title: Genome-wide expression analysis of human fibroblasts and converted neurons

status: Public on Jan 16 2014

city: Dallas

first: Chun-Li

last: Zhang

state: TX

address: 6000 Harry Hines Blvd

country: USA

institute: UT Southwestern

summary: Human fibroblasts can be directly converted into cholinergic neurons by Neurogenin 2 (Neurog2 or NGN2) under the treatments of small molecules. Genome-wide analysis of gene expression was performed to examine the similarity of converted neurons to samples from human brain or spinal cord.

overall_design: Total RNA obtained from isolated human fetal lung fibroblasts or converted neurons at 21 days. Commercially available total RNAs from adult human brains and spinal cords were used as controls.

first: Meng-Lu

last: Liu


title: Affect of Socs2 loss-of-function on liver regeneration

status: Public on Feb 01 2014

city: Boston

first: Michael Todd

last: Valerius

state: MA

address: 4 Blackfan Circle, Harvard Institute of Medicine, HIM-550

department: Renal Division

institute: Brigham and Women's Hospital

summary:
SOCS2 Ensures Metabolic Function and Mass Restoration During Liver Regeneration - SOCS2 plays distinct and contrasting roles during liver regeneration.  Early after injury, SOCS2 expression increases and limits the rate of regeneration, preserving metabolic activity.  Surprisingly, at later times, the role of SOCS2 reverses to promote liver regeneration by stimulating GH release from the pituitary via effects on serum levels of insulin-like growth factor 1.  Loss of SOCS2 promotes GH signaling by increasing growth hormone receptor levels and driving phosphorylation of proteins in the GH pathway, establishing a state of hyper-responsiveness to GH.  These findings suggest a single protein can play contrasting roles at different times after liver injury and modulation of GH signaling achieves an optimal rate of liver regeneration to balance metabolic and restorative needs.
To further understand the mechanism by which SOCS2 increases early liver regeneration, we performed microarray analysis of Socs2-null mice wildtype mice at 24 and 36 hours after hepatectomy.

overall_design: C57BL/6 mice where used as wildtype controls. Socs2-null animals were maintained on a C57BL/6 background. Both wildtype and Socs2-null adult mice were subjected to 2/3 hepatectomy and liver tissue isolated at 24 hours and 36 hours post hepatectomy. Time zero was without hepatectomy in age-matched mice for each genotype. Total RNA isolated from collected liver tissues was pooled for three animals at each time point and two biological replicates (3 pooled liver RNAs each) were labeled for array analysis. This results in a total of 12 microarrays.

first: Ryota

last: Masuzaki

first: Sophia

last: Zhao

first: M

middle: T

first: Daisuke

last: Tsugawa

first: Yuki

last: Oya

first: Kevin

middle: C

last: Ray

first: Seth

middle: J

last: Karp


title: Interferon Signature in the Blood in Inflammatory Common Variable Immune Deficiency [Training Set]

status: Public on Jan 09 2014

first: Indira

last: Munagala

address: 3434 Live Oak street

department: BIIR

institute: Baylor healthcare

summary: Transcriptional profiling was used to characterize the immunologic networks in subjects with CVID who have inflammatory complications to identify clues as to pathogenesis and potentially better modes of treatment.

overall_design: CVID subjects who fulfilled the standard diagnostic criteria, including significantly decreased levels of IgG, IgA, and/or IgM and poor or absent specific antibody production were enrolled. They were classified into, with or without  characteristic inflammatory complications, as previously designated (hematologic or organ-specific autoimmunity, biopsy-proven granulomatous disease,  or interstitial lung disease, lymphoid hyperplasia/ with splenomegaly or gastrointestinal inflammatory disease). 59 patients were included in the training set and 21 healthy controls and for test set 32 patients and 15 healthy controls. Disease controls included 6 X-linked agammaglobulinemia (XLA) patients and 15 healthy controls were included. Blood was taken before the interval intravenous immune globulin (Ig) infusions, or between subcutaneous administrations. The blood was collected using Tempus tubes and processed for microarray analysis.

first: Joon

last: Park

first: Hui

last: Xu

first: Derek

last: Blankenship

first: Patrick

last: Maffucci

first: Damien

last: Chaussabel

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

first: Charlotte

last: Cunningham-Rundles


title: Interferon Signature in the Blood in Inflammatory Common Variable Immune Deficiency [Test Set]


title: A Genomic Portrait of the Genetic Architecture and Regulatory Impact of microRNA Expression in Response to Infection (functional investigation of the role of miR-29)

status: Public on Jan 17 2014

city: Paris

first: Katherine

last: Siddle

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Investigation of the role of miR-29 on transcriptional responses to Mycobacterium tuberculosis (MTB) infection in human dendritic cells using gain- and loss-of-function approaches and microarray expression profiling.

overall_design: We assessed the impact of miR-29 perturbation on mRNA expression levels before and after MTB infection in dendritic cells using cells collected from 4 unrelated individuals. Cells were transfected using either a miR-29a mimic or miR-29 family inhibitor before infection with H37Rv for 24 hours. Gene expression was profiled by array and 4 technical replicates were performed to confirm reproducibility.

first: K

last: Deschamps

first: L

last: Tailleux

first: Y

last: Nédélec

first: J

last: Pothlichet

first: G

last: Lugo-Villarino

first: V

last: Libri

first: B

last: Gicquel

first: O

last: Neyrolles

last: Laval

first: E

last: Patin

middle: B

last: Barreiro

last: Quintana-Murci


title: Interferon Signature in the Blood in Inflammatory Common Variable Immune Deficiency

first: Indira

last: Munagala

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

overall_design: Refer to individual Series


title: Fetal transcripts in maternal blood

status: Public on Jan 08 2014

city: Medford

first: Donna

middle: K

last: Slonim

address: 161 College Ave.

department: Computer Science

institute: Tufts University

summary:
The discovery of fetal mRNA transcripts in maternal circulation holds great promise for noninvasive prenatal diagnosis. To identify potential fetal biomarkers, we studied whole blood and plasma transcripts common to term pregnant women and their newborns but reduced or absent in the postpartum mothers.
In whole blood, 157 potentially-fetal transcripts were identified.  RT-PCR confirmed the presence of specific transcripts, SNP analysis confirmed the presence of fetal transcripts in maternal circulation.  Comparison of whole blood and plasma samples from the same women suggested that placental genes are more easily detected in plasma.  We conclude that fetal and placental mRNA circulates in the blood of pregnant women.

overall_design:
[I] We profiled whole antepartum (A), postpartum (P), and umbilical cord (U) blood samples from each of 9 mothers and their 10 newborns (1 set of twins, denoted as a and b after the sample names).
[II] We also profiled plasma samples (A, P, and U) from three of those mothers to allow for a direct comparison between blood and plasma.

first: Jill

middle: L

last: Maron

first: Kirby

last: Johnson

first: Chao-Qiang

last: Lai

first: Marco

last: Ramoni

first: Gil

last: Alterovitz

first: Zina

last: Jarrah

first: Zinger

last: Yang

first: Diana

middle: W

last: Bianchi


title: Global gene expression profiles of synoviocytes and macrophages in patients with rheumatoid arthritis and osteoarthritis

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: Rheumatoid synoviocytes, which consist of fibroblast-like synoviocytes (FLS) and synovial macrophages (SM), are crucial for the progression of rheumatoid arthritis (RA). Particularly, FLS of RA patients (RA-FLS) exhibit invasive characteristics reminiscent of cancer cells, destroying cartilage and bone, although it remains unresolved how RA-FLS exhibit invasive phenotype. RA-FLS and SM originate differently from mesenchymal and myeloid cells, respectively, but share many pathologic functions. However, the molecular signatures and biological networks representing the distinct and shared features of the two cell types are unknown. Presently, we performed global transcriptome profiling of FLS and SM obtained from RA and osteoarthritis patients. By comparing the transcriptomes, we identified distinct molecular signatures and cellular processes defining invasiveness of RA-FLS and pro-inflammatory properties of RA synovial macrophages (RA-SM), respectively. Interestingly, under interleukin1β-stimulated condition, RA-FLS newly acquired pro-inflammatory signature mimicking RA-SM without losing invasive properties. We next reconstructed a network model that delineates the shared, RA-FLS-dominant (invasive), and RA-SM-dominant (inflammatory) processes. From the network model, we selected 13 genes, including POSTN and TWIST1, as novel regulator candidates responsible for FLS invasiveness. Of note, POSTN and TWIST1 expressions were elevated in independent RA-FLS and were further instigated by interleukin1β. In vitro functional assays demonstrated the requirement of POSTN and TWIST1 for migration and invasion of RA-FLS stimulated with interleukin1β. Taken together, our systems approach to rheumatoid synovitis provides a basis for identifying novel regulators responsible for pathological features of RA-FLS and RA-SM, demonstrating how a certain type of cells acquires functional redundancy under chronic inflammatory conditions.

overall_design: To identify molecular signatures of FLS and MLS in RA joints, we isolated FLS from synovial tissues of RA and osteoarthritis (OA) patients, obtained synovial macrophages from synovial fluid of RA patients, and differentiated control macrophages from peripheral blood of healthy subjects. Also, we stimulated FLS with IL1β, and then analyzed gene expression profiles of both IL1β-stimulated RA-FLS and OA-FLS

first: Jong

middle: D

last: Ji

first: Daehee

last: Hwang

first: Wan-Uk

last: Kim


title: Gene expression analysis upon UGT1A_i2 knockdown

city: Quebec

first: Chantal

last: Guillemette

state: Qc

address: 2705 boul laurier

department: Pharmacy

country: Canada

institute: Laval University

summary: Evaluate modulation in gene expression modulation upon UGT1A_i2 knockdown in basal conditions and also under pharmacological treatment (SN-38)

overall_design: 6 samples in duplicate (12 samples total); HT115 colorectal cell line was infected with either UGT1A_i2 shRNA or non-target shRNA and left untreated or treated with either vehicle or SN-38 (0.5 uM)

first: Joannie

last: Roberge

first: Mélanie

last: Rouleau

first: Judith

last: Bellemare


title: Similarities and differences between human activated macrophages II

status: Public on Jan 03 2014

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

country: United Kingdom

institute: University of Surrey

summary:
We compare, in human macrophages, stimuli considered to induce M1 or M2 type of activation, also termed classical and alternative activation.
This dataset highlights key differences between the M1 and M2 stimuli pointing to the need of a revision of the paradigm.
Macrophages were left untreated or stimulated with IL-4 and IL-13 (prototypic M1 stimuli), Dexamethasone (Glucocorticoid receptor agonist) which has been hitherto considered M2, IL-10 which also falls under the M2 umbrella, and LPS and Interferon Gamma considered M1 stimuli.

overall_design:
Total RNA obtained from autologous serum monocyte-derived macrophages exposed to:

SAMPLE 1	Untreated
SAMPLE 2	Dexamethasone 100nM
SAMPLE 3	LPS 10 ng/ml
SAMPLE 4	IL-10 20 ng/ml
SAMPLE 5	IL-13 20 ng/ml
SAMPLE 6	IL-4 20 ng/ml
SAMPLE 7	IFNy 20 ng/ml

last: Martinez

first: Siamon

last: Gordon


title: Effect of FOXA1 overexpression in prostate cancer

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: FOXA1 is a transcription factor which aids AR function in prostate. There is controversary over the effect of high FOXA1 level has on prostate cancer so we forced the overexpression in the LNCaP prostate cancer cell line.

overall_design: LNCaP prostate cancer cell line was transfected with GFP control plasmid or plasmid containing FOXA1 full length cDNA. The effect on gene expression was assessed by microarray.

first: Jessica

last: Robinson

first: Thomas

last: Carroll

first: Jason

first: David

last: Neal


title: Genome-wide gene expression analysis by TEAD4 knockdown in a gastric cancer cell line SNU216

status: Public on Jan 02 2014

city: Daejeon

first: Byungho

last: Lim

address: Medical Genomics Research Center, KRIBB, 125 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: To access oncogenic roles of TEAD4 in gastric cancer, TEAD4-regulated genes were investigated using a SNU216 cell line in which TEAD4 expression was knockdown by shRNA.

overall_design: To compare control to TEAD4 knockdown cell, total RNA was extracted from two cell lines generated by non-silencing shRNA control and TEAD4 knockdown.

first: Yong-Sung

first: Seon-Young


title: Gene expression profiling of prostate cancer cells upon JMJD2A or ETV1 knockdown

status: Public on Jan 01 2014

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary: Gene expression profiling of LNCaP prostate cancer cells that have JMJD2A knockdown (JMJD2A shRNA #3; JMJD2A shRNA #5) or ETV knockdown (ETV shRNA #1; ETC shRNA #5) were compared to non-targeted control (sh-cm) cells.

overall_design: Total RNA was isolated from transformed LNCaP human prostate cancer cells containing a non-trageting control vector (sh-cm), vectors containing shRNA sequences for JMJD2A or ETV1 genes.


title: Gene profile from RND1-knock down in MDF10A cells

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Microarray analysis was performed to get gene expression profiles induced by knock-down RND1 gene in MCF10A cells

overall_design: total RNA extracted from MCF10A cells carrying either sh-RNA targetting RND1 gene (sh-34 or sh-35) or scramble control were subjected to Microarray analysis


title: Nuclear phosphatidylinositol-5-phosphate regulates ING2 stability at discrete chromatin targets in response to DNA damage [expression]

status: Public on Dec 31 2013

city: Stanford

first: Dennis

middle: Jacob

last: Bua

address: Gilbert Building, Room 109, 371 Serra Mall

department: Biology

institute: Stanford University

summary: ING2 (inhibitor of growth family member 2) is a component of a chromatin-regulatory complex that represses gene expression and is implicated in cellular processes that promote tumor suppression.  However, few direct genomic targets of ING2 have been identified and the mechanism(s) by which ING2 selectively regulates genes remains unknown. Here we provide evidence that direct association of ING2 with the nuclear phosphoinositide phosphatidylinositol-5-phosphate (PtdIns(5)P) regulates a subset of ING2 targets in response to DNA damage.  At these target genes, the binding event between ING2 and PtdIns(5)P is required for ING2 promoter occupancy and ING2-associated gene repression.  Moreover, depletion of PtdIns(5)P attenuates ING2-mediated regulation of these targets in the presence of DNA damage.  Taken together, these findings support a model in which PtdIns(5)P functions as a sub-nuclear trafficking factor that stabilizes ING2 at discrete genomic sites.

overall_design: Genome-wide expression profiling of HT1080 cells stably transduced with ING2 or a ING2 lipid binding mutant in the presence of vehicle (DMSO) or etoposide.  Each condition is tested in triplicate

first: Gloria

last: Mas Martin

first: Olivier

last: Binda

first: Or

last: Gozani


title: Nuclear phosphatidylinositol-5-phosphate regulates ING2 stability at discrete chromatin targets in response to DNA damage

type: Genome binding/occupancy profiling by genome tiling array


title: Genome-wide analysis of each stage of EPCs differentiation

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

summary: Analysis of regulators of endothelial progenitor cells (EPCs) differentiation at gene expression level. Results provide information of gene expression pattern and critical biological processing during EPCs differentiation. Taken together, we define the network of regulators of cord blood-derived EPCs during EPCs differentiation, which can be used to identify genes involved in vascular pathology. Furthermore, we select the critical regulators and then observe these selected regulator's functionality in vitro and in vivo.

overall_design: Total RNA obtained from isolated cord blood-derived EPCs at different time points after the beginning of the EPCs culture under endothelial differentiation condition.

first: Jihye

first: Young-Guen

last: Kwon

first: Daehee

last: Hwang


title: PRDM14 promotes active DNA demethylation through the Ten-eleven translocation (TET)–mediated base excision repair pathway in embryonic stem cells

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

summary: Ten-eleven translocation (TET) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytsosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired by the base excision repair (BER) pathway, implicating 5mC oxidation in active DNA demethylation. Genome-wide DNA methylation is erased in the transition from metastable states to ground state of embryonic stem cells (ESCs) and in migrating primordial germ cells (PGCs), while some resistant regions become demethylated only in gonadal PGCs. Understanding the mechanisms underlying global hypomethylation in naïve ESCs and developing PGCs will be useful for realizing cellular pluripotency and totipotency. In this study, we found that PRDM14, the PR-domain-containing transcriptional regulator, accelerates the TET-BER cycle, resulting in the promotion of active DNA demethylation in ESCs. Induction of PRDM14 expression rapidly removed the 5mC associated with transient elevation of 5hmC at pluripotency-associated genes, germline-specific genes, and imprinted loci but not across the entire genome, which resemble second wave of DNA demethylation in gonadal PGCs. PRDM14 physically interacts with TET1/TET2 and enhances the recruitment of TET1/TET2 at target loci. Knockdown of Tet1/Tet2 impaired transcriptional regulation and DNA demethylation by PRDM14. The repression of the BER pathway by administration of pharmacological inhibitors against APE1 and PARP1 and the knockdown of thymine DNA glycosylase (TDG) also impaired DNA demethylation by PRDM14. Furthermore, DNA demethylation induced by PRDM14 normally takes place in the presence of aphidicolin, which is an inhibitor of G1/S progression. Together, our analysis provides mechanistic insight into DNA demethylation in naive pluripotent stem cells and developing PGCs.

overall_design: To investigate the function of TET1/TET2 in transcriptional regulation by PRDM14 in ESCs, we exploited microarray analysis using total mRNA derived from Scramble, Scramble + PRDM14, Tet1/Tet2 KD, Tet1/Tet2 KD + PRDM14 mouse ESC.

first: Naoki

last: Okashita

first: Yuich

last: Kumaki

first: Kuniaki

last: Ebi

first: Miyuki

last: Nishi

first: Yoshinori

last: Okamoto

first: Megumi

last: Nakayama

first: Shota

last: Hashimoto

first: Tomohumi

last: Nakamura

first: Kaoru

last: Sugasawa

first: Nakao

last: Kojima

first: Tatsuyuki

last: Takada

first: Masaki

last: Okano


title: Peripheral blood gene expression in human experiencing primary EBV infection (HT12)

city: Minneapolis

first: Samantha

last: Dunmire

state: MN

address: 2101 6th St SE

institute: University of Minnesota

summary: Epstein Barr virus causes linfectious mononucleosis and establishes lifelong infection associated with cancer and autoimmune disease.  To better understand immunity to EBV, we performed a prospective study of natural infection in healthy humans.  These anlyses were undertaken in order to determine what gene expression changes occur as the result of primary Epstein Barr virus infection.  Samples were taken both before and following acquisition of the virus for direct comparison of samples for single subjects.  These data provide an important first description of the response to natural herepesvirus infection in humans.

overall_design: PBMC were taken before acquisition of EBV, during acute infection, and during latency

first: Kristin

last: Hogquist


title: Peripheral blood gene expression in human experiencing primary EBV infection


title: Characterization of mRNA and microRNA expression profiles in solid-pseudopapillary neoplasm of pancreas, ductal adenocarcinoma and pancreatic neuroendocrine tumors

city: seoul

first: minhee

last: park

address: shinchondong

institute: student

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

first: Hoguen

last: Kim

first: Minhee

last: Park

first: Minhyung


title: Expression profiles of IRF-1 silenced ovarian cancer cell lines

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Ovarian cancer cells treated with CDDP showed up-regulation of IRF-1 and IRF-7. The expression of putative IRF-1 target genes was modulated. CDDP triggered nuclear translocation of IRF-1 and IRF-1 silencing re-orchestrated the expression profiles of CDDP treated cells.

overall_design: Using microarrays, we evaluated the expression profiles of IRF-1 silenced SK-OV-3.

first: Simona

last: Pavan

first: Martina

last: Olivero

first: Davide

last: Corà

first: MariaFlavia

last: DiRenzo


title: Gene expression of pancreatic tumors

summary:
Solid-pseudopapillary neoplasm of pancreas(SPN), ductal adenocarcinoma(PCA), neuroendocrine tumor(NET) and non-neoplastic pancreas.
To investigate the specific gene expression of SPN compared to other types of pancreatic tumor, we analyzed large-scale gene expressioin analysis to identify the molecular signature that may affect SPN tumorigenesis. Differentially expressed genes were analyzed on SPNs, PCAs, NETs and Non-neoplastic tissues.

overall_design: Solid-pseudopapillary neoplasm (SPN) is an uncommon pancreatic tumor with distinct clinicopathologic features. SPNs are characterized by mutations in exon 3 of CTNNB1. However, little is known about the gene and microRNA expression profiles of SPNs. Thus, we sought to characterize SPN-specific gene expression and identify the signaling pathways activated in these tumors. The mRNA expression profile of 14 SPNs, 6 pancreatic adenocarcinomas (PCAs), 6 pancreatic neuroendocrine tumors (NETs), and five non-neoplastic pancreatic tissues were analyzed.


title: Gene expression profile of YAP1, TEAD1 and KLF5 in hepatocellular carcinoma cell line (SK-Hep1)

city: Houston

first: Yun-Yong

address: 7435 Fannin St.

department: Systems Biology

institute: UT, MD Anderson Cancer Center

summary: Hippo signaling pathway is pivotally involved in human cancer. Among the Hippo components, YAP1 is highly active while function of MST1,2 and SAV1 was lost in liver cancer. Based on systematic analysis, we identified KLF5 as YAP1 binding partner in silico. To investigate KLF5 in liver cancer, we performed the gene expression microarray after knocked down YAP1, TEAD1 and KLF5 in SK-Hep1 cell line.

overall_design: To identify the role of YAP1, TEAD1 and KLF5 in hepatocellular carcinoma cell line, we performed microarray after knocking down YAP1, TEAD1 and KLF5 in hepatocellular carcinoma cell line (3 siLuc, 3 siYAP1, 3 siTEAD1, 3 siKLF5)

first: Sang

first: Ju-seog

last: Lee


title: LNCAP/AR and a LnCAP/AR subline (LREX') with acquired resistance to 2nd generation antiandrogens

status: Public on Dec 27 2013

first: Vivek

middle: Kumar

last: Arora

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary: The treatment of advanced prostate cancer has been transformed by novel antiandrogen therapies such as enzalutamide.  Using the LnCaP/AR xenograft model, we identified induction of glucocorticoid receptor (GR) expression as a common feature of drug resistant tumors.  From a resistant xenograft tumor, we derived a GR expressing resistant subline called LREX' which maintains the resistant phenotype.  mRNA expression was used to characterize resistant tissues.

overall_design: LnCaP/AR cells were injected into castrate mice and tumors were established.  Mice were then treated with vehicle (Con), 4 days of anti-androgen (ARN-509 10mgkg), or were maintained on anti-androgen (10mg/kg ARN-509 or enzalutamide) until emergence of resistance.  Resistant tissues continued to be exposed to anti-androgen through time of harvest.  LREX' (LnCaP/AR Resistant to Enzalutamide Xenograft Derived) was derived from an enzalutamide resistant xenograft and was re-injected into castrate mice undergoing continual treatment with enzalutamide.  The GR probe on the Illumina array failed to detect GR expression.  Therefore, GR expression as determined by qPCR is annotated separately.  Of the 10 control tissues, 8 were analyzed twice (technical duplicates annotated as A and B).

first: Emily

last: Schenkein

first: John

last: Wongvipat

first: Charles

last: Sawyers


title: shRNA kinome screen identifies TBK1 as therapeutic target for HER2+ breast cancer

status: Public on Dec 26 2013

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

summary: Microarray analysis was performed at the UHN Microarray Centre (UHNMAC, Ontario, Canada) using Illumina HumanHT-12 v4 BeadChip with 500 ng of total RNA prepared by RNeasy mini kit (QIAGEN, Cat. No. 74104). Samples from HCC1954 cells with 3-day treatment of TBK1-II at 4 uM were used to compare with vehicle-treated controls.  Microarray data was processed and normalized by lumi package from BioConductor in R with Quantile Method.  Difference between the samples were calculated by Bayesian statistic using limma package from BioConductor in R to obtain Moderated T value for subsequent Pathway analysis.

overall_design: Total RNA extracted from HER2+ HCC1954 cells after 3 days treatment of TBK1-II inhibitor compared with vehicle control

first: Tao

last: Deng

first: Eldad

last: Zacksenhaus


title: JMJD1C knockdown (H9_CT2_JMJD1C-KD_Microarray_JW)

status: Public on Dec 24 2013

city: Farmington

first: Ren-he

last: Xu

state: CT

address: 263 FARMINGTON AVE MC 6403

department: Genetics and developmental biology

institute: university of Connecticut health center

summary: It has been recently reported that the pluripotency factor OCT4, the early neural inducing factor NR2F2, and the pluripotency-associated miRNA miR-302 are linked in a regulatory circuitry that critically regulate both pluripotency and neural differentiation of human embryonic stem cells (hESCs). We show here that JMJD1C, a H3K9 demethylase expressed in undifferentiated hESCs, plays a key role in the regulatory circuitry. hESCs with JMJD1C knockdown (KD) retain the state of self-renewal and pluripotency, but express lower miR-302c than control hESCs. JMJD1C directly binds to the miR-302 promoter in hESCs and reduces H3K9 methylation on the promoter. Upon withdrawal of bFGF (an inhibitor of neural initiation) from a defined culture medium, the KD, but not control, hESCs differentiate into neural progenitors within three days – the fastest ever reported, accompanied by rapid increase of NR2F2 expression. A miR-302c analogue or an inhibitor of H3K9 methylation reduces neural induction from the KD hESCs, whereas a miR-302c inhibitor promotes hESC differentiation. Together, our findings suggest that JMJD1C plays a central role in control of neural differentiation from hESCs, which involves sustained miR-302c expression, and that inhibition of JMJD1C is sufficient to rapidly induce neural progenitors from hESCs in the defined medium depleted of bFGF. This is also the first evidence, to our knowledge, for epigenetic modification of miR-302 in hESCs.

overall_design: 6 human ES cell lines were used in this microarray assay. Each line has two replicates.

first: J

last: Wang

first: X

first: R


title: Heat-shock factor 2 is a suppressor of prostate cancer invasion

status: Public on Dec 23 2013

city: Turku

first: Matthias

last: Nees

address: Itäinen Pitkäkatu 4C

department: Biotechnology

country: Finland

institute: VTT

summary: Heat-shock factors (HSFs) are key transcriptional regulators in cell survival. Although HSF1 has been identified as a driver of carcinogenesis, HSF2 has not been explored in malignancies. Here, we report that HSF2 suppresses tumor invasion of prostate cancer (PrCa). In three-dimensional organotypic cultures and the in vivo xenograft chorioallantoic membrane model HSF2 knockdown perturbs organoid differentiation and promotes invasiveness. Gene expression profiling together with functional studies demonstrated that the molecular mechanism underlying the effect on tumor progression originates from HSF2 steering the switch between acinar morphogenesis and invasion. This is achieved by the regulation of genes connected to, for example, GTPase activity, cell adhesion, extracellular matrix and actin cytoskeleton dynamics. Importantly, low HSF2 expression correlates with high Gleason score, metastasis and poor survival of PrCa patients, highlighting the clinical relevance of our findings. Finally, the study was expanded beyond PrCa, revealing that the expression of HSF2 is decreased in a wide range of cancer types. This study provides the first evidence for HSF2 acting as a suppressor of invasion in human malignancies.

overall_design: HSF1 and HSF2 siRNA transfection was performed in triplicates (biological replicates), for 5 and 8 days prior to harvesting total RNA; and compared to PC-3 cells transfected with scrambled control siRNAs for 5 and 8 days, respectively.

first: Johanna

last: Björk

first: Malin

last: Åkerfeld

first: Jenny

last: Joutsen

first: Mikael

last: Puustinen

first: F

last: Cheng

first: Lea

last: Sistonen


title: Chronic low dose-rate versus acute ionizing radiation induced gene expression in primary derived prostate fibroblasts

status: Public on Dec 20 2013

city: Menlo Park

first: J. Tyson

last: McDonald

address: 333 Ravenswood Avenue

institute: SRI International

summary: Using a novel flood source construct, we performed a direct comparison of genome-wide gene expression regulations resulting from exposure of primary human prostate fibroblast cultures to acute (10cGy and 200cGy) and longer-term chronic (1.0-2.45cGy cumulative over 24hr) exposures.

overall_design: Samples were collected at 24 hours after an acute 10cGy or 200cGy exposure (48cGy per minute) versus immediately after an accumulated 24 hour chronic 1.0 to 2.45cGy low dose-rate exposure (7 to 17µGy per minute).  Control 0cGy samples were collected at the same time.  A total of 4 independent experimental replicates were used for each sample resulting in (2 individuals × 4 experimental conditions × 4 experimental replicates) 32 microarrays.


title: Glucocorticoid Receptor Confers Resistance to Anti-Androgens by Bypassing Androgen Receptor Blockade.

first: Vivek

last: Arora

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

overall_design: Refer to individual Series


title: Genome-wide expression profiling in 293T cells upon depletion of H1.2, Cul4A or PAF1

first: Kyunghwan

last: Kim

state: California

address: 1450 Biggy Street NRT6517

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary: Increasing evidence suggests that linker histone H1 can influence distinct cellular processes by acting as a gene-specific regulator. However, the mechanistic basis underlying such H1 specificity and whether H1 acts in concert with other chromatin-altering activities remain unclear. To investigate the cooperative role of H1.2, Cul4A and PAF1  on gene regulation, genome-wide gene expression analysis is carried out in 293T cells expressing control shRNA, H1.2 shRNA, Cul4A shRNA or PAF1 shRNA.

overall_design: Total RNA was isolated from 293T cells expressing NCsh, H1.2sh, Cul4Ash, or PAF1sh

first: Bomi

last: Lee

first: Jaehoon

first: Jongkyu

last: Choi

first: Jin-Man

first: Yue

last: Xiong

first: Robert

middle: G

last: Roeder

first: Woojin

last: An


title: Androgen and Glucocorticoid stimulation of LREX' cells in vitro

summary: The treatment of advanced prostate cancer has been transformed by novel antiandrogen therapies such as enzalutamide.  Using the LnCaP/AR xenograft model, we identified induction of glucocorticoid receptor (GR) expression as a common feature of drug resistant tumors.  From a resistant xenograft tumor, we derived a GR expressing resistant subline called LREX.  In this model, activation of GR and AR activate a similar but distinguishable set of target genes.

overall_design: LREX' cells were cultured in steroid depleted media and then treated for 8 hours with the indicated drugs in biological triplicates.

first: Emily

last: Schenkein

first: Charles

last: Sawyers


title: Expression Profile of R. capsulatus under heat and cold stress

status: Public on Dec 19 2013

city: Ankara

first: Muazzez

last: Gurgan

address: Üniversiteler Mahallesi

department: Biological Sciences

country: Turkey

institute: Middle East Technical University

summary: The effects of temperature stress on transcriptome of purple non sulfur bacterium R. capsulatus were investigated by comparing expression profiles under optimum hydrogen production condition (30°C), heat (42°C) and cold (4°C) stress conditions.

overall_design: Bacteria were grown anaerobically under continuous illumination (200 W/m2) in 150 ml volume photobioreactors at 30°C for 48 hours. Then cold stress (4°C) and heat stress (42°C) were applied in parallel. For microarray analysis, RNA samples from 1.5x109 cells were collected after 2 hours and 6 hours of stress applications.  A microarray chip for Rhodobacter capsulatus was not commercially available. For that reason, a GeneChip® array was custom designed and manufactured by Affymetrix, Santa Clara, California. The nucleotide sequence of the bacterium is available in GenBank with the accession numbers CP001312 for the chromosome and CP001313 for the plasmid pRCB133. The feature size of the antisense DNA array was 11 micron and the format was 100-3660. A total of 4,052 probe sets for open reading frames (ORFs) and 200 intergenic sequences with longer than 300bp were placed on the microarray. The cDNA synthesis, labeling, and hybridization protocols were performed according to the Affymetrix Expression Analysis Technical Manual given for prokaryotic samples

first: M

first: N

last: Erkal

first: E

last: Ozgur

last: Yucel


title: Expression data from ES cells

city: Ann Arbor

first: Yibin

last: Chen

state: MI

address: 1115 w medical drive

institute: university of Michigan

summary:
H2A.B is a unique histone H2A variant that shares only 40 ~ 50 % sequence identity with canonical H2A. It has only been identified in mammals and has quickly evolved with remarkable sequence diversity among different species. H2A.B is ubiquitously expressed in most cells and tissues. It is mainly deposited in gene body region.The localization of H2A.B is associated with methylated CpG islands in mouse ES cells.H2A.B facilitates transcription elongation to go through methylated CpG islands in the gene bodies. One typical example is that H2A.B regulates transcription elongation at imprinted loci.
We used microarray to test the function of H2A.B on gene expression.

overall_design: Mouse ES cells infected with control knockdown(KD) or H2A.B KD virus were treated with G418. ES cells were extracted for RNA and hybridization on Affymetrix microarrays.

first: Qiang

first: Xiaochun

last: Yu


title: Dexamethasone treatment of VCaP prostate cells

first: Vivek

summary: The treatment of advanced prostate cancer has been transformed by novel antiandrogen therapies such as enzalutamide.  We identified glucocorticoid receptor (GR) activity as modulator of enzalutamite sensitivity in the VCaP prostate cancer cell line.  The GR agonist dexamethasone was sufficient to confer enzalutamide resistance whereas a GR antagonist restored sensitivity.  These expression profiling data demonstrate that GR transcriptional activity overlaps with that of AR in the VCAP model.

overall_design: VCAP cells growing in complete media were treated with the indicated drugs in biological triplicates for 24 hours prior to harvest.


title: Directed differentiation of human pluripotent stem cells into cortical interneurons

first: Jeffrey

last: Zhao

department: Genomics Core

summary: Here we demonstrate the highly efficient derivation of human cortical interneurons in a NKX2.1::GFP hESC reporter line. Manipulating the timing of SHH activation yields three distinct GFP+ populations with specific transcriptional profiles, neurotransmitter phenotypes and migratory behaviors.

overall_design: Total RNA was isolated at day 18 of differentiation from FACS sorted NKX2.1::GFP+ cells from three varying differentiation conditions and a “No SHH” condition (no sonic hedgehog treatment) that did not contain any GFP-expressing cells (Trizol, Sigma). Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

first: Asif

last: Maroof

first: Yosif

last: Ganat

first: Lorenz

last: Studer


title: Narrow-band UVB phototherapy for psoriasis

city: Umeå

first: Xiaolian

last: Gu

state: västerbotton

address: Building 6M, 2nd floor, Umeå University

department: Medical Biosciences

country: Sweden

institute: Umeå University

summary: Psoriasis is a common chronic inflammatory and hyperproliferative immune-mediated skin disorder. Narrow-band UVB (NB-UVB) phototherapy is a convenient first-line treatment of psoriasis, though the mechanisms underlying its efficacy have not been completely elucidated. In order to improve our understanding of NB-UVB phototherapy, gene expression profiling was used to characterize gene expression in lesional epidermis from psoriasis patients undergoing NB-UVB phototherapy. Increased expression of melanogenesis pathway genes was observed to be the earliest response. At the end of treatment, genes involved in diverse biological processes were affected, such as pigmentation, cell adhesion, ectodermal development and metabolism. The relationship between gene expression and treatment outcome was further studied using Partial Least Squares Discriminant Analysis (PLS-DA). Gene ontology analysis showed that genes responding to phototherapy and highly correlated to treatment outcome were involved in oxidation reduction, growth and mitochondria organization. In particular SPATA18, a key regulator of mitochondria quality, was found to be significantly downregulated in psoriasis, and its upregulation following phototherapy was required for optimal clinical improvement. Our data suggest that oxidation reduction is a critical event for the resolution of psoriatic plaques.

overall_design: Twelve patients diagnosed with plaque type psoriasis were recruited to the study. NB-UVB irradiation was administered to the whole body two to three times a week. Treatment comprising approximately 24 sessions was given during two to three months. A total of six 4 mm diameter punch biopsies were taken from lesions on each psoriasis patient: two prior to UV treatment (pre-UV), two at the middle stage of UV treatment (after about one month of treatment, mid-UV) and two before the last treatment session (post-UV). Twelve healthy age-, sex- and skin type-matched volunteers were also recruited and two punch biopsies were taken from the buttocks. RNA was extracted from Laser capture microdissected epidermis.

first: Elisabet

last: Nylander

first: Philip

last: Coates

first: Karin


title: Human breast cancer associated fibroblasts exhibit subtype specific gene expression profiles

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary: Breast cancer is a heterogeneous disease for which prognosis and treatment strategies are largely governed by the receptor status (estrogen, progesterone and Her2-neu) of the tumor cells.  Gene expression profiling of whole breast tumors further stratifies breast cancer into several molecular subtypes which also co-segregate with the receptor status of the tumor cells.  We postulated that cancer associated fibroblasts (CAFs) within the tumor stroma may exhibit subtype specific gene expression profiles and thus contribute to the biology of the disease in a subtype specific manner. Several studies have reported gene expression profile differences between CAFs and normal breast fibroblasts but in none of these studies were the results stratified based on tumor subtypes.  To address whether gene expression in breast cancer associated fibroblasts varies between breast cancer subtypes, we compared the gene expression profiles of early passage primary CAFs isolated from twenty human breast cancer samples representing three main subtypes; seven ER+, seven triple negative (TNBC) and six Her2+.  We observed significant expression differences between CAFs derived from Her2+ breast cancer and CAFs from TNBC and ER+ cancers, particularly in pathways associated with cytoskeleton and integrin signaling.  In the case of Her2+ breast cancer, the signaling pathways found to be selectively up regulated in CAFs may contribute to the more invasive properties and unfavorable prognosis of Her2+ breast cancer. These data demonstrate that in addition to the distinct molecular profiles that characterize the neoplastic cells, CAF gene expression is also differentially regulated in distinct subtypes of breast cancer.

overall_design: We isolated CAFs from twenty primary breast cancer samples representing three main subtypes (ER+ (n=7), TNBC (n=7), Her2+ (n=6)) and performed gene expression profile analyses on RNA isolated from these early passage CAFs.  Those samples were done in two batches with 4 samples repeated in both batches. One TNBC sample was found to be an outlier and not used in the analysis.

first: J

last: Tchou

first: AV

last: Kossenkov

first: L

last: Chang

first: C

last: Satija

last: Herlyn

first: LC

last: Puré


title: Borderline Changes in Renal Allografts: Molecular Diagnostics Identifies Risks for Graft Dysfunction

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

summary: The significance of borderline changes (BL) in kidney allograft biopsies is widely debated. We examined differences in gene expression patterns between early clinical biopsy tissue and 3-month protocol biopsy tissue, all of which had histological BL changes and identified specific molecular BL patterns associated with poor graft outcome. The expression profiles were analyzed in training set of patients and next data were validated in validation cohort using RT-qPCR. Using the Illumina microarray technology, we observed greater expression of immunity- and inflammation-related genes in tissues from early clinical biopsies compared to 3-month protocol biopsies with BL findings. In tissues with early clinically manifested BL changes, graft deterioration within 24 months due to chronic rejection was associated with increased activation of immune, defense, and inflammatory processes, specifically with higher donor age and expression of macrophage receptor CLEC5A. In the 3-month protocol biopsies with BL changes, graft dysfunction was associated with increased expression of fibrinogen complex transcripts. This study highlights the molecular differences between clinical and subclinical biopsies with similar histological findings. The data also support a recommendation for frequent patient monitoring, especially in those who received grafts from expanded criteria donors (ECDs).

overall_design: The experiments were performed with total RNA derived from the renal graft biopsy samples of 28 different patients who had undergone a kidney transplantation.  Only the patients with diagnosis of borderline changes early (≤2 months) or protocolar (3 months) were included in the study.  RNA profiles of patients with stable and deteriorated graft function during 2 years after transplantation were compared. As microarray platform,  Illumina HumanHT-12 v4.0 Expression BeadChips (Illumina) was used. The chip scanning was performed with a BeadStation 500 instrument (Illumina Inc), and the raw data were extracted with the BeadStudio Data Analysis Software (Illumina). The R software lumi package was used to further process the raw data. The quantile method was used for normalization.

first: Ondrej

last: Viklicky

first: Irena

last: Brabcova

first: Zdenek

last: Krejcik

first: Viktor

last: Stranecky

first: Roman

last: Zachoval

first: Eva

last: Honsova


title: Gene expression data from human fibroblasts and induced Pluripotent Stem cells from Parkinson's Disease patients

status: Public on Dec 18 2013

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: We have generated human induced Pluripotent Stem cells (hiPSc) from Parkinson's Disease patients, using retrovirus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays.

overall_design: human iPSc lines were derived from human dermal fibroblasts from 2 Parkinson's Disease patients with heterozygous glucocerebrosidase mutations (GBA N370S) mutations,  and 2 idiopathic Parkinson's Disease patients. SNP datasets from the 2 control individuals used in this study have been published previously [PMID 23951090 GSE45472; PMID:24586273 GSE43904]

first: H

last: Fernandes

first: E

middle: M

last: Hartfield

last: Badger

last: Christian

last: Emmanoulidou

last: Vowles

first: S

last: Evetts

first: K

last: Vekrellis

last: Talbot

first: M

last: Hu

first: W

last: James

first: R

last: Wade-Martins


title: Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies

status: Public on Dec 12 2013

city: London

first: Charles

last: Mein

address: Charterhouse Square

department: Genome Centre

institute: Queen Mary University

summary: To seek effects of inflammatory status and 5-aminosalicylic acid (5-ASA, mesalazine) exposure ex vivo on mRNA levels within rectal mucosal biopsies from patients with ulcerative colitis.

overall_design: A total of 12 biopsies were analysed, 3 biological replicates in each of 4 categories (inflamed with or without 5-ASA, non-inflamed with or without 5-ASA).

first: Tammie

middle: S

last: MacFie

first: Tatjana

last: Boitsova

first: Anke

last: Nijhuis

first: Rosamond

last: Nuamah

first: Andrew

middle: R

last: Silver

first: James

last: Lindsay


title: Genome-wide transcriptional analysis of HT1080 cells stably transfected with PTK7 constructs

status: Public on Dec 16 2013

city: La Jolla

first: Vladislav

last: Golubkov

address: 10901 N. Torrey Pines Rd.

institute: Sanford-Burnham Medical Research Institute

summary:
Full-length membrane PTK7 and its N-terminal and C-terminal proteolytic fragments induced differential transcriptional profiles in HT1080 cells.
Pseudokinase PTK7 is an essential regulator of planar cell polarity (PCP) and directional cell motility in the course of vertebrate development and embryogenesis, and regulates both the non-canonical Wnt/PCP and canonical Wnt pathways. In contrast to its well-appreciated, crucial role in embryo development, the functional importance of the intact full-length PTK7 in malignancy is still a matter of debate. In humans, the full-length membrane PTK7 consists of seven extracellular immunoglobulin-like (Ig) domains, a transmembrane region, a juxtamembrane region and a catalytically inert cytoplasmic tyrosine kinase (PTK) domain. Because pericellular proteolysis plays a primary role in cell migration, especially in the directional locomotion of tumor cells, it is likely that proteolysis and PCP converge to promote efficient directed cancer cell migration. In agreement, the functionality of PTK7 is directly regulated by proteolysis. Ubiquitous membrane type-1 matrix metalloproteinase (MT1-MMP), arguably the primary enzyme in pericellular proteolysis and cancer cell migration, cleaves the PKP621↓LI sequence in the seventh Ig-like domain of membrane PTK7 and this cleavage results in the liberation of the N-terminal soluble PTK7 fragment (sPTK7). MT1-MMP proteolysis is followed by the cleavage of the C-terminal residual portion of PTK7 by ADAMs, including ADAM17. The ectodomain shedding is a prerequisite for the intramembrane cleavage of PTK7 by γ-secretase. This cleavage releases the C-terminal cytoplasmic tail fragment of PTK7, which is then either degraded by the proteasome or transported to the nucleus.The limited pre-existing data suggest that the full-length membrane PTK7 and its proteolytic products cause an opposing effect on the efficiency of cell migration. Thus, the continuing presence of the full-length membrane PTK7 on the plasma membrane down-regulated the myosin light chain (MLC) phosphorylation (a downstream event of the Wnt/PCP pathway) and, in agreement, reduced migration efficiency of fibrosarcoma HT1080 cells. MT1-MMP proteolysis of PTK7 reversed the inhibitory effect of the full-length membrane PTK7, resulted in the accumulation of the stable N-terminal sPTK7 fragment in the extracellular milieu and promoted cell invasion of HT1080 cells. Expression of the Chz PTK7 mutant that exhibited an additional PEK↓LK503 MT1-MMP cleavage site in the junction region between the fifth and the sixth Ig-like domains stimulated cell migration even further. These effects suggest the existence of the intriguing and specific downstream mechanisms by which the intact PTK7, its digest fragments and the homo- and heterodimeric complexes between the PTK7 membrane, soluble and intracellular portions control cell function. These mechanisms, however, have not been precisely investigated in the earlier works by us and others. Understanding of these mechanisms will shed additional light on the role that PTK7 alone as well as in its combination with MT1-MMP, ADAMs and γ-secretase plays in cancer cell migration.

overall_design: To evaluate in detail the effects of PTK7 and its proteolytic fragments on genome-wide transcriptional regulation, we specifically employed fibrosarcoma HT1080 cells. These highly invasive cells express low endogenous levels of PTK7 but high levels of active MT1-MMP and ADAMs. Because of these parameters, we could manipulate this preudokinase functionality using HT1080 cells transfected with the recombinant PTK7 constructs. The cells we employed included the PTK7 knock-out cells (shPTK7 cells), cells with the enforced overexpression of the original membrane PTK7 (PTK7 cells) and its Chuzhoi (Chz) mutant that exhibited an additional PEK↓LK503 MT1-MMP cleavage site (Chz cells), and the cells, which overexpresssed multiple deletion species of PTK7. These species represented the soluble (sPTK7), membrane and cytoplasmic C-terminal digest fragments that resulted because of PTK7 cleavage by MT1-MMP (cPTK7/622-1070) and ADAM/gamma–secretase (cPTK7/726-1070). Expression of these constructs allowed us to specifically determine the downstream effect of PTK7 proteolysis on gene expression. HT1080 cells were stably transfected with the PTK7 constructs. Cells (1 x 10^4/ml) were plated in DMEM- 10% FBS in a 100-mm dish and grown for 72 h to produce a subconfluent culture. Total cellular RNA was extracted using a Direct-zol RNA MiniPrep kit (Zymo Research). Biotin-labeled cRNA samples were prepared using the Illumina RNA Amplification Kit (Ambion). The labeled cRNA (750 ng) was hybridized for 18 h at 58°C to the HumanHT-12 v4 Expression BeadChip (Illumina). BeadChips were then developed using fluorolink streptavidin-Cy3 (GE Healthcare). Array chips were scanned using an Illumina BeadArray Reader. The initial data extraction and normalization were performed using the BeadArray Reader and GeneSpring GX software (Agilent).


title: Expression Profile of R. Capsulatus on different nitrogen sources and different concentrations of acetate

status: Public on Dec 14 2013

first: Nilufer

last: Erkal

institute: Mİddle East Technical University

summary: The  influence of different nitrogen sources on transcriptome of Purple non sulfur bacterium R. Capsulatus was investigated by comparing expression profile on 5mM ammonium chloride and 2 mM glutamate. Carbon source was 40mM acetate on both conditions. To study the effect of different acetate concentrations,  40mM and 80mM acetate were used with 2 mM glutamate as nitrogen source.

overall_design: Bacteria were grown anaerobically under continuous illumination (200 W/m2)  in 150 ml volume photobioreactors at 30°C.   For microarray analysis, RNA samples were collected after 16h of inoculation from 1.5x109 cells.  A microarray chip for Rhodobacter capsulatus was not commercially available. For that reason, a GeneChip® array was custom designed and manufactured by Affymetrix, Santa Clara, California. The nucleotide sequence of the bacterium is available in GenBank with the accession numbers CP001312 for the chromosome and CP001313 for the plasmid pRCB133. The feature size of the antisense DNA array was 11 micron and the format was 100-3660. A total of 4,052 probe sets for open reading frames (ORFs) and 200 intergenic sequences with longer than 300bp were placed on the microarray. The cDNA synthesis, labeling, and hybridization protocols were performed according to the Affymetrix Expression Analysis Technical Manual given for prokaryotic samples

first: Muazzez

last: Gurgan

first: Ebru

last: Ozgur

first: Meral

last: Yucel


title: Transcriptome analysis of primary monocytes from HIV+ patients with differential responses to therapy

status: Public on Dec 30 2013

city: Sydney

first: Nitin

last: Saksena

state: new south wales

address: Darcy Road

department: Center for Virus Research

country: Australia

institute: Westmead Millennium Institute,Westmead Hospital

summary:
This study aimed at investigating the monocytic transcriptome distinction between patients with sustained virus suppression (BDL) and patients with virological failure during highly active antiretroviral therapy (HAART).
This study provides the first transcriptomic distinctions in monocytes between viremic patients and BDLs on HAART. Our results reflected the outcome balanced between subversion of monocyte transcriptome by HIV and compensatory effect adapted by host cells.

overall_design: Total RNA obtained from primary monocytes from five HIV+ patients on HAART who sustainably controlled HIV below detection level (BDL), five HIV+ patients on HAART who consecutively experienced viremia and four healthy HIV sero-negative controls were compared against each other.

first: Jing

middle: Q

last: Wu

first: Tara

last: Sassé

first: Monica


title: Biologic characterization of adult MYC-positive mature B-cell lymphomas other than molecular Burkitt lymphoma

city: Regensburg

first: Christian

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

type:
Expression profiling by array
Third-party reanalysis

summary: MYC translocations are the biologic hallmark of Burkitt lymphomas but also occur in other mature B-cell lymphomas. If accompanied by chromosomal breaks targeting the BCL2 and/or BCL6 oncogenes, these MYC translocation-positive (MYC+) lymphomas are called double-hit lymphomas (DHLs); otherwise, the term single-hit lymphoma (SHL) is applied. In order to characterize the biologic features of these MYC+ lymphomas other than Burkitt lymphomas, we explored, after exclusion of molecular Burkitt lymphoma (mBL) as defined by gene expression profiling (GEP), the molecular, pathological and clinical aspects of 80 MYC translocation (MYC+) lymphomas (31 SHL, 26 BCL2+/MYC+, 14 BCL6+/MYC+, 6 BCL2+/BCL6+/MYC+ and 3 MYC+ lymphomas with unknown BCL6 status). Comparison of SHL and DHL revealed no difference in frequency of MYC partner (IG/non-IG), genomic complexity or MYC expression and no differences in GEP. DHL showed a more frequent GCB-like GEP and higher IGH and MYC mutation rates. GEP revealed 130 differentially expressed genes between BCL6+/MYC+ and BCL2+/MYC+ DHL. BCL2+/MYC+ DHL showed a more frequent GCB-like GEP. Analysis of all lymphomas according to MYC partner (IG/non-IG) revealed no substantial differences. In contrast to mBL and lymphomas without MYC break, SHL and DHL patients had similar poor outcome. Our data suggest that after excluding mBL, MYC+ lymphomas could be biologically widely lumped without further need for subclassification.

overall_design:
32 diffuse large B-cell lymphoma samples were hybridized to HG-U133A Affymetrix GeneChips. In addition, this study contains 30 already published samples, which contribute to GSE4475 (Hummel et al. 2006 (PMID 16760442)), as well as 18 already published samples from GSE22470 (Salaverria et al. 2011 (PMID 21487109)). No re-normalisation of the published samples was performed.

The complete dataset representing: (1) the 32 diffuse large B-cell lymphoma Samples, (2) the 30 Samples from GSE4475 and (3) the 18 Samples from GSE22470, is linked below as a supplementary file

first: Sietse

last: Aukema

first: Markus

last: Kreuz

first: Maciej

last: Rosolowski

first: Dirk

last: Hasenclever

first: Michael

last: Hummel

first: Ralf

last: Küppers

first: Dido

last: Lenze

first: Christiane

last: Pott

first: Julia

last: Richer

first: Andreas

last: Rosenwald

first: Monika

last: Szczepanowski

first: Carsten

last: Schwaenen

first: Harald

last: Stein

first: Heiko

last: Trautmann

first: Swen

last: Wessendorf

first: Lorenz

last: Trümper

last: Loeffler

first: Rainer

last: Spang

first: Philip

last: Kluin

first: Wolfram

last: Klapper

first: Reiner

last: Siebert


title: Measurement of temperature affects on Arabidopsis transcription and decay rates

status: Public on Dec 07 2013

city: Exeter

first: Steven

last: Penfield

address: Stocker Raod

department: Biosciences

institute: University or Exeter

summary: The goal of this study is to measure Arabidopsis mRNA transcription and mRNA decay rates genome wide at two temperatures, and thus to calculate the temperature coefficient of both processes. Sensing and response to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes to transcription or decay rates and whether passive or active temperature regulation is involved.  Results  Using a base analogue labelling method we directly measured the temperature coefficient (Q10) of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional mechanism process exists for the activethat controls of mRNA abundance by temperature/

overall_design: The design of this expreiment is thus: at time zero (dawn) 3 biological replicate samples were harvested, and then the base analogue 4-thiouracil (4SU) was added to three remaining biological replicate samples. At time T these were harvested and the latter biotinylated and separated into 4SU-containing (labelled) and 4SU non-containing (unlabelled) fractions by passage through a streptavidin column. Total RNA for both timepoints was hybridisaed on the chips, as were the separated fractions from time T, giving 12 chips in total. This design was  repeated at a second temperature, giving 24 hybridisations. The two tempertaures were 27C and 17C and time T was 1 hour after dawn at 27C and two hours after dawn at 17C.

first: Kate

last: Sidaway-Lee


title: Gene expression of A53T and corrected IPSC driven to DA neurons and exposed to paraquat and maneb

status: Public on Dec 05 2013

city: Guelph

first: Scott

last: Ryan

state: ON

address: 50 Stone Rd E

institute: University of Guelph

summary: Parkinson disease (PD) is characterized by extensive loss of A9 dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). A strong association has been reported between PD and exposure to mitochondrial toxins such as the environmental pesticides paraquat, maneb, and rotenone. Here, using a robust, patient-derived, stem cell model of PD that allows comparison of -synuclein ( -syn) mutant cells and isogeneic mutation-corrected controls, we identify mitochondrial toxin-induced perturbations specific to A53T -syn mutant A9-DA neurons (hNs). We report a novel molecular pathway whereby basal as well as toxin-induced oxidative and nitrosative stress inhibits the MEF2C-PGC1 transcription network in A53T hNs compared to corrected controls, contributing to mitochondrial dysfunction and apoptotic cell death. Our data provide mechanistic insight into gene-environmental interaction (GxE) in the pathogenesis of PD. Furthermore, using small molecule high-throughput screening, we identify the MEF2C-PGC1 pathway as a new drug target for therapeutic benefit in PD.

overall_design: In the current study, isogenic hiPSCs differing exclusively at a single amino acid (A53T) were exposed to either 2.8uM paraquat in combination with 1uM maneb for 24h or PBS vehicle control. Gene expression profile was analysed to assess the effect of both the genotype and exposure regiment on gene expression.

first: Stuart

last: Lipton

first: Rajesh

last: Ambasudan


title: Activated T cell gene expression profile associated with Psoriasis

status: Public on Dec 02 2013

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

summary:
Psoriasis is a Tcell-mediated disease characterized by the chronic inflammation of skin. Gene expression analyses on skin biopsies and freshly isolated PBMCs have provided important insights into Psoriasis pathophysiology.
In the present study we analyze, for the first time, the gene expression profile of in vitro activated T cells in Psoriasis compared to normal heatlhy controls.

overall_design: T cells from PBMCs isolated from patients and healthy controls were in vitro activated with anti-CD3 and anti-CD28 for 72 hours. After T cell activation, cells were harvested and RNA extracted for microarray analysis.

first: N

last: Palau

first: L

last: Puig

first: C

last: Ferrandiz

first: A

first: S

last: Marsal


title: Hepatocytes-HepaRG reprogramming.

city: Rennes

first: Hélène

last: Dubois-Pot-Schneider

address: Hopital Pontchaillou, rue Henri Le Guilloux

institute: INSERM UMR 991

summary: To identify the molecular mechanisms and environmental inducers contributing to reprogramming of hepatocytes into progenitors in HCC context, we used the HepaRG cell line as model.

overall_design: We performed transcriptomic analysis at various time-points during this process; 0h, 1h, 4h, 8h, 12h, 16h, 24h and 48h.

first: Anne

last: Colu

first: Seiichi

last: Ishida


title: Transcriptome wide target profiling for miR-199a-5p and miR-424-3p.

city: Herston

first: Nicole

last: Cloonan

state: Queensland

address: 300 Herston Road

institute: QIMR Berghofer Medical Research Institute

summary: Whole transcriptome Identification of  direct targets of miR-199a-5p and miR-424-3p using biotinylated pull-downs found that both miRNAs are likely to have a role in the cell cycle.

overall_design: HEK293T cells were transfected with biotinylated miRNAs (either miR-199a-5p or miR-424-3p). The miRNAs and target mRNA were pulled down with streptavidin and compared to the input control.


title: Expression data of control (F/F) and Snai1 knockout (KO) Flk1+/- cells

status: Public on Dec 10 2013

city: Bethesda

first: Yongshun

last: Lin

state: MD

address: 10 Center Dr.

institute: National Heart, Lung, and Blood Institute

summary:
Snai1 is a master factor of epithelial to mesenchymal transitioin (EMT), however, its role in embryonic stem cell (ESC) differentiation and lineage commitment remains undefined.
We used microarrays to compare the global programme of gene expression between control and Snai1 knockout Flk1+ and Flk1- cells sorted from 4 day EBs.

overall_design: Control and Snai1 knockout ESCs were cultured as embryoid bodies in spotaneous differentiation media, 4 days EBs were dissociated and sorted by anti-Flk1 antibody to separated Flk1+ and Flk1- cells, total RNA were collected for Affymetrix microarrays

first: Stephen

last: Weiss


title: Small Molecules Screened via Conversion Kinetics Analyses Facilitate Single Factor-mediated Hepatic Transprogramming

status: Public on Dec 03 2013

city: Cambridge

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

summary: Recent studies have shown that defined hepatic factors could lead to the direct conversion of fibroblasts into induced hepatocytes (iHeps). However, reported conversion efficiencies are vey low and the underlying mechanism of the hepatic lineage conversion is largely unknown. Here, we report that direct conversion into iHeps is a stepwise transition involving erasure of somatic memory, mesenchymal-to-epithelial transition, and induction of hepatic cell fate in a sequential manner. Throughout screening for additional factors that could potentially enhance the kinetics of the MET and hepatic programs, we have found that c-Myc and Klf4 (CK) dramatically accelerate the conversion kinetics, resulting in remarkably improved generation of iHeps (>87 fold). Furthermore, we identified small molecules that could replace the roles of CK and thus led to the highly efficient generation of iHeps without CK. Finally, we show that a single factor (Hnf1α) supported by small molecules is sufficient to robustly induce transprogramming of fibroblasts into functional hepatocyte-like cells with high yield. This novel approach might help to fully elucidate the direct conversion process and also facilitate the translation of iHep into clinic.

overall_design: Cells transduced with different combinations of factors were cultured in standard Hep medium. Epithelial colonies were observed within 5 days with much higher numbers in the presence of additional factor, c-Myc and Klf4, compared to control group, indicating the number of epithelial colony was dramatically increased in the presence of additional stem cell factors. In this study, the established iHep lines (4a3, 4a1CK, and 4a3CK at passage 10) were compared with MEFs and primary hepatocytes in whole transcriptome levels.

first: Kyung

middle: T

first: Seung

last: Lee

first: Dong

last: Han


title: Gene expression and genotype data from human fibroblasts and induced Pluripotent Stem cells from Parkinson's Disease patients

first: Sally

last: Cowley

type:
Expression profiling by array
SNP genotyping by SNP array

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

overall_design: Refer to individual Series

first: H

last: Fernandes

first: E

last: Hartfield

first: J

last: Badger

middle: C

last: Christian

last: Emmanoulidou

last: Vowles

last: Evetts

first: K

last: Vekrellis

last: Talbot

first: M

last: Hu

first: W

last: James

first: R

last: Wade-Martins


title: Gene induction in STAT1-/- fibroblasts transduced with lentiviruses expressing human cGAS

status: Public on Dec 01 2013

city: Dallas

first: John

last: Schoggins

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

summary: The hypothesis tested was that lentiviral driven cGAS expression activates antiviral gene expression.

overall_design: Cells were transduced with lentiviruses expressing cGAS or a control (firefly luciferase). Total RNA was harvested 48 h post-transduction and processed for Illumina BeadArray.


title: Gene expression profiles of stromal cells in ovarian cancer co-culture models

city: Los Angeles

first: Kate

last: Lawrenson

state: CA

address: 1450 Biggy Street

department: Preventive Medicine

institute: University of Southern California

summary: Goal: to profile gene expression change that occur when cancer-associated firboblast precursor cells are co-cultured with normal epithelial cells (IOSE4) or epithelial ovarian cancer cells (HeyA8)

overall_design: MSCs and INOF cells were co-cultured with IOSE4 cells or Hey.A8 EOC cells. 1000 stromal cells were plated into 6 well plates and 10,000 epithelial cells plated into porous inserts (pore size 1μm, Greiner BioOne). After 24hrs, cells were refed and epithelial cell inserts added to the stromal cell cultures. Cells were grown in 50% INOF medium and 50% MSC medium for 7 days before harvesting RNA

first: Simon

last: Gayther

first: Joshua

last: Millstein


title: Gene expression profiles of mammary epithelial and breast cancer cells following fever range hyperthermia

city: El Paso

first: Brad

middle: Allen

last: Bryan

state: Texas

address: 5001 El Paso Drive

department: Biomedical Sciences

institute: Texas Tech University Health Sciences Center

summary: Preclinical and clinical studies have shown for decades that tumor cells demonstrate significantly enhanced sensitivity to “fever range” hyperthermia (increasing the intratumoral temperature to 42-45oC) than normal cells, although it is unknown why cancer cells exhibit this distinctive susceptibility. To address this issue, mammary epithelial cells and three malignant breast cancer lines were subjected to hyperthermic shock and microarray analysis of the global transcription changes was subsequently performed.

overall_design: MCF10A (mammary epithelial cells) and MCF7, MDA231, and MDA468 breast cancer cells were grow at normal growth temperatures or subjected to 30 minutes of hyperthermic (45oC) shock followed by replacement with conditioned media at normal growth temperatures.  RNA was collected 4 hours after shock and subjected to microarray analysis.

first: Dianne

last: Mitchell


title: DNA Methylation Changes in Allergic Patients Correlate with Symptom Severity  [gene expression]

city: Linkoping

first: Colm

middle: Eamonn

last: Nestor

address: KEF, Hälsuniversitetet

institute: Linkoping University

summary: Altered DNA methylation patterns in CD4+ T-cells indicate the importance of epigenetic mechanisms in inflammatory diseases. However, the identification of these alterations is complicated by the heterogeneity of most inflammatory diseases. Seasonal allergic rhinitis (SAR) is an optimal disease model for the study of DNA methylation because of its well-defined phenotype and etiology. We generated genome-wide DNA methylation (Npatients = 8, Ncontrols = 8) and gene expression (Npatients= 9, Ncontrols = 10) profiles of CD4+ T-cells from SAR patients and healthy controls using Illumina’s HumanMethylation450 and HT-12 microarrays, respectively. DNA methylation profiles clearly and robustly distinguished SAR patients from controls, during and outside the pollen season. Moreover, we found that this methylation signature correlated with symptom severity. In agreement with previously published studies, gene expression profiles of the same samples failed to separate patients and controls. Separation by methylation (Npatients = 12, Ncontrols = 12), but not by gene expression (Npatients = 21, Ncontrols = 21) was also observed in an in vitro model system in which purified PBMCs from patients and healthy controls were challenged with allergen. We observed changes in the proportions of memory T-cell populations between patients (Npatients = 35) and controls (Ncontrols= 9), which could explain the observed difference in DNA methylation. Our data highlight the potential of epigenomics in the stratification of immune disease and represents the first successful molecular classification of SAR using CD4+ T cells.

overall_design: Total RNA was isolated from CD4+ T-cells of patients with seasonal allergic rhinitis and healthy controls both during and outside the pollen season. Total RNA was amplified and hybridized to Illumina HT12 version 4 human whole-genome arrays (Illumina, San Diego, CA).

middle: E

first: Mikael

last: Benson


title: The miRNA miR-139-5p is a regulator of metastatic pathways in breast cancer.

first: Nicole

last: Cloonan

summary: Whole transcriptome Identification of  direct targets of miR-139-5p using biotinylated pull-downs found that this miRNA has roles in breast cancer invasion and migration.

overall_design: MCF7 cells were transfected with biotinylated miR-139-5p. The miRNAs and target mRNA were pulled down with streptavidin and compared to the input control.


title: Imperfect centered miRNA binding sites are common and can mediate functional repression of target mRNAs [microarray]

summary: Whole transcriptome Identification of  direct targets identify a new class of miRNA::mRNA interactions.

overall_design: HEK293T cells were transfected with biotinylated miRNAs. The miRNAs and target mRNA were pulled down with streptavidin and compared to a mock transfected control.


title: VGLL4 is a novel regulator of survival in human embryonic stem cells

city: Santa Clara

first: Adriana

last: Tajonar

address: 3707 Poinciana Drive

institute: Harvard University

summary:
Human embryonic stem cells (hESCs) are maintained in a self-renewing state by an interconnected network of mechanisms that sustain pluripotency, promote proliferation and survival, and prevent differentiation. We sought to find novel genes that could contribute to one or more of these processes by using a gain-of-function screen of a large collection of human open reading frames. We identified Vestigial-like 4 (VGLL4), a co-transcriptional regulator with no previously described function in hESCs, as a positive regulator of survival in hESCs. Specifically, VGLL4 overexpression in hESCs significantly decreases cell death in response to dissociation stress. Additionally, VGLL4 overexpression enhances hESC colony formation from single cells. These effects may be attributable, in part, to a decreased activity of initiator and effector caspases observed in the context of VGLL4 overexpression. Additionally, we show an interaction between VGLL4 and the Rho/Rock pathway, previously implicated in hESC survival. This study introduces a novel gain-of-function approach for studying hESC maintenance and presents VGLL4 as a previously undescribed regulator of this process.
The goal of this experiment was to compare the global transcriptional profile of hESCs overexpressing VGLL4 to wild-type hESCs in order to understand the transcriptional differences behind the phenotype exhibited by VGLL4-overexpressing cells. This list was then used for subsequent analysis where genes were filtered individually, but also per sample, such that only genes with a pvalue of detection of less than 0.05 on at least 5 of the samples were kept. Next, the SAM statistical suite was used to generate a list of genes that are expressed at a significantly higher level in the 4 Vgll4 samples compared to the 4 WT samples using an FDR of 7% for discovery purposes.

overall_design: RNA was purified from total cultures of HUES6 human embryonic stem cells (wildtype vs cells overexpressing VGLL4 from a lentiviral vector). Samples were collected in quadruplicates (biological replicates) using a Qiagen RNeasy kit and 200 ng of starting material were used as input for the Illumina TotalPrep Amplification Kit. Human ES cells were grown in the presence of mouse embryonic fibroblasts.

first: Rene

last: Maehr

first: Guang

first: Julie

middle: B

last: Sneddon

first: Jose

last: Rivera-Feliciano

first: Dena

last: Cohen

first: Stephen

middle: J

last: Elledge

first: Douglas

last: Melton


title: Gene expression profiling of CD4+ T-cell subsets in follicular lymphoma.

status: Public on Nov 21 2013

city: Houston

first: Min

last: Zhang

address: 7455 Fannin Street

institute: MD Anderson Cancer Center

summary: CD4+ T-cells from three follicular lymphoma tumors were sorted by flow cytometry into three subsets based on high (hi), intermediate (int), or low (lo) levels of PD-1 and CXCR5 expression and whole genome gene expression profiling was performed.

overall_design: This set contains three samples for PD-1hiCXCR5hiCD4+ T cells, two samples for PD-1intCXCR5intCD4+ T cells, and three samples for PD-1loCXCR5loCD4+ T cells.

first: Zhiqiang

last: Wang

first: Fuliang

last: Chu

first: Yanli

last: Gao

first: Sattva

last: Neelapu

first: Richard

last: Davis


title: Effect of histamine on human keratinocytes

city: Oxford

last: Taylor

address: Headington

institute: CBRG

summary: Genome-wide analysis of gene expression after stimulation with histamine  to assess the main processes, molecular functions and cellular components affected as well as genes related to skin barrier function.

overall_design: HaCaT cells were exposed to histamine (1ug/ml) for 24h. The cells were lysed, total RNA was extracted and microarray study was performed on Illumina HT12 platform.

first: Graham

last: Ogg

first: Danuta

last: Gutowska-Owsiak


title: Cancer stem cells from lobular infiltrating breast tumor metastasize to bone and acquire a gene signature associated to bone tropism

status: Public on Nov 30 2013

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary: We investigated the role of breast cancer stem-like cells (CSCs-like), isolated from primary tumor, in promoting bone metastases in a human-in-mice model. Luciferase-transduced CD44+CD24- breast CSCs-like were injected through subcutaneous (SC) and intracardiac (IC) route in nonobese/severe combined immunodeficient (NOD/SCID) mice carrying subcutaneous human bone implants. The implanted bone was viable, active and human neo-vascularization was present. By in vivo luciferase imaging, we monitored tumor growth and detected bone-localized breast CSCs-like, both after SC and IC injection. Bone metastatic lesions were histologically evident, and tumor cells expressed epithelial markers and vimentin. Bone metastatic cells isolated from bone implants showed a CD44-CD24+ phenotype and re-created tumors and bone metastases after injection in secondary mice. A “bone tropism” expression signature was found to distinguish bone-colonizing cells from parental CSCs-like and to persist at subsequent passages also in the absence of surrounding bone tissue. The bone tropism signature displayed significant enrichment in genes discriminating bone metastases of breast cancer from metastases at other organs. Our results demonstrate the ability of breast CSCs-like to promote bone metastasis and provide a CSCs-like bone tropism signature, with potential prognostic value.

overall_design: C10 breast cancer stem-like cells (CSCs-like) were derived as mammospheres from a lobular-infiltrating breast carcinoma (ER+, HER2-). Samples are organized in the following groups: (i) Breast CSCs-like (C10, duplicate); (ii) Luciferase-transduced CSCs-like (C10L, simplicate); (iii) Bone-isolated C10L metastatic cells (C10-bone, duplicate) and subsequently (iv) grown in vitro as spheroids (C10-CSC, simplicate) or (v) re-grown in subcutaneous implants (C10-SC, duplicate).

first: Claudio

last: Isella

first: Ilaria

last: Roato


title: Glutamine sensitivity analysis identifies the xCT antiporter as a common triple negative breast tumor therapeutic target.

status: Public on Nov 22 2013

city: San Francisco

first: Luika

middle: Ann

last: Timmerman

address: 2340 Sutter Street,  Room N361

department: Cancer Center

institute: UCSF / HDF Comprehensive Cancer Center

summary: A small number of tumor-derived cell lines have formed the mainstay of cancer therapeutic development, yielding drugs with impact typically measured as months to disease progression.  To develop more effective breast cancer therapeutics, and more readily understand their potential clinical impact, we constructed a functional metabolic portrait of 46 independently-derived breast tumorigenic cell lines, contrasted with purified normal breast epithelial subsets, freshly isolated pleural effusion breast tumor samples and culture-adapted, non-tumorigenic mammary epithelial cell derivatives.  We report our analysis of glutamine uptake, dependence, and identification of a significant subset of triple negative samples that are glutamine auxotrophs.  This NCBI GEO submission comprises a small datasest generated to compare the expression profiles of the above nontumorigenic, purified normal and purified pleural effusion samples with 10 established breast cancer-derived cell lines.  This dataset was subsequently merged with a previously published expression dataset derived from 45 independent breast cancer derived cell lines (Neve, et al 2006), and analyses contrasting various subsets of the merged dataset were published.

overall_design: Expression data from 26 samples, no replicates: purified normal human mammary epithelial breast cellular subsets CD10+, BerEP4+, and remaining stromal cell samples from 3 independent anonymous donors; 3 anonymous purified human breast cancer pleural effusion samples; 4 HMEC-derived culture adapted but not transformed samples (184A1, 184B5, HMLE, HMLE-PR); and 10 established human breast cancer cell lines.

first: Thomas

last: Holton

first: Mariia

last: Yuneva

first: Raymond

last: Louie

first: Mercè

last: Padró

last: Hu

first: Denise

last: Chan

middle: P

last: Ethier

first: Laura

last: van't veer

first: Kornelia

last: Polyak

first: Frank

last: McCormick

first: Joe

middle: W

last: Gray


title: Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [time course]

status: Public on Nov 19 2013

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

institute: university of eastern finland

summary:
Here, we have focused on studying the link between metabolic changes driven by the differentiation into mature adipocytes of a human preadipocyte cell line (SGBS) and their regulation, through a combined experimental and computational approach.
By collecting data on gene expression, PPARg, CEBPa, LXR and H3K4me3 genome-wide ChIP-seq profles and transcriptome-wide microRNA target identification for miR-27a, miR29a and miR-222, and using constraint-based modeling to estimate metabolic reaction activity, we obtained a comprehensive set of information highlighting how epigenetic, transcriptional and post-transcriptional regulation impacts the metabolic network.

overall_design:
Illumina HT12 microarrays: Time series of differentiation (20 samples, 7 time points in duplicate or triplicate)

This is the Illumina Gene Expression part of the study.


title: Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [T0901317]

overall_design:
Illumina HT12 V3.0 microarrays: LXR ligand activation with 1 microM T0901317 for 4 h in SGBS day 10 differentiated adipocytes (6 samples, treatment vs control, in triplicate)

This submission represents transcriptome component of study.


title: Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [miR]

overall_design:
Illumina HT12 V4.0 microarrays: Transcriptome analysis 24 hours following overexpression of indicated microRNAs or control siRNAs on indicated time points of differentiation (D0 or D4 + 24 hours) (7 conditions in triplicate, total of 21 samples + siLamin transfection as positive control in duplicate)

This submission represents transcriptome component of study.


title: Expression data from Arabidopsis root in response to boron limitation

status: Public on Nov 13 2013

city: Bunkyo-ku

first: Mayuki

last: Tanaka

state: Tokyo

address: 1-1-1 Yaoyoi

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

summary:
Boron is essential for plants, and boron availability in soil is an important determinant of agricultural production. Boron availability in soil is limited at many regions in the world, including Japan. Under boron deficient conditions, leaf expansion and root elongation, apical dominance, flower development,and fruit and seed sets are inhibited.
In this work, we analyzed the mRNA expression of genes containing AUGUAA motif in their 5′-UTR, which is induced by boron. We used microarrays to detail the global gene expression underlying boron deficiency in roots.

overall_design: Plants were grown on solid medium containing 1% (w/v) sucrose, 1.5% (w/v) gellan gum and 100 µM boron for 10 days and then transferred to 0.3 and 100 µM boron for 2 days. Plates were placed vertically at 22°C in a growth chamber under long-day conditions (16 h light/8 h dark cycle). We analyzed the transcript profiles in roots by microarray analysis (Affymetrix ATH1 Genome Array).

first: Toru

last: Fujiwara

first: Masami

middle: Y

last: Hirai


title: Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study

status: Public on Nov 20 2013

city: Tucson

first: Vincent

last: Gardeux

state: AZ

address: 1657 East Helen Street, PO Box 210240

department: Medicine

institute: University of Arizona

summary:
Background: Genome-wide transcriptome profiling generated by microarray and RNA-Seq often provides deregulated genes or pathways applicable only to larger cohort. On the other hand, individualized interpretation of transcriptomes is increasely pursued to improve diagnosis, prognosis, and patient treatment processes. Yet, robust and accurate methods based on a single paired-sample remain an unmet challenge.

Methods: “N-of-1-pathways” translates gene expression data profiles into mechanism-level profiles on single pairs of samples (one p-value per geneset). It relies on three principles: i) statistical universe is a single paired sample, which serves as its own control; ii) statistics can be derived from multiple gene expression measures that share common biological mechanisms assimilated to genesets; iii) semantic similarity metric takes into account inter-mechanisms’ relationships to better assess commonality and differences, within and cross study-samples (e.g. patients, cell-lines, tissues, etc.), which helps the interpretation of the underpinning biology.

Results: In the context of underpowered experiments, N-of-1-pathways predictions perform better or comparable to those of GSEA and Differentially Expressed Genes enrichment (DEG enrichment), within- and cross-datasets. N-of-1-pathways uncovered concordant PTBP1-dependent mechanisms across datasets (Odds-Ratios≥13, p-values≤1×10-5), such as RNA splicing and cell cycle. In addition, it unveils tissue-specific mechanisms of alternatively transcribed PTBP1-dependent genesets. Furthermore, we demonstrate that GSEA and DEG Enrichment preclude accurate analysis on single paired samples.

Conclusions: N-of-1-pathways enables robust and biologically relevant mechanism-level classifiers with small cohorts and one single paired samples that surpasses conventional methods. Further, it identifies unique sample/ patient mechanisms, a requirement for precision medicine.

overall_design:
Cell lines, culture conditions: The epithelial human breast cancer cell line MDA-MB231 (ER-/ PR-/ HER2-) were obtained from the American Type Culture Collection (Manassas, VA). The epithelial human ovarian tumor cell line A2780 was received as a generous gift from Dr. Thomas C. Hamilton (Fox Chase Cancer Center, Philadelphia, PA) Cancer Center, Philadelphia, PA). Cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine in a humid environment at 37°C, with 5% CO2. Both cell lines were free of Mycoplasma species and were maintained for no longer than 10 weeks in culture after recovery from frozen stocks. Mycoplasma levels were checked periodically using the MycoAlert® Mycoplasma Detection Kit (Lonza Inc., Allendale, NJ). The authenticity of cell lines was assessed by the ATCC carrying out short tandem repeat (STR) analysis (Verified STR Profiling Service, ATCC® 135-XV). Additionally, we compared A2780 to the original STR profile collected by the European Collection of Cell Culture (Catalogue number 93112519).

Doxycycline-inducible knockdown of PTBP1 regulated by small hairpin RNA (shRNA): In order to analyze the effect of PTBP1 depletion, two consecutive viral transductions were performed in both MDA-MB231 and A2780 cell lines. Cells were plated on 24-well plate (10-20×104 cells/well), maintained in culture for 16 hours, and then medium containing LV-tTR/KRAB-Red lentiviral particles was added. Following 16 h of incubation, cells were transduced a second time by LV-THM/PTBshRNA or LV-THM/LUCshRNA lentiviral particles. Clones expressing both red and green fluorescent protein (dsRED and GFP respectively) were selected and expanded. Following 16 h of incubation, cells were washed and split in two subcultures, one without doxycycline (PTBP1/-DOX; Control in Figure 1) and the other with Doxycycline (DOX) at a final concentration of 1 μg/ml (PTBP1/+DOX; PTBP1-KD in Figure 1). Doxycycline was prepared according to the manufacturer’s recommendations (Sigma-Aldrich, St. Louis, MO). Five days later, cells were analyzed by fluorescence microscopy, and PTBP1 gene expression was assessed using PCR and Western Blotting (data not shown). The cells that were transduced by LV-LUCshRNA express PTBP1 regardless of the presence of DOX (LUCshRNA/+DOX). Constructs and lentivirus preparation were performed as previously described in literature [He X et al., Knockdown of polypyrimidine tract-binding protein suppresses ovarian tumor cell growth and invasiveness in vitro, Oncogene 2007, 26(34):4961-4968].

Microarray Analysis: For each of the cell lines, MDA-MB231 and A2780, total RNAs were extracted from four biological replicates of PTBP1-depleted cells, PTBP1-KD (4× PTBP1/+DOX) and eight biological replicates control cells (4× PTBP1/-DOX and 4× LUCshRNA/+DOX) by Direct-zol RNA kit (Zymo Research, Irvine, CA). All paired samples consist of PTBP1-depleted cells (PTBP1-KD) and matched control cells. Qualities of RNA were assessed based on the RNA quality indicator (RQI ≥ 8) using Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA). Gene expression microarray measurements were performed using the GeneChip PrimeView Human Gene Expression Array that contains 49,395 probes and measures 36,000 transcripts and variants per sample. Labeling and hybridization were performed following Affymetrix protocols. The raw data were normalized according to the Robust Multiple-array Average (RMA) technique, using Affymetrix Power Tools (APT).

biological replicate: Ovarian_LucsH_DOX_1, Ovarian_LucsH_DOX_2, Ovarian_LucsH_DOX_3, Ovarian_LucsH_DOX_4

biological replicate: Ovarian_PTBsh1_NODOX_1, Ovarian_PTBsh1_NODOX_2, Ovarian_PTBsh1_NODOX_3, Ovarian_PTBsh1_NODOX_4

biological replicate: Ovarian_PTBsh1_DOX_1, Ovarian_PTBsh1_DOX_2, Ovarian_PTBsh1_DOX_3, Ovarian_PTBsh1_DOX_4

biological replicate: Breast_LucsH_DOX_1, Breast_LucsH_DOX_2, Breast_LucsH_DOX_3, Breast_LucsH_DOX_4

biological replicate: Breast_PTBsh1_NODOX_1, Breast_PTBsh1_NODOX_2, Breast_PTBsh1_NODOX_3, Breast_PTBsh1_NODOX_4

biological replicate: Breast_PTBsh1_DOX_1, Breast_PTBsh1_DOX_2, Breast_PTBsh1_DOX_3, Breast_PTBsh1_DOX_4

first: Ahmet

middle: D

last: Arslan

first: Ikbel

last: Achour

first: Tsui-Ting

last: Ho

first: William

last: Beck

first: Yves

middle: A

last: Lussier


title: DNA-damaging agent and immune inducer synergistically induced defence gene expression in Arabidopsis

status: Public on Nov 14 2013

city: Durham

first: Shunping

last: Yan

state: North Carolina

address: 127 Science Dr.

institute: Duke University

summary: We used microarrays to identify differentially expressed genes after DNA-damaging agent bleomycin (BLM) and/or immune inducer 2, 6-dichloroisonicotinic acid (INA) treatment. We focused on those genes that were synergistically induced by co-treatment (BLM+INA).

overall_design: Arabidopsis seedlings were treated with 4 μg/ml BLM and/or low INA (10 μM). There are 4 treatments: control (CK), INA, BLM and BLM+INA. Each treatments have three biological replicates. There are 12 samples in total.

first: Wei

last: Wang

first: Xinnian

last: Dong


title: Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas

status: Public on Nov 16 2013

city: Heidelberg

first: Marcus

last: Renner

address: Im Neuenheimer Feld 224

department: General Pathology

institute: Institute of Pathology

type:
Expression profiling by array
Methylation profiling by array

overall_design: Refer to individual Series

first: Thomas

last: Wolf

first: Gunhild

last: Mechtersheimer


title: Fibroblast Major TF KDs

status: Public on Nov 12 2013

city: Yokohama

first: Yasuhiro

last: Tomaru

state: Kanagawa

address: 1-7-22 Suehicho

department: Omics Science Center

institute: RIKEN

summary: Knock down of fibroblast specific TF, FOXD1, HOXC4, LHX9, OSR1, PRRX1, TBX3, TWIST2 and NC(negative control siRNA) in fibroblast

overall_design: 24 Samples total.

first: Y

last: Nishinura


title: Gene expression profiling of tumor biopsies before and after pidilizumab therapy in patients with relapsed follicular lymphoma grade 1 or grade 2.

first: Min

last: Zhang

summary: Endogenous or iatrogenic antitumor immune responses can improve the course of follicular lymphoma (FL), but may be diminished by immunoregulatory mechanisms in the tumor microenvironment. These may include effects of programmed death (PD)-1, a coinhibitory receptor that impairs T-cell function and is highly expressed on intratumoral T cells. In a Phase II trial, we tested the efficacy of pidilizumab, a humanized anti-PD-1 monoclonal antibody, with rituximab in patients with rituximab-sensitive FL relapsed after 1-4 prior therapies. Pidilizumab was administered at 3 mg/kg every 4 weeks for 4 infusions, plus 8 optional infusions every 4 weeks for patients with stable disease or better. Starting 2 weeks after the first infusion of pidilizumab, rituximab was given at 375 mg/m2 weekly for 4 weeks. Peripheral blood and tumor biopsies were studied to assess immunological effects of pidilizumab. The combination was well-tolerated, with no grade 3/4 toxicities. Overall (66%) and complete (52%) response rates in 29 evaluable patients were high, with tumor regression in 86% of patients. Median progression-free survival was 18.8 months, and was not reached for the 19 responders. Peripheral blood immunophenotyping showed increased memory CD4+ T cells and activation of NK cells after pidilizumab therapy. Tumor response and progression-free survival were associated with T-cell activation gene signatures in tumor gene expression profiling data, both at baseline and in changes induced by pidilizumab. The efficacy of pidilizumab with rituximab compared favorably to historical retreatment with rituximab monotherapy in patients with relapsed FL. Pidilizumab may benefit patients with pre-existing endogenous antitumor immune responses.

overall_design: This set contains 26 samples in total. 8 pairs of pre- and post-treatment samples, and 10 additional pre-treatment samples.

first: Zhiqiang

first: Wencai

last: Ma

first: Fuliang

last: Chu

first: Jason

last: Westin

first: Sattva

last: Neelapu

first: Richard

last: Davis


title: Basic data set for advanced transdifferentiation from fibroblast

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


title: Blood PD-1+ CXCR3- CXCR5+ CD4 T cells and active GC Tfh cells share a transcriptional profile signature

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

first: M

last: Locci

first: E

last: Haddad

first: S

last: Crotty

first: K

last: Ghneim

last: Cameron

first: P