status: Public on Jan 30 2010

city: Houston

first: Richard

last: Kellermayer

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
Comparison of murine colonic mucosal gene expression between postanatal day 90 (P90) to postnatal day 30 (P30) by whole genomic expression microarray.
Gene expression profiling of colonic mucosal DNA between P90 and P30 mice. Agilent Technologies two-color labelling kit and genomic hybridization protocol was utilized.

overall_design: 4 independent P90 to P30 comparisons were performed as follows. RNA (0.4ug) samples were processed and labelled with Cy3 and Cy5 (Quick Amp labelling kit, two color, Agilent technologies)  and 4 independent P90 to P30 comparisons were done on Agilent tecnologies 4x44k whole genomic expression microarray G2519F, Amadid:014868)

first: Kellermayer

last: Richard


title: Interferon-γ-responsive non-hematopoietic cells regulate the immune response to Mycobacterium tuberculosis

status: Public on Nov 25 2009

city: New York

first: Ludovic

last: Desvignes

state: NY

address: 522 First Avenue

department: Medicine

country: USA

institute: New York University School of Medicine

summary: Immunity to Mycobacterium tuberculosis in humans and in mice requires interferon gamma (IFNγ).  Wheras IFNγ has been studied extensively for its effects on macrophages in tuberculosis, we determined that protective immunity to tuberculosis also requires IFNγ-responsive non-hematopoietic cells.  Bone marrow chimeric mice with IFNγ-unresponsive lung epithelial and endothelial cells exhibited earlier mortality and higher bacterial burdens than control mice, under-expressed indoleamine-2,3-dioxygenase (Ido1) in lung endothelium and epithelium and over-expressed interleukin-17 (IL-17) with massive neutrophilic inflammation in the lungs.  We also found that the products of IDO catabolism of tryptophan selectively inhibit IL-17 production by Th17 cells, by inhibiting the action of IL-23.  These results reveal a previously-unsuspected role for IFNγ responsiveness in non-hematopoietic cells in regulation of immunity to M. tuberculosis, and reveal a mechanism for IDO inhibition of Th17 cell responses.

overall_design: Bone marrow chimera were created by γ-irradiation (10 Gy) of recipient mice, Ifngr+/+ (W) or Ifngr-/- (K), and reconstitution by i.v. injection of Ifngr+/+ (W) bone marrow cells. After 6 weeks, the two groups of chimera W→W and W→K were infected via the aerosol route with 100 colony forming units of Mycobacterium tuberculosis strain H37Rv. At 63 days post-infection, 4 W→W mice and 4 W→K mice were euthanized, their lung left lobe removed and processed for total RNA isolation and microarray. The 4 samples from the W→W mice were pooled together and used as control sample whereas the 4 samples from the W→K mice were pooled together and used as experimental sample. The same harvest and sample processing was conducted on day 97 after infection, using 5 W→W mice and 6 W→K mice.

first: Joel

middle: D

last: Ernst


title: Mouse ES cell neural differentiation

status: Public on Nov 04 2009

city: shanghai

first: Huang

last: Chengyang

address: Yue Yang Road 320

country: China

institute: Institute of biochemistry and cell biology

summary: Gene expression profiles of mouse ES cells (D0) and neural precusor cells (D6)

overall_design: The mouse ES cell line R1 was grown on mitotically inactive fibroblast feeder layers in DMEM containing 15% FBS and LIF (1000 U/ml). Direct neural differentiation of ES cells was performed as described. (Watanabe et al., 2005)

first: Chengyang

last: Huang

first: Yang

last: Xiang

first: Degui

last: Chen

first: Naihe

last: Jing


title: Patterns of gene expression and copy-number alterations in VHL disease-associated and sporadic ccRCC

status: Public on Jun 02 2009

city: Boston

first: Rameen

last: Beroukhim

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

type:
Expression profiling by array
Genome variation profiling by SNP array

summary:
Recent insights into the role of the VHL tumor suppressor gene in hereditary and sporadic clear cell carcinoma of the kidney (ccRCC) have led to new treatments for patients with metastatic ccRCC, although virtually all patients eventually succumb to the disease. We performed an integrated, genome-wide analysis of copy-number changes and gene expression profiles in 90 tumors, including both sporadic and VHL disease-associated tumors, in hopes of identifying new therapeutic targets in ccRCC. We identified 14 regions of nonrandom copy-number change, including 7 regions of amplification (1q, 2q, 5q, 7q, 8q, 12p, and 20q) and 7 regions of deletion (1p, 3p, 4q, 6q, 8p, 9p, and 14q). An analysis aimed at identifying the relevant genes revealed VHL as one of 3 genes in the 3p deletion peak, CDKN2A and CDKN2B as the only genes in the 9p deletion peak, and MYC as the only gene in the 8q amplification peak. An integrated analysis to identify genes in amplification peaks that are consistently overexpressed among amplified samples confirmed MYC as a potential target of 8q amplification and identified candidate oncogenes in the other regions. A comparison of genomic profiles revealed that VHL disease-associated tumors are similar to a subgroup of sporadic tumors, and thus more homogeneous overall. Sporadic tumors without evidence of biallelic VHL inactivation fell into 2 groups: one group with genomic profiles highly dissimilar to the majority of ccRCC, and a second group with genomic profiles that are much more similar to tumors with biallelic inactivation of VHL.

Keywords: comparative genomic hybridization

overall_design: 90 clear cell renal cell carcinomas and 21 renal cancer cell lines were subject to 250K SNP analysis.

first: Sabina

last: Signoretti


title: Expression data from paclitaxel and salinomycin-treated HMLER breast cancer cells

status: Public on Aug 20 2009

city: Cambridge

first: Piyush

middle: B.

last: Gupta

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research/MIT

summary: Screens for agents that specifically kill epithelial cancer stem cells (CSCs) have not been possible due to the rarity of these cells within tumor cell populations and their relative instability in culture. We describe here an approach to screening for agents with epithelial CSC-specific toxicity. We implemented this method in a chemical screen and discovered compounds showing selective toxicity for breast CSCs. One compound, salinomycin, reduces the proportion of CSCs by >100-fold relative to paclitaxel, a commonly used breast cancer chemotherapeutic drug. Treatment of mice with salinomycin inhibits mammary tumor growth in vivo and induces increased epithelial differentiation of tumor cells. In addition, global gene expression analyses show that salinomycin treatment results in the loss of expression of breast CSC genes previously identified by analyses of breast tissues isolated directly from patients. This study demonstrates the ability to identify agents with specific toxicity for epithelial CSCs

overall_design: Experimentally transformed HMLER breast cancer cells were treated in culture with either paclitaxel (10nM) or salinomycin (1uM) for one week. There were three biologic replicates for each treatment condition.

middle: B

first: Tamer

middle: T

last: Onder

first: Robert

middle: A

last: Weinberg

first: Eric

middle: S

last: Lander


title: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-1"

status: Public on Apr 15 2009

city: Seattle

first: Dan

last: Tenenbaum

state: WA

institute: Institute for Systems Biology

summary: By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea.   Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1.  Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms).  The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle.  Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.

overall_design: This publication consists of five experiments, known as A, B, C, Control-1, and Control-2. A,B, and C are entrained as described in the publication, and Control-1 and Control-2 were not entrained.

first: Kenia

last: Whitehead

first: Min

last: Pan

first: Ken-Ichi

last: Masumura

last: Bonneau

first: Nitin

last: Baliga


title: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "C"

first: Richard


title: Gene expression in GLN versus PDLN in NOD mice

status: Public on Apr 23 2009

city: Stanford

first: Remi

middle: J

last: Creusot

state: CA

address: 269 Campus Dr, CCSR 2240

institute: Stanford University

summary: Comparison of the gene expression in the two pancreatic lymph nodes: gastric lymph node (GLN) and pancreatico-duodenal lymph node (PDLN) in NOD mice. The analysis was done in an attempt to explain the preferential homing of bone marrow-derived dendritic cells to the GLN after intravenous injection.

overall_design: GLN and PDLN were excised from 4 individual 12-wk old female NOD mice and RNA was extracted after tissue homogenization in Trizol for processing onto microarray (Agilent 4x44K). Each array corresponds to one single mouse, thus this study comprise 4 biological replicates.

first: Garry

last: Fathman


title: Distinct roles of FOXA2 and FOXA3 in allergic airway disease

status: Public on Aug 21 2009

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary:
Allergen challenge induced mucus metaplasia modify the expression of two transcription factors belonging to the FOXA family: FOXA2 and FOXA3. Foxa2 expression is decreased during allergic airway disease whereas, Foxa3 expression is increased by allergen.
Therefore, we asked whether persistent expression of Foxa2 prevents mucus and whether absence of Foxa3 affects mucus or other features asociated with allergic airway disease.
We analyzed the effects of these changes in FOXA transcription factor expression using Foxa2 transgenic mice and Foxa3-/- mice. We found that persistent expression of FOXA2 reduced mucus but the absence of FOXA3 had no effect on mucus production induced by allergen challenge.
However, the absence of FOXA3 decreased airway hyperreactivity and increased IgE production and eosinophilic inflammation but none of these features were affected by persistent expression of FOXA2. These results indicate that FOXA3 has functions distinct from those of FOXA2 in the allergic response.

Keywords: gene expression comparison between Foxa3-/- and littermate control mice both challenged with OVA

overall_design: DNA miocroarrays were used to analyze lung mRNA expression of Foxa3 KO and littermate control mice challenged with saline or OVA. The experiment incorporated a 1 color design and used Agilent arrays that contained roughly 44,000 60mer probes that provide complete coverage of the mouse genome. 11 arrays were hybridized and represent 3 lung samples for groups WT saline, WT OVA and KO OVA. There are 2 lung samples for the KO saline group.

first: David

last: Erle

first: Sung-Woo

last: Park

first: Catherine

last: Verhaeghe


title: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "A"

status: Public on Apr 14 2009


title: Profiling of immortalized human lung epithelial cells following infection with oncogenic KRAS (G12V)

status: Public on Oct 21 2009

city: La Jolla

first: Pablo

last: Tamayo

address: 3855 Health Sciences Drive MC 0658

department: Moores Cancer Center

institute: UCSD

summary:
The purpose of the dataset is to analyze expression of genes induced by KRAS
The proto-oncogene KRAS is mutated in a wide array of human cancers, most of which are aggressive and respond poorly to standard therapies. Although the identification of specific oncogenes has led to the development of clinically effective, molecularly targeted therapies in some cases, KRAS has remained refractory to this approach. An alternative strategy for targeting KRAS is to identify gene products that, when suppressed or inhibited, result in cell death only in the presence of an oncogenic allele. Here we have used systematic RNA interference (RNAi) to detect synthetic lethal partners of oncogenic KRAS and found that the non-canonical IkB kinase, TBK1, was selectively essential in cells that harbor mutant KRAS. Suppression of TBK1 induced apoptosis specifically in human cancer cell lines that depend on oncogenic KRAS expression. In these cells, TBK1 activated NF- B anti-apoptotic signals involving cREL and BCL-XL that were essential for survival, providing mechanistic insights into this synthetic lethal interaction. These observations identify TBK1 as a potential therapeutic target in KRAS mutant tumors and establish a general approach for the rational identification of co-dependent pathways in cancer.

overall_design: Profiling of KRAS activation (mutant), KRAS WT and control in AALE cells (Lundberg et al., Oncogene 2002;21:4577)

first: Jesse

last: Boehm


title: Microarray analysis of splenic reservoir monocytes and their blood counterparts

status: Public on Aug 03 2009

first: Martin

last: Etzrodt

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Massachusetts General Hospital

summary:
A current paradigm states that monocytes circulate freely and patrol blood vessels, but differentiate irreversibly into dendritic cells or macrophages upon tissue entry. Here we show that bona fide undifferentiated monocytes reside in the spleen and outnumber their equivalents in circulation. The reservoir monocytes are relatively immotile, assemble in clusters in the cords of the subcapsular red pulp, and are distinct from macrophages and dendritic cells. In response to ischemic myocardial injury, splenic monocytes increase their motility, exit the spleen en masse, accumulate in injured tissue and participate in wound healing. These observations uncover a role for the spleen as a site for storage and rapid deployment of monocytes, and identify the splenic monocyte reservoir as a resource that the body exploits to regulate inflammation.
The goal of this gene expression study was to compare the gene expression of Ly-6C hi inflammatory monocytes residing in the spleen and their circulating counterparts in the blood.

overall_design: Monocyte subsets of a group of four mice (C57BL/6, 8-12 weeks) were isolated by fluorescence activated cell sorting (FACS Aria, BD biosciences) as CD11bhi (CD90/B220/CD49b/NK1.1/Ly-6G)lo (F4/80/I-Ab/CD11c)lo Ly-6Chi (all antibodies BD biosciences) cells. Samples of 1,000 Ly-6Chi blood and Ly-6Chi splenic monocytes of each mouse were collected directly into 20 µl lysis buffer of the PicoPure RNA isolation kit (Arcturus). RNA extraction was subsequently performed according to the manufacturer’s instructions (Arcturus). RNA quality was assessed using RNA pico lab chips on the Agilent Bioanalyzer. For all samples a RIN above 8 could be achieved. All further steps were performed at the UCSF Shared Microarray Core Facilities according to standard protocols (http://www.arrays.ucsf.edu and http://www.agilent.com).

first: Filip

middle: K

last: Swirski

first: Matthias

last: Nahrendorf

first: Moritz

last: Wildgruber

first: Virna

last: Cortez-Retamozo

first: Peter

last: Panizzi

first: Jose

middle: L

last: Figueiredo

first: Rainer

last: Kohler

first: Aleksey

last: Chudnovskiy

last: Waterman

first: Elena

last: Aikawa

first: Thorsten

last: Mempel

last: Libby

first: Ralph

last: Weissleder

first: Mikael

last: Pittet


title: Hepatocyte-specific deletion of SIRT1 alters fatty acid metabolism

status: Public on Apr 07 2009

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Hepatic metabolic derangements are key components in the development of fatty liver, insulin resistance, and atherosclerosis. SIRT1, a NAD+-dependent protein deacetylase, is an important regulator of energy homeostasis in response to nutrient availability. Here we demonstrate that hepatic SIRT1 regulates fatty acid metabolism by positively regulating PPAR-alpha. Hepatocyte-specific deletion of SIRT1 impairs PPAR-alpha signaling and decreased fatty acid beta-oxidation in the liver. When challenged with a high-fat diet, liver-specific SIRT1 knockout mice develop hepatic steatosis, hepatic inflammation, and endoplasmic reticulum stress. Taken together, our data indicate that SIRT1 plays a vital role in the regulation of hepatic lipid homeostasis.

overall_design: ix Lox control and six Liver-specific SIRT1 KO (SIRT1 LKO) mice in 95% C57BL/6 background were fed ad libitum with free access to water and food. They were then sacrificed at 4:00pm to analyze PPAR-alpha mediated phenotypes under physiologically relevant conditions. Livers from these mice were then dissected and RNA was isolated with a Qiagen RNA easy mini kit with on-column DNAseI treatment. RNA quality was validated with the Agilent 2100 Bioanalyzer in the microarray facility. RNA samples were then pooled with 2 animals/replicate and analyzed by Agilent Whole Mouse arrays. Data are generated by the Rosetta Resolver Error Model.

first: Aparna

last: Purushotham

first: Qing

last: Xu

first: Xiaoling

last: Li

first: Jennifer

last: Collins


title: Comparative gene expression profile of Cux2 knock-out cortex

status: Public on Feb 25 2009

city: madrid

first: Ana

last: Dopazo

address: Melchor Fdez Almagro

department: Genomics Unit

country: Spain

institute: CNIC

summary:
Gene expression profiles of Cux2 ko cortex was compared to the profile of WT cortex.

Keywords: tissue comparison

overall_design: Cerebral cortex of WT and Cux2 ko animals were dissected and total RNA was obtained. Gene expression profiles were obtained for each sample and compared.

first: Marta

last: Nieto

first: Beatriz

last: Cubelos

first: Sebastian

last: Alvaro


title: Time-course of gene expression in BMDCs stimulated with gamma-PGA nanoparticles

status: Public on Mar 05 2009

city: Kagoshima

first: Takayuki

last: Hamasaki

state: Kagoshima

address: 8-35-1 Sakuragaoka

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Kagoshima University

summary: The gene expression levels in murine bone marrow-derived dendritic cells treated with γ-PGA NPs were examined by oligonucleitide microarray at 6, 12 and 24 hours. The gene expression of proinflammatory chemokines, cytokines, and costimulatory molecules was upregulated considerably in DCs treated with γ-PGA NPs at 6 hours.

overall_design: The gene expression in murine bone marrow-derived dendritic cell was measured at 6, 12 and 24 hours after exposure to  γ-PGA NPs (300 µg/ml).  Three independent experiments were performed.

first: Masanori

last: Baba


title: Gene expression in the pancreatic lymph node of Deaf1 knock out mice vs. BALB/c controls

status: Public on Jul 15 2009

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

summary:
A microarray study performed in the pancreatic lymph nodes of Deaf1 knock-out and BALB/c control mice to identify genes that are regulated by the transcriptional regulator Deaf1.  These experiments constitute a portion of the study described below:

Abstract:
Type 1diabetes (T1D) can result from a breakdown in peripheral tolerance which is controlled by peripheral tissue antigen (PTA) expression in lymph nodes.  Here, we identified a transcriptional regulator, deformed epidermal autoregulatory factor 1 (Deaf1), which regulates the expression of various PTAs in the pancreatic lymph node (PLN). We found, by microarray, that Deaf1 controls the expression of ~600 genes in the PLN.  In the non-obese diabetic (NOD) mouse model of T1D, we identified a wild-type form of Deaf1 (DF1) and a truncated alternatively spliced variant (DF1-VAR1) that hetero-dimerizes with and decreases the transcriptional activity of DF1. The expression of DF1 correlates with the expression of various pancreatic PTAs such as insulin, and during the onset of destructive insulitis in NOD mice, DF1 expression is downregulated, while the DF1-VAR1 expression is upregulated in the PLN.  A reduction in DF1-controlled PTA expression in the PLN, leading to decreased peripheral tolerance, could underlie the pathogenesis of NOD disease.

overall_design: Deaf1-KO mice (4 wk old) and age-matched BALB/c control mice were sacrificed, and the PLN were removed and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA quality was assessed using the Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer’s instructions.  Control and Deaf1-KO mouse RNA was amplified, labeled with Cy3 and Cy5, respectively, and combined with spike A and spike B mix, respectively, using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies).  The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific).   Samples were prepared with the gene expression hybridization kit (Agilent Technologies) and two color microarrays were performed using the whole mouse genome (4x44K) Oligo microarray kit, according to manufacturer’s instructions.  Microarray chips were washed and scanned using the DNA microarray scanner (Agilent Technologies).  Data was processed with Feature Extraction Software (Agilent Technologies), and analyzed using GeneSpring GX 7.3 Software (Agilent Technologies).  This submission shows the data obtained from two individual Deaf1 knockout mice measured against a pool of 4 BALB/c control mice.

first: Rémi

last: Creusot

first: Leon

last: Su

first: Deqiao

last: Sheng

first: Pearl

last: Chang

first: Margaret

last: Czesak

first: Paul

middle: R

last: Albert

first: Ai-Ris

last: Collier

first: Shannon

last: Turley

last: Fathman


title: Transcriptome analysis of J774A.1 macrophages undergoing amino acid deprivation

status: Public on Feb 05 2009

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Phagocytosis represents a mechanism used by macrophages to remove pathogens and cellular debris. Recent evidence suggested that amino acid or glucose deprivation may cause an increase in phagocytosis of heat-inactivated Escherichia coli and Staphylococcus aureus by macrophages, but not the uptake of platelets, apoptotic cells or beads. Increased phagocytosis of bacteria could be blocked by phagocytosis inhibitors and depended on p38 MAP kinase activity. To examine potentially important downstream pathways linked to EBSS-induced starvation and p38 MAP kinase activation, a full genome microarray representing over 41,000 mouse genes or transcripts was probed with cDNA isolated from J774A.1 macrophages that were treated with EBSS, EBSS supplemented with the p38 inhibitor SB202190 or control medium supplemented with 10% fetal bovine serum.

Keywords: autophagy, heterophagy, p38 MAP kinase, scavenger receptor A, starvation

overall_design: Prior to RNA isolation, J774A.1 macrophages were incubated in RPMI 1640 medium supplemented with (i) 10% fetal bovine serum, (ii) Earle’s Balanced Salt Solution (EBSS) or (iii) EBSS supplemented with 10 µM SB202190 for 6 hours.

first: Wim

last: Martinet

first: Dorien

last: Schrijvers

first: Jean-Pierre

last: Timmermans

first: Arnold

last: Herman

first: Guido

last: De Meyer


title: Lymphoid tissue specific homing of bone marrow-derived dendritic cells

first: Remi

summary:
Because of their potent immunoregulatory capacity, dendritic cells (DCs) have been exploited as therapeutic tools to boost immune responses against tumors or pathogens, or dampen autoimmune or allergic responses. Murine bone marrow-derived DCs (BM-DCs) are the closest known equivalent of the blood monocyte-derived DCs that have been used for human therapy. Current imaging methods have proven unable to properly address the migration of injected DCs to small and deep tissues in mice and humans. This study presents the first extensive analysis of BM-DC homing to lymph nodes (and other selected tissues) after intravenous and intraperitoneal inoculation. Following intravenous delivery, DCs accumulated in the spleen, and preferentially in the pancreatic and lung-draining lymph nodes. In contrast, DCs injected intraperitoneally were found predominantly in peritoneal lymph nodes (pancreatic in particular), and in omentum-associated lymphoid tissue. This uneven distribution of BM-DCs, independent of the mouse strain and also observed within pancreatic lymph nodes, resulted in the uneven induction of an immune response in different lymphoid tissues. These data have important implications for the design of systemic cellular therapy with DCs, and in particular underlie a previously unsuspected potential for specific treatment of diseases such as autoimmune diabetes and pancreatic cancer.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Stress-dependent CHIP/Daxx interaction suppresses the p53 apoptotic program

status: Public on Jun 15 2009

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary:
Our previous studies have implicated CHIP as a co-chaperone/ubiquitin ligase, whose activities yield protection against stress-induced apoptotic events. In this report, we demonstrate a stress-dependent interaction between CHIP (carboxyl terminus of Hsp70-interacting protein) and Daxx, death domain-associated protein. This interaction interferes with the stress-dependent association of HIPK2 with Daxx, blocking phosphorylation of serine 46 in p53 and inhibiting the p53-dependent apoptotic program. Microarray analysis confirmed suppression of the p53-dependent transcriptional portrait in CHIP (+/+) but not in CHIP (-/-) heat shocked MEFs. The interaction between CHIP and Daxx results in ubiquitination of Daxx which is then partitioned to an insoluble compartment of the cell. In vitro ubiquitination of Daxx by CHIP revealed that Ub chain formation utilizes non canonical lysine linkages associated with resistance to proteasomal degradation. CHIP's ubiquitination of Daxx utilizes lysines 630 and 631 and competes with the cell's sumoylation machinery at these residues. These studies implicate CHIP as a stress-dependent regulator of Daxx that counters Daxx's pro-apoptotic influence in the cell. By abrogating p53-dependent apoptotic pathways and by ubiquitination competitive with Daxx sumoylation, CHIP integrates the cell's proteotoxic stress response with cell cycle pathways that influence cell survival.

Keywords: p53, apoptosis, cell stress, ubiquitination

overall_design: We utilized a “sample x reference” experimental design strategy in which RNA extracted from mouse embryonic fibroblasts was hybridized to the microarray slide in the presence of labeled Universal Mouse Reference RNA (UMRR, Stratagene, LaJolla, CA).  A total of 24 RNA samples were used in this analysis.  Briefly, five hundred nanograms of total RNA were used for gene expression profiling following reverse transcription and T-7 polymerase-mediated amplification/labeling with Cyanine-5 CTP.  Labeled subject cRNA was co-hybridized to Agilent G4112F Whole Mouse Genome 4x44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Slides were hybridized, washed, and scanned on an Axon 4000b microarray scanner.  The data were processed using Feature Extaction software (Agilent, Santa Clara, CA).

first: Holly

last: McDonough

first: Peter

last: Charles

first: Eleanor

middle: G

last: Hilliard

first: Shu-bing

last: Qian

first: Jin-Na

last: Min

first: Andrea

last: Portbury

first: Douglas

middle: M

last: Cyr

first: Cam

last: Patterson


title: IL-4-primed bone marrow macrophages isolated from  C57Bl6/J or Balb/cAnNCrl mice

status: Public on Aug 10 2009

city: Regensburg

first: Carol

last: El Chartouni

address: Franz-Josef-Strauß Allee 11

department: Hematology and oncology

country: Germany

institute: University Hospital Regensburg

summary:
To compare the expression profile of differentiated mouse bone marrow macrophages (BMM) in response to IL-4, we have employed whole genome microarray expression profiling. For this purpose, bone marrow cells were isolated from 8 to 12 weeks old C57BL6/J and Balb/cAnNCrl mice and cultured in the presence of the macrophage colony-stimulating factor (M-CSF). After seven days of culture, IL-4 was added for 4 and 18 hours.

Keywords: Mice strain comparison; Gene expression profiling

overall_design: IL-4 induced gene expression was investigated in mouse bone marrow macrophages (BMM) of C57BL6/J and Balb/cAnNCrl mice. Differentiated BMM were incubated with mouse recombinant IL-4 for 4 or 18 hours or without for 18 hours. Two independent experiments were performed at each time (mock, 4 and 18 hours) using different mice littermates for each experiment.

first: Michael

last: Rehli


title: Transcript expression data from glioblastoma subcutaneous xenografts and non-neoplastic control brain

status: Public on Mar 07 2009

first: Graeme

last: Hodgson

department: Neurological Surgery

institute: UCSF

summary:
Development of model systems that recapitulate the molecular heterogeneity observed amongst GBM tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from The Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7-gain/chromosome-10-loss, a poor prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBMs genomic amplification and overexpression of known GBM oncogenes such as EGFR, MDM2, CDK6 and MYCN, and novel genes including NUP107, SLC35E3, MMP1, MMP13 and DDX1. The transcriptional signature of GBMX tumors, which was stable over multiple subcutaneous passages, was defined by overexpression of genes involved in M-phase, DNA Replication, and Chromosome organization (MRC) and was highly similar to the poor-prognosis mitosis-and-cell-cycle-module (MCM) in GBM. Assessment of gene expression in TCGA-derived GBMs revealed overexpression of MRC cancer genes AURKB, BIRC5, CCNB1, CCNB2, CDC2, CDK2, and FOXM1, which form a transcriptional network important for G2/M- progression and/or -checkpoint activation. In conclusion, our study supports propagation of GBM tumors as subcutaneous xenografts as a useful approach for sustaining key molecular characteristics of patient tumors, and highlights therapeutic opportunities conferred by this GBMX tumor panel for testing targeted therapeutic strategies for GBM treatment.
Keywords: Disease state analysis

overall_design: RNA expression was assessed in 38 samples: 34 GBM xenograft tumors (29 independent tumors with hybridization replicates for 5 tumors) and 4 non-neoplastic control brain samples

first: J

first: Ru-Fang

last: Yeh


title: Aldehyde oxidase homologue 2 (Aoh2) knockout mouse and retinoic acid synthesis

status: Public on Jan 01 2009

city: Milano

first: Maddalena

last: Fratelli

address: Via La Masa, 19

country: Italy

institute: "Mario Negri" Institute

summary:
The mouse aldehyde oxidase, Aoh2 (aldehyde oxidase homolog 2), is a molybdo-flavoenzyme.  Harderian glands are the richest source of Aoh2, although  the protein is detectable also in sebaceous glands, epidermis and other keratinized epithelia.  The levels of Aoh2 in the Harderian gland and skin are controlled by genetic background, being maximal in CD1 or C57BL/6 and minimal in DBA/2, CBA or 129/Sv strains.  Testosterone is a negative regulator of Aoh2 in Harderian glands.  Homogenously purified Aoh2 oxidizes retinaldehyde into retinoic acid efficiently, while it is devoid of pyridoxal oxidizing activity, unlike other aldehyde oxidases.  Aoh2  knockout mice are viable and fertile, although they have an absolute deficit of retinaldehyde oxidase activity in the Harderian gland, decreased retinoic acid levels, and down-regulation of retinoid-dependent genes.  The Harderian gland’s transcriptome of knockout mice is characterized by perturbations in pathways controlling lipid homeostasis and cellular secretion.  This is particularly evident in sexually immature animals.  Lower amounts of retinoic acid are also observed in the skin of Aoh2-/- animals.  Knockout mice have thickening of the epidermis in basal conditions and after UV light exposure.  This has correlates in the skin transcriptome, which shows enrichment and overall up-regulation of genes involved in hypertrophic responses.

Keywords: Gene knockout study

overall_design:
Harderian Gland - Animals were divided into four groups: male and female, before and after sexual maturation (5-6 and 7-9 weeks, respectively). 3-5 animals per group were used. Each couple of samples from WT and KO mice, age and sex matched, and where possible, from brothers, were hybridized on the same slide, in dye-swapped duplicates, for a total of 30 microarrays.

Skin – Skin samples from 4 WT and 4 KO adult female animals were taken, age matched (sisters, whenever possible), and hybridized on the same slide with a balanced dye design, for a total of 4 microarrays.

first: Mineko

last: Terao

first: Maria

last: Barzago

first: Mami

last: Kurosaki

first: Renzo

last: Bagnati

first: Antonio

last: Bastone

first: Chiara

last: Giudice

first: Eugenio

last: Scanziani

first: Alessandra

last: Mancuso

first: Cecilia

last: Tiveron

first: Enrico

last: Garattini


title: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "B"

first: Dan

last: Tenenbaum

first: Kenia

last: Whitehead

first: Min

last: Pan

first: Ken-Ichi

last: Masumura

first: Richard

last: Bonneau

first: Nitin

last: Baliga


title: Single intestinal stem cells build crypt-villus structures in vitro without a cellular niche

status: Public on Apr 03 2009

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

summary:
The intestinal epithelium is the most rapidly self-renewing tissue in adult mammals. We have recently demonstrated the presence of approximately six cycling Lgr5+ stem cells at the bottoms of small intestinal crypts1. We have now established long-term culture conditions under which single crypts undergo multiple crypt fission events, whilst simultanously generating villus-like epithelial domains in which all differentiated cell types are present. Single sorted Lgr5+ stem cells can also initiate these crypt-villus organoids. Tracing experiments indicate that the Lgr5+ stem cell hierarchy is maintained in organoids. We conclude that intestinal crypt-villus units are self-organizing structures, which can be built from a single stem cell in the absence of a non-epithelial cellular niche.

Keywords: expression profiling

overall_design: Freshly isolated small intestinal crypts from two mice were divided into two parts. RNA was directly isolated from one part (RNeasy Mini Kit, Qiagen), the other part was cultured for one week according to the conditions described in the associated paper, followed by RNA isolation. We prepared labeled cRNA following the manufacturer’s instruction (Agilent Technologies). Differentially labelled cRNA from small intestinal crypts and organoids were hybridised separately for the two mice on a 4X44k Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays.

first: Toshiro

last: Sato

middle: E

first: Hans

last: Clevers


title: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-2"


title: Expression data of MCF7 cells following short-term E deprivation, ER-alpha siRNA knockdown and oxidant treatments

status: Public on Nov 03 2008

city: Novato

first: Christina

last: Yau

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

summary:
To investigate the oxidant sensitivity of E/ER regulated gene expression, E/ER regulated genes are identified using E deprivation or
ER-alpha siRNA knockdown; and oxidative stress responsive is determined by 8hr exposure to diamide, hydrogen peroxide and menadione
Keywords: biomarker identification

overall_design: MCF7 cells were treated under various conditions to identifiy oxidative stress responsive E/ER regulated genes.  Association of these genes with respect to tumor phenotypes are assessed

first: Christopher

last: Benz


title: 16MB binding of H3ac, H4ac, STAT1, IRF1 antibodies in IFNg treated and untreated HeLa cells using nimblegen array

status: Public on Jan 15 2009

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital

type: Genome binding/occupancy profiling by genome tiling array

summary:
Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucletide probes at 30bp intervals tiling over non-repetitive 16MB gene locus(HG17)
Keywords: ChIP-chip

overall_design: three replicates for each marker at each state.

first: Zhaodong

last: Xu

first: Tao

last: Yu

first: Katherine

last: Huang


title: Mouse heart cells' gene expression difference compared with that of MEF cells

status: Public on Apr 01 2009

city: Shanghai

first: Jing

last: Liao

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology  Shanghai Institutes for Biological Sciences  Chinese Academy of Science

summary: Mouse somatic heart cell had different gene expression level compared with that of the MEF cells. This difference gave the mouse somatic heart cell unique characteristics which could then be compared with the mouse ES cells by genes comparison to show the gene expression difference between mouse somatic heart cells and mouse ES cells.

overall_design: There were two replicates sample of the mouse somatic heart cell named 1, 2. And the control cells were the MEF cells. Mouse somatic heart cells samples were labled with Cy3 and the MEF cells were labled with Cy5. The data was process to show the mouse somatic heart cells' gene expression difference compared with that of MEF cells.

first: Lei

last: Xiao

first: Chun

last: Cui

first: Huasheng

first: Xiaokun

last: Teng

first: Yi

last: Zhang


title: Mouse lung cells' gene expression difference compared with that of MEF cells

department: Institute of Biochemistry and Cell Biology

summary: Mouse somatic lung cell had different gene expression level compared with that of the MEF cells. This difference gave the mouse somatic lung cell unique characteristics which could then be compared with the mouse ES cells by genes comparison to show the gene expression difference between mouse somatic lung cells and mouse ES cells.

overall_design: There were two replicates sample of the mouse somatic lung cell named 1, 2. And the control cells were the MEF cells. Mouse somatic lung cells samples were labled with Cy3 and the MEF cells were labled with Cy5. The data was process to show the mouse somatic lung cells' gene expression difference compared with that of MEF cells.


title: Comparison of gene expression in BMDCs stimulated with gamma-PGA nanoparticles, LPS and unparticulate gamma-PGA

first: Takayuki

last: Hamasaki

summary: The gene expression levels in murine bone marrow-derived dendritic cells treated with γ-PGA NPs were examined by oligonucleitide microarray and compared with those in the cells treated with other adjuvants. The gene expression of proinflammatory chemokines, cytokines, and costimulatory molecules was upregulated considerably in DCs treated with γ-PGA NPs. The upregulation pattern was similar to that in DCs treated with LPS but not in DCs treated with unparticulate γ-PGA. The activation of DCs by γ-PGA NPs was confirmed by real-time RT-PCR analysis for the genes related to TLR signaling. The effect of γ-PGA NPs on DCs was not annihilated by treating with polymixin B, an inhibitor of LPS. Furthermore, the immunization of mice with γ-PGA NPs carrying OVA significantly induced Ag-specific CD8+ T cells and Ag-specific production of IL-2, TNF-α, and IFN-γ from the cells. Such activities of γ-PGA NPs were more prominent, when compared to the immunization with OVA plus aluminum hydroxide or OVA plus CFA. These results suggest that γ-PGA NPs induce a CD8+ T cell response through activating innate immunity in a fashion different from that of LPS. Thus, γ-PGA NPs may be an attractive adjuvant to be further developed for vaccine therapy.

overall_design: The gene expression in murine bone marrow-derived dendritic cell was measured at 6 hours after exposure to  γ-PGA NPs (300 µg/ml), LPS(1 µg/ml ), or unparticulate γ-PGA(300 µg/ml).  Three independent experiments were performed.

first: Masanori

last: Baba


title: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon

first: Dan

last: Tenenbaum

institute: Institute for Systems Biology

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

first: Kenia

last: Whitehead

first: Min

last: Pan

first: Ken-Ichi

last: Masumura

first: Richard

last: Bonneau

first: Nitin

last: Baliga


title: Expression data of control-shRNA and SATB1-shRNA expressing MDA-MB-231 cells from 2D and 3D culture system

status: Public on Jan 31 2008

city: Berkeley

first: Terumi

last: Kohwi-shigematsu

address: 1 Cyclotron road

department: Life Science

institute: LBNL

summary:
We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells.
Keywords: Comparative studies on Control_shRNA and SATB1_shRNA1 expressing MDA-MB-231 from 2D or 3D culture.

overall_design: We examined control_shRNA-MDA-MB-231 cells and SATB1_shRNA1-MDA-MB-231 cells under two culture condition;on plastic dish(2D culture) and on Matrigel coated dish(3D culture). When SATB1 was depleted by RNAi technology, these normally aggressive cells exhibited normal breast like morphology on 3D. We used two different microarray platforms (Codelink and Affymetrix) to make expression data. Initial analysis of data and cross-platform comparison were performed using Codelink expression analysis and GeneSpring software. We provide ratio for control_shRNA/SATB1_shRNA1-MDA-MB-231 cells for 2D and 3D on this series.

first: Han

last: Hye-Jung

first: Kohwi

last: Yoshinori

first: Kohwi-Shigematsu

last: Terumi


title: Mouse ES cells' gene expression difference compared with that of the MEF cells

first: Jing

last: Liao

summary: Mouse ES cells had different gene expression level compared with that of the MEF cells. This difference gave the mouse ES cells unique characteristics which could then be compared with other species' ES cells or iPS cells like human ES cells and Rat iPS cells by the homologue genes comparison to show which species' ES cells or iPS cells were more competitive with the other.

overall_design: There were three replicates sample of the mouse ES cells named 1, 2, 3. And MEF cells were named MEF. Mouse ES cells samples were labled with Cy3 and the mix2 were labled with Cy5. The data was process to show the mouse ES cells' gene expression difference compared with that of MEF cells.

first: Lei


title: Analysis of the effects of loss of E-cadherin and cell adhesion on human mammary epithelial cells

status: Public on Jan 15 2008

city: Boston

first: Tamer

last: Onder

address: One Blackfan Circle

institute: Children's Hospital Boston

summary:
Loss of the epithelial adhesion molecule E-cadherin is thought to enable metastasis by disrupting intercellular contacts - an early step in metastatic dissemination.  To further investigate the molecular basis of this notion, we use two methods to inhibit E-cadherin function that distinguish between E-cadherin's cell-cell adhesion and intracellular signaling functions.  While the disruption of cell-cell contacts alone does not enable metastasis, the loss of E-cadherin protein does, through induction of an epithelial-to-mesenchymal transition, invasiveness and anoikis-resistance. We find the E-cadherin binding partner beta-catenin to be necessary but not sufficient for induction of these phenotypes. In addition, gene expression analysis shows that E-cadherin loss results in the induction of multiple transcription factors, at least one of which, Twist, is necessary for E-cadherin loss-induced metastasis.  These findings indicate that E-cadherin loss in tumors contributes to metastatic dissemination by inducing wide-ranging transcriptional and functional changes.
Keywords: E-cadherin knockdown, dominant-negative E-cadherin expression, E-cadherin and Beta-catenin double knockdown

overall_design:
Gene expression changes induced by knockdown of E-cadherin, expression of dominant-negative E-cadherin and double knockdown of E-cadherin and Beta-catenin in immortalized human mammary epithelial cells
Four groups, three biological replicates per group. shCntrl expressing cells are the control group

first: Piyush

last: Gupta

first: Sendurai

last: Mani

last: Yang

first: Eric

last: Lander

first: Robert

last: Weinberg


title: Halobacterium NRC-1 oxygen, light and vng0019h perturbation

status: Public on Jan 03 2008

city: Seattle

first: Marc

last: Facciotti

address: 1441 North 34th Street

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng0019h was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation

overall_design: 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.


title: Halobacterium NRC-1 oxygen, light and kinA2 perturbation, experiment 2

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of kinA2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and zim perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of zim was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and vng1296C perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng1296C was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen and light  perturbation

summary:
A 50ml culture of Halobacterium NRC-1 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response


title: Halobacterium NRC-1 oxygen, light and htr8 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of htr8 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and kinA2 perturbation


title: Halobacterium NRC-1 oxygen, light and htr1 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of htr1 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and boa4 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of boa4 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and phoR perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of phoR was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and ark perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of ark was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and gap perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of gap was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and sop2 perturbation, experiment 2

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of sop2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and vng0750C perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng0750C was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and htlD perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of htlD was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and afsQ2 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of afsQ2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and sop2 perturbation


title: Halobacterium NRC-1 oxygen, light and phr2 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of phr2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and bop perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of bop was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and boa1 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of boa1 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 Diurnal experiment

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


title: Halobacterium NRC-1 oxygen, light and phr1/phr2 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletions of phr1 and phr2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Genome-wide expression profiling of cells infected with control or RPS14 shRNAs

status: Public on Jan 17 2008

first: Pablo

last: Tamayo

address: 3855 Health Sciences Drive MC 0658

institute: UCSD

summary:
We performed genome-wide expression profiling of cells infected with control or RPS14 shRNAs.
Keywords: controls vs. shRNA treated

overall_design: The purpose of the dataset is to profile analyze the effect of silencing RPS14

first: Benjamin

last: Ebert


title: Halobacterium NRC-1 oxygen, light and phr1 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of phr1 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation

first: Min

last: Pan


title: Halobacterium NRC-1 oxygen, light and vng2334C perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng2334c was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 oxygen, light and ura3 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3  was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1 General transcription factor perturbation

summary:
Halobacterium cells, specified general transcription factor knock-out strains or plasmid expressed 6-His tagged general transcription factor strains, were grown to mid-log phase.  RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  .  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method. Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: genetic perturbation

overall_design: each knockout or perturbed expression strain was analyzed at a single point during growth.  This sample was analyzed on duplicate microarrays as a dye flip (2 microarrays per sample).


title: Halobacterium NRC-1 Diurnal experiment Light 2

summary:
The wild type strain of Halobacterium salinarium strain NRC-1 was used for the diel growth experiments.  For experiment, cultures were started at an OD >> 0.001.  Cultures were grown anaerobically at a temperature of 38° C under light:dark cycles (12:12 hrs) for 120 hours then grown under constant light.  Average light intensity was 150 μE/m2/sec. Time course sampling began 84 hours into the light:dark phase.  Samples were collected every 3 hours for 72 hours.   At each time point, culture was withdrawn by syringe and replaced with nitrogen gas.  Aliquots of the culture were centrifuged and the cell pellet flash-frozen in a dry ice/ethanol bath after decanting the supernatant.
RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  For this experiment 3 μl of ULYSIS Alexa Fluor 594 and 6 μl of 660 dyes (Molecular Probes) were used for labeling.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.  Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response

overall_design: 25 conditions were analyzed on duplicate arrays (50 total microarrays) as dye-flips.

first: Kenia

last: Whitehead


title: Halobacterium NRC-1 Diurnal experiment Dark 3

summary:
The wild type strain of Halobacterium salinarium strain NRC-1 was used for the diel growth experiments.  Culturing from colony was done under constant light in a liquid Complete Medium (CM; at 37 ºC with shaking at 220 rpm).  For experiment, cultures were started at an OD = 0.005.  Cultures were grown aerobically (shaking at 120 rpm) and a temperature of 37° C under light:dark cycles (12:12 hrs) for 72 hours then grown in complete darkness.  Light intensity was 150 μE/m2/sec.  Time course sampling began after the 72 hour light:dark phase.  A second culture was also sampled as a control and was grown under complete darkness (no light:dark cycle) before sampling began.
Samples from both the experimental and control cultures were collected after 83 hours of exposure to the light:dark cycle every 1 to 3 hours for another 25 hours.   Aliquots of the cultures were centrifuged and the cell pellet flash-frozen in liquid nitrogen after decanting the supernatant. RNA extractions were performed using the Stratagene Absolute RNA kit and RNA quality checked with the Agilent Bioanalyzer and with PCR.  Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1. Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 5 μg of RNA from the sample and reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.  Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response

overall_design: 24 conditions were analyzed on duplicate microarrays as dye-flips (48 total microarrays).

first: Nitin

last: Baliga


title: Halobacterium NRC-1 Diurnal experiment Dark 2

summary:
The wild type strain of Halobacterium salinarium strain NRC-1 was used for the diel growth experiments.  Culturing from colony was done in a liquid Complete Medium (CM; at 42 ºC with shaking at 100 rpm).  For experiment, cultures were started at an OD >> 0.001.  Cultures were grown aerobically (shaking at 100 rpm) and a temperature of 42° C under light:dark cycles (12:12 hrs) for 72 hours then grown in complete darkness.  Light intensity was 150 μE/m2/sec.
Time course sampling began after the 72 hour light:dark phase.  Samples were collected every 1 to 3 hours for 65 hours.   Aliquots of the culture were centrifuged and the cell pellet flash-frozen in a dry ice/ethanol bath after decanting the supernatant. RNA extractions were performed using the Stratagene Absolute RNA kit and RNA quality checked with the Agilent Bioanalyzer and with PCR.  Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1. Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method. Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response

overall_design: 18 conditions were assayed on duplicate arrays (36 total microarrays) as dye flips.


title: Halobacterium NRC-1 Diurnal experiment Dark 1

summary:
The wild type strain of Halobacterium salinarium strain NRC-1 was used for the diel growth experiments.  Culturing from colony was done in a liquid Complete Medium (CM; at 42 ºC with shaking at 100 rpm).  For experiment, cultures were started at an OD << 0.001.  Cultures were grown aerobically (shaking at 100 rpm) and a temperature of 42° C under light:dark cycles (12:12 hrs) for 72 hours then grown in complete darkness.  Light intensity was 150 μE/m2/sec.  Time course sampling began after the 72 hour light:dark phase.
Samples were collected approximately every 4 hours for 68 hours.   Aliquots of the culture were centrifuged and the cell pellet flash-frozen in a dry ice/ethanol bath after decanting the supernatant. RNA extractions were performed using the Stratagene Absolute RNA kit and RNA quality checked with the Agilent Bioanalyzer and with PCR.  Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1.  Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.
Keywords: environmental response

overall_design: A total of 18 conditions were assayed on duplicate microarrays (total 36 microarrays) as dye flips.


title: Halobacterium NRC-1 oxygen, light and htr2 perturbation

summary:
A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of htr2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions.  Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively.  Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively.  Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light.

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility.  The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference.  RNA from the final time point of a replicate experiment was used as the reference.  Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip).  Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: environmental response, genetic perturbation


title: Halobacterium NRC-1, H2O2 Stress Response

summary:
50mM H2O2 was added to mid-log phase Halobacterium NRC-1 cultures. After
constant stress of H2O2 for 30 minutes, cultures were spun down and
pellets were resuspended in same volume of GN101 media. Samples for RNA
preparation were collected during recovery time points at 0, 10, 20, 30,
40, 60 and 120 minutes.
Keywords: stress response

overall_design: 16 samples (8 exposed to H2O2 and 8 non-exposed controls) were each hybridized on duplicate arrays (as dye-flips) against the same standard control sample.