title: Transcriptome analysis of the phytobacterium Xylella fastidiosa growing under xylem-based chemical conditions

status: Public on Dec 30 2006

city: Santo André

first: Luiz

last: Nunes

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

institute: UFABC - Universidade Federal do ABC

summary:
Xyllela fastidiosa (Xf) is a xylem-limited bacterium responsible for important plant diseases, such as citrus variegated chlorosis (CVC) in Brazil and grapevines Pierce´s disease in the USA. One intriguing aspect of this microorganism is its capacity to grow in an extremely harsh environment such as the xylem, mainly composed of water, minerals and few organic salts. In vitro growth of Xf cells in chemically-defined media that mimic xylem fluid has been recently achieved, allowing more detailed studies of metabolic processes used by xylem-dwelling bacteria to thrive in such a nutrient-poor environment. We employed microarray hybridization experiments to compare the transcriptomes of Xf cells grown in 3G10-R, a medium that resembles grape sap and in Periwinkle Wilt (PW), the complex medium traditionally used to cultivate Xf. We identified 317 transcripts modulated in response to growth in either of the two media. Some of these genes seem to be involved in plant colonization, virulence and competition with other microorganisms, and have also been shown, in independent studies, to be up-regulated in cells directly isolated from the xylem of infected plants. Xf cells also show an increase in aerobic respiration when cultivated in PW, which can be associated with enhanced bacterial growth rates. This finding raises the question of weather such a metabolic switch might be related to the onset of CVC in infected plants, when Xf population seems to increase dramatically.
Keywords: Diefential growth conditions

overall_design: To evaluate and compare the bacterial transcriptome profiles from bacteria cultured in PW and 3G10R media, bacterial cultures were  harvested for total RNA extraction at day 3 (PW) and day 13 (3G10R), which allowed us to compare bacterial cultures grown into similar cellular densities. Samples from the resulting RNAs were then used in competitive hybridizations against Xf microarrays. Replicated experiments were performed with two independent RNA preparations from cells cultivated in each medium and since each microarray carried two replicas of each spotted gene, we ended up with a series of 8 independent readings for each gene present in the microarrays. Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with median values lower than the median local background plus two Standard Deviations have been flagged and excluded from further analyses. Replicated experiments were performed with two independent RNA preparations from cells cultivated in each medium. For each pair of RNA preparations, two independent hybridizations were performed, with dye swaps within each pair. The results from each hybridization were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array. Finally, the results from each individual experiment were loaded into the software TIGR Multi-Experiment Viewer (TMEV), v.3.01. Experiments were then normalized and genes that displayed statistically significant modulation were identified with the aid of the one-class option of the Significance Analysis of Microarrays (SAM) test, described by Tusher et al. (2001). The δ factor of the SAM test was adjusted to guarantee a False Discovery Rate (FDR) < 1.

first: Regina

last: Oliveira


title: Yeast FAIRE_BY4741 on Oligo Arrays

status: Public on Aug 11 2006

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Department of Biology

country: USA

institute: University of North Carolina at Chapel Hill

type: Genome binding/occupancy profiling by genome tiling array

summary:
The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence.
Keywords: FAIRE

overall_design: The yeast strain BY4741 was subjected to FAIRE, followed by microarray detection on higher-resolution oligonucleotide arrays.

first: Gregory

middle: J

last: Hogan

first: Cheol

middle: K

last: Lee


title: DNaseI/Array GM06990

status: Public on Jul 27 2006

city: Seattle

first: Michael

middle: Scott

last: Kuehn

state: WA

address: 1705 NE Pacific St #K-357

department: Genome Sciences

institute: University of Washington

summary:
The goal of this study was to map DNaseI sensitivity and DNaseI hypersensitive sites over the ENCODE regions in human lymphoblastoid cells (GM06990, Coriell).
Keywords: DNase/Array

overall_design: DNA fragments released from DNaseI cut sites in nuclear chromatin were collected and hybridized to the Nimblegen ENCODE array.  DNaseI-fragmented naked DNA was used as a control.


title: Expression analysis of hns mutant Salmonella

status: Public on Jun 08 2006

first: William

middle: Wiley

last: Navarre

address: 1959 NE Pacific Street Room K455

department: Laboratory Medicine

summary:
Transcriptome analysis of two independently derived hns mutants compared to an isogenic wild-type Salmonella (strain 14028s - lab ID# WN153).  Note: both the wild-type and hns strains carry an additional mutation in the rpoS locus (encoding the stationary phase sigma factor) resulting in a deletion of amino acids 61-65 that diminish its activity.
Keywords: cell type comparison

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

platform_organism:
Salmonella
Salmonella enterica

overall_design:
Comparison of wild-type Salmonella typhimurium to isogenic hns mutants.  Strains were grown to OD 2.0 (600nm), before RNA was harvested.  cDNA was labeled with Cy3 or Cy5 fluorophores incoroporated during reverse transcription.  The array was hybridized with a standard Cy3/Cy5 dye-swap protocol with the exact conditions outlined in the heading for each of the samples.

The data in this series represents four biological replicates, with 6 technical replicates for each biological replicate (3 for each of 2 dye-swaps). Two of the biological replicates compare hns-mutant strain WN342 to the wild-type.  Two of the biological replicates compare hns-mutant strain WN341 to the wild-type.  This was done to account for the possibility that suppressor mutations might arise in the slower growing hns strain.  WN341 and WN342 were thought to be identical but later analysis revealed that WN341 had acquired a large deletion in the pagC/pagD region which should be accounted for when looking at the data.

middle: W

first: Steffen

last: Porwollik

first: Yipeng

last: Wang

first: Henry

last: Rosen

last: McClelland

first: Stephen

last: Libby

first: Ferric

middle: C

last: Fang


title: Sex-dependent and STAT5b-dependent Liver Gene Expression

status: Public on Jul 26 2006

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary:
A series of dual-channel gene expression profiles obtained using Rosetta/Merck Mouse TOE 75k microarrays was used to examine the sex-dependent and STAT5b-dependent differences in gene expression in adult mouse liver. This series is comprised of 4 pools of 3 randomly chosen independent wildtype male and female mouse liver cDNA samples and 4 pools of 3 randomly chosen independent STAT5b-deficient male and female mouse liver cDNA samples, totaling 16 pools. The pools were paired randomly to generate 4 comparisons of M-WT:F-WT, M-WT:M-KO, F-KO:F-WT, and F-KO:M-KO.  Comparison of the set of sex-dependent genes with the set of genes responsive to the loss of STAT5b in males shows that 75% of the sex-specific genes were also regulated by STAT5b in males.  Only 20% of the sex-specific genes retained sex-specificity in the absence of STAT5b, indicating a large role for STAT5b in sex-specific liver gene expression.
Keywords: genetic knockout and sex response

overall_design: A pool of cDNA from 3 mice is Cy3-labeled and compared to another pool of cDNA from 3 mice that is Cy5-labeled.  The pools are then dye-swapped and compared again.  The two pairs of data are averaged together, the averages are normalized across the fluorescent reverse pairings, and the log2 value is reported for each average as well as the anti-log.  This is replicated 3 times with independent pools of cDNA for each pair of conditions being compared.  There are a total of 4 pairs of conditions compared for a grand total of 12 samples.

first: Karl

middle: H

last: Clodfelter

first: Minita

middle: G

last: Holloway

first: Paul

last: Hodor

first: Soo-Hee

last: Park

last: Ray


title: MYC binding sites in HeLa cells

status: Public on Mar 09 2006

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

summary:
MYC binding sites determined in HeLa cells using ChIP-chip
Keywords: ChIP-chip

overall_design: ChIP-chip

first: Shally

last: Xu

first: Peggy

last: Farnham

last: Singer

first: Roland

last: Green


title: Yeast FAIRE_Cell Cycle Study

first: Jason

last: Lieb

overall_design: We arrested cells in late G1 using the mating pheromone α-factor, released the cells into fresh YPD, and collected synchronized cells at seven time points spanning a single cell cycle. The collected time-point samples were then subjected to FAIRE, followed by microarray detection.

first: Gregory

last: Hogan

first: Cheol

last: Lee


title: HeLa E2F1 ChIP on 24,000 Promoters

status: Public on Mar 03 2006

summary:
2 biological replicates (array 59066 and array 64695) of HeLa E2F1 ChIP vs matched Total DNA
Keywords: ChIP

overall_design: 2 replicates allow comparison of signals, partial determination of E2F1 role


title: HeLa E2F1 ChIP-chip experiments

status: Public on Feb 28 2006

summary:
These are three biological replicates. HeLa cells were crosslinked on separate days. In each case, a matched total from the same crosslinking was produced in parallel. Amplicons were made from each and hybridized onto ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green.
Keywords: ChIP-chip

overall_design:
Goal was determination of E2F1 binding sites in HeLa cells by using ChIP-chip methodology.
See Farnham Lab website for downloadable protocol for ChIP or supplementary file (Chip_protocol.txt) below.
NimbleGen performed all array processing. See NimbleGen website for information on array procedures.

first: Mike


title: Expression Profiling of MAP Kinase-Mediated Meiotic Progression in C. elegans

status: Public on Aug 01 2006

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

summary:
A unique allele of MAP kinase, mpk-1(ga111), displays a reversible, temperature-sensitive, tissue-specific defect in progression through meiotic prophase I.  We performed gene expression profiling on mpk-1(ga111) animals at multiple times after shift to permissive temperature to identify candidate downstream effectors of MPK-1 signaling in the germline.  This analysis delineated a cohort of genes whose expression requires MPK-1 (MAP kinase) signaling in germ cells in the pachytene stage of meiosis I.
Keywords: Timecourse of C. elegans mpk-1 mutants

overall_design: We analyzed six timepoints after MAP kinase mpk-1(ga111) mutants were shifted to a temperature permissive for meiotic progression.  Each timepoint was sampled in triplicate.  Control (mpk-1+) animals were sampled in triplicate at the beginning and end of the time series.  All samples were compared to a common reference sample made of a mixture of both control samples.

first: Stefanie

last: Leacock


title: Invasive lobular and ductal carcinomas of the breast

status: Public on Jan 06 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
This set of experiments includes 38 IDCs, 21 ILCs, 2 lymphnode metastases, and 3 normal breast samples. It is designed to compare gene expression profiles of IDCs and ILCs. Total RNAs from all samples were isolated using TRIzol, amplified using optimized T7 linear amplification protocol, and labeled with Cy5. Stratagen Universal Human Reference RNA was amplified the same way and labeled with Cy3.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Youngran

last: Ji

first: Hongjuan

last: Zhao

first: Anita

last: Langerod


title: An Integrated Fingerprinting platform for the study of Chinese Medicineal Herb Cordyceps sinensis

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

summary:
The traditional Chinese medical formulas have been in clinical use for thousands of years and their therapeutic effects were documented in ancient Chinese pharmacopoeias. High-throughput biological analysis on cell line models has been demonstrated as a useful alternative to elucidate intricate molecular mechanisms associated with drug actions in a number of pharmacogenomic studies. This microarray study is aimed to provide a reliable and feasible means to explore the healing philosophy of Chinese herbalism.
Keywords: Pharmacogenetics

overall_design: Loop-designed microarray experiments were performed in our study. Eight samples are arranges as a double loop, with eight microarray slides for each loop. Four technical replicates were performed for each sample and the dye assignments were balanced. One sample was duplicated as an internal control. This set of loop-designed microarray experiment contains a control untreated sample and seven herbal drug-treated samples that include a repeated sample as internal control.

first: MinLung

last: Tsai

first: YuLing

last: Hsieh


title: ENCODE ChIP-chip for BAF170 on Human Hela S3 Cells

status: Public on Nov 04 2005

city: Woodbridge

first: Can

last: Bruce

address: 5 Chestnut Lane

institute: Sciomix

summary:
BAF170 ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaced every 38bps (overlapping by 12nts).  Goal is to identify binding sites for BAF170.
Keywords = Transcription Factor Binding, BAF170, ChIP-chip, Human, Genome Tiling Arrays
Keywords: ChIP-chip

overall_design: DNA from immunoprecipitated chromatin or total genomic DNA was hybridized to a Nimblegen ENCODE tiling array containing overlapping 50 nt oligonucleotide probes.  Samples are four biological replicates.

first: Ghia

last: Euskirchen

first: Zhengdong

last: Zhang

first: Joel

middle: S

last: Rozowsky

middle: B

last: Gerstein

first: Michael

middle: P

last: Snyder


title: ENCODE ChIP-chip for BAF155 on Human Hela S3 Cells

summary:
BAF155 ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaced every 38bps (overlapping by 12nts).  Goal is to identify binding sites for BAF155.
Keywords = Transcription Factor Binding, BAF155, ChIP-chip, Human, Genome Tiling Arrays
Keywords: ChIP-chip

first: Mark


title: Analysis of mRNA expression profiles in bovine endometrium during the pre-attachment period using monocygotic twin pairs

status: Public on Dec 07 2005

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary:
To get new insights into molecular mechanisms underlying the embryo-maternal communication during the pre-implantation period endometrium samples from Day 18 pregnant vs. non-pregnant twin cows were analyzed using a combination of subtracted cDNA libraries and cDNA array hybridization.
Keywords: Comparison of endometrium of pregnant versus control animals

overall_design: Endometrial tissue samples of day 18 pregnant cows (ET, n=5) were compared to non-pregnant controls (ST, n=5). Pair wise comparison was done within twin pairs (one pregnant twin versus the corresponding control twin). First, subtracted cDNA libraries were produced enriched for cDNAs of genes upregulated in pregnant animals starting from endometrial tissue samples of one twin pair (405/406). Overall 4608 clones of every library were picked and PCR-amplified cDNA fragments were spotted on three arrays. These three arrays were then simultaneously hybridized with P-33 labeled probes derived from the 10 tissue samples. cDNA clones with an upregulation of 2-fold or higher in at least 4 out of five twin pairs were set as interesting. Signals of these cDNA clones were manually evaluated to eliminate false-positive signal differences. These cDNA clones and some additional interesting cDNA clones were sequenced.

first: Claudia

last: Klein

first: Susanne

middle: E

last: Schmidt

first: Horst-Dieter

last: Reichenbach

first: Helmut

last: Blum

first: Eckhard

last: Wolf


title: Gene Expression Profiles with Common Translocations in Acute Myeloid Leukemia (AML) using SAGE

status: Public on Dec 01 2005

city: Evanston

first: San Ming

last: Wang

state: IL

address: 1001 University Place

department: Center for Functional Genomics

institute: ENH Research Institute, Northwestern University

summary:
SAGE was used to profile gene expression in leukemic myeloid progenitor cells of AML patients with t(8;21), t(15;17), t(9;11) and inv(16).
Keywords: SAGE analysis of gene expression in leukemic myeloid progenitor cells isolated from bone marrow

overall_design: Bone marrow cells from 4 patients with de novo t(9;11), 3 with treatment-related t(9;11), and 5 each with inv(16), t(15;17), t(8;21) were used for the study. Each sample contained at least 75% affected  cells with no other chromosome abnormalities at cytogenetic level. Mononuclear cells were purified from bone marrow cells for each sample, and CD15+ myeloid progenitor cells were isolated from these mononuclear cells. Poly A+ RNA were isolated from CD15+ myeloid progenitor cells of each sample for SAGE tag collection.

first: Sanggyu

last: Lee

first: Jianjun

last: Chen

first: Guolin

last: Zhou

first: Run

middle: Z

last: Shi

first: Gerrard

last: Bouffard

first: Masha

last: Kocherginsky

first: Xijin

last: Ge

first: Miao

last: Sun

first: Nimanthi

last: Jayathilaka

first: Yeong

last: Kim

first: Neelmini

last: Emmanuel

last: Bohlander

last: Minden

first: Paul

last: Liu

first: Justin

last: Kline

first: Ozden

last: Ozer

first: Richard

last: Larson

first: Michelle

last: LeBeau

first: Eric

last: Green

first: Jeffery

last: Trent

first: Theodore

last: Karrison

first: San

middle: M

last: Wang (Correspondence)

first: Janet

last: Rowley (Correspondence)


title: Yeast FAIRE_testing wild-type and mutant strains

first: Jason

middle: D

last: Lieb

overall_design: Two wild-type strains, eleven strains harboring deletions for histone modification enzymes, and four histone tail deletion strains were subjected to FAIRE.

first: Gregory

last: Hogan

first: Cheol

last: Lee


title: The expression profiles of promastigotes and axenic amastigotes in Leishmania donovani

status: Public on Dec 20 2005

city: Shanghai

first: qiaoli

last: li

address: 800 Dongchuan Rd.

department: School of Life Sciences

country: China

institute: Shanghai Jiao Tong University

summary:
In this study, we examined the transcriptome of Leishmania donovani promastigotes and axenic amastigotes to identify differentially regulated mRNAs utilizing the serial analysis of gene expression
Keywords: stage differentiation; axenic amastigotes

overall_design: Our approach was to identify Leishmania genes developmentally expressed during the promastigote and amastigote stages. Our assumption was that genes which expressed a difference between the promastigote and amastigote stages were likely to be essential to the transformation and the survival of the parasite within its human host.

first: Qiaoli

last: Li

first: Yangxing

last: Zhao

first: Zhiming

last: Zhang

first: Wangjie

last: Xu

first: Ming

last: Lu

first: Zhaoxia

last: Wang

first: Zhongdong

last: Qiao


title: ENCODE ChIP-chip for FOS on Human Hela S3 Cells

status: Public on Oct 19 2005

first: Can

last: Bruce

summary:
FOS ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts).  Goal was to identify FOS-binding sites.
Keywords = Transcription Factor Binding, FOS, ChIP-chip, Human, Genome Tiling Arrays
Keywords: ChIP-chip

overall_design: DNA from immunoprecipitated chromatin or total genomic DNA was hybridized to a Nimblegen ENCODE tiling array containing overlapping 50 nt oligonucleotide probes.  Samples are three biological replicates.

first: Peter

last: Kraus

first: Ghia

last: Euskirchen

first: Zhengdong

first: Joel

last: Rozowsky

first: Mark

last: Gerstein

first: Michael

last: Snyder


title: Gene expression diversity among Mycobacterium tuberculosis clinical isolates

status: Public on Aug 26 2005

last: Stanford Microarray Database

summary:
While several groups, including our own, have examined variability of M. tuberculosis at the DNA level, this is the first systematic survey of variability in mRNA expression among clinical isolates of M. tuberculosis. Genes whose expression varies among isolates when assayed under a single growth condition may make poor drug targets and vaccine antigens and may affect molecular diagnostics, so they can be used to narrow down lists of candidate molecules. Because the measurement of gene expression is extremely sensitive to environmental conditions, comparison of gene expression is labour intensive. In this study, we surveyed 12 strains. These strains are a subset of those for which we have already published genomic deletion information (Kato-Maeda et al., 2001). In order to ensure maximum reproducibility of the experiments and avoid complications caused by differences in growth conditions, we measured gene expression under well-controlled in vitro conditions. Our aims were to provide an overview of gene expression variability among clinical isolates under a single growth condition and to test whether gene functional classes are related to variability in expression.
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design:
Biological Replicate
Computed

first: Qian

last: Gao


title: ENCODE ChIP-chip for JUN on Human Hela S3 Cells

summary:
JUN ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaced every 38bps (overlapping by 12nts).  Goal is to identify binding sites for JUN.
Keywords = Transcription Factor Binding, JUN, ChIP-chip, Human, Genome Tiling Arrays
Keywords: ChIP-chip


title: Prion infected ScN2a and GT1

status: Public on Aug 24 2005

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
A comparison of prion infected and non-infected samples from neuroblastoma cells (N2a), and a
comparison of prion infected and non-infected samples from hypothalmus cells (GT1).
11 dual-color DNA-chip hybridizations of cDNAs were made.
Keywords: other

first: Alex

last: Greenwood

first: Marion

last: Horsch

first: Johannes

last: Beckers


title: Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome

status: Public on Jul 26 2005

summary:
The chromosomes of several widely used laboratory derivatives of Streptomyces coelicolor A3(2) were found to have 1.06 Mb inverted repeat sequences at their termini (i.e. long-terminal inverted repeats; L-TIRs), which are 50 times the length of the 22 kb TIRs of the sequenced S. coelicolor strain M145. The L-TIRs include 1005 annotated genes and increase the overall chromosome size to 9.7 Mb. The 1.06 Mb L-TIRs are the longest reported thus far for an actinomycete, and are proposed to represent the chromosomal state of the original soil isolate of S. coelicolor A3(2). S. coelicolor A3(2), M600 and J1501 possess L-TIRs, whereas approximately half the examined early mutants of A3(2) generated by ultraviolet (UV) or X-ray mutagenesis have truncated their TIRs to the 22 kb length. UV radiation was found to stimulate L-TIR truncation. Two copies of a transposase gene (SCO0020) flank 1.04 Mb of DNA in the right L-TIR, and recombination between them appears to generate strains containing short TIRs. This TIR reduction mechanism may represent a general strategy by which transposable elements can modulate the structure of chromosome ends. The presence of L-TIRs in certain S. coelicolor strains represents a major chromosomal alteration in strains previously thought to be genetically similar.
A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s).
Keywords: dose_response_design

first: Nitsara

last: Karoonuthaisiri

first: David

last: Weaver

first: Ryan

last: Fong

first: Mai-Lan

last: Ho


title: loss of paradormancy in underground adventitious buds of leafy spurge (Euphorbia esula)

status: Public on Jun 15 2005

city: Fargo

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary:
This study is a time course of growth induction (0, 12, 24, 48, and 72 hrs) following the breaking of paradormancy in underground buds of the perennial weed leafy spurge (Euphorbia esula).
Keywords: Time course, growth induction, apical dominance, paradormancy, root buds, leafy spurge

platform_organism:
Manihot esculenta
Euphorbia esula

overall_design: Two independently isolated samples for each time point was compared to a single control sample (also independently isolated) collected from paradormant underground adeventitious buds. Dye swaps were done for each time point (not each biological replicate).

first: James

middle: V

last: Anderson

first: Mauricio

last: Soto-Suárez


title: ENCODE (HG17) region-wide binding of a few antibodies in IFg treated and untreated HeLa cells using nimblegen array

city: San Diego

first: Chunxu

last: Qu

department: Gene Regulation

institute: Ludwig Institute for Cancer Research

summary:
Genome-wide location analysis of trimethyl-K4 histone H3 and RNA polymerase II binding in interferon gamma-induced for 30 minutes HeLa cells and uninduced HeLa cells was done using 50mer oligonucletide probes at 38bp intervals tiling over non-repetitive ENCODE regions (HG17, NCBI build 35).
Keywords: ChIP-chip

overall_design: There are three replicates for each marker at each state.

first: Bing

last: Ren


title: Prediction of drug sensitivity

status: Public on Jul 30 2005

summary:
Tumor cell lines and drug-resistant counterparts.  These data support the publication Gyorffy et al, Oncogene 2005 (July), Prediction of doxorubicin sensitivity in breast tumors based on gene expression profiles of drug-resistant cell lines correlates with patient survival.
We contrasted the expression profiles of 13 different human tumor cell lines of gastric (EPG85-257), pancreatic (EPP85-181), colon (HT29) and breast (MCF7 and MDA-MB-231) origin and their counterparts resistant to the topoisomerase inhibitors daunorubicin, doxorubicin or mitoxantrone. We interrogated cDNA arrays with 43 000 cDNA clones ( approximately 30 000 unique genes) to study the expression pattern of these cell lines.
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
Keywords: cell_type_comparison_design

overall_design: Using regression correlation

first: Mitchell

last: Garber


title: RIZ1 repression is associated with insulin-like growth factor-1 signaling activation in chronic myeloid leukemia...

status: Public on Jun 04 2005

city: Saskatoon

first: Matthew

last: Bainbridge

state: SK

address: 20 Campus Drive

department: Computer Science

institute: U of Saskatchewan

summary:
Replicate experiments with dye flips to observe the effect of forcing the expression of riz1 (prdm2) in erythroleukemia cell line k562.
Keywords: repeat sample

first: Wei-feng

last: Dong

first: Naoto

last: Takahashi

first: Andrea

last: Hull

first: Elodie

last: Pastural

first: Shi

last: Huang

first: John

middle: F

last: DeCoteau

first: C

middle: R

last: Geyer


title: ENCODE: GWLA analysis of a few promoter and enhancer markers in HeLa cells

status: Public on Jun 03 2005

summary:
GWLA analysis of a few promoter and enhancer markers in Hela cells.
Keywords: ChIP/chip

overall_design: Using tiling array covered non-repetitive encode regions, ChIP/chip was done using chromatin extracted from both induced and uninduced HeLa cells and a few antibodies.

first: Nate

last: Heintzman

first: Sara

last: van Calcar

first: Rhona

last: Stuart


title: ENCODE: GWLA analysis of SUZ12 and triMeH3K27 binding in HeLa cells

status: Public on Jun 12 2005

summary:
Genome-wide location analysis of SUZ12 and  TriMeH3K27 binding in HeLa  cells (human cervix epithelial adenocarcinoma cells) using RenLab ENCODE PCR tiling array.
Keywords: ChIP-chip

overall_design: For each antibody, there are three replicates.

first: Kun

last: Wang


title: Characterization of human regulatory T cells (TReg)

status: Public on Jan 31 2006

city: Braunschweig

first: Susanne

last: Pfoertner

address: Mascheroder Weg 1

institute: German Research Centre for Biotechnology (GBF)

summary:
Here, we describe the development and application of a new oligonucleotide microarray to analyze human TReg cells. Using whole genome transcription data from human and mouse TReg cells we have compiled a unique microarray consisting of 350 TReg specific genes (Human TReg Chip). Highly purified CD4+CD25+ and CD4+CD25- T cells were isolated from peripheral blood of 11 healthy volunteers and used for expression profiling to highlight the impact of molecular changes.
Keywords: cell type comparison

overall_design: 11 healthy volunteers; at least duplicates, mostly triplicates --> overall: 59 samples


title: ENCODE ChIP-chip for STAT1 on Human Hela S3 Cells

status: Public on May 27 2005

first: Joel

last: Rozowsky

address: 266 Whitney Ave, Bass 437

department: Molecular Biophysics & Biochemistry

institute: Yale University

summary:
STAT1 ChIP-chip performed on Human Hela S3 Cells for three different platforms. Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts) (5 biological replicates), custom maskless array tiling most of ENCODE with 50mer oligonucleotides end-to-end (3 biological replicates) and custom maskless array tiling most of ENCODE with 36mer oligonucleotides end-to-end (2 biological replicates). The chromatin-immunoprecipitation protocol is the same for all samples, however the labelling and hybridization protocols differ between Nimblegen and custom maskless arrays.
Keywords = Transcription Factor Binding, STAT1, ChIP-chip, Human, Genome Tiling Arrays
Keywords: other

first: Ghia

last: Euskirchen

first: Stephen

last: Hartman

first: Sherman

last: Weissman

first: Mark

last: Gerstein

first: Michael

last: Snyder


title: ENCODE Transcript Mapping for Human Placental Poly(A)+ RNA

status: Public on May 18 2005

type: Expression profiling by genome tiling array

summary:
Transcript Mapping on Affymetrix ENCODE arrays for 3 different biological replicates of Placental Poly(A)+ RNA (each with either 2 or 3 technical replicates)
Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays
Keywords: other

first: Zheng

last: Lian

first: Philipp

last: Kapranov

first: Olof

last: Emanuelsson

first: Ugrappa

last: Nagalakshmi

first: Alex

last: Urban

first: Jill

last: Cheung

first: Tom

last: Gingeras


title: ENCODE: Histone H3 acetylation and K4 methylation in IMR90 cells

status: Public on Dec 16 2004

first: Chunxu

last: Qu

summary:
ChIP-on-Chip data using histone H3 acetylation antibody and H3K4 methylation antibody. Each in triplicate.
Keywords: other

first: Tae

last: Kim

first: Leah

middle: O

last: Barrera

first: Sara

last: van Calcar

first: Bing

last: Ren


title: A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells

status: Public on Apr 21 2005

type: Genome binding/occupancy profiling by array

summary:
Genome-wide location analysis of transcription factor of c-Myc and Max was conducted using RenLab Hu6K array in Daudi cells.  In comparison, the GWLA was also done for general transcription factor RNA polymerase II and TAF1, and sequence specific transcription factor E2F1 in the same cell line.
Keywords = GWLA
Keywords = RenLab
Keywords = Hu6K
Keywords = Myc
Keywords = Max
Keywords: other

first: Zirong

last: Li

first: Webster

middle: K

last: Cavenee

middle: Q

last: Zhang


title: Normal and injured liver sinusoidal endothelial cells

status: Public on Oct 01 2004

city: Tokyo

first: Hidenori

last: Nonaka

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

country: Japan

institute: University of Tokyo

summary:
Comparison of C57BL/6J 8-10 weeks male mouse liver sinusoidal endothelial cells (LSEC) from normal liver and from liver injured by carbon tetrachloride administration.
Keywords: other

first: H

first: Sumio

last: Sugano

first: Atsushi

last: Miyajima


title: NCI cDNA microarray-human 60 cell lines

status: Public on Nov 24 2004

city: Research Triangle Park

first: Jennifer

last: Fostel

institute: NIEHS

summary:
We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs.
Keywords: parallel sample

first: John

middle: N

last: Weinstein

first: Uma

middle: T

last: Shankavaram


title: SADE analysis of microdissected kidney

status: Public on Nov 14 2003

city: 91191 Gif/ Yvette Cedex

first: Jean-Marc

last: Elalouf

department: IBITEC-S

country: France

institute: CEA Saclay

summary: Libraries generated from microdissected kidney samples from the healthy pole of cancerous kidneys. Donors were from either sex. Libraries were  generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Danielle

last: Chabardès-Garonne

first: Arnaud

last: Méjean

first: Jean-Christophe

last: Aude

first: Lydie

last: Cheval

first: Antonio

last: Di Stefano

first: Marie-Claude

last: Gaillard

first: Martine

last: Imbert-Teboul

first: Monika

last: Wittner

first: Chanth

last: Balian

first: Véronique

last: Anthouard

first: Catherine

last: Robert

first: Béatrice

last: Ségurens

first: Patrick

last: Wincker

first: Jean

last: Weissenbach

first: Alain

last: Doucet


title: Cx expression profiling

city: Atlanta

first: Martin

last: Steinau

state: GA

institute: CDC

summary:
Microarray expression profiling of cervical exfoliated cells (10k genes)
Keywords: repeat sample

overall_design: We used whole genome microarrays (25,353 unique genes) to compare the transcription profiles from seven samples of normal exfoliated cells and one cervical tissue.

first: Daisy

last: Lee

first: Mangalathu

last: Rajeevan

first: Suzanne

last: Vernon

first: Mack

last: Ruffin

first: Elizabeth

last: Unger


title: 4 WT individual mice kidneys versus 5th WT kidney, their littermate

status: Public on Jul 27 2004

city: Munich - Neuherberg

first: Johannes

last: Beckers

state: Bavaria

address: Ingolstaedter Landstr. 1

institute: GSF - National Research Center

summary:
Every individual (W1-W4) was hybridised 4 times, including 2 dye swaps:
W1: 23573-23576;
W2: 23577-23580;
W3: 23581-23584;
W4: 23585-23588.
Only 2 of 4 hybridisations wer made at the same preparation
Keywords: parallel sample

first: Alexei

middle: L

last: Drobyshev

first: Isabelle

last: Frey


title: 4 Slc15a2 KO individual mice kidneys versus pool of 5 WT mice kidneys

summary:
Every individual kidney was hybridised 4 times including 2 dye swaps:
K1: 23557-23560
K2: 23561-23564
K3: 23565-23568
K4: 23569-23572
Only 2 of 4 hybridisations were made at one sample preparation.
Keywords: parallel sample


title: ENCODE Transcript Mapping for Total RNA from Human NB4 Cells untreated, treated with RA, and treated with TPA

status: Public on May 19 2005

city: New Haven

first: Joel

last: Rozowsky

summary:
Transcript Mapping on Affymetrix ENCODE arrays for Total RNA from 4 different samples (2 or 3 technical replicates of each). All of the four same NB4 samples have also been treated with Retanoic Acid (RA) (2 or 3 technical replicates of each). Three of the four same NB4 samples have also been treated with TPA (2 or 3 technical replicates of each). RA treated NB4 cells can be partially differentiated to Neutrophils and TPA treated NB4 cells can be differentiated to Monocytes.
Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays
Keywords: parallel sample

middle: S

first: Zheng

last: Lian

first: Philipp

last: Kapranov

first: Olof

last: Emanuelsson

first: Ugrappa

last: Nagalakshmi

first: Alex

last: Urban

first: Jill

last: Cheung

first: Sherman

last: Weissman

first: Mark

last: Gerstein

first: Tom

last: Gingeras

first: Michael

last: Snyder


title: ENCODE Transcript Mapping for Human Neutrophil (PMN) Total RNA

summary:
Transcript Mapping on Affymetrix ENCODE arrays for 10 different biological replicates of Neutrophil (PMN) Total RNA (each with 2 technical replicates). Each biological sample is from a different individual.
Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays
Keywords: other


title: Global analysis of RAR-responsive genes in the Xenopus neurula

status: Public on Mar 05 2005

city: Irvine

first: Yongchol

last: Shin

address: 4115 McGaugh Hall

department: Developmental and Cell Biology

institute: University of California, Irvine

summary:
Retinoid signaling is important for patterning the vertebrate hindbrain and midaxial regions. We recently showed that signaling through retinoic acid receptors (RARs) is essential for anteroposterior patterning along the entire body axis. To further investigate the mechanisms through which RARs act, we employed microarray analysis to investigate the effects of modulating RAR activity on target gene expression. We identified 334 upregulated genes (92% of which were validated) including known RA responsive genes, known genes that have never been proposed as RA targets and many hypothetical and unidentified genes (n = 166). 67 validated downregulated genes were identified including known RA responsive genes and anterior marker genes. The expression patterns of selected upregulated genes (n = 45) were examined at neurula stages using whole mount in situ hybridization. We found that most of these genes were expressed in the neural tube and many were expressed in anterior tissues such as neural crest, brain, eye anlagen, and cement gland. Some were expressed in tissues such as notochord, somites, pronephros and blood islands, where retinoic acid (RA) plays established roles in organogenesis. Members of this set of newly identified RAR target genes are likely to play important roles in neural patterning and organogenesis under the control of RAR signaling pathways and their further characterization will expand our understanding of RA signaling during development.
Keywords = retinoid
Keywords = microarray
Keywords = RAR
Keywords = neurula
Keywords = anteroposterior patterning
Keywords = and organogenesis
Keywords: repeat sample

first: Kayo

last: Arima

first: Jason

last: Shiotsugu

first: Ron

last: Niu

first: Bruce

last: Blumberg

first: Tetsuya

last: Koide


title: ENCODE: GWLA of TAF1, RNA PolII binding in four cell lines

status: Public on Sep 21 2004

first: Chunxu

last: Qu

summary:
Genome-wide location analysis of TAF1 and RNA polymerase II binding in ENCODE regions of IMR90, HCT116, HeLa and THP1 cell lines.  There are a total of 8 experiments, each with three replicates.
Details of chromatin immunoprecipitation and data analysis can be found at
Li Z, van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B (2003) A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. PNAS, 100:8184-8169.
Keywords: other

first: Tae Hoon

last: Kim

first: Leah

last: Barrera

first: Sara

last: van Calcar

first: Bing

last: Ren


title: Myoblast stimulation with angiotensin II

status: Public on Jul 28 2004

city: San Francisco

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

summary:
Quiescent C2C12 myoblasts and myoblasts that were stimulated with Angiotensin II for 12 h or 24 h
Keywords = Angiotensin II
Keywords: parallel sample

first: Myint

last: Hlaing


title: Gene expression of bovine embryo

city: Tsukuba City

first: Koichi

last: Ushizawa

state: Ibaraki

address: Ikenodai 2

department: Animal Science Department

institute: National Institute of Agrobiological Sciences

summary:
The objective of the present study was to use our own fabricated bovine embryo cDNA microarray to profile genome-wide expression patterns of genes during the implantation period. Duplicate readings were obtained by hybridization of a Cy3/Cy5 probe mixture for each sample. Data normalization was performed the local background intensity of each array spot was smoothed by the local weight regression (lowess) smoother and subtracted from spot intensity data. The subtracted intensity data were subjected to non-parametric regression and local variance normalization because non-parametric regression can reduce intensity-depended biases. Accuracy is improved, when compared to linear regression, if the points in the scatter plot of Cy3 vs. Cy5 are not distributed around a straight line.
Keywords = Gene expression
Keywords = embryo
Keywords = fetus
Keywords = fetal membrane
Keywords = implantation period
Keywords: time-course

first: Chandana

middle: B

last: Herath

first: Kanako

last: Kaneyama

first: Satoshi

last: Shiojima

first: Akira

last: Hirasawa

first: Toru

last: Takahashi

first: Kei

last: Imai

first: Kazuhiko

last: Ochiai

first: Tomoyuki

last: Tokunaga

first: Yukio

last: Tsunoda

first: Gozo

last: Tsujimoto

first: Kazuyoshi

last: Hashizume


title: Erbb2-transfected mice fibroblasts

status: Public on Jun 04 2004

first: Johannes

last: Beckers

summary:
Group of 5 experiments (including 2 independent cell preparations and 2 dye swaps) of Erbbr (Her2, Neu) transfected fibroblasts versus normal cells
Keywords: parallel sample

first: Sandra

last: Rieger

first: Barbara

last: Seliger


title: Eosinophils and basophils

status: Public on Feb 21 2004

first: Michael

last: Salazar

summary:
Ten male 4get mice were infected with N. brasiliensis and single-cell suspensions of total lung tissue were prepared 9 days after infection. Cells were stained for CD3, CD19, c-kit and CCR3 and sorted for CD3-CD19-c-kit-GFP+CCR3+SSChi (eosinophils) and CD3-CD19-c-kit- GFP+CCR3-SSClo (basophils) using a MoFlo high-speed cell sorter (Cytomation, Fort Collins, CO). Total RNA was isolated from 2 x 106 eosinophils and 1.75 x 105 basophils using the Total RNA Isolation Kit (Fluka, Buchs, Switzerland) and amplified by two rounds of in vitro transcription using the Amino Allyl MessageAmpTM aRNA kit (Ambion, Austin, TX). Universal Mouse Reference RNA (#740100; Stratagene, La Jolla, CA) was amplified in the same way. Aminoallyl-UTP was incorporated during the second round of amplification and 5 µg of amplified RNA was coupled to Cy3 and Cy5 fluorescent dyes (CyScribeTM dye labeling kit, Amersham Biosciences, Peapack, NJ). Probes were hybridized to spotted glass oligonucleotide (70-mer) arrays which cover just over 16,400 unique genes (Mouse Genome Set Version 2.0, Qiagen, Germany). The arrays were prehybridized in 1% BSA (Invitrogen), 5 x SSC, 0.1% SDS for 2 hr at 42°C, washed in water and hybridized with the Cy3/Cy5-labeled probes in 2.8 x SSC, 0.2% SDS, 0.6 mg/ml Cot-1 DNA (Invitrogen), and 0.8 mg/ml yeast tRNA, at 63°C for 45 hr. Slides were washed sequentially in 0.03%SDS/1 x SSC, 0.2 x SSC and 0.05 x SSC, dried and scanned on an Axon 4000B scanner using Genepix 3.0 software (Axon Instruments, Inc.). Data were normalized using the R package Bioconductor software and ?lowess? normalization on the pixel medians without background subtraction (Ihaka and Gentleman, 1996).
Keywords = Eosinophils
Keywords = Basophils
Keywords = Nippostrongylus
Keywords = Lung
Keywords = Type 2 immunity
Keywords: other

first: David

last: Voehringer

first: Kanade

last: Shinkai

first: Richard

last: Locksley


title: Differential Gene Expression by Memory T Helper Cells Bearing the Gut-Homing Receptor Integrin α4β7

status: Public on Feb 13 2004

summary:
This series represents mature CD4+ lymphocytes with high and low expression of integrin α4β7 isolated from human subjects.
Keywords = lymphocyte, integrin α4β7 , differential gene expression, microarray
Keywords: parallel sample

middle: J

last: Erle

first: Madeleine

middle: W

last: Rodriguez


title: 18h before puparium formation vs. puparium formation tissue comparisons

status: Public on Jul 23 2003

first: Tong-Ruei

last: Li

address: 333 Cedar St. Rm#NSB386

department: Department of Genetics

institute: Yale University School of Medicine

summary:
Samples at 18h before puparium formation were compared to samples at puparium formation for each the following tissues: epidermis with attached muscle, salivary gland, wing disc, midgut, and central nervous system.
Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development
Keywords: other

first: Kevin

middle: P

last: White


title: Midgut metamorphosis timecourse

summary:
A midgut reference sample is compared to midgut samples taken at various stages before (18h, 4h), at (0h), and after (2h, 3h, 4h, 5h, 6h, 8h, 10h, 12h) puparium formation.
Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development
Keywords: other


title: Whole animal vs. tissues at 18h before puparium formation

summary:
Comparisons between whole animal and epidermis with attached muscle, salivary gland, wing disc, midgut, and central nervous system tissues at approximately 18 hours before pupariation.
Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development
Keywords: other


title: Genome-wide regulation by TFIID and SAGA

status: Public on Feb 27 2004

city: Ithaca

first: B. Franklin

last: Pugh

email: fp265@cornell.edu, bfp2@psu.edu

state: NY

address: 465 Biotechnology Bldg.

department: Molecular Biology and Genetics

institute: Cornell University

summary:
TFIID and SAGA share a common set of TAFs, regulate chromatin, and deliver TBP to promoters.  Here we examine their relationship within the context of the Saccharomyces cerevisiae genome-wide regulatory network. We find that while TFIID and SAGA make overlapping contributions to the expression of all genes, TFIID function predominates at ~90% and SAGA at ~10% of the measurable genome.  Strikingly, SAGA-dominated genes are largely stress-induced and TAF-independent, and are down-regulated by the coordinate action of a variety of chromatin, TBP, and RNA polymerase II regulators.  In contrast, the TFIID-dominated class is less regulated, but is highly dependent upon TAFs including those shared between TFIID and SAGA.  These two distinct modes of transcription regulation might reflect the need to balance inducible stress responses with the steady output of housekeeping genes.
Keywords = Taf1
Keywords = Spt3
Keywords = Gcn5
Keywords: other

first: Kathryn

last: Huisinga


title: EcR mutant midgut comparison

summary:
Comparisons between EcR mutant midgut and a reference control sample from mixed-stage normal midgut
Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development
Keywords: other


title: sage gene RNAi experiment

summary:
Comparisons between the salivary glands upon the RNAi of sage gene vs. the control.
Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development
Keywords: other


title: MicroRNAs in the miR-106b family regulate p21/CDKN1A and promote cell cycle progression.

status: Public on Feb 19 2009

city: Seattle

first: Irena

last: Ivanovska

address: 401 Terry Ave N

institute: Merck

summary: microRNAs in the miR-106b family are overexpressed in multiple tumor types and are correlated with the expression of genes that regulate the cell cycle. Consistent with these observations, miR-106b family gain of function promotes cell cycle progression, whereas loss of function reverses this phenotype. Microarray profiling uncovers multiple targets of the family, including the cyclin-dependent kinase inhibitor p21/CDKN1A. We show that p21 is a direct target of miR-106b and that its silencing plays a key role in miR-106b-induced cell cycle phenotypes. We also show that miR-106b overrides a doxorubicin-induced DNA damage checkpoint. Thus, miR-106b family members contribute to tumor cell proliferation in part by regulating cell cycle progression and by modulating checkpoint functions.

overall_design: HCT116 Dicerex5 cells were transfected with microRNAs in six-well plates, and RNA was isolated 10 h after transfection. Transcripts containing the miR-106b family hexamers in their 3' UTRs were identified.  By microarray analysis, 103 transcripts that contained miR-106b family complementary hexamers in their 3' UTRs were down-regulated by miR-106b, miR-106a, miR-20b, and miR-17-5p within 10 h of transfection.

first: Alexey

last: Ball

first: Robert

last: Diaz

first: Jill

last: Magnus

first: Miho

last: Kibukawa

first: Janell

middle: M

last: Schelter

first: Sumire

last: Kobayashi

first: Lee

last: Lim

first: Julja

last: Burchard

first: Aimee

last: Jackson

first: Peter

last: Linsley

first: Michele

middle: A

last: CLeary


title: Characterization of early stages of human B cell development by gene expression profiling

status: Public on Mar 04 2009

city: Oslo

first: June

middle: Helen

last: Myklebust

address: Montebello

department: Immunology

country: Norway

institute: The National Hospital

summary: We have characterized several stages of normal human B cell development in adult bone marrow by gene expression profiling of hemopoietic stem cells, early B (E-B), pro-B, pre-B, and immature B cells, using RNA amplification and Lymphochip cDNA microarrays (n = 6). Hierarchical clustering of 758 differentially expressed genes clearly separated the five populations. We used gene sets to investigate the functional assignment of the differentially expressed genes. Genes involved in VDJ recombination as well as B lineage-associated transcription factors (TCF3 (E2A), EBF, BCL11A, and PAX5) were turned on in E-B cells, before acquisition of CD19. Several transcription factors with unknown roles in B lymphoid cells demonstrated interesting expression patterns, including ZCCHC7 and ZHX2. Compared with hemopoietic stem cells and pro-B cells, E-B cells had increased expression of 18 genes, and these included IGJ, IL1RAP, BCL2, and CD62L. In addition, E-B cells expressed T/NK lineage and myeloid-associated genes including CD2, NOTCH1, CD99, PECAM1, TNFSF13B, and MPO. Expression of key genes was confirmed at the protein level by FACS analysis. Several of these Ags were heterogeneously expressed, providing a basis for further subdivision of E-B cells. Altogether, these results provide new information regarding expression of genes in early stages of human B cell development.

overall_design: Total RNA was extracted from HSC, E-B (CLP), pro-B, pre-B, and IM-B cell populations from human BM, 6 different donors from each population. Total RNA was also extracted from naive B cells, centroblasts, centrocytes or memoty B cells from tonsils, each population was pooled from 4 different donors). The total RNA was amplified, and hybridized to Lymphochip cDNA microarrays

first: Marit

middle: E

last: Hystad

middle: H

first: Trond

last: Boe

first: Einar

last: Sivertsen

first: Edith

last: Rian

first: Lise

last: Forfang

first: Else

last: Munthe

first: Andreas

last: Rosenwald

first: Michael

last: Chiorazzi

first: Inge

last: Jonassen

first: Louis

last: Staudt

first: Erlend

last: Smeland