportional hazards models were fit for OS and PFS as function of the statistically significant ASCAT variables, IDH1, MGMT, KPS and 1p19q codeletion. Multivariable Cox models also were fit for OS as a function of the statistically significant ASCAT variables, IDH1, MGMT, KPS, and surgery type.  Model assumptions were checked and verified.  Statistical analyses were performed using SAS 9.4 (SAS Institute Inc., Cary, NC), and statistical significance was assessed at the 0.05 level.

first: Geoffrey

middle: H

last: Smith

first: Jennifer

last: Hauenstein


title: Liver X Receptor α Activation Enhances Cholesterol Secretion in Lactating Mammary Epithelium

status: Public on Mar 05 2019

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

summary:
We profiled differential gene expression in vivo between pregnant day 14 (secretory differentiation) and lactation day 4 (established secretory activation) using isolated mouse mammary epithelial cells depleted of the mammary adipocytes.
Liver-X-Receptors are ligand-dependent transcription factors activated by cholesterol metabolites. These receptors induce a suite of target genes required for de novo synthesis of triglycerides and cholesterol transport in many tissues. Two different isoforms -LXRα and LXRβ- have been well characterized in liver, adipocytes, macrophages and intestinal epithelium among others, but their contribution to cholesterol and fatty acid efflux in the lactating mammary gland is poorly understood. We hypothesize that LXR regulates lipogenesis during milk fat production in lactation. Global mRNA analysis of mouse mammary epithelial cells (MECs) revealed multiple LXR/RXR targets are upregulated sharply at the onset of lactation compared to mid-pregnancy. LXRα is the primary isoform and its protein levels increase throughout lactation in MECs. The LXR agonist GW3965 markedly induced several genes involved in cholesterol transport and lipogenesis and enhanced cytoplasmic lipid droplet accumulation in the HC11 MEC cell line. Importantly, in vivo pharmacological activation of LXR increased the milk cholesterol percentage and induced Srebp1c and Abca7 expression in MECs. Cumulatively, our findings identify LXRα as an important regulator of cholesterol incorporation into the milk through key nodes of de novo lipogenesis, suggesting a potential therapeutic target in women with difficulty initiating lactation.

overall_design: The isolated mammary epithelial cells from pregnant day 14 and lactation day 4 mice were investigated

first: Diego

middle: Y

last: Grinman

first: Valeria

middle: P

last: Careaga

first: Elizabeth

last: Wellberg

first: M

middle: V

last: Dansey

first: Edith

middle: C

last: Kordon

first: Steven

middle: M

last: Anderson

first: Marta

middle: S

last: Maier

first: Gerardo

last: Burton

first: Paul

last: MacLean

first: Adali

last: Pecci


title: Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo

status: Public on Dec 19 2018

city: Santa Cruz

first: Susan

last: Carpenter

state: CA

address: 1156 High Street

department: Molecular Cell and Developmental Biology

institute: University of California Santa Cruz

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

overall_design: Refer to individual Series


title: Integrated DNA methylation and gene expression profiling  across multiple brain regions implicate novel genes in Alzheimer’s  disease

status: Public on Jan 31 2019

city: Baltimore

first: Stephen

last: Semick

state: MD

address: 655 W Baltimore St S

institute: University of Maryland School of Medicine

type: Methylation profiling by genome tiling array

summary: Late-onset Alzheimer’s disease (AD) is a complex age-related neurodegenerative disorder that likely involves epigenetic  factors. To better understand the epigenetic state associated with AD, we surveyed 420,852 DNA methylation (DNAm) sites  from neurotypical controls (N = 49) and late-onset AD patients (N = 24) across four brain regions (hippocampus, entorhinal  cortex, dorsolateral prefrontal cortex and cerebellum). We identiied 858 sites with robust diferential methylation collectively  annotated to 772 possible genes (FDR < 5%, within 10 kb). These sites were overrepresented in AD genetic risk loci  (p = 0.00655) and were enriched for changes during normal aging (p < 2.2 × 10−16), and nearby genes were enriched for  processes related to cell-adhesion, immunity, and calcium homeostasis (FDR < 5%). To functionally validate these associations,  we generated and analyzed corresponding transcriptome data to prioritize 130 genes within 10 kb of the diferentially  methylated sites. These 130 genes were diferentially expressed between AD cases and controls and their expression was  associated with nearby DNAm (p < 0.05). This integrated analysis implicates novel genes in Alzheimer’s disease, such as  ANKRD30B. These results highlight DNAm diferences in Alzheimer’s disease that have gene expression correlates, further  implicating DNAm as an epigenetic mechanism underlying pathological molecular changes associated with AD. Furthermore,  our framework illustrates the value of integrating epigenetic and transcriptomic data for understanding complex disease.

overall_design: We measured DNA methylation (DNAm) levels from dorsolateral prefrontal cortex (DLPFC), hippocampus (HIPPO), entorhinal cortex (ERC), and cerebellum (CRB) of postmortem brain donors diagnosed with Alzheimer's disease (N=24) and neurotypical controls (N=49). For additional demographic information, please refer to Table S1 of the corresponding publication.

first: Andrew

middle: E

last: Jaffe


title: Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (macrophages)

summary: Here we amplified a region in exon 5 of Ptgs2 that contains SNPs to allow us to differenitate between the C57 allele and the MOLF allele

overall_design: primers were designed to a region in exon 5 that contained SNPs what once sequenced could be separated into C57 and MOLF alleles. Regions were amplified from a WT/MOLF and LincRNA-Cox2/MOLF macrophages and Mi-seq was performed. From the fastq files sequences with SNPs were grepped out from the file and counted to determine the number of reads that corresponded to the C57 (WT or KO allele) versus the MOLF


title: Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs and spleens)

summary:
Here we compare gene expression profiles between lungs and spleens following LPS in vivo injection into Wild type, lincRNA-Cox2 knockout and lincRNA-Cox2 mutant mice
The aim of the experiment is to determine the cis and trans functions for lincRNA-Cox2 following in vivo LPS challenge within the spleen and lung

overall_design: Lungs and spleens were extracted  from 8 week old wild type, lincRNA-Cox2 knockout and mutant mice following 6h of LPS treatment (20mg/kg) and placed directly in Trizol. RNA was isolated and sequenced


title: NKL homeobox gene NKX2-2 is aberrantly expressed in Hodgkin lymphoma

status: Public on Jan 22 2019

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

institute: Leibniz Institute DSMZ

summary: NKL homeobox genes encode basic transcriptional regulators of cell and tissue differentiation. Recently, we described a hematopoietic NKL-code comprising particular NKL homeobox genes expressed in normal hematopoietic stem cells and during lymphopoiesis, highlighting their physiological role in the development of T-, B- and NK-cells. Here, we describe aberrant expression of the neural non-hematopoietic NKL homeobox gene NKX2-2 in 10% of both classical Hodgkin lymphoma (HL) and nodular lymphocyte predominant (NLP) HL patients. NKX2-2 expressing NLPHL cell line DEV served as a model by analysing chromosomal configurations and expression profiling data to reveal activating mechanisms and downstream targets of this developmental regulator. While excluding chromosomal rearrangements at the locus of NKX2-2, we identified t(3;14)(p21;q34) resulting in overexpression of the IL17 receptor gene IL17RB via juxtaposition to the IGH-locus. SiRNA-mediated knockdown experiments demonstrated that IL17RB activated NKX2-2 transcription. Overexpression of IL17RB-cofactor DAZAP2 via chromosomal gain of 12q13 and deletion of its proteasomal inhibitor SMURF2 at 17q24 supported expression of NKX2-2. IL17RB activated transcription factors FLI1 and FOXG1 which in turn mediated NKX2-2 expression. In addition, overexpressed chromatin-modulator AUTS2 contributed to NKX2-2 activation as well. NKX2-2 inhibited transcription of lymphoid NKL homeobox gene MSX1 and activated expression of basic helix-loop-helix factor NEUROD1 which may disturb B-cell differentiation processes via reported interaction with TCF3/E2A. Taken together, our data reveal in HL ectopic activation of a neural gene network showing NKX2-2 at a central position, highlighting oncogenic impacts of NKL homeobox genes in B-cell malignancies.

overall_design: Hodgkin lymphoma cell line characterisation.

first: Stefan

last: Nagel


title: Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs)

summary:
Here we compare gene expression profiles between lungs taken from a Wild type mouse to lungs from a lincRNA-Cox2 knockout mouse
The aim of the experiment is to determine what impact lincRNA-Cox2 has on gene expression within the lung

overall_design: Lungs were extracted  from 4 months old wild type and lincRNA-Cox2 knockout mice after CO2 euthanasia and cervical neck dislocation, snap frozen, homogenized in liquid nitrogen and resuspended in Trizol.

first: John

last: Rinn


title: Microarray expression data on cultured dermal fibroblasts from patients affected with classical Ehlers Danlos syndrome (cEDS)

status: Public on Jan 21 2019

city: Brescia

first: Nicola

last: Chiarelli

state: Lombardy

address: Viale Europa 11

department: Molecular and Translational Medicine

country: Italy

institute: University of Brescia

summary:
Gene expression profiling of cultured skin fibroblasts obtained from patients affected with classical Ehlers Danlos syndrome (cEDS)
Transcriptome-wide expression profiling using the Affymetrix Gene 1.0 ST platform comparing the gene expression pattern of cultured skin fibroblasts from 4 cEDS patients with those of 9 healthy individuals

overall_design: Comparison of transcriptome profiling of human cultured skin fibroblasts from 4 cEDS patients and 9 healthy individuals


title: Bulk RNA sequencing of chemical-induced intermediate cells

status: Public on Nov 19 2018

city: Hangzhou

first: Yishan

last: Chen

address: #866 Yuhangtang Road

institute: Zhejiang University

summary: This study aims to investigate the individual effect of cocktail VCRTc on the direct reprogramming process.We collected cells as follows: mouse chondrocytes (mchons), mouse embryonic fibroblasts(MEFs), MEFs treated by a chemical cocktail VCRTc for 3 days (3d-VCRTc) and 6 days (6d-VCRTc), and MEFs treated by individual chemical V, C, R, T, ce for 6 days, respectively. Then we did RNA extraction,reverse transcription and library preperation before bulk RNA seq. We uncovered that MEFs treated with chemicals have an upregulation of chondrocytes enriched genes; and a downregulation of MEF enriched genes,indicating that chemical treatment drove MEF toword chondrogenic lineage before the 2nd stage of differentiation.

overall_design: RNA-seq was modified from a previous method. Briefly, RNA was extracted from samples by Trizol reagent (TAKARA), reverse transcription was conducted by SuperScript II reverse transcriptase (Invitrogen), double strand cDNA was conducted using NEBNext mRNA second strand synthesis kit (NEB), double strand DNA was cleaned with AMPure XP beads (Beckman Coulter). 3’end enriched sequencing library was constructed with Nextera XT kit (Illumina) and sequenced on Illumina X-Ten platform.  There were 3 samples for each group and 5 replicates of sequencing library for each sample.

first: Hongwei

last: Ouyang


title: Similarities and differences in the regulation of HoxD genes during chick and mouse limb development.

status: Public on Nov 27 2018

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus


title: RIPK3-dependent transcriptional program in flavivirus-infected neurons

status: Public on Nov 06 2018

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

summary: Here, we characterize RIPK3-dependent transcriptional responses in cortical neurons following infection with neurotropic flaviviruses. Neurons were infected with either Zika virus (ZIKV) strain MR766 at an MOI of 0.1,  West Nile virus (WNV) strain TX 2002-HC at an MOI of 0.001, or a saline mock solution. Neurons were derived from mice lacking RIPK3 expression (Ripk3-/-) or wildtype controls. These studies revealed a number of antiviral genes whose upregulation following viral infection is absent in neurons lacking RIPK3, a subset of which were validated using qRT-PCR.

overall_design: Primary cortical neuron cultures derived from WT or Ripk3-/- mice were infected with ZIKV MR766, WNV TX 2002-HC, or a saline control. Total RNA was collected at 24 hours post infection for subsequent analysis. Three independent replicates were included per condition (genotype/infection).

first: Brian

last: Daniels

last: Oberst


title: A novel population of Hopx-dependent basal radial glial cells in the developing mouse neocortex

status: Public on Oct 10 2018

city: Dresden

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

institute: MPI-CBG

summary: A specific subpopulation of neural progenitor cells, the basal radial glial cells (bRGCs) of the outer subventricular zone (OSVZ), are thought to have a key role in the evolutionary expansion of the mammalian neocortex. In the developing lissencephalic mouse neocortex, bRGCs exist at low abundance and show significant molecular differences from bRGCs in developing gyrencephalic species. Here, we demonstrate that the developing mouse medial neocortex (medNcx), in contrast to the canonically studied lateral neocortex (latNcx), exhibits an OSVZ and an abundance of bRGCs similar to that in developing gyrencephalic neocortex. Unlike bRGCs in developing mouse latNcx, the bRGCs in medNcx exhibit human bRGC-like gene expression, including expression of Hopx, a human bRGC marker. Disruption of Hopx expression in mouse embryonic medNcx and forced Hopx expression in mouse embryonic latNcx demonstrate that Hopx is required and sufficient, respectively, for a bRGC abundance as found in developing gyrencephalic neocortex. Taken together, our data identify a novel bRGC subpopulation in developing mouse medNcx that is highly related to bRGCs of developing gyrencephalic neocortex.

overall_design: mRNA profiles of basal radial glial cells isolated from E18.5 mouse medial neocortex were generated by deep sequencing, in quadruplicate, using Illumina.

first: Samir

last: Vaid

first: Lena

last: Hersemann

first: Holger

last: Brandl

first: Wieland

middle: B

last: Huttner

first: Takashi

last: Namba


title: Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [ChIP-Seq]

summary: Hoxd genes are important for limb development in all tetrapods examined thus far. In mouse, they are controlled by a complex bimodal regulation, which regulates first the proximal patterning, then the distal structure, allowing at the same time the formation of the wrist and ankle articulations. We analyzed the existence of this regulatory mechanism in chicken, i.e. in an animal where large morphological differences exist between fore- and hindlimbs. We report that while this bimodal regulation is globally conserved between mammals and avian, some important modifications evolved at least between these two model systems, in particular regarding the activity of specific enhancer and the position of the TAD boundary and the forelimb versus hindlimb comparative regulations. Some aspects of these regulations seem to be more conserved between chick and bats than with the mouse situation, which may relate to the extent to which forelimbs and hindlimbs of these various animals differ in their functions.

overall_design: ChIP analysis of H3K27ac, H3K27me3, H3K4me1 and CTCF from chick and mouse limb tissues

first: N

first: A

last: Necsulea

first: D

last: Duboule


title: Single cell dissection of Chemical Reprogramming from Fibroblasts into functional Chondrocytes

summary: We used single cell analysis to systematically dissect the sequential changes of cellular phenotypes during fibroblast-chondrocyte direct reprograming.1401 single-cell transcriptomes were measured in total (232 MEFs of day0, 577 chemical-induced intermediate cells (ci-ICs) of day6, 311 ci-chons of day 34, 281 mouse primary chondrocytes (mchons) as positive control). We found that ci-chons and mchons shared similar subpopulation with specifically expression of cartilage-related markers. The findings also indicated that in the early induction, fibroblasts to lose their original features, and transit into a cartilage progenitor intermediate state.

overall_design: Single cells (MEFs, ci-ICs, ci-chons and primary mouse chondocytes) were captured using FluidigmTM C1 high-throughput IFC. Therefore, the sorted single-cell suspension was loaded on a microfluidic RNA-seq chip. We checked the cells by a microscope for captured cell number confirmation. Then cell lysis, reverse transcription and cDNA pre-amplification were performed on the chip according to Fluidigm’s standard protocol. Illumina libraries were Illumina Nextera XT DNA Sample Preparation kit according to the protocol supplied by Fluidigm. Cell libraries were pooled and sequenced 150 bp paired-end on one lane of Illumina HiSeq xten.


title: High-Resolution Dissection of Chemical Reprogramming from Fibroblasts into Functional Articular Chondrocytes


title: Subcutaneous adipose gene expression from men in the METSIM cohort

status: Public on Jul 31 2019

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: The University of North Carolina at Chapel Hill

summary: We analyzed the abdominal subcutaneous adipose tissue of 434 male human subjects from the METSIM study, via RNA-sequencing. The METSIM study was approved by the Ethics Committee of the University of Eastern Finland and Kuopio University Hospital in Kuopio, Finland and carried out in accordance with the Helsinki Declaration. Written informed consent was obtained from all participants. Here, we provide the expression values by gene for each subject and relevant covariates. Raw fastq files will be contributed to dbGaP, as they require controlled access.

overall_design: Subcutaneous adipose gene expression profiles, measured via RNAseq, for 434 men from the METSIM cohort

first: Chelsea

middle: K

last: Raulerson

first: Markku

last: Laakso


title: RNA transcriptome sequencing analysis of MKN45 cells transfected with tcons_00001221 shRNA or control shRNA

status: Public on May 12 2018

city: Shanghai

first: Ming

middle: zhe

last: Ma

state: Shanghai

address: 270 DongAn Road

department: Department of Gastric Surgery

institute: Fudan University Shanghai Cancer Center

summary: An RNA transcriptome sequencing analysis was performed in MKN45 cells that were transfected with tcons_00001221 shRNA or control shRNA.

overall_design: mRNA profiles of MKN45 cells transfected with tcons_00001221 shRNA or control shRNA.

first: Mingzhe


title: Role of Chromogranin A on renal function in a mouse model of failing kidney

status: Public on Oct 25 2018

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

summary:
Chromogranin A (CHGA) is elevated in plasma of patients with renal failure and several CHGA polymorphisms are associated with hypertensive renal disease. Therefore, we investigated the role of CHGA in kidney disease using the partial nephrectomy model of kidney failure. Mice under surgery to remove 2/3rds of the left kidney and the entire right kidney. Control mice received the sham surgery. Wild-type and CHGA-/- mice used.
To model the changes in vitro, CRL-1927 kidney cells were treated with or without CHGA in vitro.

overall_design:
WT and CHGA-/- mice underwent sham or 5/6ths nephrectomy and were followed for 10 weeks. At the end of the study, tissue was harvested and RNA extracted for expression profiling by microarray on Nimblegen mm9 12x135K array.
CRL-1927 kidney cells were treated with or without CHGA in vitro, and RNA extracted for expression profiling by microarray on Nimblegen mm9 12x135K array.

first: Sucheta

last: Vaingankar

first: Nicholas


title: Cooperative Regulation of Normal and Neoplastic Hepatocyte Proliferation by Myc and ChREBP

status: Public on Aug 09 2018

city: Pittsburgh

first: Edward

last: Prochownik

state: PA

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

summary: By analogy to the c-Myc (Myc)/Max family of transcription factors, there also exists a “parallel” network of structurally and functionally related bHLH-ZIP proteins with certain Myc-like functions. Two closely related “Myc-like” paralogs termed Mondo A and MondoB/ChREBP (ChREBP) positively regulate gene expression in heterodimeric association with the Max-like factor Mlx.  Myc is necessary to support liver cancer cell growth but not for normal hepatocyte proliferation. Here, we investigated the role for ChREBP and its relationship to Myc in these processes. Unlike Myc, ChREBP loss conferred a marked proliferative disadvantage to normal hepatocytes as did the loss of both ChREBP and Myc. In addition, hepatoblastomas (HBs) originating in myc-/-, chrebp-/- or myc-/-/chrebp-/- backgrounds grew significantly more slowly. Metabolic studies performed on livers and HBs arising in all three backgrounds showed marked differences in oxidative phosphorylation, fatty acid -oxidation (FAO) and the activity of pyruvate dehydrogenase. RNAseq of livers and HBs indicated seven distinct forms of target transcript regulation. Gene ontology analysis indicated that many transcripts de-regulated in the chrebp-/- background encode enzymes functioning in glycolysis, the TCA cycle and - and-FAO whereas those in myc-/- background encode enzymes for glycolysis, glutaminolysis and sterol biosynthesis. Transcript de-regulation in the double knockout group was similar but also included those involved in peroxisomal - and -FAO. Finally, we identified cooperative positive regulation by Myc and ChREBP of virtually all ribosomal protein genes. Our findings define the global proliferative, metabolic and transcriptional roles for the more general “Extended Myc Network” under both normal and neoplastic conditions.

overall_design: Total 40 samples from 8 groups, 5 repeat in each group. Group 1( wild type liver-control), Group 2 ( Myc KO Liver), Group 3 (ChREBP KO Liver), Group 4 ( Myc KO plus ChREBP KO Liver--Double  KO Liver), Group 5( wild type hepatoblastomasl), Group 6 ( Myc KOhepatoblastomas), Group 7 (ChREBP KO hepatoblastomas), Group 8 ( Myc KO plus ChREBP KO hepatoblastomas--Double  KO hepatoblastomas)

first: Huabo

last: Wang


title: Development of lncRNA and mRNA expression signatures for gastric cancer cells under hypoxic conditions

status: Public on Aug 06 2018

summary: To further development of lncRNA and mRNA expression signatures for gastric cancer cells under hypoxic conditions, we have employed  microarray expression profiling as a discovery platform to identify lncRNAs that are differentially expressed upon hypoxia.

overall_design: Hypoxia induced lncRNA expression in human gastric cancer cells was measured at 24 hours after exposure to hypoxia (1% oxygen).  Two independent experiments were performed for each experiment.


title: Next Generation Sequencing Facilitates Quantitative Analysis of conventional and ischemia-free liver transplantation Transcriptomes

status: Public on Apr 12 2018

city: Guangzhou

first: Xiaoshun

last: He

address: NO.58 Zhongshan Er Road

department: Organ Transplant Center

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the transcriptomes of conventional liver transplantation liver allografts and ischemia-free liver transplantation livers by comparing samples of post-reperfusion and at the end of preservation.

overall_design: Liver allograft mRNA profiles of the end of preservation and post-reperfusion were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: X

first: Z

last: Guo

first: S

last: Huang


title: Expression data from progesterone receptor knockout versus heterozygous mouse ovaries: granulosa cells

status: Public on Apr 20 2018

city: St Lucia

first: Lisa

last: Akison

state: QLD

address: Sir William MacGregor Building

department: Biomedical Sciences

country: Australia

institute: University of Queensland

summary:
Ovulation requires sequential molecular events and structural remodeling in the ovarian follicle for the successful release of a mature oocyte capable of being fertilised. Critical to this process is progesterone receptor (PGR), a transcription factor highly yet transiently expressed in granulosa cells of preovulatory follicles. Progesterone receptor knockout (PRKO) mice are anovulatory, with a specific and complete defect in follicle rupture. Therefore, this model was used to examine the critical molecular and biochemical mechanisms necessary for successful ovulation.
We used microarrays to identify putative PGR-regulated genes in granulosa cells at a time when PGR expression is maximal (eCG + 8h hCG) and the preovulatory follicle is undergoing the final changes necessary for successful ovulation.

overall_design: The mutant strain used in this experiment were PRlacZ knock-in mice which originated from Assoc Prof John Lydon, Baylor College of Medicine, Houston TX, USA. The lacZ insertion results in disruption of transcription of both isoforms of PGR (Ismail et al, 2002, Mol Endocrinol 16:2475-2489), and therefore mice homozygous for the lacZ insertion are a phenocopy of the knockout strain described by Lydon et al. (1995, Genes Dev. 9:2266-2278) and are hereafter referred to as PRKO. Heterozygous mice (PR+/-) are a phenocopy of WT and have normal fertility (Ismail et al, 2002) and are therefore appropriate controls. Granulosa cells were collected by puncturing antral follicles from the ovaries of pre-pubertal PRKO and PR+/- mice 8 h after a standard protocol for hormonal induction of ovulation. Day 21-23 old mice were injected i.p. with 5IU of equine chorionic gonadotropin (eCG) to stimulate follicle growth, followed 44-47 h later by i.p. injection of 5 IU of human chorionic gonadotropin (hCG) to trigger ovulatory processes. Granulosa cells from 15 animals were collected per genotype, with cells from 3 animals pooled per sample for a total of n = 5 samples per genotype.

first: Darryl

last: Russell

first: Rebecca

last: Robker


title: Expression data from progesterone receptor knockout versus heterozygous mouse ovaries: cumulus oocyte complexes

summary:
Ovulation requires sequential molecular events and structural remodeling in the ovarian follicle for the successful release of a mature oocyte capable of being fertilised. Critical to this process is progesterone receptor (PGR), a transcription factor highly yet transiently expressed in granulosa cells of preovulatory follicles. Progesterone receptor knockout (PRKO) mice are anovulatory, with a specific and complete defect in follicle rupture. Therefore, this model was used to examine the critical molecular and biochemical mechanisms necessary for successful ovulation.
Although PGR is not expressed in the cumulus cells or oocyte of the preovulatory cumulus oocyte complex (COC), it is well known that the COC responds to the cascade of gene expression changes that occurs in preovulatory granulosa cells. We used microarrays to identify putative ‘ovulation’ genes in preovulatory COCs at a time when PGR expression is maximal in granulosa cells (eCG + 8h hCG) and the preovulatory COC and follicle are undergoing the final changes necessary for successful ovulation.

overall_design: The mutant strain used in this experiment were PRlacZ knock-in mice which originated from Assoc Prof John Lydon, Baylor College of Medicine, Houston TX, USA. The lacZ insertion results in disruption of transcription of both isoforms of PGR (Ismail et al, 2002, Mol Endocrinol 16:2475-2489), and therefore mice homozygous for the lacZ insertion are a phenocopy of the knockout strain described by Lydon et al. (1995, Genes Dev. 9:2266-2278) and are hereafter referred to as PRKO. Heterozygous mice (PR+/-) are a phenocopy of WT and have normal fertility (Ismail et al, 2002) and are therefore appropriate controls. Cumulus oocyte complexes (COCs) were collected by puncturing antral follicles from the ovaries of pre-pubertal PRKO and PR+/- mice 8 h after a standard protocol for hormonal induction of ovulation. Day 21-23 old mice were injected i.p. with 5IU of equine chorionic gonadotropin (eCG) to stimulate follicle growth, followed 44-47 h later by i.p. injection of 5 IU of human chorionic gonadotropin (hCG) to trigger ovulatory processes. COCs from 12 animals were collected per genotype, with cells from 3 animals pooled per sample for a total of n = 4 samples per genotype.


title: PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage

status: Public on Feb 28 2018

city: Milan

first: Dmitry

last: Penkov

address: Via Adamello 16

institute: IFOM

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

overall_design: Refer to individual Series


title: PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [RNA-Seq]

summary: Down-regulation (DR) of PREP1 (aka PKNOX1) tumor suppressor induces H2Ax foci in human fibroblasts. Here we have analyzed the effect of PREP1 DR on DNA replication using cell cycle analysis, Repliseq, DNA combing, ChIP-seq, RNA-seq and immunofluorescence (IF). In human cells, PREP1 DR similarly affects both the rate of DNA replication and the progression of cells through the S phase. Genome wide, PREP1 DR induces late to early DNA replication shifts in normally late-replicated genomic regions amounting to 25% of the genome, in addition to unscheduled origins firing. A concomitant strong increase of unidirectional replication forks explains the appearance of DNA damage foci. The DNA target of PREP1 DR is the Lamin Associated DNA, in agreement with the simultaneous decrease of Lamin B1. Therefore PREP1 is a novel regulator of replication timing and Lamin B1 level, which ChIP-seq and RNA-seq data indicate as independent from its transcriptional activity. This activity must constitute the basis for its tumor suppression function.

overall_design: RNA-seq of HeLa cells transfected with siPrep1 and siLuc (control cells)

first: Francesco

last: Blasi

first: Angela

last: Palmigiano

last: Santaniello


title: Reconstitution of the human pancreatic niche stimulates differentiation of hESCs into beta cells and reveals new signals for pancreatic endocrine cell maturation

status: Public on Jun 01 2018

city: Houston

first: Malgorzata

last: Borowiak

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: RNA-seq was performed for hESC-derived endocrine progenitors (EPs) treated with WNT5A for short-term (12h) and long-term (5 days) to investigate the downstream targets of WNT5A in EPs. Sequencing of untreated cells and those treated with WNT5A for 12h, which are at EP stage, and for 5 days, which are at beta cell stage, allowed for observation of developmental changes during in vitro differentiation.

overall_design: Two controls as 12h or 5 days untreated (maintained in B27) and two 12h or 5 days WNT5A-treated EPs.

first: Diane

last: Yang

first: Jolanta

last: Chmieloweic

first: Marissa

last: Scavuzzo


title: PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [ChIP-Seq]

overall_design: ChIP-seq of HeLa cells performed using PREP1 Ab.


title: PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [Repli-Seq]

overall_design: Repli-seq of HeLa cells transfected with siPrep1 and siLuc (control cells)


title: Transcriptome profiles in peripheral white blood cells at the time of artificial insemination discriminate beef heifers with different fertility potential

status: Public on Jan 13 2018

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary:
Background: Infertility is a longstanding limitation in livestock production with important economic impact for the cattle industry. Female reproductive traits are polygenic and lowly heritable in nature, thus selection for fertility is challenging. Beef cattle operations leverage estrous synchronization in combination with artificial insemination (AI) to breed heifers and benefit from an early and uniform calving season. A couple of weeks following AI, heifers are exposed to bulls for an opportunity to become pregnant by natural breeding (NB), but they may also not become pregnant during this time period. Focusing on beef heifers, in their first breeding season, we hypothesized that: a- at the time of AI, the transcriptome of peripheral white blood cells (PWBC) differs between heifers that become pregnant to AI and heifers that become pregnant late in the breeding season by NB or do not become pregnant during the breeding season; and b- the ratio of transcript abundance between genes in PWBC classifies heifers according to pregnancy by AI, NB, or failure to become pregnant.
Results: We generated RNA-sequencing data from 23 heifers from two locations (A: six AI-pregnant and five NB-pregnant; and B: six AI-pregnant and six non-pregnant). After filtering out lowly expressed genes, we quantified transcript abundance for 12,538 genes. The comparison of gene expression levels between AI-pregnant and NB-pregnant heifers yielded 18 differentially expressed genes (DEGs) (ADAM20, ALDH5A1, ANG, BOLA-DQB, DMBT1, FCER1A, GSTM3, KIR3DL1, LOC107131247, LOC618633, LYZ, MNS1, P2RY12, PPP1R1B, SIGLEC14, TPPP, TTLL1, UGT8, eFDR≤0.02). The comparison of gene expression levels between AI-pregnant and non-pregnant heifers yielded six DEGs (ALAS2, CNKSR3, LOC522763, SAXO2, TAC3, TFF2, eFDR≤0.05). We calculated the ratio of expression levels between all gene pairs and assessed their potential to classify samples according to experimental groups. Considering all samples, relative expression from two gene pairs correctly classified 10 out of 12 AI-pregnant heifers (P=0.0028) separately from the other 11 heifers (NB-pregnant, or non-pregnant).
Conclusion: The transcriptome profile in PWBC, at the time of AI, is associated with the fertility potential of beef heifers. Transcript levels of specific genes may be further explored as potential classifiers, and thus selection tools, of heifer fertility.

overall_design: Peripheral white blood cells (PWBC) were collected from heifers at the time of artificial insemination. We generated transcriptome data from PWBC and contrasted the gene expression values between heifers that became pregnant and did not became pregnant.

first: Sarah

last: Dickinson


title: Microarray expression data obtained from human skin fibroblasts derived from patients affected with vascular Ehlers Danlos syndrome (vEDS)

status: Public on Jan 03 2018

first: Nicola

last: Chiarelli

summary:
Analysis of gene expression profiling of cultured skin fibroblasts obtained from patients affected with vascular Ehlers Danlos syndrome (vEDS)
Transcriptome-wide expression profiling using the Affymetrix Gene 1.0 ST platform comparing the gene expression pattern of cultured skin fibroblasts derived from three patients with vEDS with those of nine healthy individuals

overall_design: Comparison of transcriptome profiling of human cultured skin fibroblasts from three vEDS patients and nine healthy individuals


title: Gene expression profiling of intact individual planarians during homeostatic tissue turnover after inhibition of myoD or nkx1-1

status: Public on Nov 22 2017

city: Cambridge

first: Peter

middle: W

last: Reddien

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: MyoD is a conserved myogenic factor which controls formation of longitundinal muscle fibers in planarians. nkx1-1 is a conserved transcription factor which controls formation of circular muscle fibers in planarians.

overall_design: Polyadenylated RNA was isolated from individual animals from planarians following RNAi (10 dsRNA feedings) of a control gene (C.elegans unc-22; 6 replicates) and myoD (6 replicates) or following RNAi (12 dsRNA feedings) of a control gene (C. elegans unc-22; 5 replicates) and nkx1-1 (7 replicates).

first: M

last: Scimone

first: Lauren

last: Cote


title: Orthogonal muscle fibres have different instructive roles in planarian regeneration


title: RNA-protein dynamics of high CO2-adapted, iron-phosphorus co-limited Trichodesmium reveals nutrient-limited molecular architecture of a globally significant marine nitrogen fixer in a future ocean

status: Public on Oct 23 2017

city: Los Angeles

first: Eric

middle: Alva

last: Webb

address: 3616 Trousdale Parkway

institute: University of Southern California

summary: Our paper presents the results of a study in which we used Illumina RNA-Seq (i.e. transcriptomics) and high-CO2 nutrient limitation experiments to examine transcriptional variation of iron-limited, phosphorus-limited, and iron-phosphorus co-limited cultures following long-term (~7 years) low- (380 µatm CO2) and high-CO2 (750 µatm CO2) selection. Hence, we describe the molecular physiology of the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

overall_design: A single IMS101 population, originally isolated from an individual Trichodesmium colony, was split into low (380-selected) and high (750-selected) CO2 treatments of 6 biological replicates each, and grown for ~7 years (~1,000 and ~1,500 generations for 380- and 750-selected, respectively). Semi-continuous culturing methods were used with a light-dark cycle of 12:12 (light:dark) at 26 C in a modified Aquil medium (devoid of fixed nitrogen) containing standard vitamins and trace metals with 250 nM Fe and 10 µM phosphate (PO43-). Next, Fe/P co-limited treatments were generated by sub-culturing 3 biological replicates from each CO2 treatment and incubating them in the aforementioned media except with co-limiting levels of Fe (10 nM) and PO43- (0.25 µM ) for >1 year. To then mimic episodic pulses of Fe or P experienced by Fe/P co-limited microbes in the oligotrophic ocean , either Fe or P was added at replete concentrations to subcultures of the Fe/P co-limited cell lines to generate P and Fe limited lines at both CO2 levels, respectively. Following a two-month acclimation period to create steady-state conditions, the lines were sampled for molecular analyses. All samples for transcriptomics (biological duplicates) were taken by filtering cells onto 5-µm polycarbonate filters during the middle of the photoperiod, flash frozen, and stored in liquid nitrogen until extraction.

first: Nathan

middle: G

last: Walworth


title: Gene expression profiling of regenerating planarian tails after inhibition of myoD and follistatin

summary: MyoD is a conserved myogenic factor which controls formation of longitundinal muscle in planarians. myoD(RNAi) animals do not regenerate after amputation due to the lack of expression of a conserved TGF-beta inhibitor follistatin.

overall_design: Polyadenylated RNA was isolated from dissected wound faces of tail fragments at  0, 6, 24, and 48 hours post-amputation (hpa) from planarians following RNAi (8 dsRNA feedings) of a control gene (C.elegans unc-22; 3 replicates) and myoD (3 replicates) or following RNAi (6 dsRNA feedings) of a control gene (C. elegans unc-22; 3 replicates) and follistatin (3 replicates).


title: microRNA profiling of trifluridine resistant colorectal cancer cell lines and parental cell lines

status: Public on Sep 25 2017

city: tokushima

first: kenta

last: tsunekuni

state: tokushima

address: Ebisuno Hiraishi, Kawauchi-cho

department: Translational Research Laboratory

institute: taiho parmaceutical

summary: microRNA and mRNA profiling was conducted for parental cell lines and cell lines resistant to trifluridine in 3 colorectal cell lines (DLD-1, HCT-116, RKO). We hypothesized that a detailed comparison between miRNA and mRNA expression might reveal the mechanism for acquired resistant to trifluridine in colorectal cancer.

overall_design: miRNA (1 mg) was extracted from parental cell lines and cell lines resistant to trifluridine in 3 colorectal cancer cell lines (DLD-1, HCT-116, RKO) using miRNeasy mini kit. The extracted RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit. The labeled RNAs were hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc. Fluorescent array images were acquired with 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) and Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).　The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Expression ratios were analyzed using normalized signal intensity.

first: Kenta

last: Tsunekuni

first: Masamitsu

last: Konno

first: Ayumu

last: Asai

first: Takashi

last: Kobunai

first: Teiji

last: Takechi

first: Yuichiro

last: Doki

first: Masaki

last: Mori

first: Hideshi

last: Ishii


title: mRNA profiling of trifluridine resistant colorectal cancer cell lines and parental cell lines

overall_design: mRNA (1 mg) was extracted from parental cell lines and cell lines resistant to trifluridine in 3 colorectal cancer cell lines (DLD-1, HCT-116, RKO) using miRNeasy mini kit. cDNA and Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye (Cy5) Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc. The labeled samples were hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc. Fluorescent array images were acquired with 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) and Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan). The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Expression ratios were analyzed using normalized signal intensity.


title: Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [cohort 3273]

status: Public on Mar 12 2018

city: Lund

first: Lao

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

summary:
PURPOSE
In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification.

METHODS
In total, 3,678 patients with BC were studied. For 405 tumors, a comprehensive multi-rater histopathologic evaluation was performed. Using RNA-seq data, single-gene classifiers and multigene classifiers (MGCs) were trained on consensus histopathology labels. Trained classifiers were tested on a prospective population-based series of 3,273 BCs that included a median follow-up of 52 months (Sweden Cancerome Analysis Network—Breast [SCAN-B], ClinicalTrials.gov identifier: NCT02306096), and results were evaluated by agreement statistics and Kaplan-Meier and Cox survival analyses.

RESULTS
Pathologist concordance was high for ER, PgR, and HER2 (average κ, 0.920, 0.891, and 0.899, respectively) but moderate for Ki67 and NHG (average κ, 0.734 and 0.581). Concordance between RNA-seq classifiers and histopathology for the independent cohort of 3,273 was similar to interpathologist concordance. Patients with discordant classifications, predicted as hormone responsive by histopathology but non–hormone responsive by MGC, had significantly inferior overall survival compared with patients who had concordant results. This extended to patients who received no adjuvant therapy (hazard ratio [HR], 3.19; 95% CI, 1.19 to 8.57), or endocrine therapy alone (HR, 2.64; 95% CI, 1.55 to 4.51). For cases identified as hormone responsive by histopathology and who received endocrine therapy alone, the MGC hormone-responsive classifier remained significant after multivariable adjustment (HR, 2.45; 95% CI, 1.39 to 4.34).

CONCLUSION
Classification error rates for RNA-seq–based classifiers for the five key BC biomarkers generally were equivalent to conventional histopathology. However, RNA-seq classifiers provided added clinical value in particular for tumors determined by histopathology to be hormone responsive but by RNA-seq to be hormone insensitive.

overall_design:
Illumina paired-end RNA-sequencing and expression estimation were performed for two cohorts: a training cohort with 405 samples (GSE81538), and a validation cohort with 3273 samples (of which 136 cases have technical replicates) (GSE96058).  A comprehensive histopathological evaluation was performed on the 405-cohort to estimate inter-pathologist variability on original diagnostic slides as well as on repeat immunostains, leading to consensus scores for five clinical biomarkers.  Subtyping was performed using the PAM50 gene list.

Please note that there are "primary sample" (e.g F30) and "technical replicate" (e.g. F30repl) of the same BioSample.  The technical replicates in herein are primarily newly constructed and sequenced libraries from the same RNA extraction as the primary sample, with the remaining replicates being re-sequencings of the same library as the respective primary sample.

Due to the patient consent, Swedish law, the potential that the sequencing data contains personally-identifiable information and hereditary mutations, and the right to privacy, the submitter cannot make available the raw sequence data in a public repository.

first: Christian

last: Brueffer

first: Johan

last: Vallon-Christersson

first: Dorthe

last: Grabau

first: Anna

last: Ehinger

first: Jari

last: Häkkinen

first: Cecilia

last: Hegardt

first: Janne

last: Malina

first: Yilun

last: Chen

first: Pär-Ola

last: Bendahl

first: Jonas

last: Manjer

first: Martin

last: Malmberg

first: Christer

last: Larsson

first: Niklas

last: Loman

first: Lisa

last: Rydén

first: Åke

last: Borg


title: mRNA and microRNA profiling of trifluridine resistant colorectal cancer cell lines and parental cell lines

first: kenta

last: tsunekuni

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


title: Targeting the androgen receptor N-terminus via the cochaperone Bag-1L [RNA-seq C-terminal mutant]

status: Public on Aug 23 2017

city: Boston

first: Laura

last: Cato

address: 450 Brookline Ave., D728

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Targeting the activation function-1 (AF-1) at the N-terminus of the androgen receptor (AR) is an attractive therapeutic alternative to the current approaches to inhibit AR action in prostate cancer (PCa). Here we show that the AR AF-1 is bound by the BAG domain of the cochaperone Bag-1L. Mutations in this domain or loss of Bag-1L abrogates AR signaling and reduces PCa growth. Correspondingly, Bag-1L protein levels increase with progression of primary prostate tumors to castration-resistant PCa, correlating inversely with patient response to abiraterone therapy. Intriguingly, BAG domain residues important for its interaction with the AR AF-1 overlap a potentially druggable pocket of this protein. Bag-1L is therefore a putative therapeutic target for the inhibition of AR AF-1 activity.

overall_design: We performed transcriptome analysis (RNA-Seq) of 2 cell lines (LNCaP Bag-1L WT and LNCaP Bag-1L CMut) cultured under hormone-starvation conditions for 72 h and then treated with vehicle (ethanol, EtOH) or 10 nM Dihydrotestosterone (DHT) for 16 h. Biological duplicate samples were analyzed for each cell line and each treatment condition.

first: Antje

last: Neeb

first: Olivier

last: Armant

first: Victor

last: Gourain

first: Andrew

first: Myles

last: Brown


title: Targeting the androgen receptor N-terminus via the cochaperone Bag-1L


title: Targeting the androgen receptor N-terminus via the cochaperone Bag-1L [ChIP-Seq]

overall_design: Androgen receptor (AR) ChIP-seq was carried out in LNCaP Talen Control, Bag-1L KO, Bag-1L KO plus Vector (control), Bag-1L KO plus (wild-type) Bag-1L, LNCaP plus wild-type Bag-1L and LNCaP plus CMut Bag-1L cells. Cells were cultured under hormone-starvation conditions for 72 h and then treated with vehicle (ETOH) or 10 nM DHT for 4 h prior to cell fixation and harvest. Experiments in LnCaP Talen Control and Bag-1L KO cells were carried out in duplicate.

first: Jennifer

last: Wu


title: Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [superseries]

first: Lao

last: Saal

summary:
This SuperSeries is composed of the SubSeries GSE81538 [cohort 405] and GSE96058 [cohort 3273] linked to below.

PURPOSE
In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification.

METHODS
In total, 3,678 patients with BC were studied. For 405 tumors, a comprehensive multi-rater histopathologic evaluation was performed. Using RNA-seq data, single-gene classifiers and multigene classifiers (MGCs) were trained on consensus histopathology labels. Trained classifiers were tested on a prospective population-based series of 3,273 BCs that included a median follow-up of 52 months (Sweden Cancerome Analysis Network—Breast [SCAN-B], ClinicalTrials.gov identifier: NCT02306096), and results were evaluated by agreement statistics and Kaplan-Meier and Cox survival analyses.

RESULTS
Pathologist concordance was high for ER, PgR, and HER2 (average κ, 0.920, 0.891, and 0.899, respectively) but moderate for Ki67 and NHG (average κ, 0.734 and 0.581). Concordance between RNA-seq classifiers and histopathology for the independent cohort of 3,273 was similar to interpathologist concordance. Patients with discordant classifications, predicted as hormone responsive by histopathology but non–hormone responsive by MGC, had significantly inferior overall survival compared with patients who had concordant results. This extended to patients who received no adjuvant therapy (hazard ratio [HR], 3.19; 95% CI, 1.19 to 8.57), or endocrine therapy alone (HR, 2.64; 95% CI, 1.55 to 4.51). For cases identified as hormone responsive by histopathology and who received endocrine therapy alone, the MGC hormone-responsive classifier remained significant after multivariable adjustment (HR, 2.45; 95% CI, 1.39 to 4.34).

CONCLUSION
Classification error rates for RNA-seq–based classifiers for the five key BC biomarkers generally were equivalent to conventional histopathology. However, RNA-seq classifiers provided added clinical value in particular for tumors determined by histopathology to be hormone responsive but by RNA-seq to be hormone insensitive.

overall_design: Refer to individual Series.


title: microRNA  expression profiles of reticulocytes for hereditary persistence of fetal hemoglobin and β-thalssemia minor with high fetal hemoglobin.

status: Public on Jan 01 2018

city: Nanning

first: Ketong

last: Lai

address: Shuangyong Road

department: Department of Pediatrics

institute: the First Affiliated Hospital of Guangxi Medical University

summary: We used microarrays to investigate differential microRNA (miRNA) expression in reticulocytes comparing reticulocytes from control individuals with normal fetal hemoglobin (HbF) level to hereditary persistence of fetal hemoglobin (HPFH) and β-thalssemia minor with high HbF, and try to find out some miRNAs associated with the mechanisms of HbF induction.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Reticulocytes were isolated from whole blood of control individuals (n=7) and individuals of HPFH and β-thalssemia minor with high HbF (n=7). All 14 samples were analyzed for miRNA expression.

first: Yunyan

last: He


title: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha

status: Public on Mar 27 2017

city: Durham

first: John

middle: F

last: Rawls

address: 213 Research Drive

institute: Duke University School of Medicine

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional profile of E2 response of CD-1 mouse uterus

status: Public on Apr 01 2017

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Transcriptional responses of the CD-1 mouse strain following treatments with E2 or the short acting estrogen estriol (E3) were evaluated by microarray and compared to our previous profiles done in C57Bl6 mice. The pattern of response was similar in both strains, with early (2h) responses to E2 or E3 appearing very similar. The later (24h) response revealed that E2 exhibits a more robust response than E3, illustrating the short-acting nature of E3.

overall_design: E2 or E3 regulation of uterine transcription was evaluated in triplicate samples from CD-1 mouse uterus.

first: Sylvia

last: Hewitt

first: Kenneth

last: Korach


title: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha (Mouse ChIP-seq, RNA-seq, and DNase-seq)

summary: We profiled transcriptome and chromatin landscapes in jejunal mouse intestinal epithelial cells (IECs) from mice reared in the absence (Germ Free or GF) or presence (Conventionalized or CV) of microbiota.  We show that  microbiota colonization results in changes in histone modifications at hundreds of enhancers that are associated with microbiota-regulated genes. Furthermore, we show that microbiota colonization is associated with a drastic genome-wide reduction in Hnf4a and Hnf4g binding.

overall_design: Generation and analysis of RNA-seq, DNase-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, Hnf4a ChIP-seq, and Hnf4g ChIP-seq datasets from primary IECs isolated from the jejunum of GF and CV mice.

first: James

last: Davison

first: Colin

middle: R

last: Lickwar

first: Lingyun

last: Song

first: Ghislain

last: Breton

first: Gregory

last: Crawford


title: DNA-Binding Mutant EAAE-ER alpha Genome-Wide Binding in the Uterus

city: Research Triangle Park

address: 111 Alexander Dr

department: RDBL

summary: Transcription factors (TFs) influence cell function by interpreting information contained within cis-regulatory elements in chromatin. Whereas ChIP-sequencing has been used to identify and map transcription factor-DNA interactions, it has been difficult to assign functionality to the binding sites identified. Thus, in this study we probed the transcriptional activity, DNA-binding competence and functional activity of select nuclear receptor (NR) mutants in cellular and animal model systems and used this information to define the sequence constraints of functional steroid nuclear receptor (sNR) cis-regulatory elements. Analysis of the architecture within sNR chromatin interacting sites revealed that only a small fraction of all sNR chromatin interacting events are associated with transcriptional output, and that this functionality is restricted to elements that vary from the consensus palindromic elements by one or two nucleotides. These findings define the transcriptional grammar necessary to predict functionality from linear genome sequences.

overall_design:
ERa binding of  DBD-mutant ERa (EAAE) 2 samples; pools of  15 EAAE uteri (V or E2 treated)

Please note that the precise mouse strain information is, unfortunately, not known. The original ES cells used to make the mice was a mixture of 129P2/OlaHsd and mice were subsequently bred to C57BL/6. The official strain name (B6;129P2-Esr1tm2.1Gsc/J) accounts for this mixture, but no one has determined the relative contribution of each.

first: Laurel

middle: A

last: Coons

first: Adam

last: Burkholder

first: Donald

last: McDonnell


title: Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche

status: Public on Dec 06 2016

city: Detroit

first: Katherine

last: Gurdziel

address: 6135 Woodward Ave.

department: Institute of Environmental Health Sciences

institute: Wayne State University

summary: In this work, we generated early human amnion-like tissues by culturing human pluripotent stem cells (hPSCs) in a bioengineered implantation-like niche in vitro. To explore the gene expression profile of hPSC-derived amnion-like cells (hPSC-amnion), we performed mRNA-sequencing for both undifferentiated hPSCs and hPSC-amnion. Here we show that hPSC-amnion differs from hPSCs by actively regulating a comprehensive set of transcriptional regulation network and developmental signaling pathways such as BMP-SMAD signaling.

overall_design: hPSCs cultured in conventional maintenance condition (mTeSR1-based feeder-free culture system; three biological replicates) as well as in the engineered implantation-like niche (the Gel-3D system composed of mTeSR1 and Geltrex; three biological replicates) were harvested and subjected to RNA-seq.

first: Yue

last: Shao

first: Kenichiro

last: Taniguchi

first: Ryan

last: Townshend

first: Deborah

last: Gumucio

first: Jianping

last: Fu


title: Targeting the androgen receptor N-terminus via the cochaperone Bag-1L [RNA-Seq KO]

first: Laura

last: Cato

overall_design: We performed transcriptome analysis (RNA-Seq) of 2 cell lines (LNCaP-Talen Control and LNCaP-Talen Bag1L KO) cultured in full medium (FM), or under hormone-starvation conditions for 72 h and then treated with vehicle (ethanol, EtOH) or 10 nM Dihydrotestosterone (DHT) for 16 h. Biological duplicate samples were analyzed for each cell line and each treatment condition.

first: Antje

last: Neeb

first: Olivier

last: Armant

first: Victor

last: Gourain

first: Andrew

first: Myles

last: Brown


title: Shear stress activates YAP to promote motility in human prostate cancer cells

status: Public on Mar 08 2017

first: Pamela

last: Wenzel

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharmacology

institute: University of Texas Health Science Center at Houston

summary: Biophysical features of the microenvironment such as stiffness of extracellular matrix (ECM), nanotopography, and biomechanical force are critical regulators of cellular potential and behavior, yet the effects of extrinsic mechanical cues on tumor cells remain poorly understood. Here we demonstrate that frictional force, or wall shear stress (WSS), caused by fluid flow supports invasive behavior in cancer cells through activation of negative effectors of the Hippo tumor suppressor pathway, YAP and TAZ. In biomimetic models of lymphatic vasculature, WSS stimulated motility. These effects were accompanied by YAP dephosphorylation at ser-127, YAP and TAZ nuclear localization, and transactivation of YAP/TAZ downstream targets, including CTGF, AMOTL2, and ANKRD1. YAP, but not TAZ, was strictly required for WSS-enhanced motility, as knockdown of YAP or blockade of YAP-TEAD interactions by a small molecule inhibitor, verteporfin, reduced cellular velocity to levels observed in static controls. YAP-mediated effects on motility were dependent upon Rho-associated kinase (ROCK) and LIM-domain kinase (LIMK), as pharmacological inhibition of their activity led to activation of the actin-severing protein cofilin and blocked YAP dephosphorylation by WSS, thereby impairing migration. These data provide a signaling mechanism whereby biomechanical forces may influence cancer cell metastasis and implicate YAP as a core component of mechanosensitive machinery that modulates cancer progression.

overall_design: The human prostate cancer cell line PC3 was tested for response to fluid wall shear stress (WSS). One day after seeding in a 6 well plate, cells of siRNA groups were transfected with control siRNA or YAP1 siRNA at 25nM using DharmaFect reagent. 24 hours after transfection, both tranfected cells and normal PC3 cells (10^5 cells per channel; surface area of each channel equaled 248 cm^2) were transferred into each polydimethylsiloxane (PDMS) channel (2.2 MPa surface stiffness) and permitted to attach for 24 hours. Fluid flow was then applied to each channel using a Harvard Apparatus PHD ULTRA programmable syringe pump. Cells were exposed either to static or WSS (0.05 dyne/cm^2) for 3 hours. Upon collection of cells with RLT lysis buffer (QIAGEN RNeasy kit), three channels of identical treatment were pooled to comprise a single sample. 12 samples total are included in this study. In detail, samples included at 3 hours: 3 static, 3 WSS, 3 WSS with siCTL and 3 WSS with siYAP. Sample labels end with the replicate number, i.e., WSS3 for the third replicate of the WSS sample.


title: Microarray expression data from five Ehlers-Danlos Syndrome Hypermobility type/Joint Hypermobility Syndrome (EDS-HT/JHS) patients' skin fibroblasts

status: Public on Aug 05 2016

city: Brescia

first: Nicola

last: Chiarelli

address: Viale Europa 11

department: Molecular and Translational Medicine

institute: University of Brescia

summary:
To unravel the molecular mechanisms potentially associated with the pathogenesis of the EDS-HT/JHS.
Transcriptome-wide expression profiling using the Affymetrix Gene 1.0 ST platform comparing the gene expression patterns of skin fibroblasts of five  EDS-HT/JHS patients with those of six healthy individuals

overall_design: Comparison between five EDS-HT/JHS human fibroblasts and six healthy individuals


title: ISL1 and JMJD3 synergistically control cardiac differentiation of embryonic stem cells

status: Public on Apr 25 2016

city: Beijing

first: Yang

last: Wang

state: Beijing

address: Xueyuan Road 38#

department: Molecular Biology and Biochemistry

institute: Peking University Health Science Center

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


title: microRNA expression profile from five Ehlers-Danlos Syndrome Hypermobility type/Joint Hypermobility Syndrome (EDS-HT/JHS) patients' skin fibroblasts

summary:
To screen for potential miRNA that may contribute to the etiopathogenesis of EDS-HT/JHS
miRNA expression profiling was performed using the Affymetrix GeneChip® miRNA 3.0 Array and comparing the miRNA expression changes of skin fibroblasts of five EDS-HT/JHS patients with those of six healthy individuals

overall_design: Comparison of miRNA expression profiles between five EDS-HT/JHS human fibroblasts and six  controls


title: A genetic screen identifies hypothalamic Fgf15/19 as a regulator of glucagon secretion

status: Public on Nov 07 2016

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: The counterregulatory response to hypoglycemia, which restores normal blood glucose levels to ensure sufficient provision of glucose to the brain, is critical for survival. To discover underlying brain regulatory systems, we performed a genetic screen in recombinant inbred mice for quantitative trait loci (QTL) controlling glucagon secretion in response to neuroglucopenia. We identified a QTL on the distal part of chromosome 7 and combined this genetic information with transcriptomic analysis of hypothalami. This revealed Fgf15 as the strongest candidate to control the glucagon response. Fgf15 was found to be expressed by neurons of the dorsomedial hypothalamus and the perifornical area. Intracerebroventricular injection of FGF19, the human ortholog of Fgf15, reduced activation by neuroglucopenia of dorsal vagal complex neurons and of the parasympathetic nerve, leading to a lower glucagon secretion. These data show that Fgf15 in hypothalamic neurons is a regulator of vagal nerve activity in response to neuroglucopenia.

overall_design: 36 BXD strains + 4 parental strains, 1 time point, basal condition without treatment

first: Alexandre

last: Picard

first: Josselin

last: Soyer

first: Xavier

last: Berney

first: David

last: Tarussio

first: Simon

last: Quenneville

first: Maxime

last: Jan

first: Frédéric

first: Eric

last: Grouzmann

first: Mark

last: Ibberson

first: Bernard

last: Thorens


title: Microarray and miRNA expression data from five Ehlers-Danlos Syndrome Hypermobility type/Joint Hypermobility Syndrome (EDS-HT/JHS) patients' skin fibroblasts

platform_organism:
Homo sapiens
synthetic construct


title: ISL1 and JMJD3 synergistically control cardiac differentiation of embryonic stem cells (ChIP-Seq)

summary: ISL1 is expressed in cardiac progenitor cells and plays critical roles in cardiac lineage differentiation and heart development. Cardiac progenitor cells hold great potential for clinical and translational applications. However the mechanisms underlying ISL1 function in cardiac progenitor cells have not been fully elucidated. Here we uncover a hierarchical role of ISL1 in cardiac progenitor cells, showing that ISL1 directly regulates hundreds of potential downstream targets that are implicated in cardiac differentiation, through an epigenetic mechanism. Specifically, ISL1 promotes the demethylation of tri-methylation of histone H3K27 (H3K27me3) at the enhancers of key downstream target genes, including Myocd and Mef2c, which are core cardiac transcription factors. ISL1 physically interacts with JMJD3, a H3K27me3 demethylase, and conditional depletion of JMJD3 leads to impaired cardiac progenitor cell differentiation, phenocopying that of ISL1 depletion. Interestingly, ISL1 is not only responsible for the recruitment of JMJD3 to specific target loci during cardiac progenitor differentiation, but also modulates its demethylase activity. In conclusion, ISL1 and JMJD3 partners to alter the cardiac epigenome, instructing gene expression changes that drive cardiac differentiation.

overall_design: Examination of ISL1 and JMJD3 genome-wide distribution in day 7 EBs of cardiac differentiated from mESCs.

first: Chunyan

last: Zhou


title: LIM-Domain-Binding 1 maintains the terminally-differentiated state of pancreatic β-cells

status: Public on Dec 31 2016

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Utilize high-throughput transcriptomic and cistromic analysis to determine the functional requirement for LDB1 and ISL1 in mature murine pancreatic β-cells while simultaneously assessing their functional interdependence at the chromatin level.

overall_design: The total RNA profiles for FACS-enriched populations of WT, Ldb1-negative, and Isl1-negative β-cells isolated from tamoxifen-induced male mice at post-natal day (P) 56, P56, and P49, respectively, were generated by RNA-seq. The LDB1 and ISL1 whole pancreatic islet cistromes from 8-10-week-old male CD1 mice were generated by ChIP-seq.

first: Benjamin

middle: N

last: Ediger

first: Kyoung-Jae

last: Won

first: Doris

last: Stoffers


title: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha (zebrafish RNA-seq)

first: John

last: Rawls

summary: We performed RNA-seq from 6 days post fertilization hnf4a-/- and hnf4a+/+ zebrafish larval digestive tracts raised in the absence (Germ Free, GF) or presence (Conventionalized, CV) of microbiota.  We found that zebrafish hnf4a activates almost half of the microbiota-suppressed genes, indicating that the microbiota supress Hnf4a trans-activity.  We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis.

overall_design: Generation and analysis of RNA-seq from hnf4a-/- and hnf4a+/+ zebrafish larvae in the absence (Germ Free, GF) or presence (Conventionalized, CV) microbiota.

first: James

last: Davison

first: Colin

last: Lickwar

first: Lingyun

last: Song

first: Ghislain

last: Breton

first: Gregory

last: Crawford


title: Expression data from maturing soybean seeds

status: Public on Jan 21 2016

city: Wageningen

first: Renake

last: Nogueira Teixeira

state: Gelderland

address: Drovendaalsesteeg 1

department: Plant Physiology

country: Netherlands

institute: Wageningen University

summary:
Environmental stresses such as drought, salinity and both high and low temperature are frequently faced by crops all over the world and can be considered major limiting factors for plant geographical distribution and productivity. Breeding has allowed creation of crops more adapted to some of the adverse environmental conditions and to overcome the geographical limitation without major consequences to productivity. However, due to the climate changes observed in the last few decades, some agricultural areas have experienced the “green seed problem” characterized by chlorophyll retention in mature seeds. This is problematic in oil seed crops such as soybean and canola since it is related to lower seed and oil quality, resulting in serious financial losses. Besides the environmental factors, there are also genetic components controlling the susceptibility of different cultivars to green seed production. Understanding the molecular mechanisms controlling chlorophyll retention in seeds is crucial to allow advanced molecular breeding techniques and genetic engineering as a way to increase tolerance to this growing problem.
We have used maturing soybean seeds of the cultivar MG/BR 46, harvested in R6, R7 and R8,  produced under non-stressed and stressed environmental conditions, to understand he molecular basis of chlorophyll degradation and, consequently, its retention during soybean seed maturation.

overall_design: Soybean seeds were produced under stressed and non-stressed conditions and harvested in 3 different stages of maturation: R6 non-stressed, R7 non-stressed, R8 non-stressed, R6 stressed, R7 stressed, R8 stressed.

first: Teixeira

last: Renake Nogueira

first: Silva

last: Edvaldo Aparecido Amaral da

first: Hilhorst

last: Henk

first: Ligterink

last: Wilco


title: Transcript level coordination of carbon pathways during silicon-starvation induced lipid accumulation in the diatom Thalassiosira pseudonana

status: Public on Nov 30 2015

city: La Jolla

first: Raffaela

last: Abbriano

address: 9500 Gilman Dr

department: Scripps Institution of Oceanography

institute: University of California San Diego

summary: To characterize the transcript level component of metabolic regulation, genome-wide transcript level changes were documented in the model diatom Thalassiosira pseudonana over a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of co-regulated genes as a key feature of global gene regulation in T. pseudonana. The identity of key enzymes for carbon metabolic pathway inputs (photosynthesis) and outputs (growth and storage) reveals these clusters are organized to synchronize these processes.

overall_design: 24 hour timecourse of silicon starvation, 7 timepoints in biological duplicate

first: Sarah

last: Smith

first: Corine

last: Gle

first: Jesse

last: Traller

first: Aubrey

last: Davis

first: Maria

last: Vernet

first: Emily

last: Trentacoste

first: Andrew

last: Allen

first: Mark

last: Hildebrand


title: Janus kinase 1 is essential for inflammatory cytokine signaling and mammary gland remodeling

status: Public on Apr 08 2016

city: Daejeon

first: Taemook

last: Kim

address: 291 Daehak-ro, Yuseong-gu

department: Biological sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Jak1 is a ubiquitously expressed tyrosine kinase that transduces extracellular signals from a variety of cytokines and their receptors to downstream signal transducers and activators of transcription (STATs). Since deficiency in Jak1 causes early neonatal lethality, we generated Jak1 conditional knockout mice to  study the biological role of this kinase during the development of the mammary gland in adult females

overall_design: Total RNA was extracted from flash-frosen mammary gland tissues of seven conditional knockout females(3 lactation, 4 second day of involution) and six wildtype control mice(3 lactating, 3 involution)

first: Kazuhito

last: Sakamoto

first: Barbara

last: Wehde

first: Kyung-Hyun

last: Ryu

first: Ha-Youn

last: Shin

first: Aleata

last: Triplett

first: Nirakar

last: Rajbhandari

first: Channabasavaiah

last: Gurumurthy

first: Fabian

last: Schuler

first: Andreas

last: Villunger

first: Keunsoo

last: Kang

first: Lothar

last: Hennighausen

first: Kay-Uwe

last: Wagner


title: microRNA expression profiles from three arterial tortuosity syndrome (ATS) patients' skin fibroblasts with recessive SLC2A10 mutations [miRNA]

status: Public on Sep 21 2015

first: Nicola

last: Chiarelli

summary:
To screen for potential miRNA that may contribute to the pathomechanisms of ATS
miRNA expression profiling using the Affymetrix GeneChip® miRNA 3.0 Array comparing the miRNA expression changes of skin fibroblasts of three ATS patients with those of three healthy individuals

overall_design: Comparison of miRNA expression profiles between three ATS human fibroblasts and three healthy individuals


title: Genome-wide DNA methylation signature in lung adenocarcinomas has prognostic impact [gene expression]

status: Public on Nov 13 2015

city: Oslo

first: Maria

middle: Moksnes

last: Bjaanæs

address: Ullernchausseen 70

department: Department of genetics

country: Norway

institute: Oslo Universitetssykehus

summary:
Purpose: DNA methylation alterations are early events in tumorigenesis and important in the regulation of gene expression in cancer cells. Lung cancer has in general a poor prognosis, and a deeper insight into the epigenetic landscape in lung adenocarcinoma tumors and its prognostic implications is needed.

Experimental Design: We determined whole-genome DNA methylation profiles of 164 lung adenocarcinoma samples and 19 samples of matched normal lung tissue samples using the Illumina Infinium 450K array [GSE66836]. The methylation levels were correlated with gene expression levels analyzed by the Agilent 60K mRNA expression array. Methylation changes were studied specifically in tumors from never-smoking patients, and in tumors with mutations in the EGFR-, KRAS- or TP53 genes, and survival analyses were performed.

Results: We identified a large number of differentially methylated CpGs in lung adenocarcinoma tissue, and different methylation profiles in tumors from smokers and never-smokers. Specific methylation profiles were observed in tumors with mutations in the EGFR-, KRAS- or TP53 gene. Both positive and negeative correlations between DNA methylation levels and mRNA expression levels were seen. Methylation profiles of the tumor samples identified clusters of patients with distinct prognosis. A prognostic index based on the methylation levels of 33 CpGs was established, and validated in an independent cohort of lung adenocarcinoma patients from the TCGA project. Among the CpGs in the prognostic signature, some were localized in the HOX B and HOX C gene clusters.

Conclusions: Methylation differences mirror biological important features the etiology of lung adenocarcinomas and influence prognosis.

overall_design:
We determined mRNA expression in 121 lung adenocarcinoma samples using the Agilent 60K mRNA expression array. These data was correlated with the whole-genome DNA methylation profiles of matched lung adenocarcinomas to investigate the correlation of the CpG methylation to the mRNA expression. We identified a large number of both negative and positive correlations. Negative correlations between gene expression and DNA methylation were most often found when the methylated loci were located in the promoter region, while positive correlations were most often found outside promoter regions

Please note that the sample numbers are matched between the methylation study [GSE66836] and this study.

first: Thomas

last: Fleischer

first: Ann

last: Halvorsen

first: Antoine

last: Daunay

first: Florence

last: Busato

first: Steinar

last: Solberg

first: Lars

last: Jørgensen

first: Elin

last: Kure

first: Hege

last: Edvardsen

first: Anne-Lise

last: Børresen-Dale

first: Odd

middle: T

last: Brustugun

first: Jörg

last: Tost

first: Vessela

last: Kristensen

first: Åslaug

last: Helland