title: AML1/ETO-transduced_rep3

status: Public on Mar 21 2007

city: Hanover

first: Nancy

middle: Asmussen

last: Speck

state: NH

address: 311 Vail Bldg

department: Biochemistry

institute: Dartmouth Medical School

description: Primary bone marrow mononuclear cells were harvested from 5-6 week old C57BL/6 mice (Jackson Labs, Bar Harbor, ME) and subjected to immunomagnetic negative selection using the Lineage cell depletion Kit (Miltenyi Biotech, Auburn, CA) to enrich for stem and progenitor cells (Lin- cells).  To further enrich the stem cell compartment, Lin- cells underwent positive selection for the expression of Sca1 (Lin-Sca1+;LS) using the Anti-Sca-1 MicroBead Kit (Miltenyi Biotech). LS cells (6x105 in 3ml) were plated in ultra-low adhesion 6-well plates (Costar, Corning, NY) and incubated overnight at 37oC, 5% CO2 in transplant media [RPMI, 20% FCS, penicillin and streptomycin, 10 ng/ml IL-3, 20 ng/ml IL-6 (R&D Systems, Minneapolis, MN), 10 ng/ml SCF (Stem Cell technologies, Vancouver, Canada)]. Twelve hours later, 6x105 cells in 2ml of fresh transplant media were added to 6-well plates (Cellstar, GBO, NC) coated with 100 mg Retronectin (Takara, Madison WI). Independent retroviral transductions were performed on three samples using AML1/ETO retrovirus.  Retroviral (AML1/ETO) supernatants (2 ml), 4 µl of 40 mg/ml polybrene and 40µl 1M Hepes were added to each well and the cells centrifuged for 90 minutes at 1400 g, 37oC. Cells were subjected to a second round of transduction 24 hours later as described above.  48 hours following the second transduction, cells were collected (kept as independent samples) and stained with PE conjugated anti-cKit (BD Bioscience), APC conjugated anti-Sca1 (Ebioscience), and biotin conjugated anti-lineage cocktail (Miltenyi Biotech).  PerCP Cy5.5 conjugated Streptavidin (BD Bioscience) was added to identify differentiated cells marked with biotin conjugated antibodies.  7-AAD (Molecular Probes) was used to exclude dead cells from the sort.  25,000 transduced (GFP+), live, Lin- (7-AAD/PerCP Cy5.5-), Sca1+ cKit+ (APC-PE ++) cells were sorted directly into 600ul of RLT RNA lysis buffer (Qiagen) using a BD FACSAria cell sorter (BD Bioscience).

hyb_protocol: Hybridization was performed according to manufacturer's (Affymetrix) instructions

scan_protocol: Scanning was performed according to manufacturer's (Affymetrix) instructions

data_processing: RMA

source_name: AML1/ETO-transduced, live, lineage-negative, Sca1 cKit double-positive bone marrow cells

label_protocol: 50ng of total RNA from each sample was amplified using the RiboAmp RNA amplification kit (Arcturus).  First-round aRNA was converted into double-strand cDNA again using the Arcturus RiboAmp kit.  Second-round dscDNA was then biotinylated in a second amplification using the Enzo High Yield T7 transcription kit according to the manufacturer's instructions.  Labeled cRNA was purified using Qiagen Rneasy mini-columns.

extract_protocol: Lin- Sca1+ cKit+ GFP+ (transduced) mouse bone marrow cells were sorted using a BD FACSAria directly into RLT RNA lysis buffer with 2-ME (Qiagen).  Total RNA was Dnase1-treated on Rneasy mini-columns according to manufacturer's instructions (Qiagen Rneasy mini-kit).  Total RNA quantity and integrity were verified using Agilent Technologies Bioanalyzer 2100.

tag: C57BL/6, 5-6 weeks old


title: W692A-transduced_rep2

type: RNA

country: USA

description: Primary bone marrow mononuclear cells were harvested from 5-6 week old C57BL/6 mice (Jackson Labs, Bar Harbor, ME) and subjected to immunomagnetic negative selection using the Lineage cell depletion Kit (Miltenyi Biotech, Auburn, CA) to enrich for stem and progenitor cells (Lin- cells).  To further enrich the stem cell compartment, Lin- cells underwent positive selection for the expression of Sca1 (Lin-Sca1+;LS) using the Anti-Sca-1 MicroBead Kit (Miltenyi Biotech). LS cells (6x105 in 3ml) were plated in ultra-low adhesion 6-well plates (Costar, Corning, NY) and incubated overnight at 37oC, 5% CO2 in transplant media [RPMI, 20% FCS, penicillin and streptomycin, 10 ng/ml IL-3, 20 ng/ml IL-6 (R&D Systems, Minneapolis, MN), 10 ng/ml SCF (Stem Cell technologies, Vancouver, Canada)]. Twelve hours later, 6x105 cells in 2ml of fresh transplant media were added to 6-well plates (Cellstar, GBO, NC) coated with 100 mg Retronectin (Takara, Madison WI). Independent retroviral transductions were performed on four samples using W692A retrovirus.  Retroviral (W692A) supernatants (2 ml), 4 µl of 40 mg/ml polybrene and 40µl 1M Hepes were added to each well and the cells centrifuged for 90 minutes at 1400 g, 37oC. Cells were subjected to a second round of transduction 24 hours later as described above.  48 hours following the second transduction, cells were collected (kept as independent samples) and stained with PE conjugated anti-cKit (BD Bioscience), APC conjugated anti-Sca1 (Ebioscience), and biotin conjugated anti-lineage cocktail (Miltenyi Biotech).  PerCP Cy5.5 conjugated Streptavidin (BD Bioscience) was added to identify differentiated cells marked with biotin conjugated antibodies.  7-AAD (Molecular Probes) was used to exclude dead cells from the sort.  25,000 transduced (GFP+), live, Lin- (7-AAD/PerCP Cy5.5-), Sca1+ cKit+ (APC-PE ++) cells were sorted directly into 600ul of RLT RNA lysis buffer (Qiagen) using a BD FACSAria cell sorter (BD Bioscience).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: W692A-transduced, live, lineage-negative, Sca1 cKit double-positive bone marrow cells


title: AML1/ETO-transduced_rep2


title: GFP-transduced_rep1

description: Primary bone marrow mononuclear cells were harvested from 5-6 week old C57BL/6 mice (Jackson Labs, Bar Harbor, ME) and subjected to immunomagnetic negative selection using the Lineage cell depletion Kit (Miltenyi Biotech, Auburn, CA) to enrich for stem and progenitor cells (Lin- cells).  To further enrich the stem cell compartment, Lin- cells underwent positive selection for the expression of Sca1 (Lin-Sca1+;LS) using the Anti-Sca-1 MicroBead Kit (Miltenyi Biotech). LS cells (6x105 in 3ml) were plated in ultra-low adhesion 6-well plates (Costar, Corning, NY) and incubated overnight at 37oC, 5% CO2 in transplant media [RPMI, 20% FCS, penicillin and streptomycin, 10 ng/ml IL-3, 20 ng/ml IL-6 (R&D Systems, Minneapolis, MN), 10 ng/ml SCF (Stem Cell technologies, Vancouver, Canada)]. Twelve hours later, 6x105 cells in 2ml of fresh transplant media were added to 6-well plates (Cellstar, GBO, NC) coated with 100 mg Retronectin (Takara, Madison WI). Independent retroviral transductions were performed on three samples using control (GFP/MigR1) retrovirus.  Retroviral (GFP) supernatants (2 ml), 4 µl of 40 mg/ml polybrene and 40µl 1M Hepes were added to each well and the cells centrifuged for 90 minutes at 1400 g, 37oC. Cells were subjected to a second round of transduction 24 hours later as described above.  48 hours following the second transduction, cells were collected (kept as independent samples) and stained with PE conjugated anti-cKit (BD Bioscience), APC conjugated anti-Sca1 (Ebioscience), and biotin conjugated anti-lineage cocktail (Miltenyi Biotech).  PerCP Cy5.5 conjugated Streptavidin (BD Bioscience) was added to identify differentiated cells marked with biotin conjugated antibodies.  7-AAD (Molecular Probes) was used to exclude dead cells from the sort.  25,000 transduced (GFP+), live, Lin- (7-AAD/PerCP Cy5.5-), Sca1+ cKit+ (APC-PE ++) cells were sorted directly into 600ul of RLT RNA lysis buffer (Qiagen) using a BD FACSAria cell sorter (BD Bioscience).

source_name: GFP/MigR1 (vector-only)-transduced, live, lineage-negative, Sca1 cKit double-positive bone marrow cells


title: W692A-transduced_rep1


title: W692A-transduced_rep3


title: W692A-transduced_rep4


title: GFP-transduced_rep2


title: AML1/ETO-transduced_rep1


title: GFP-transduced_rep3


title: NM9 healthy control

status: Public on Mar 20 2007

city: Singapore

first: Yi

last: Hong

email: hong.yi@sgh.com.sg, fbap8570@yahoo.com

address: Outram Road

department: Colorectal Surgery

country: Singapore

institute: Singapore General Hospital

description: DNA chip technology was used to systematically search for genes differentially expressed in early onset CRC. We report a panel of 7 over-expressed genes in the normal appearing colonic mucosa of young patients without dominant family history compared to that of HC that could potentially predict early onset CRC.

data_processing: GCOS software, MAS5, scaled to 500

label: fluorescent

organism: Homo sapiens

source_name: biopsies from healthy individuals undergoing colonoscopic examination, snap-frozen immediately, stored at -80ºC

tag: Tissue

value: Mucosa


title: Peripheral Blood Mononuclear cells (C2_graCNV)

status: Public on Mar 29 2007

type: genomic

city: Columbus

first: David

middle: Lawrence

last: Newsom

state: OH

address: 700 Children's Drive

department: Microbial Pathogenesis

institute: Nationwide Children's Hospital

description: Peripheral Blood Mononuclear cells

hyb_protocol: see the Functional Genomics Core website (dnaarrays.org) of Ohio State University. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: The data was analyzed with WPP as described in the associated publication.

molecule: genomic DNA

source_name: Peripheral Blood Mononuclear cells

extract_protocol: Spin Doctor Genomic DNA Isolation kit (Gerard Biotech, Oxford, OH).

tag: Female, Caucasian


title: NM4 healthy control


title: 4145M patient’s mucosa

source_name: mucosa collected and archived within 30 mins after surgery


title: NM3 healthy control


title: NM24 healthy control


title: NM22 healthy control


title: NM16 healthy control


title: 3950M patient’s mucosa


title: NM19 healthy control


title: 3446M patient’s mucosa


title: 3798M patient’s mucosa


title: 3838M patient’s mucosa


title: 3578M patient’s mucosa


title: 3335M patient’s mucosa


title: 3216M patient's mucosa

tag: Gender

value: F

tag: Age


title: NM18 healthy control


title: NM20 healthy control


title: NM14 healthy control


title: 4160M patient’s mucosa


title: 3416M patient's mucosa


title: 3894M patient’s mucosa


title: 2965M patient's mucosa

description: we used DNA chip technology to systematically search for genes differentially expressed in early onset CRC. We report a panel of 7 over-expressed genes in the normal appearing colonic mucosa of young patients without dominant family history compared to that of HC that could potentially predict early onset CRC.

data_processing: GCOS software,MAS5, scaled to 500

source_name: mucosa collected and archived within 30 mins after sugery


title: 5IDC_normal_lobular

status: Public on Mar 16 2007

city: Olomouc

first: Jan

last: Bouchal

address: Hnevotinska 3

department: Department of Clinical and Molecular Pathology

country: Czech Republic

institute: Palacky University

description: Amplified total RNA from microdissected normal lobular cells from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)

hyb_protocol: The biotinylated cRNA preparation was fragmented, assessed by gel electrophoresis, and placed in hybridization cocktail containing biotinylated hybridization controls (GeneChipTM Eukaryotic Hybridization Control Kit, Affymetrix). Sample was first hybridized to Test3 Arrays for 16 hours, washed, stained using antibody-mediated signal amplification and scanned. After passing this quality control stage, the sample was hybridized onto the large Human Genome U133 Plus 2.0 Array.

scan_protocol: see associated EXP file

data_processing: GCOS with the default settings exept that the target signal was set to 100

source_name: breast, flash-frozen, microdissected normal lobular cells

label_protocol: Fifty nanograms of total RNA were reverse transcribed and amplified by Microarray Target Amplification Kit (Roche diagnostics, Basel, Switzerland). In brief, total RNA (50 ng) was converted into cDNA using a modified oligo (dT) primer (TAS-T7 Oligo (dT)24). A unique Target Amplification Sequence (TAS) with no homology to any known sequences in public databases generated the 3´ anchor on the cDNA for subsequent PCR amplification. In order to include a 5´ anchor sequence on the cDNA, the TAS-(dN)10 primer was used for the initiation of the second strand cDNA synthesis. After purification using the Microarray Target Purification Kit (Roche), PCR was performed using the TAS primer and Expand PCR Enzyme Mix which is optimized for long (>1kb) and unbiased PCR products. In order to ensure that messages were not amplified to saturation, the optimal number of PCR cycles was estimated by preliminary PCR and agarose electrophoresis of PCR products from cycles 21, 24, 27, 30 and 33. After purification with the Microarray Target Purification Kit (Roche), the PCR products were labeled with biotin-14-CTP (Invitrogen, CarlsBad, CA, USA) and biotin-16-UTP (Roche) by in vitro transcription using Microarray RNA Target Synthesis Kit T7 (Roche). The labelled cRNA was purified using the Microarray Target Purification Kit (Roche), quantified by spectrophotometer and checked by agarose electrophoresis. The entire amplification and labelling process was monitored by GeneChip® Eukaryotic Poly-A RNA Control Kit (Affymetrix, Santa Clara, CA, USA) with exogenous positive controls which were spiked into the total RNA before cDNA synthesis and finally detected on Human Genome U133 Plus 2.0 Arrays (Affymetrix).

extract_protocol: At least 1000 normal ductal cells were microdissected from cryosections using the VeritasTM Laser Capture Microdissection System (Arcturus Bioscience, Inc., USA) according to standard protocols. Caps with captured cells were directly placed in 100 ul lysis buffer (Qiagen, Hilden, Germany). Total cellular RNA was isolated (RNeasy® Micro Kit, Qiagen) according to manufacturer´s recommendations and subsequently quantified on a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

tag: normal tissue from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)


title: 3IDC_tumor ductal

description: Amplified total RNA from microdissected tumor cells from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)

label: biotin-14-CTP (Invitrogen, CarlsBad, CA, USA) and biotin-16-UTP (Roche)

source_name: breast, flash-frozen, microdissected ductal tumor cells

tag: tumor tissue from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)


title: 5IDC_tumor ductal


title: 4IDC_tumor ductal


title: 5IDC_normal_ductal

description: Amplified total RNA from microdissected normal ductal cells from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)

source_name: breast, flash-frozen, microdissected normal ductal cells


title: 4IDC_normal_lobular


title: 3IDC_normal_lobular


title: 4IDC_normal_ductal


title: 2IDC_tumor_ductal


title: 3IDC_normal_ductal


title: 1IDC_normal_ductal


title: 2IDC_normal_lobular


title: 10ILC_normal_ductal

description: Amplified total RNA from microdissected normal ductal cells from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)

tag: normal tissue from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)


title: 2IDC_normal_ductal


title: 1IDC_tumor_ductal


title: 1IDC_normal_lobular


title: 8ILC_tumor_lobular

description: Amplified total RNA from microdissected tumor cells from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)

source_name: breast, flash-frozen, microdissected lobular tumor cells

tag: tumor tissue from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)


title: 8ILC_normal_lobular

description: Amplified total RNA from microdissected normal lobular cells from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)


title: 10ILC_normal_lobular


title: 8ILC_normal_ductal


title: 7ILC_tumor_lobular


title: 7ILC_normal_lobular


title: 7ILC_normal_ductal


title: 9ILC_normal_lobular


title: 9ILC_tumor_lobular


title: Pilocytic astrocytoma chip 8031

status: Public on Mar 14 2007

city: Saint Louis

first: Mukesh

middle: K

last: Sharma

state: MO

address: 4566 Scott Avenue, room 306

department: Neurology

institute: Washington University School of Medicine in Saint Louis

description: Pilocytic astrocytoma.  Chip ID 8031

data_processing: Transformation procedure used:GCOS1.4.  Array scaled so that the average probe set hybridization signal intensity value (target intensity) was 1500.

label: biotinylated aRNA

source_name: Pilocytic astrocytoma

tag: Brain tumor, WHO grade I, Pilocytic astrocytoma


title: 6ILC_tumor_lobular


title: 6ILC_normal_ductal


title: Pilocytic astrocytoma chip 8030

description: Pilocytic astrocytoma.  Chip ID 8030


title: Pilocytic astrocytoma chip 8027

description: Pilocytic astrocytoma.  Chip ID 8027


title: Pilocytic astrocytoma chip 8461

description: Pilocytic astrocytoma.  Chip ID 8461


title: Pilocytic astrocytoma chip 8029

description: Pilocytic astrocytoma.  Chip ID 8029


title: Pilocytic astrocytoma chip 8035

description: Pilocytic astrocytoma.  Chip ID 8035


title: Pilocytic astrocytoma chip 8033

description: Pilocytic astrocytoma.  Chip ID 8033


title: Pilocytic astrocytoma chip 8032

description: Pilocytic astrocytoma.  Chip ID 8032


title: Pilocytic astrocytoma chip 8036

description: Pilocytic astrocytoma.  Chip ID 8036


title: Pilocytic astrocytoma chip 8028

description: Pilocytic astrocytoma.  Chip ID 8028


title: Pilocytic astrocytoma chip 8025

description: Pilocytic astrocytoma.  Chip ID 8025


title: Pilocytic astrocytoma chip 8026

description: Pilocytic astrocytoma.  Chip ID 8026


title: Pilocytic astrocytoma chip 8023

description: Pilocytic astrocytoma.  Chip ID 8023


title: Pilocytic astrocytoma chip 8020

description: Pilocytic astrocytoma.  Chip ID 8020


title: Pilocytic astrocytoma chip 8021

description: Pilocytic astrocytoma.  Chip ID 8021


title: 6ILC_normal_lobular


title: Pilocytic astrocytoma chip 8024

description: Pilocytic astrocytoma.  Chip ID 8024


title: Pilocytic astrocytoma chip 8022

description: Pilocytic astrocytoma.  Chip ID 8022


title: Pilocytic astrocytoma chip 7764

description: Pilocytic astrocytoma.  Chip ID 7764


title: Pilocytic astrocytoma chip 7767

description: Pilocytic astrocytoma.  Chip ID 7767


title: Pilocytic astrocytoma chip 7766

description: Pilocytic astrocytoma.  Chip ID 7766


title: Pilocytic astrocytoma chip 7761

description: Pilocytic astrocytoma.  Chip ID 7761


title: Pilocytic astrocytoma chip 7757

description: Pilocytic astrocytoma.  Chip ID 7757


title: Pilocytic astrocytoma chip 7760

description: Pilocytic astrocytoma.  Chip ID 7760


title: Pilocytic astrocytoma chip 7756

description: Pilocytic astrocytoma.  Chip ID 7756


title: Pilocytic astrocytoma chip 7758

description: Pilocytic astrocytoma.  Chip ID 7758


title: Pilocytic astrocytoma chip 7755

description: Pilocytic astrocytoma.  Chip ID 7755


title: Pilocytic astrocytoma chip 7759

description: Pilocytic astrocytoma.  Chip ID 7759


title: Pilocytic astrocytoma chip 7750

description: Pilocytic astrocytoma.  Chip ID 7750


title: Pilocytic astrocytoma chip 8034

description: Pilocytic astrocytoma.  Chip ID 8034


title: Pilocytic astrocytoma chip 7765

description: Pilocytic astrocytoma.  Chip ID 7765


title: Pilocytic astrocytoma chip 7749

description: Pilocytic astrocytoma.  Chip ID 7749


title: Pilocytic astrocytoma chip 7753

description: Pilocytic astrocytoma.  Chip ID 7753


title: Pilocytic astrocytoma chip 7748

description: Pilocytic astrocytoma.  Chip ID 7748


title: 9ILC_normal_ductal


title: Pilocytic astrocytoma chip 7752

description: Pilocytic astrocytoma.  Chip ID 7752


title: Cerebellar astrocyte 2

description: Cerebellar astrocyte chip 2.  CHIP ID 10490

source_name: Cerebellar astrocyte 2

tag: Postnatal day 1


title: Cerebellar astrocyte 3

description: Cerebellar astrocyte chip 3.  CHIP ID 10491

source_name: Cerebellar astrocyte 3


title: Pilocytic astrocytoma chip 7751

description: Pilocytic astrocytoma.  Chip ID 7751


title: Pilocytic astrocytoma chip 7746

description: Pilocytic astrocytoma.  Chip ID 7746


title: Pilocytic astrocytoma chip 7745

description: Pilocytic astrocytoma.  Chip ID 7745


title: Neocortical astrocyte 3

description: Neocortical astrocyte chip 3.  CHIP ID 10488

source_name: Neocortical astrocyte 3

tag: strain

value: ICR


title: Pilocytic astrocytoma chip 7744

description: Pilocytic astrocytoma.  Chip ID 7744


title: Pilocytic astrocytoma chip 7743

description: Pilocytic astrocytoma.  Chip ID 7743


title: Pilocytic astrocytoma chip 7747

description: Pilocytic astrocytoma.  Chip ID 7747


title: Neocortical astrocyte 2

description: Neocortical astrocyte chip 2.  CHIP ID 10487

source_name: Neocortical astrocyte 2

tag: Strain


title: 10ILC_tumor_lobular


title: Neocortical astrocyte 1

description: Neocortical astrocyte chip 1. CHIP ID 10486

data_processing: Transformation procedure used: GCOS1.4.  Array scaled so that the average probe set hybridization signal intensity value (target intensity) was 1500.

source_name: Neocortical astrocyte 1


title: Baboon brain lcpufa L3 2

status: Public on Mar 10 2007

city: Ithaca

first: Kumar

last: Kothapalli

state: NY

address: Savagae Hall

institute: Cornell University

description: The expression data were analyzed by MAS5 statistical algorithms resident in GCOS; in short, the signal intensity for each gene was calculated as the average intensity difference, represented by [Σ(PM - MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92). GCOS-generated detection and change calls were used to identify robust expression changes.

hyb_protocol: The cRNA pellet was resuspended in 10 ul RNase-free H2O and 10.0 ug was fragmented by ion-mediated hydrolysis at 95oC for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16hr at 45oC to GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix), which cover over 47,000 human transcripts and variants representing approximately 39,000 of the best characterized human genes (Affymetrix). Arrays were washed at 25oC with 6 X SSPE (0.9M NaCl, 60 mMNaH2PO4, 6 mM EDTA + 0.01% Tween 20) followed by a stringent wash at 50oC with 100 mM MES, 0.1M [Na+], 0.01% Tween 20.  The arrays were then stained with phycoerythrein-conjugated streptavidin (Molecular Probes) and the fluorescence intensities were determined using the GCS 3000 high-resolution confocal laser scanner (Affymetrix).

scan_protocol: The arrays were then stained with phycoerythrein-conjugated streptavidin (Molecular Probes) and the fluorescence intensities were determined using the GCS 3000 high-resolution confocal laser scanner (Affymetrix).  The scanned images were analyzed using programs resident in GeneChip Operating System (GCOS; Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250 for all arrays used.

label: biotinylated UTP & CTP

organism: Papio anubis

source_name: precentral gyrus brain, L3, 3X LCPUFA (1.00%DHA-0.67%ARA)

label_protocol:
First and second strand cDNA were synthesized from 15 ug of total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) primer (PrOligo) according to the manufacturer’s instructions.
cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.). Briefly, double stranded cDNA synthesized from the previous steps were washed twice with 70% ethanol and resuspended in 22 ul RNase-free H2O. The cDNA was incubated with 4 ul each of 10X Reaction Buffer, Biotin-labeled Ribonucleotides, DTT, RNase Inhibitor Mix and 2 ul 20X T7 RNA Polymerase for 5 hr at 37oC. The labeled cRNA was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and ethanol precipitated at –20oC for 1 hr to overnight.

extract_protocol: Total RNA was isolated from approximately 50-100 mg of tissue from each animal using RNA STAT-60 according to the manufacturer's instructions (Tel Test Inc) [RNA Stat-60 is the same as Trizol reagent].

tag: Female, Age

value: 83 Days at Necropsy, Tissue:Brain


title: Cerebellar astrocyte 1

description: Cerebellar astrocyte chip 1.  CHIP ID 10489

source_name: Cerebellar astrocyte 1


title: small intestine EPI-MES Epi B

status: Public on Mar 12 2007

city: Ann Arbor

first: Xing

last: Li

state: MI

address: 109 Zina Pitcher Place,045 BSRB

department: Bioinformatics Program & CDB

institute: Universtiy of Michigan

description: There are 6 chips in the microarray experiment. 3 for epithilium of mouse small intestine; 3 for mesenchyme of mouse small intestine.

hyb_protocol: samples were bybridized according to affymetrix protocols: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: microarray was scanned according to affymetrix protocols.

data_processing: Microarray CEL files was processedusing RMA to get gene expression values

source_name: mouse small intestine E18.5 days epithelium

label_protocol:
samples were labelled according to affymetrix protocols:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

extract_protocol: Tissue separation was done as previously described.  Briefly, E18.5 embryos from C57BL/6 females were removed from the yolk sac and amnion and placed into ice-cold PBS containing penicillin/streptomycin.  The entire small intestine, from duodenum to cecum, was isolated, cut open longitudinally, placed into 1.0 ml of cold Cell Recovery Solution (BD Biosciences) in a 12-well plate and incubated for nine hours at 4°C.  On ice, each plate was agitated by hand for 30 to 45 minutes until all epithelium sloughed off, as determined by microscopic examination.  The mesenchyme was gently removed from the more delicate epithelial fragments with sterile forceps and rinsed in a dish of sterile PBS to remove any remaining epithelial cells.  Mesenchyme from three embryos was pooled into a 15 ml conical tube then snap frozen in liquid nitrogen; six such pooled samples were prepared.  The remaining epithelial tissue was washed twice with 10 ml of cold PBS and collected by gentle centrifugation (100xg for 7 minutes at 4°C).  Intestinal epithelium from three embryos was pooled into a 15 ml conical tube then snap frozen in liquid nitrogen; six pooled samples were prepared.  Each pool of tissue was subsequently homogenized in 1.0 mls TRIzol (Invitrogen), on ice, and RNA prepared per the TRIzol protocol.  Total RNA was further purified using the RNeasy Mini Kit (Qiagen), and quality assessed by electrophoresis of 2.0 µg RNA on a 1% agarose gel.  To assess epithelial vs. mesenchymal purity of RNA, we performed RT-PCR for both epithelial-specific mRNAs (Vil1 and Prkg2) and mesenchymal-specific mRNAs (Vim, Madcam1, and Actg2).  Three epithelial and three mesenchymal RNA fractions exhibiting no or minimal contamination with mesenchymal and epithelial mRNAs, respectively, were selected from among the samples for Affymetrix microarray analysis.

tag: Mouse small intesine (E18.5) was separated to epithelium and mesenchyme.


title: Baboon brain lcpufa L3 4

value: 84 Days at Necropsy, Tissue:Brain


title: Baboon brain lcpufa L 4

source_name: precentral gyrus brain, L, 1× LCPUFA (0.33%DHA-0.67%ARA)

value: 85 Days at Necropsy, Tissue:Brain


title: human embryonic carcinoma cells

city: changsha

first: sheng

last: yang

address: xiangya Road

country: China

institute: Institute of Human Reproduction & Stem Cell Engineering, Central South University

description: Gene expression data from human embryonic carcinoma cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: human embryonic carcinoma cells cultured in vivo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The NTERA-2 cells were cultured without feeder cells and planted with the density of 7X104/cm2 and every 3 days the cells were passaged by the typsine enzyme digest.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Undifferentiate human embryonic carcinoma cells (NTERA-2) were  collected , transferred to a EP tube, rinsed with PBS and placed in the RNA protection solution (GibcoBRL)..

tag: karyotype

value: aberrant

tag: passage number:not clear


title: small intestine Mes A

scan_protocol: icroarray was scanned according to affymetrix protocols.

source_name: mouse small intestine E18.5 days mesenchyme A


title: small intestine Mes C

source_name: mouse small intestine mesenchyme C

tag: mouse small intestine E18.5 days mesenchyme


title: Baboon brain lcpufa L3 1


title: small intestine EPI-MES Epi A

source_name: small intestine epithilum A

tag: mouse small intestine epithilum, at day E18.5


title: Baboon brain lcpufa L 2

tag: Male, Age


title: Baboon brain lcpufa L3 3


title: human embryonic stem cells 2

description: Gene expression data from aberrant human embryonic stem cells

source_name: simple duplication karyotype human embryonic stem cells cultured in vivo

growth_protocol: chHES-3 cell line was isolated by mechanical dissection in 2002, and cultured in mouse embryonic fibroblast feeder cells isolated by our institute.The chHES-3 lines were  were passaged by the mechanical methods every 6 days.

treatment_protocol: simple duplication human embryonic stem cells (chHES-3) were  collected inverted microscopes,Selected human embryonic stem cells were transferred to a EP tube, rinsed with PBS and placed in the RNA protection solution (GibcoBRL).

tag: passage number:53


title: human embryonic stem cells 3

source_name: complex karytoype human embryonic stem cells cultured in vivo

treatment_protocol: complex karyotypic human embryonic stem cells (chHES-3) were  collected inverted microscopes,Selected human embryonic stem cells were transferred to a EP tube, rinsed with PBS and placed in the RNA protection solution (GibcoBRL)..

tag: passage number:172


title: small intestine EPI-MES Epi C

source_name: mouse small intestine E18.5 days epithelium C

tag: Mouse small intesine (E18.5) was separated to epithelium and mesenchyme. This sample is EPI C.


title: Baboon brain lcpufa control 3

source_name: precentral gyrus brain, control, no DHA-ARA


title: small intestine Mes B

source_name: mouse small intestine E18.5 days mesenchyme B

tag: Mouse small intesine (E18.5) was separated to epithelium and mesenchyme. This sample is Mes B


title: Baboon brain lcpufa L 3

value: 87 Days at Necropsy, Tissue:Brain


title: Baboon brain lcpufa control 1


title: Baboon brain lcpufa L 1


title: Baboon brain lcpufa control 2

source_name: Brain Tissue,Control 2


title: Treated with IL1b PRB11920 (HGU133P)

status: Public on Mar 09 2007

city: South San Francisco

first: Kenneth

last: Jung

state: CA

address: 1 DNA Way MS93

institute: Genentech

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: Normal human epidermal keratinocytes

label_protocol: Standard Affymetrix procedure

extract_protocol: Qiagen RNeasy Mini Kit

tag: Treated with IL1b


title: Baboon brain lcpufa control 4


title: Treated with KGF PRB11913 (HGU133P)

description: KGF

tag: Treated with KGF


title: Treated with IL1b PRB11919 (HGU133P)


title: human embryonic stem cells 1

description: Gene expression data from human embryonic stem cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45? on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: normal karyotype human embryonic stem cells cultured in vivo

growth_protocol: chHES-20 cell line was isolated by mechanical dissection in 2005, and cultured in human embryonic fibroblast feeder cells isolated by our institute.  At initially isolation phase, the density of bFGF was 50ng/ml, at passage 4, the density decreased to 4ng/ml,at last, the chHES-20 lines were  were passaged by the mechanical methods every 6 days.

treatment_protocol: Undifferentiate human embryonic stem cells (chHES-20) were  collected inverted microscopes,Selected human embryonic stem cells were transferred to a EP tube, rinsed with PBS and placed in the RNA protection solution (GibcoBRL).

tag: normal karyotype:46,XX

tag: passage number:11


title: Treated with KGF PRB11915 (HGU133P)

description: KGF


title: Treated with IL26d PRB11910 (HGU133P)

tag: Treated with IL26d


title: Treated with IL24 PRB11907 (HGU133P)

tag: Treated with IL24


title: Treated with IL26d PRB11912 (HGU133P)


title: Treated with IFNg PRB11916 (HGU133P)

description: IFNg

tag: Treated with IFNg


title: Treated with IFNg PRB11917 (HGU133P)

description: IFNg


title: Treated with IL22 PRB11906 (HGU133P)

tag: Treated with IL22


title: Treated with IL22 PRB11904 (HGU133P)


title: Treated with IL19 PRB11900 (HGU133P)

tag: Treated with IL19


title: Treated with IL22 PRB11905 (HGU133P)


title: Treated with IL26d PRB11911 (HGU133P)


title: Treated with IL24 PRB11908 (HGU133P)


title: Treated with IL19 PRB11898 (HGU133P)


title: Treated with IL20 PRB11902 (HGU133P)

tag: Treated with IL20


title: Treated with IL24 PRB11909 (HGU133P)


title: Treated with IL19 PRB11899 (HGU133P)


title: Treated with IL20 PRB11903 (HGU133P)


title: Untreated PRB11895 (HGU133P)

description: Untreated

tag: Untreated


title: Untreated PRB11896 (HGU133P)

description: Untreated


title: Treated with IL20 PRB11901 (HGU133P)


title: Untreated PRB11897 (HGU133P)

description: Untreated


title: MLV VLP

status: Public on Mar 08 2007

city: Baltimore

first: Catherine

last: Scollick

state: MD

address: 615 N. Wolfe St.

institute: Johns Hopkins University School of Public Health

description: MLV VLP gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 12.5 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip® Operating Software v1.4 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

molecule: polyA RNA

source_name: MLV VLP

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

extract_protocol: Qiagen extraction of m RNA was performed according to the manufacturer's instructions.

treatment_protocol: no treatment

tag: Transfected HEK 293 cells, n = 1


title: oxt6:AtCPSF30 line 6, biological rep2

status: Public on Mar 07 2007

city: Lexington

first: Arthur

middle: G

last: Hunt

state: KY

address: 301A Plant Science Building

department: Dept. of Plant and Soil Sciences

institute: University of Kentucky

description: Gene expression data from oxt6 mutant plants expressing an AtCPSF30 transgene

hyb_protocol: Following fragmentation, 20 ug of biotin-labeled cRNA were hybridized for 16 hr at 45C on the ATH1-121501 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner.

data_processing: The data were analyzed with ArrayAssist 3.2 (Stratagene) using the PLIER normalization algorithm.   For this, the default settings were applied:  HZ=4 VZ=4 BG=2 SmoothFactorBG=100.000000 Epsilon=0.500000 BF= Gamma1L=0.004500 Gamma1H=0.004500 Gamma2L=0.006000 Gamma2H=0.006000 Perturbation=1.100000

organism: Arabidopsis thaliana

source_name: leaves from xt6:AtCPSF30 line 6 Arabidopsis plants, soil-grown for 30 days

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 ug total RNA.

growth_protocol: Arabidopsis plants were seeded and grown in soil at 22-26 °C in an 8 hr light/16 hr dark regime (under Phillips F40CW 34W fluorescent lights, with an intensity of 55 µmol m-2 sec-1).

extract_protocol: RNA was isolated using the Invitrogen Trizol Reagent (cat 15596-018) and further purified with the Qiagen RNeasy Plant Mini Kit (cat 74903), and tested for quality by gel electrophoresis and inspection of the stable RNA bands.

tag: Genotype

value: wild-type Columbia background

tag: 30 day-old soil grown plants


title: KO mouse 1_heart_basal

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

description: All hybridization were performed at the McGill University and Genome Quebec Innovation Centre. Affymetrix array technology involves the in-situ synthesis of hundreds of thousands of distinct oligonucleotide sequences onto a glass array using photolithography and combinatorial chemistry. Each 25-mer oligonucleotide is represented by millions of copies in a specific area. Each transcriptional sequence is spanned by 11-20 pairs of oligonucleotide probes randomly spaced throughout the array. All sequences designed on the array are selected from GenBank, dbEST and RefSeq. Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

scan_protocol: Refer to the protocols on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech). An Affymetrix GeneChIP 3000 scanner was used.

data_processing: The signal intensities shown in the VALUE column are a measure of abundance of transcript and calculated from combined, background adjusted perfect match and mismatched values of the probe set. The raw data is in MAS 5.0 format.

source_name: KO mouse heart under basal conditions

extract_protocol: Qiagen Fibrous Tissue Midi kit (mortar and pestle)

tag: Strain

tag: Gender

value: male

tag: Age

value: 2-3 months

tag: Tissue

value: heart


title: KO mouse 3_heart_basal

hyb_protocol: Refer to the protocols on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech).


title: WT mouse 3_heart_basal

source_name: WT mouse heart under basal conditions

label_protocol: Refer to the protocols on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech).

extract_protocol: Qiagen Fibrous Tissue Midi Kit (mortar and pestle)

value: Male


title: KO mouse 2_heart_basal


title: WT mouse 1_heart_basal

description: All hybridization were conducted at the McGill University and Genome Quebec Innovation Centre. Affymetrix array technology involves the in-situ synthesis of hundreds of thousands of distinct oligonucleotide sequences onto a glass array using photolithography and combinatorial chemistry. Each 25-mer oligonucleotide is represented by millions of copies in a specific area. Each transcriptional sequence is spanned by 11-20 pairs of oligonucleotide probes randomly spaced throughout the array. All sequences designed on the array are selected from GenBank, dbEST and RefSeq. Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

scan_protocol: Refer to protocols describe on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech). An Affymetrix GeneChIP 3000 scanner was used.

tag: Age:2-3 months


title: MLV Cellular

description: MLV VLP gene expression

label: ENZO BioArray HighYield RNA Transcript Labeling Kit

source_name: MLV Cellular

extract_protocol: Trizol extraction of mRNA was performed according to the manufacturer's instructions.


title: WT mouse 2_heart_basal

hyb_protocol: Refer to protocols describe on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech).


title: oxt6:AtCPSF30 line 6, biological rep1


title: wild-type Arabidopsis, biological rep1

description: Gene expression data from wild-type plants

source_name: leaves from wild-type Arabidopsis plants, soil-grown for 30 days


title: HIV1 Cellular

description: HIV1 VLP gene expression

source_name: HIV1 Cellular


title: oxt6 mutant, biological rep1

description: Gene expression data from oxt6 mutant plants

source_name: leaves from oxt6 mutant Arabidopsis plants, soil-grown for 30 days


title: oxt6:AtCPSF30 line 5, biological rep2

source_name: leaves from oxt6:AtCPSF30 line 5 Arabidopsis plants, soil-grown for 30 days


title: oxt6 mutant, biological rep3


title: wild-type Arabidopsis, biological rep2


title: Pilocytic astrocytoma chip 7754

description: Pilocytic astrocytoma.  Chip ID 7754

source_name: Pilocytic astrocytoma

tag: Brain tumor, WHO grade I, Pilocytic astrocytoma


title: HIV1 VLP

description: HIV1 VLP gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 12.5 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours GeneChip Expression Analysis Technical Manul- Affymetrix)

source_name: HIV1 VLP

extract_protocol: Qiagen extraction of mRNA was performed according to the manufacturer's instructions.


title: wild-type Arabidopsis, biological rep3


title: oxt6 mutant, biological rep2


title: HBEC3-KT

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

description: Immortalized with CDK4 and hTERT

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250

source_name: Human Bronchial Epithelial Cell

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocol from 5 microgram total RNA

growth_protocol: KSFM supplemented with EGF and BPE

extract_protocol: Qiagen RNeasy kit including DNase1 treatment

tag: Histology

value: immortalized normal

tag: Sex

tag: Race:


title: HBEC4-KT

description: Immortalized with CDK4 and hTERT


title: HBEC3-ET

description: Immortalized with CDK4 and hTERT


title: HBEC5-KT

description: Immortalized with CDK4 and hTERT

tag: Age:


title: Adherent Glioma Cell Line R8

status: Public on Mar 06 2007

city: Regensburg

first: Christoph

middle: P.

last: Beier

address: Universitatsstrasse 84

country: Germany

institute: University of Regensburg

description: Adherent human glioblastoma driven by CD133- cancer stem cells

hyb_protocol: Thereafter, the labeled cRNA was purified and fragmented by incubation at 94°C for 35 min. The quality of cRNA and the fragmentation were checked by microcapillary electrophoresis on an Agilent 2100 bioanalyzer, and 15 µg of biotinylated cRNA were hybridized to HG-U133plus 2.0 GeneChip® arrays for 16 h at 45°C with constant rotation at 60 rpm. All microarrays were processed in an Affymetrix GeneChip® Fluidics Station 400. Following staining with streptavidin R-phycoerythrin conjugate and washing cycles,

scan_protocol: The microarrays were scanned using the GeneChip® Scanner 3000 7G.

data_processing: Expression signals for each transcript and comparisons between different samples were calculated with the Affymetrix GeneChip® Operating Software GCOS1.4 and exported into Microsoft Excel.

source_name: Adherent human glioblastoma

label_protocol: In detail, 2,5 µg of total RNA was converted to cDNA using a T7-oligo-d(T)24 primer and SuperScript II reverse transcriptase. Second strand cDNA synthesis and blunt ending was performed using RNase H, E.coli DNA polymerase I, E.coli DNA ligase and T4 DNA Polymerase. Following cleanup, cDNA was used for in vitro transcription amplification reaction using T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix to produce biotinylated cRNA.

growth_protocol: DMEM-F12 Medium supplemented with EGF, FGF, LIF and B27

extract_protocol: Quiagen RNAeasy according to manufactors protocoll

tag: Driven by CD133- cancer stem cells


title: HBEC2-KT

description: Immortalized with CDK4 and hTERT

value: M


title: FOG-1-independent transcripition by GATA-1(V205G) in G1E cells, 0h

status: Public on Mar 05 2007

city: Madison

first: Kirby

middle: Dean

last: Johnson

state: WI

address: 1300 University Avenue

department: Pharmacology

institute: University of Wisconsin-Madison

data_processing:
Affymetrix standard protocol.  University of Chicago Microarray Facility
1) normalization method: scale to 500

 2) data selection procedures and parameters, transformation algorithm: GCOS  default setting

3)  scaling parameters: 500

source_name: G1E cells expressing ER-GATA-1(V205G); prior to estradiol treatment

extract_protocol: RNA was isolated with Trizol from up 10 million cells.  Further purification was achieved via Qiagen RNeasy column purification.

treatment_protocol: samples represent untreated controls for comarison to cells treated for 24 h with 1 uM estradiol.

tag: GATA-1-null G1E erythroid precursor cells expressing a GATA-1 V205G mutant as a fusion to the estrogen receptor ligand binding domain.


title: Adherent glioma stem cell line R46


title: Treated with KGF PRB11914 (HGU133P)

description: KGF

tag: Treated with KGF


title: Neurosphere-like glioma cell line R28

description: Neurosphere-like human glioblastoma driven by CD133+ cancer stem cells

source_name: Neurosphere-like human glioblastoma

tag: Driven by CD133+ cancer stem cells


title: Adherent glioma cell line R43


title: Neurosphere-like glioma Cell Line R18


title: Met5A control 1h

city: Solna

first: Penny

last: Nymark

state: Stockholm

address: Nobels väg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description: The data was used together with similar data from other cell lines exposed to asbestos to analyze asbestos-specific changes in gene expression. An article with the results has been submitted.

data_processing: raw data from the .CEL file

source_name: cell line Met5A

tag: human

tag: pleural mesothelial

tag: immortalized


title: HBEC2-E

description: Immortalized with CDK4 and hTERT


title: Met5A control 48h

description: The data was analyzed to find gene expression changes related to asbestos exposure.

data_processing: raw-data extracted from the .CEL file


title: Met5a asbestos exposed 48h replicate


title: Beas2B control 0h

source_name: cell line Beas2B

tag: bronchial epithelial


title: Neurosphere-like glioma Cell Line R11


title: Met5A asbestos exposed 1h


title: Beas2B asbestos exposed 24h replicate


title: Beas2B control 48h


title: Beas2B asbestos exposed 48h


title: Beas2B control 6h


title: FOG-1-independent transcripition by GATA-1(V205G) in G1E cells; 24h

data_processing:
Affymetrix standard protocol.  University of Chicago Microarray Facility
1)  normalization method: scale to 500

2) data selection procedures and parameters, transformation algorithm: GCOS default setting

3) scaling parameters: 500

source_name: G1E cells expressing ER-GATA-1(V205G); 24 h estradiol treatment

extract_protocol: RNA was isolated with Trizol from up 10 million cells. Further purification was achieved via Qiagen RNeasy column purification.

treatment_protocol: samples represent cells treated for 24 h with 1 uM estradiol.

tag: GATA-1-null G1E erythroid precursor cells expressing a GATA-1 V205G mutant as a fusion to the estrogen receptor ligand binding domain.  Treated with 1 uM estradiol for 24 h.


title: Beas2B control 1h


title: Beas2B control 24h


title: Met5A asbestos exposed 48h


title: Beas2B asbestos exposed 24h


title: A549 asbestos exposed 48h

source_name: cell line A549

tag: 58 year old Caucasian male

tag: lung carcinoma


title: A549 control 7 days


title: A549 control 24h


title: A549 control 0h


title: Beas2B asbestos exposed 6h


title: Beas2B asbestos exposed 1h


title: A549 control 48h


title: A549 control 6h


title: A549 asbestos exposed 7 days


title: A549 asbestos exposed 6h


title: A549 control 1h


title: A549 asbestos exposed 48h replicate

description:
The mean signal value from 2 replicates of this sample was used in the analysis.
The data was used together with similar data from other cell lines exposed to asbestos to analyze asbestos-specific changes in gene expression. An article with the results has been submitted.


title: MASMC_WT_PDGF_T0

status: Public on Mar 01 2007

city: Seattle

first: Michael

middle: T

last: Chin

state: WA

address: 815 Mercer Street

department: Medicine

institute: University of Washington

description: Gene expression data from Hey2 KO and WT MASMCs treated with PDGF for varying amounts of time.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Model 3000 scanner

source_name: MASMC WT cells treated with PDGF

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 0 minutes.

extract_protocol: After the appropriate length of treatment, the cells were washed one time with phosphate buffered saline and RNA was harvested with the Qiagen RNeasy protocol according to the manufacturerÕs instructions (Qiagen).

treatment_protocol: Mouse aortic smooth muscle cells were isolated from adventitia stripped, explanted aortas by mincing followed by enzymatic digestion. Cells were plated onto fibronectin coated dishes and cultured in DMEM with serum. Purity was checked by immunostaining for sm alpha actin and calponin.

tag: Genetic background

value: Mixed C57BL/6 and 129SvJ

tag: Passage


title: MASMC_WT_PDGF_T240

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 240 minutes.


title: MASMC_WT_PDGF_T30

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for the length of time indicated by the experiment.


title: A549 asbestos exposed 24h


title: MASMC_WT_PDGF_T15

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 15 minutes.


title: MASMC_WT_PDGF_T180

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 180 minutes.


title: MASMC_WT_PDGF_T60

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 60 minutes.


title: MASMC_WT_PDGF_T120

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 120 minutes.


title: A549 asbestos exposed 1h

source_name: Cell line A549


title: MASMC_WT_PDGF_T480

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 480 minutes.


title: MASMC_Hey2_KO_PDGF_T480

source_name: MASMC Hey2 KO cells treated with PDGF


title: MASMC_Hey2_KO_PDGF_T30

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 30 minutes.


title: MASMC_Hey2_KO_PDGF_T15


title: oxt6:AtCPSF30 line 5, biological rep1

tag: Genotype

tag: 30 day-old soil grown plants


title: MASMC_Hey2_KO_PDGF_T60


title: MASMC_Hey2_KO_PDGF_T180

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 180 minutes


title: MASMC_Hey2_KO_PDGF_T0

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for the 0 minutes.


title: MASMC_Hey2_KO_PDGF_T120

growth_protocol: For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 120 minutes


title: GUYT_50257 (HG-U133PLUS2)

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

description: Tumor samples from tamoxifen treated primary breast cancer patients.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA Bioconductor

source_name: breast

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)

tag: samplename

tag: ID

tag: series

value: GUYT

tag: age

tag: grade

tag: size

tag: er

tag: pgr

tag: node


title: GUYT_50237 (HG-U133PLUS2)


title: GUYT_50246 (HG-U133PLUS2)


title: GUYT_50254 (HG-U133PLUS2)


title: GUYT_50251 (HG-U133PLUS2)


title: GUYT_50230 (HG-U133PLUS2)


title: GUYT_50228 (HG-U133PLUS2)


title: GUYT_50238 (HG-U133PLUS2)


title: GUYT_50243 (HG-U133PLUS2)


title: GUYT_50236 (HG-U133PLUS2)


title: GUYT_50252 (HG-U133PLUS2)


title: GUYT_50239 (HG-U133PLUS2)


title: GUYT_50233 (HG-U133PLUS2)


title: MASMC_Hey2_KO_PDGF_T240


title: GUYT_50218 (HG-U133PLUS2)


title: GUYT_50223 (HG-U133PLUS2)


title: GUYT_50193 (HG-U133PLUS2)


title: GUYT_50248 (HG-U133PLUS2)


title: GUYT_50235 (HG-U133PLUS2)


title: GUYT_50210 (HG-U133PLUS2)


title: GUYT_50190 (HG-U133PLUS2)


title: GUYT_50213 (HG-U133PLUS2)


title: GUYT_50211 (HG-U133PLUS2)


title: GUYT_50221 (HG-U133PLUS2)


title: GUYT_50219 (HG-U133PLUS2)


title: GUYT_50192 (HG-U133PLUS2)


title: GUYT_50183 (HG-U133PLUS2)


title: GUYT_50204 (HG-U133PLUS2)


title: GUYT_50181 (HG-U133PLUS2)


title: GUYT_50184 (HG-U133PLUS2)


title: GUYT_50174 (HG-U133PLUS2)


title: GUYT_50176 (HG-U133PLUS2)


title: GUYT_50177 (HG-U133PLUS2)


title: GUYT_50179 (HG-U133PLUS2)


title: GUYT_50173 (HG-U133PLUS2)


title: GUYT_50178 (HG-U133PLUS2)


title: GUYT_50160 (HG-U133PLUS2)


title: GUYT_50188 (HG-U133PLUS2)


title: GUYT_50200 (HG-U133PLUS2)


title: GUYT_50166 (HG-U133PLUS2)


title: GUYT_50168 (HG-U133PLUS2)


title: GUYT_50182 (HG-U133PLUS2)


title: GUYT_50155 (HG-U133PLUS2)


title: GUYT_50163 (HG-U133PLUS2)


title: GUYT_50158 (HG-U133PLUS2)


title: GUYT_50159 (HG-U133PLUS2)


title: GUYT_50156 (HG-U133PLUS2)


title: GUYT_50172 (HG-U133PLUS2)


title: GUYT_50150 (HG-U133PLUS2)


title: GUYT_50169 (HG-U133PLUS2)


title: GUYT_50162 (HG-U133PLUS2)


title: GUYT_50153 (HG-U133PLUS2)


title: GUYT_50151 (HG-U133PLUS2)


title: GUYT_50154 (HG-U133PLUS2)


title: GUYT_50148 (HG-U133PLUS2)


title: GUYT_50137 (HG-U133PLUS2)


title: GUYT_50146 (HG-U133PLUS2)


title: GUYT_50143 (HG-U133PLUS2)


title: GUYT_50126 (HG-U133PLUS2)


title: GUYT_50134 (HG-U133PLUS2)


title: GUYT_50131 (HG-U133PLUS2)


title: GUYT_50135 (HG-U133PLUS2)


title: GUYT_50149 (HG-U133PLUS2)


title: GUYT_50138 (HG-U133PLUS2)


title: GUYT_50125 (HG-U133PLUS2)


title: GUYT_50128 (HG-U133PLUS2)


title: GUYT_50130 (HG-U133PLUS2)


title: GUYT_50122 (HG-U133PLUS2)


title: GUYT_50119 (HG-U133PLUS2)


title: GUYT_50136 (HG-U133PLUS2)


title: GUYT_50118 (HG-U133PLUS2)


title: GUYT_50124 (HG-U133PLUS2)


title: GUYT_50117 (HG-U133PLUS2)


title: GUYT_50112 (HG-U133PLUS2)


title: GUYT_50111 (HG-U133PLUS2)


title: GUYT_50116 (HG-U133PLUS2)


title: GUYT_50132 (HG-U133PLUS2)


title: GUYT_50247 (HG-U133PLUS2)


title: GUYT_50110 (HG-U133PLUS2)


title: GUYT_50109 (HG-U133PLUS2)


title: GUYT_50107 (HG-U133PLUS2)


title: GUYT_50105 (HG-U133PLUS2)


title: GUYT_50115 (HG-U133PLUS2)


title: GUYT_50108 (HG-U133PLUS2)


title: Col-0 +ABA repl2

city: San Diego

first: Julian

last: Schroeder

address: 9500 Gilman Drive

institute: University of California San Diego

description: Wild type (Col) plants were treated with ddH2O including 50 micromolar Abscisic Acid for 4 hours.

data_processing: Affymetrix MAS5 software

source_name: Columbia wild-type leaves, Abscisic Acid treatment

label_protocol: 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: 500 mg of green plant tissue of 4-week old plants was frozen and ground in liquid nitrogen. Total RNA was extracted using the TRIzol method (Invitrogen) and purified by RNeasy kit (Qiagen).

treatment_protocol: Sprayed plant with ddH2O containing 50 micromolar ABA, incubation for 4 hours

tag: Arabidopsis thaliana, ecotype Columbia, leaves of 4 week-old plants, sprayed with Abscisic Acid (ABA)


title: abh1 -ABA repl1

description: abh1 plants were mock-treated with ddH2O for 4 hours.

source_name: abh1 mutant leaves, no treatment

treatment_protocol: Sprayed plant with ddH2O (mock treatment)

tag: Arabidopsis thaliana, ABA hypersensitive 1 (abh1) mutant, leaves of 4 week-old plants, no treatment


title: GUYT_50102 (HG-U133PLUS2)


title: skeletal muscle

status: Public on Feb 23 2007

city: St. Louis

middle: Martin

last: Murphy

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

description: The RNA for the Liver, Brain, Thymus, Heart, Lung, Spleen, Testicle, Ovary, and Kidney hybridizations were used from the Total RNA: Mouse Normal Tissue purchased from Ambion (Austin, TX). The RNA for the Placenta, Day 7 Embryo, Eye, Uterus, Stomach, Lymph Node, and Skeletal Muscle were used from the Mouse Total RNA Master Panel purchased from BD Clontech (Palo Alto, CA)

source_name: skeletal muscle


title: abh1 +ABA repl2

description: abh1 plants were treated with ddH2O containing 50 micromolar Abscisic Acid for 4 hours.

source_name: abh1 mutant leaves, Abscisic Acid treatment

treatment_protocol: Sprayed plants with ddH2O containing 50 micromolar ABA, incubation for 4 hours

tag: Arabidopsis thaliana, ABA hypersensitive 1 (abh1) mutant, leaves of 4 week-old plants, sprayed with Abscisic Acid (ABA)


title: abh1 -ABA repl2


title: submax gland

source_name: submax gland


title: testis

source_name: testis


title: abh1 +ABA repl1


title: GUYT_50106 (HG-U133PLUS2)


title: thymus

source_name: thymus


title: Col-0 -ABA repl1

description: Wild type (Col) plants were mock-treated with ddH2O for 4 hours.

source_name: Columbia wild-type leaves, no treatment

tag: Arabidopsis thaliana, ecotype Columbia, leaves of 4 week-old plants, no treatment


title: stomach

source_name: stomach


title: placenta

source_name: placenta


title: Col-0 -ABA repl2


title: Col-0 +ABA repl1


title: ovary

source_name: ovary


title: spleen

source_name: spleen


title: kidney

source_name: kidney


title: heart

source_name: heart


title: lung

source_name: lung


title: eye

source_name: eye


title: lymph node

source_name: lymph node


title: liver

source_name: liver


title: GUYT_50225 (HG-U133PLUS2)

source_name: breast


title: embryo_d7


title: brain

source_name: brain


title: CD4+ naive

source_name: CD4+ naive


title: IMR-32_pCMV-DPP3_48hr_rep 2

status: Public on Feb 22 2007

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: standard Affymetrix procedures using the GeneChip Fluidics Station 450

scan_protocol: standard Affymetrix procedures using the GeneChip 3000 scanner

data_processing: gcRMA

label_protocol: cDNA synthesis and amplification employed the Affymetrix 3' IVT protocol.

extract_protocol: Human neuroblastoma cells IMR-32 (ATCC) were grown in DMEM medium supplemented with 10% FBS and treated as described above.  RNA was isolated using the RNeasy Kit from Qiagen.


title: RBP2-/- MEF(2)

city: New Haven

first: Qin

last: Yan

state: CT

address: Department of Pathology, PO Box 208023

institute: Yale School of Medicine

description:
Study the effect of RBP2 inactivation in gene expression
Analysis name: WK2006060808

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing:
Analysis of the raw gene expression profiling was performed using dChip software. Please see the following paper for details.
Klose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P, Gilliland DG, Zhang Y, Kaelin WG. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell (2007)

label: Biotin

source_name: RBP2-/- MEF

label_protocol: Affymetrix

extract_protocol: Total RNA isolation using RNeasy mini kit with on-column DNase digestion (Qiagen).

tag: Subconfluent RBP2-/- primary mouse embryonic fibroblasts at passage 3.


title: IMR-32_pCMV-SQSTM1_48hr_rep 1


title: wild type MEF(2)

description:
Study the effect of RBP2 inactivation in gene expression
Analysis name: WK2006060807

source_name: wild type MEF

tag: Subconfluent wild type primary mouse embryonic fibroblasts at passage 3.


title: RBP2-/- MEF(1)

description:
Study the effect of RBP2 inactivation in gene expression
Analysis name: WK2006060806


title: IMR-32_pCMV-DPP3_48hr_rep 1


title: wild type MEF(1)

description:
Study the effect of RBP2 inactivation in gene expression
Analysis name: WK2006060805

data_processing:
Analysis of the raw gene expression profiling was performed using dChip software. Please see the following paper for details.
Klose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P, Gilliland DG, Zhang Y, Kaelin WG. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell  (2007)


title: IMR-32_pCMV_48hr_rep 2


title: hBSMC_control_rep2

status: Public on Feb 20 2007

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

institute: Laval University

description: Human primary bronchial smooth muscle cells were grown to near confluence, starved for 24 hours (medium containing 0.1% FBS) and then treated with vehicle (0.05% ethanol) for an additional 24 hours before RNA extraction.

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G and the data was extracted using Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: Expression values were extracted using the Robust Multichip Average method (Irizarry RA, Hobbs B, Collin F, et al. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-64)

source_name: human bronchial smooth muscle cell_vehicle_24h

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

growth_protocol: Cells were growth in Smooth muscle Growth Medium (SmGM-2 Bulletkit, Cambrex) which included Smooth muscle Basal Medium (SmBM) supplemented with 5 % Fetal Bovine Serum (FBS), hEGF (0.5 ng/ml), hFGF (2 ng/ml), insulin (5 µg/ml) and GA-1000 (100 ng/ml of Gentamicin and 0.1 ng/ml of Amphotericin-B), according to manufacturer's instructions.

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry (Ultrospec 2100 pro).

treatment_protocol: BSMCs were grown in 25 cm2 flasks in SmGM and starved for 24 hours (SmBM supplemented with 0.1% FBS) before stimulation. Supernatant was removed and cells were incubated for 24 hours in fresh growth factor-free medium with vehicle (ethanol at 0.05%).

tag: ethnicity

value: Hispanic

tag: Gender

tag: Age

tag: Tissue

value: primary human bronchial smooth muscle cells


title: hBSMC_vitamin D_rep3

description: Human primary bronchial smooth muscle cells were grown to near confluence, starved for 24 hours (medium containing 0.1% FBS) and then treated with 100 nM of vitamin D (1alpha,25-Dihydroxyvitamin D3) for an additional 24 hours before RNA extraction.

source_name: human bronchial smooth muscle cell_VitD_100nM_24h

treatment_protocol: BSMCs were grown in 25 cm2 flasks in SmGM and starved for 24 hours (SmBM supplemented with 0.1% FBS) before stimulation. Supernatant was removed and cells were incubated for 24 hours in fresh growth factor-free medium with 100 nM of 1alpha,25-Dihydroxyvitamin D3 (Sigma, Saint Louis, Missouri).


title: IMR-32_pCMV_48hr_rep 1


title: hBSMC_control_rep1


title: hBSMC_control_rep3


title: IMR-32_pCMV-SQSTM1_48hr_rep 2


title: hBSMC_vitamin D_rep2


title: GUYT_50120 (HG-U133PLUS2)

tag: samplename

tag: ID

tag: series


title: thymus_CD4Cre-ctnnbex3_4

status: Public on Feb 17 2007

city: Boston

first: Fotini

last: Gounari

state: MA

address: 75 Kneeland, 12th floor

department: molecular oncology research institute

institute: Tufts-New England Medical Center

description: Total RNA from thymocytes or tumor was extracted using TRIZOL reagent followed by purification with the Qiagen RNeasy mini kit. The quantity and quality of RNA were determined by spectrophotometric analysis and electrophoresis on a 2.0% agarose gel. 10 micrograms of total RNA in 10ul sterile H2O were used for first and second strand cDNA synthesis, followed by an in vitro transcription reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphatases to produce biotinylated cRNAs.

hyb_protocol: The standard protocol for Affymetrix gene chips was used. Briefly, biotinylated cRNA was hybridized onto chips in hybridization buffer overnight at 45C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that did not hybridize to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

scan_protocol: GeneChip HT as scanner

data_processing:
Normalization. Normalization of expression values ensures the comparability of gene expression estimates across different samples. In dChip, normalization is done at Perfect Match (PM) and MM (Mismatch) before the calculation of Model-Based Expression Indices (MBEIs). By default an array with median intensity is chosen as the baseline array against which other arrays are normalized at probe intensity level. The invariant set normalization method is used in which a subset of Perfect Match (PM) probes with small within-subset rank difference in the two arrays is used as a basis for the normalization.
	Transformation. We used D-Chip software to calculate expression index. Model based expression index based on PM/MM difference were calculated for each gene in each sample. The details could be found in (C Li and W Wong. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl. Acad. Sci. Vol. 98, 31-36, 2001a.). Using the combination of a pair of 25-mer probes that are designed to be perfect match (PM) and mismatch (MM) to the targets offers the balance of highest sensitivity and specificity in the presence of a complex background-especially for low abundance transcripts.
	Data selection procedures. Before analysis, the arrays were normalized at PM/MM probe level followed by computing model-base expression levels. Genes were filtered to adjust variation across samples: 0.30, Standard deviation/Mean, 10.00, P call % > =50%. Genes that showed more than 3-fold change in the thymocytes between LckCre to CD4Cre-Ctnnbex3 or CD4Cre-Ctnnbex3 pretransformed thymocytes to lymphomas were selected. Notch pathway related genes were chosen.

source_name: CD4Cre-ctnnbex3 mouse before T cell transformation

extract_protocol: Total thymocytes or lymphomas from mice were collected and homogenized for total RNA isolation with TRIZOL reagent (GIBCO BRL) and purified with Qiagen RNeasy mini kit.

treatment_protocol: thymocytes were kept in TRIZOL reagent and stored at -80C before total RNA isolation

tag: Mice with upregulation of b-catenin developed lymphomas, this mouse was killed before it had thymocyte transformation


title: thymus_control1

source_name: wild type mouse

label_protocol: The standard protocol for Affymetrix gene chips was used. Briefly, biotinylated cRNA was hybridized onto chips in hybridization buffer overnight at 45C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that did not hybridize to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

tag: This mouse was mixted background.


title: thymus_control5

tag: this mouse had a mixed gene background


title: thymus_control2

tag: this mouse was mixted geneback


title: thymus_CD4Cre-ctnnbex3_3


title: thymus_CD4Cre-ctnnbex3_1


title: thymus_CD4Cre-ctnnbex3_5


title: thymus_CD4Cre-ctnnbex3_2


title: thymus_lymphoma1

source_name: CD4Cre-ctnnbex3 mouse with lymphoma

tag: Mice with upregulation of b-catenin developed lymphomas, this mouse was mixed gene background, and had lymphoma at 99 days old.


title: hBSMC_vitamin D_rep1


title: thymus_control4


title: thymus_control3

tag: this mouse had a mixed gene backgrond


title: thymus_lymphoma2

tag: Mice with upregulation of b-catenin developed lymphomas, this mouse was mixed gene background, and had lymphoma at 75 days old.


title: thymus_lymphoma8

tag: Mice with upregulation of b-catenin developed lymphomas, this mouse was mixed gene background, and had lymphoma at 98 days old.


title: thymus_lymphoma5

treatment_protocol: thymocytes were kept in TRIZOL reagent and stored at -80 before total RNA isolation

tag: Mice with upregulation of b-catenin developed lymphomas, this mouse was mixed gene background, and had lymphoma at 65 days old


title: thymus_lymphoma4

tag: Mice with upregulation of b-catenin developed lymphomas, this mouse was mixed gene background, and had lymphoma at 93 days old.


title: thymus_lymphoma7

tag: Mice with upregulation of b-catenin developed lymphomas, this mouse was mixed gene background, and had lymphoma at 86 days old.


title: Murray_2-3_T4-APH_Rep1_ATH1

status: Public on Feb 16 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description:
DNA replication inhibitor: aphidicolin
growth media type: liquid culture media
light regime: continuous darkness
nutrients: 100 ml MS salts, 3% sucrose, 0.5 mg/l NAA, 0.05 mg/l kinetin
average daily temperature: 27oC

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T4 sample was taken at 4 hours after washing to release the block (exp. variable; time course).

tag: Developmental stage

value: early stationary phase

value: cell suspension


title: thymus_lymphoma6

tag: Mice with upregulation of b-catenin developed lymphomas, this mouse was mixed gene background, and had lymphoma at 87 days old.


title: NIXKO3 SPLEEN

status: Public on Feb 14 2007

city: Cincinnati

first: Bruce

middle: J

last: Aronow

institute: Cincinnati Children's Hospital Medical Center

description: Samples used for hybridization consisted of non-pooled (NP) RNA extracts from the two genotypic groups namely wild type controls (WT) and Nix knockout animals (Nix-/-). A total of eight hybridization experiments were performed.

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains  0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Affymetrix murine MOE 430 2.0  gene chips were used.GeneChip CEL  files were subjected to  GC-RMA  normalization (get reference) using  the  GeneSpring GX 7.3.1
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

source_name: 8 week old Nix null mice (Nix-/-) spleen

label_protocol: Standard Affymetrix one-cycle target labeling protocol.

extract_protocol:
Total RNA was extracted from the murine spleens using Trizol kit (Invitrogen) and then purified two times using RNeasy columns (Qiagen)
Quality control steps:   RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used


title: thymus_lymphoma3

tag: This was from the lymphoma of a CD4cre-ctnnbex3 mouse with mixed background. The mouse was 81 days old.


title: Murray_2-5_T8-APH_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T8 sample was taken at 8 hours after washing to release the block (exp. variable; time course).

tag: Tissue


title: Murray_2-4_T6-APH_Rep1_ATH1

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T6 sample was taken at 6 hours after washing to release the block (exp. variable; time course).


title: Murray_2-6_T10-APH_Rep1_ATH1

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T10 sample was taken at 10 hours after washing to release the block (exp. variable; time course).


title: Murray_2-7_T12-APH_Rep1_ATH1

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T12 sample was taken at 12 hours after washing to release the block (exp. variable; time course).


title: Murray_2-8_T14-APH_Rep1_ATH1

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T14 sample was taken at 14 hours after washing to release the block (exp. variable; time course).


title: NIXKO6 SPLEEN

tag: 8 week old Nix null mice (Nix-/-) spleen


title: WT6 SPLEEN

source_name: 8 week old wild type mice spleen

tag: 8 week old wild type mice spleen


title: Murray_2-9_T16-APH_Rep1_ATH1

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T16 sample was taken at 16 hours after washing to release the block (exp. variable; time course).


title: WT4 SPLEEN


title: WT5 SPLEEN


title: NIXKO10 SPLEEN


title: WT3 SPLEEN


title: NIXKO2 SPLEEN


title: Lung_Gavage_DBET_2-58

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: Sample Type: tissue, Tissue: Lung, Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade

data_processing: affylmGUI, The Walter and Eliza Hall Institute of Medical Research

source_name: lung tissue, right lobe, gavage treatment, corn oil vehicle, 13 weeks, 5 days per week, 1,2-dibromoethane, 62 mg per kg

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

treatment_protocol: in vivo Treatment: 1,2-Dibromoethane, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 62, Units of Dose or Concentration: mg/kg

tag: Array Type

value: Affymetrix Mouse 430_2

tag: Amount to Core

tag: Units of Amount

value: ul

tag: Ratio

tag: Dilution

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: Good

tag: Sample Preservation

value: RNA later

tag: Strain or Line

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State

value: Adult

tag: Sacrifice Method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: Sex

value: Female

tag: Age

tag: Units of Age

value: weeks


title: Murray_2-1_T0-APH_Rep1_ATH1

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T0 sample was taken directly after washing to release the block (exp. variable; time course).

tag: Developmental stage

tag: Tissue


title: Lung_Gavage_DBET_2-56

tag: Array Type

tag: Amount to Core


title: Lung_Gavage_DBET_2-52

tag: Units of Amount

tag: Ratio


title: Lung_Gavage_MACR_2-109

source_name: lung tissue, right lobe, gavage treatment, water vehicle, 13 weeks, 5 days per week, N-methylolacrylamide, 50 mg per kg

treatment_protocol: in vivo Treatment: N-Methylolacrylamide, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 50, Units of Dose or Concentration: mg/kg

tag: Dilution

tag: RNA Integrity Number


title: Lung_Gavage_MACR_2-106

tag: Bioanalyzer Results

tag: Sample Preservation


title: Lung_Gavage_DBET_2-54

tag: Strain or Line

tag: NCBI Taxonomy ID


title: Lung_Gavage_CMPH_2-118

source_name: lung tissue, right lobe, gavage treatment, water vehicle, 13 weeks, 5 days per week, 2-chloromethylpyridine hydrochloride, 250 mg per kg

treatment_protocol: in vivo Treatment: 2-Chloromethylpyridine hydrochloride, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 250, Units of Dose or Concentration: mg/kg

tag: Individual

tag: Developmental State


title: Lung_Gavage_CMPH_2-113

tag: Sacrifice Method

tag: Sex


title: Lung_Gavage_CMPH_2-119

tag: Age

tag: Units of Age


title: Lung_Gavage_MACR_2-102


title: Lung_Feed_DIAZ_2-25

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, diazinon, 200 ppm

treatment_protocol: in vivo Treatment: Diazinon, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 200, Units of Dose or Concentration: ppm


title: Lung_Gavage_MACR_2-101


title: Lung_Feed_MALA_2-39

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, malathion, 16000 ppm

treatment_protocol: in vivo Treatment: Malathion, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 16000, Units of Dose or Concentration: ppm


title: Lung_Gavage_COUM_2-75

source_name: lung tissue, right lobe, gavage treatment, corn oil vehicle, 13 weeks, 5 days per week, coumarin, 200 mg per kg

treatment_protocol: in vivo Treatment: Coumarin, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 200, Units of Dose or Concentration: mg/kg


title: Lung_Feed_MALA_2-33


title: Lung_Feed_MALA_2-36


title: Lung_Feed_BBMP_2-4

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, 2,2-Bis(bromomethyl)-1,3-propanediol, 1250 ppm

treatment_protocol: in vivo Treatment: 2,2-Bis(bromomethyl)-1,3-propanediol, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1250, Units of Dose or Concentration: ppm


title: Lung_Feed_DIAZ_2-21


title: Lung_Feed_DIAZ_2-24


title: Lung_Feed_BBMP_2-6


title: Lung_Feed_MALA_2-38


title: Lung_Feed_BBMP_2-10


title: Lung_Gavage_COUM_2-72


title: Lung_Gavage_COUM_2-76


title: Lung_Feed_DIAZ_2-28


title: Lung_Gavage_COUM_2-80


title: Lung_Gavage_CMPH_2-115


title: Lung_Gavage_BENZ_2-85

source_name: lung tissue, right lobe, gavage treatment, corn oil vehicle, 13 weeks, 5 days per week, benzene, 100 mg per kg

treatment_protocol: in vivo Treatment: Benzene, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 100, Units of Dose or Concentration: mg/kg


title: Lung_Gavage_BENZ_2-86


title: Lung_Feed_BBMP_2-2


title: Lung_Gavage_BENZ_2-90


title: Lung_Feed_NAAC_2-19

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, 4-nitroanthranilic acid, 10000 ppm

treatment_protocol: in vivo Treatment: 4-Nitroanthranilic acid, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 10000, Units of Dose or Concentration: ppm


title: Lung_Feed_NAAC_2-15


title: Lung_Feed_NAAC_2-17


title: Lung_Gavage_BENZ_2-82


title: Lung_Feed_NAAC_2-13


title: Lung_Gavage_CCON_2-93

source_name: lung tissue, right lobe, gavage treatment, 13 weeks, 5 days per week, corn oil vehicle control

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg


title: Lung_Gavage_CCON_2-99


title: Lung_Gavage_WCON_2-121

source_name: lung tissue, right lobe, gavage treatment, 13 weeks, 5 days per week, water vehicle control

treatment_protocol: in vivo Treatment: Distilled Water, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg


title: Lung_Gavage_CCON_2-95


title: Lung_Gavage_CCON_2-59


title: Lung_Gavage_CCON_2-97


title: Lung_Gavage_CCON_2-60


title: Lung_Gavage_CCON_2-134


title: Lung_Feed_PCNB_1-20

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, pentachloronitrobenzene, 8187 ppm

treatment_protocol: in vivo Treatment: Pentachloronitrobenzene, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 8187, Units of Dose or Concentration: ppm

value: ug


title: Lung_Feed_FCON_2-45

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, rodent chow control

treatment_protocol: in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm


title: Lung_Gavage_WCON_2-124


title: Lung_Gavage_WCON_2-129


title: Lung_Feed_FCON_2-43


title: Lung_Gavage_WCON_2-127


title: Lung_Feed_FCON_2-44


title: Lung_Feed_PCNB_1-18


title: Lung_Gavage_CCON_2-132