title: E-16-20h_H3K9Me3_3_of_3_rep_2

description: ChIP-chip of H3K9me3 in Drosophila embryos at 16-20 hours of development, E-16-20h_H3K9Me3_3_of_3_rep_2

source_name: ChIP, embryos at 16-20 hours of development, E-16-20h_H3K9Me3_3_of_3_rep_2

source_name: Input, embryos at 16-20 hours of development, E-16-20h_H3K9Me3_3_of_3_rep_2


title: E-0-4h_H3K9Me3_3_of_3_rep_3

status: Public on Mar 24 2009

type: genomic

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

country: USA

institute: University of Chicago

description: ChIP-chip of H3K9me3 in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_3

hyb_protocol: The hybridization solution is composed of 5 ug each of Cy3- and Cy5-labeled DNA, 50 ug of salmon sperm DNA, Agilent Blocking Agent and Agilent Hyb Buffer. The mixture is heated to 95*C for 3 min and then 37*C for 30 minutes immediately prior to hybridization. Samples are hybridized for 40 hours at 65*C. After hybridization the slides are washed in Agilent Wash Buffer 1 for 5 minutes at room temperature and then in Agilent Wash Buffer 2 for 5 minutes at 31*C.

scan_protocol: Channel 1 & 2 are for the Agilent arrays are scanned on Agilent's DNA Microarray Scanner G2505B at a resolution of 5 microns. Data is extracted from the images using Agilent's Feature Extraction Software 9.5.3.1.

data_processing: We preprocessed microarray data to normalize it and reduce experimental noise as described in Qi et al. (Qi et al., Nature biotechnology 2006). In short, the raw intensities from each channel was divided by the median intensity from that channel before computing a ratio to arrive at a median adjusted ratio. We further subtracted average value of negative control probes on the array and then added one as a regularization parameter.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: ChIP, embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_3

label_protocol: 2 ug of amplified IP DNA are used for random primer labeling reaction (invitrogen). Cy3-dCTP is incorporated for the ChIP samples while Cy5-dCTP is incorporated for the Input chromatin sample. After washing of the labeled material on Centricon columns, 5ug of labeled DNA is used for hybridization.

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.   2. For a 0-4 hours egg laying, new plates are added after a 2hours pre-egglaying at 10 am and flies are allowed to lay eggs for 4 hours.   3. Embryos are collected at 1.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 2 pm in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IP'd material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

treatment_protocol: No treatment

tag: tissue

value: embryos

tag: time point

value: 0-4 hours of development

tag: test

value: ChIP

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: antibody lot number

tag: replicate

source_name: Input, embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_3

tag: reference

value: Input


title: E-4-8h_H3K27Me3_3_of_3_rep_1

description: ChIP-chip of H3K27me3 in Drosohila embryos at 4-8 hours of development, E-4-8h_H3K27Me3_3_of_3_rep_1

source_name: ChIP, embryos at 4-8 hours of development, E-4-8h_H3K27Me3_3_of_3_rep_1

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 4-8 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected at 4.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 5 pm in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila embryos are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IP'd material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

value: 4-8 hours of development

value: Upstate

source_name: Input, embryos at 4-8 hours of development, E-4-8h_H3K27Me3_3_of_3_rep_1

value: input


title: E-4-8h_H3K9Me3_3_of_3_rep_1

description: ChIP-chip of H3K9me3 in Drosophila embryos at 4-8 hours of development, E-4-8h_H3K9Me3_3_of_3_rep_1

source_name: ChIP, embryos at 4-8 hours of development, E-4-8h_H3K9Me3_3_of_3_rep_1

source_name: Input, embryos at 4-8 hours of development, E-4-8h_H3K9Me3_3_of_3_rep_1


title: E-0-4h_H3K9Me3_3_of_3_rep_2

description: ChIP-chip of H3K9me3 in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_2

source_name: ChIP, embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_2

source_name: Input, embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_2


title: iPS PDB 2lox-5

status: Public on Mar 06 2009

type: RNA

city: Cambridge

first: Frank

last: Soldner

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient

hyb_protocol: Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.

data_processing: Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Virus-carrying human induced pluripotent stem cells (hIPSC)

label_protocol: 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.

growth_protocol: Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)].  Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4).

tag: parental cell line


title: iPS PDB 1lox-21Puro-20

description: Factor-free human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient.  Lentiviral vectors were excised after integration using Cre-recombinase.

source_name: Factor-free human induced pluripotent stem cells (hIPSC)

treatment_protocol: Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4).  Lentiviral vectors were then excised after integration using Cre-recombinase.


title: E-12-16h_H3K9Me3_2_of_3_rep_2

status: Public on Mar 20 2009

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_2

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_2

growth_protocol: The sequenced Drosophila strain poupulation has been amplified and cultivated in population cages. The egg lay for collecting embryos is done in the cage with apple juice agar plates. Egg lay is done for 4 hours and embryos are collected 12 hours later for chromatin extraction.

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_2


title: E-12-16h_H3K9Me3_3_of_3_rep_2

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_2

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_2

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_2


title: E-12-16h_H3K9Me3_2_of_3_rep_1

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_1

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_1

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_1


title: iPS PDB 2lox-22


title: E-12-16h_H3K9Me3_1_of_3_rep_3

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_3

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_3

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_3


title: E-12-16h_H3K9Me3_2_of_3_rep_3

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_3

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_3

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_2_of_3_rep_3


title: iPS PDB 1lox-21Puro-26


title: iPS PDB 1lox-17Puro-5


title: PDB fibroblasts

description: Fibroblasts cultured in fibroblast medium

source_name: PDB fibroblasts

growth_protocol: Fibroblasts were cultured in fibroblast medium [DMEM supplemented with 15% FBS (Hyclone), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen) and penicillin/streptomycin (Invitrogen)].

tag: Human fibroblasts


title: H13B ESC

status: Public on Dec 21 2008

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: Human Embryonic Stem Cell line

hyb_protocol: All arrays were hybridized at 45ºC for 16 hours and scanned using an   AFX GC3000 G7 scanner.

scan_protocol: AFX GC3000 G7 scanner

data_processing: RMA

source_name: Human Embryonic Stem Cells

label_protocol: Approximately 3 µg of RNA from each sample was labeled using the   MessageAmp™ Biotin II-Enhanced IVT kit (Ambion) following manufacturer’s   instructions.

growth_protocol: iPS cells were maintained on irradiated   mouse embryonic fibroblasts (MEF) as previously described.  Fibroblast cells   (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium   (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum   (HyClone Laboratories).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit   (Qiagen) with on-column DNase I digestion or Tri-Reagent (Sigma).

treatment_protocol: Lentiviral transduction of fibroblast cells was performed as   previously described.

tag: H13B passage 43 Human Embryonic Stem Cells


title: iPS PDB 2lox-17


title: E-12-16h_H3K9Me3_3_of_3_rep_3

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_3

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_3

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_3


title: hES H9

description: Human embryonic stem cells cultured with a fibroblast feeder layer; NIH Code: WA09

source_name: Human embryonic stem cells

growth_protocol: Human embryonic stem cells H9 were maintained on MMC-inactivated MEFs or on MMC-inactivated human fibroblasts (D551; American Type Culture Collection, Manassas, VA) according to the manufacturer’s protocol.

tag: Human ES cell line H9


title: H7 ESC

description: Human Embryonic Stem Cell line

tag: H7 passage 73 Human Embryonic Stem Cells


title: H9 ESC

description: Human Embryonic Stem Cell line

tag: H9 passage 50 Human Embryonic Stem Cells


title: hES BG01

description: Human embryonic stem cells cultured with a mouse embryonic fibroblast feeder layer; NIH Code: BG01

tag: Human ES cell line BG01


title: H14A ESC

description: Human Embryonic Stem Cell line

tag: H14B passage 61 Human Embryonic Stem Cells


title: E-12-16h_H3K9Me3_1_of_3_rep_2

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_2

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_2

tag: tissue

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_2


title: iPS PDB 2lox-21

source_name: Virus-carrying human induced pluripotent stem cells (hIPSC)


title: SMA 3813

description: Fibroblast cells obtained from Spinal Muscular Atrophy 1 patient

source_name: Human Fibroblast cells

tag: Human Fibroblast cells


title: E-12-16h_H3K9Me3_3_of_3_rep_1

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_1

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_1

tag: time point

tag: test

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_3_of_3_rep_1


title: SMA 3814

description: Fibroblast cells obtained from clinically normal mother of spinal muscular atrophy patients


title: E-0-4h_H3K9Me3_3_of_3_rep_1

description: ChIP-chip of H3K9me3 in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_1

source_name: ChIP, embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_1

tag: antibody

tag: antibody manufacturer

source_name: Input, embryos at 0-4 hours of development, E-0-4h_H3K9Me3_3_of_3_rep_1


title: iPS SMA 4.2

description: Generated iPS cells from primary fibroblasts from the unaffected mother following infection with lentiviral constructs encoding OCT 4, SOX   2, NANOG, and LIN 28 (WT clone)

source_name: Human iPS cells

tag: Human iPS cells


title: L1_H3K9Me3_3_of_3_rep_2

description: ChIP-chip of H3K9me3 in Drosophila L1 larvae, L1_H3K9Me3_3_of_3_rep_2

source_name: ChIP, L1 larvae, L1_H3K9Me3_3_of_3_rep_2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of first instar larvae, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. 3. L1 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

value: larvae

tag: antibody catalog number

tag: antibody lot number

tag: replicate

source_name: Input, L1 larvae, L1_H3K9Me3_3_of_3_rep_2


title: L2_H3K9Me3_3_of_3_rep_3

description: ChIP-chip of H3K9me3 in Drosophila L2 larvae, L2_H3K9Me3_3_of_3_rep_3

source_name: ChIP, L2 larvae, L2_H3K9Me3_3_of_3_rep_3

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of second instar larvae (L2), new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 24 hours. 3. L2 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

source_name: Input, L2 larvae, L2_H3K9Me3_3_of_3_rep_3

tag: reference


title: ts.noH.NO3.M3.X30562

status: Public on Oct 06 2006

city: Livermore

first: Anu

last: Chakicherla

state: CA

address: 7000 East Avenue, Mail Stop: L-446

institute: Lawrence Livermore National Lab

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30562_532

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Thiobacillus denitrificans ATCC 25259

source_name: thiosulfate.no H2.NO3.Batch M3

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: See Beller et al. (2006) [PMID: 16980503] for denitrifying growth conditions.

extract_protocol: Total RNA was extracted using the MasterPure Complete DNA and RNA Purification Kit (EpiCentre) using a modified protocol and RNAprotect (Qiagen).

treatment_protocol: Exposure conditions are shown in Table 1 (Beller et al 2013), Group VIII.  Details are provided in Beller et al. (2006) [PMID: 16980503].

tag: strain


title: ts.noH.O2.M2.X30829

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30829_532

source_name: thiosulfate.no H2.O2.Batch M2

growth_protocol: See Beller et al. (2006) [PMID: 16980503] for aerobic growth conditions.

treatment_protocol: Exposure conditions are shown in Table 1 (Beller et al 2013), Group IV.  Details are provided in Beller et al. (2006) [PMID: 16980503].


title: ts.noH.NO3.M3.X30629

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30629_532


title: E-12-16h_H3K9Me3_1_of_3_rep_1

description: ChIP-chip of H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_1

source_name: ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_1

source_name: Input, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_1


title: ts.noH.O2.M2.X30839

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30839_532


title: iPS SMA 3.6

description: Generated iPS cells from primary fibroblasts from a type 1 SMA patient following infection with lentiviral constructs encoding OCT 4, SOX   2, NANOG, and LIN 28 (Clone 3.6)


title: ts.noH.NO3.M3.X32425

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
32425_532


title: iPS PDB 1lox-17Puro-10

description: Factor-free human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient.  Lentiviral vectors were excised after integration using Cre-recombinase.

source_name: Factor-free human induced pluripotent stem cells (hIPSC)

tag: parental cell line


title: iPS SMA 3.5

description: Generated iPS cells from primary fibroblasts from a type 1 SMA patient following infection with lentiviral constructs encoding OCT 4, SOX   2, NANOG, and LIN 28 (Clone 3.5)


title: E2F1_Expt1

status: Public on Feb 27 2002

city: Tampa

first: William

middle: Douglas

last: Cress

state: FL

address: 12902 Magnolia Drive

department: Oncology

institute: Moffitt Cancer Center

description:
This sample represents quiescent NIH3T3 cells infected with an E2F1 expressing adenovirus.  Infection was for 30 hours at a multiplicity of 10 viruses per cell. This sample should be directly compared to GSM821 in which identical cells were infected with a control beta-galactosidase expressing adenovirus. The purpose of comparing these samples was to identify genes regulated by E2F1.

The E2F pathway has been proposed to regulate genes involved in the transition from quiescence into DNA synthesis.  However, this hypothesis has not been rigorously tested on a genomic scale.  Toward this end, we have infected quiescent mouse fibroblasts, which do not express E2F1, with an E2F1-expressing adenovirus and examined the expression of more than 6,000 genes using high-density microarrays.  Microarray results clearly support the current paradigm, however, they suggest that E2F1 may also regulate unanticipated cellular functions including pathways involved in apoptosis, signal transduction, transcriptional control, and membrane biology.   Most surprisingly, we identified a number of genes that are repressed by E2F1 expression, suggesting that E2F1 may have the potential to repress transcription of numerous genes through an unknown mechanism.

organism: Mus musculus

source_name: NIH3T3 fibroblasts treated with E2F1 expressing adenovirus


title: BetaGal_Expt1

description:
This sample represents quiescent NIH3T3 cells infected with a beta-galactosidase expressing adenovirus. Infection was for 30 hours at a multiplicity of 10 viruses per cell. This sample should be directly compared to GSM820 in which identical cells were infected with an E2F1-expressing expressing adenovirus. The purpose of comparing these samples was to
identify genes regulated by E2F1.

The E2F pathway has been proposed to regulate genes involved in the transition from quiescence into DNA synthesis.  However, this hypothesis has not been rigorously tested on a genomic scale.  Toward this end, we have infected quiescent mouse fibroblasts, which do not express E2F1, with an E2F1-expressing adenovirus and examined the expression of more than 6,000 genes using high-density microarrays.  Microarray results clearly support the current paradigm, however, they suggest that E2F1 may also regulate unanticipated cellular functions including pathways involved in apoptosis, signal transduction, transcriptional control, and membrane biology.   Most surprisingly, we identified a number of genes that are repressed by E2F1 expression, suggesting that E2F1 may have the potential to repress transcription of numerous genes through an unknown mechanism.

source_name: NIH3T3 fibroblasts infected with a beta-galactosidase expressing adenvirus


title: BetaGal_Exp2

description:
This sample represents quiescent NIH3T3 cells infected with a beta-galactosidase expressing adenovirus.  Infection was for 30 hours at a multiplicity of 10 viruses per cell. This sample should be directly compared to GSM823 in which identical cells were infected with an E2F1-expressing expressing adenovirus. The purpose of comparing these samples was to identify genes regulated by E2F1.

The E2F pathway has been proposed to regulate genes involved in the transition from quiescence into DNA synthesis. However, this hypothesis has not been rigorously tested on a genomic scale. Toward this end, we have infected quiescent mouse fibroblasts, which do not express E2F1, with an E2F1-expressing
adenovirus and examined the expression of more than 6,000 genes using high-density microarrays. Microarray results clearly support the current paradigm, however, they suggest that E2F1 may also regulate unanticipated cellular functions including pathways involved in apoptosis, signal transduction, transcriptional control, and membrane biology. Most surprisingly, we identified a number of genes that are repressed by E2F1 expression, suggesting that E2F1 may have the potential to repress transcription of numerous genes through an unknown mechanism.

source_name: NIH3T3 fibroblasts infected with a beta-galactosidase expressing adenovirus


title: E2F1_Expt2

description:
This sample represents quiescent NIH3T3 cells infected with an E2F1 expressing adenovirus. Infection was for 30 hours at a multiplicity of 10 virus per cell. This same should be compared to a control GSM822 that was infected with a beta-galactosidase expressing adenovirus

The E2F pathway has been proposed to regulate genes involved in the transition from quiescence into DNA synthesis.  However, this hypothesis has not been rigorously tested on a genomic scale.  Toward this end, we have infected quiescent mouse fibroblasts, which do not express E2F1, with an E2F1-expressing adenovirus and examined the expression of more than 6,000 genes using high-density microarrays.  Microarray results clearly support the current paradigm, however, they suggest that E2F1 may also regulate unanticipated cellular functions including pathways involved in apoptosis, signal transduction, transcriptional control, and membrane biology.   Most surprisingly, we identified a number of genes that are repressed by E2F1 expression, suggesting that E2F1 may have the potential to repress transcription of numerous genes through an unknown mechanism.

source_name: NIH3T3 cells infected with an E2F1-expressing adenovirus


title: ts.noH.O2.M2.X30830

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30830_532