title: rat and mouse embryos transfer to mouse together, day 7 of pregnancy replicate 3

city: Beijing

first: Xiujun

last: Fan

address: No25 Beishihuan Xilu

institute: Institute of Zoology

description: whole implantation site of rat embryos, day 7 of pregnancy in mouse uterus

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: implantation site

extract_protocol: Approximately 100mg implantation sites tissue were extracted by TRIzol following the instruction, and then purified by RNAeasy kit (Qiagen).

treatment_protocol: rat embryos were flush out at day 5 of pregnancy, mouse embryos were flushed out at day 4 of pregnancy, then transferred to day 3 pseudopregnancy ICR mouse together. The rat embryos implantation sites were collected at day 7 of pregnancy

tag: strain

value: ICR

tag: gender

value: female

tag: weight

value: 25 gram

tag: tissue

value: uterus

tag: gestation day

value: day 7

tag: treatment

value: embryos transfer

tag: rat strain

value: wistar


title: rat embryos transfer to mouse, day 7 of pregnancy replicate 1

status: Public on Dec 01 2007

type: RNA

country: China

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

treatment_protocol: rat embryos were flush out at day 5 of pregnancy, then transferred to day 3 pseudopregnancy ICR mouse. The rat embryos implantation sites were collected at day 7 of pregnancy


title: rat embryos transfer to mouse, day 9 of pregnancy replicate 1

description: whole implantation site of rat embryos, day 9 of pregnancy in mouse uterus

treatment_protocol: rat embryos were flushed out at day 5 of pregnancy, then transferred to day 3 pseudopregnancy ICR mouse. The rat embryos implantation sites were collected at day 9 of pregnancy

value: day 9


title: mouse embryos transfer to mouse, day 9 of pregnancy replicate 2

description: whole implantation site of mouse embryos, day 9 of pregnancy in mouse uterus

treatment_protocol: mouse embryos were flushed out at day 4 of pregnancy, then transferred to day 3 pseudopregnancy ICR mouse. The mouse embryos implantation sites were collected at day 9 of pregnancy


title: rat and mouse embryos transfer to mouse together, day 9 of pregnancy replicate 1

treatment_protocol: rat embryos were flushed out at day 5 of pregnancy, mouse embryos were flushed out at day 4 of pregnancy, then transferred to day 3 pseudopregnancy ICR mouse together. The rat embryos implantation sites were collected at day 9 of pregnancy


title: rat embryos transfer to mouse, day 9 of pregnancy replicate 2


title: mouse embryos transfer to mouse, day 9 of pregnancy replicate 1


title: rat and mouse embryos transfer to mouse together, day 7 of pregnancy replicate 1


title: PGC-1alpha 3

city: Boston

first: Pere

last: Puigserver

state: MA

address: 1 Jimmy Fund Way

department: Cancer Biology

country: USA

institute: Dana-Farber Cancer Institute

description: Affymetrix original enzo processing protocol

hyb_protocol: standard affymetrix hybridization protocol

data_processing:
Data were analyzed by RMA (with default settings) in BioConductor 1.2
Global scaling to TGT 150

label: Biotin

label_protocol: standard affymetrix labelling protocol

growth_protocol: TSC2-/- MEFs were cultured in DMEM containing 10%CCS.  Media was changed at time of treatment.

extract_protocol: trizol isolation

treatment_protocol: confluent TSC2-/- MEFs were infected with adenovirus expressing PGC-1alpha for 10 hours, media was changed and cells were harvested 14 hours later.

tag: Mouse embryo fibroblast tsc2--

tag: confluent TSC2-/- MEFs


title: mouse embryos transfer to mouse, day 7 of pregnancy replicate 1

description: whole implantation site of mouse embryos, day 7 of pregnancy in mouse uterus

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets

treatment_protocol: Mouse embryos were flush out at day 4 of pregnancy, then transferred to day 3 pseudopregnancy ICR mouse. The mouse embryos implantation sites were collected at day 7 of pregnancy


title: rat and mouse embryos transfer to mouse together, day 7 of pregnancy replicate 2


title: rat and mouse embryos transfer to mouse together, day 9 of pregnancy replicate 2


title: 15_0001C_Day1_40

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

description: Controls

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L 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), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C 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 EukGE-WS2v5_450. 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:
Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

organism: Homo sapiens

source_name: Whole blood from normal children.

label_protocol: 120 ng of total RNA from 2 wild type [WT] and 4 beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

extract_protocol:
Total RNA was extracted from whole blood using the PaxGene system.
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto,CA].

treatment_protocol: Samples were not manipulated.

tag: Control

tag: Survivor

value: Female


title: rat embryos transfer to mouse, day 7 of pregnancy replicate 2


title: mouse embryos transfer to mouse, day 7 of pregnancy replicate 2

description: whole implantation site of mouse embryos day 7 of pregnancy in mouse uterus


title: 17-0001A_Day1_44

description: Septic shock

source_name: Whole blood from children with septic shock.

tag: Septic shock

value: Male

tag: organism

tag: organism class


title: 15_0002C_Day1_41

description: Controls


title: 15_0005C_Day1_43

description: Controls


title: Rapamycin 2

source_name: rapamycin-treated

treatment_protocol: 14 hour 20nM rapamycin treatment


title: 15_0003C_Day1_42

description: Controls


title: 15-0011A_Day1_38

description: Septic shock

value: Staph aureus

value: Gram pos


title: 13-0002A_Day1_35

description: Septic shock


title: 11-0057A_Day1_33

description: Septic shock

value: Group A Strep


title: 11_0027C_Day1_30

description: Controls


title: 14-0004A_Day1_37

description: Septic shock

tag: Non survivor

value: Group B Strep


title: 11-0054A_Day1_32

description: Septic shock


title: 11_0013C_Day1_25

description: Controls


title: 11_0018C_Day1_27

description: Controls


title: 11_0037C_Day1_31

description: Controls


title: 12-0002A_Day1_34

description: Septic shock

value: Adenovirus

value: Viral


title: 11_0012C_Day1_24

description: Controls


title: 11_0019C_Day1_28

description: Controls


title: 07-0006A_Day1_18

description: Septic shock

value: Strep pneumo


title: 11_0009C_Day1_22

description: Controls


title: 11_0008C_Day1_21

description: Controls


title: 10-0021A_Day1_19

description: Septic shock


title: 10-0029A_Day1_20

description: Septic shock


title: 11_0014C_Day1_26

description: Controls


title: 06-0009A_Day1_17

description: Septic shock


title: 11_0011C_Day1_23

description: Controls


title: 02-0002A_Day1_16

description: Septic shock


title: 01_0049A_Day1_12

description: Septic shock


title: 01_0052A_Day1_14

description: Septic shock

tag: update


title: 01_0053A_Day1_15

description: Septic shock


title: 01_0051A_Day1_13

description: Septic shock


title: 01-0033A_Day1_10

description: Septic shock


title: 01-0066A_Day1_9

description: Septic shock


title: 01-0045A_Day1_11

description: Septic shock


title: 01-0062A_Day1_8

description: Septic shock


title: 11_0020C_Day1_29

description: Controls


title: 01-0061A_Day1_7

description: Septic shock


title: 01-0044A_Day1_3

description: Septic shock


title: 01-0059A_Day1_5

description: Septic shock


title: 765E

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description: Gene expression of brain tissue from meningioma patient. Progesterone (PR) and estrogen (ER) hormone receptors were measured via immunohistochemistry and compared with gene expression profiling results.

hyb_protocol: The mRNA was reverse transcribed to generate cDNA, which was then biotinylated and hybridized to Affymetrix U133 plus 2.0 expression arrays

scan_protocol: Affymetrix

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: brain meningioma

label_protocol: Biotinylated

extract_protocol: Tumor tissue was snap-frozen at the time of surgery and stored at –80 degrees Celsius in the Brain Tumor Tissue Bank at Brigham and Women’s Hospital. Extraction of RNA from these fresh frozen tumor specimens was performed.

tag: ER

tag: PR


title: 01-0058A_Day1_4

description: Septic shock

tag: gender


title: 01-0007A_Day1_0

description: Septic shock

value: Neisseria


title: 765F


title: 765H


title: 01-0060A_Day1_6

description: Septic shock


title: 765C


title: 711G


title: 01-0036A_Day1_1

description: Septic shock


title: 711C


title: 711D


title: 711B


title: 711E


title: 615I


title: 711A


title: 615E


title: 615H


title: 615J


title: 615G


title: 01-0043A_Day1_2

description: Septic shock


title: 615B


title: 615D


title: 711I


title: 15-0012A_Day1_39

description: Septic shock


title: 525C


title: 525D


title: 525A


title: Col-0 control 3

city: New York

first: Rafael

last: Catala

state: NY

address: 1230 York ave

department: Plan Molecular Biology

institute: The Rockefeller University

description: GeneChip Expression Analysis Technical Manual

organism: Arabidopsis thaliana

source_name: Col-0 c3

label_protocol: MessageAmp™ II-Biotin Enhanced

extract_protocol: TriZOL

tag: Ecotype

value: Columbia 0

tag: age

value: 3 weeks

tag: Condition

value: control


title: siz1-3 control 3

hyb_protocol: GeneChip Expression Analysis Technical Manual

source_name: siz1-3 c3

tag: Genotype


title: 615A


title: siz1-3 drought 3

scan_protocol: GeneChip Expression Analysis Technical Manual

source_name: siz1-3 d3

value: drought 2hr


title: siz1-3 control 2

data_processing: GeneChip Expression Analysis Technical Manual

source_name: siz1-3 c2


title: 525B


title: 478F


title: siz1-3 drought 2

source_name: siz1-3 d2


title: Col-0 drought 2

source_name: Col-0 d2


title: siz1-3 control 1

source_name: siz1-3 c1


title: Col-0 control 2

source_name: Col-0 c2


title: 478G


title: 478B


title: siz1-3 drought 1

source_name: siz1-3 d1


title: 14-0002A_Day1_36

description: Septic shock


title: Col-0 drought 3

source_name: Col-0 d3


title: 478E


title: 478D


title: 478H


title: 478C


title: Col-0 drought 1

source_name: Col 0 d1


title: Col-0 control 1

source_name: Col-0 c1

tag: Columbia 0

tag: Age

value: 21 days


title: 478A


title: HUVEC vs TNF-alpha 8hr exposure

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

hyb_protocol: Hybridized microarrays were washed according to manufacturer’s protocols and subjected to a signal enhancement protocol consisting of an initial incubation with streptavidin-phycoerythrin conjugate followed by goat anti-streptavidin biotinylated antibody and a final staining with the streptavidin-phycoerythrin conjugate.

scan_protocol: The microarrays were scanned using the GeneArray™ scanner with an argon ion laser excitation source and emission detected by a photomultiplier tube through a 570-nm long pass filter.  Digitized image data were processed using GeneChip® Operating Software.

data_processing: normalized to all data points

source_name: human umbilical vein endothelial cells

label_protocol: Ten micrograms of total RNA were subjected to first- and second-strand cRNA synthesis incorporating biotin-labeled nucleotides.  cRNA was then fragmented and subsequently hybridized overnight with microarray chips using the manufacturer’s hybridization buffer.

growth_protocol: grown in M199 culture medium supplemented with human serum at 37 degrees Celsius for 8 hours in 5% CO2

extract_protocol: Trizol reagent

treatment_protocol: 8hr culture of confluent culture of HUVECs in M199 culture medium containing 1ng/ml human TNF-alpha

tag: HUVECs cultured in M199 culture medium containing 1ng/ml TNF-alpha for 8hr


title: Normal_colon_14_12April05

city: North Ryde

first: Lawrence

middle: C

last: LaPointe

state: NSW

address: 11 Julius Ave

country: Australia

institute: Clinical Genomics

hyb_protocol: An hybridization cocktail was prepared with 15ug of cRNA (0.5 ug/uL) and hybridized to HG U133 Plus 2.0 microarrays for 16h at 45degC in an Affymetrix Hybridization Chamber 640.  Each cRNA sample was spiked with standard prokaryotic hybridization controls for quality monitoring.

scan_protocol: Hybridized microarrays were stained with streptavidin phycoerytherin and washed with a solution containing biotinylated anti-streptavidin antibodies using the Affymetrix Fluidics Station 450.  Finally, the stained and washed microarrays were scanned with the Affymetrix Scanner 3000.

data_processing: The Affymetrix software package was used to transform raw microarray image files to digitized format.  As for the Discovery set above, gene expression levels for the this data set were calculated using MAS 5.0 (Affymetrix), scaled to 100 for quality control purposes and with the RMA normalization algorithm for expression data.

source_name: colorectum, ascending

label_protocol:
To measure relative expression of mRNA transcripts, tissue RNA samples were analyzed using Affymetrix HG U133 Plus 2.0 GeneChips (Affymetrix, Santa Clara, CA USA) according to the manufacturers protocols.  Biotin labeled cRNA was prepared using 5ug (1.0 ug/uL) total RNA
(approx. 1 ug mRNA) with the One-Cycle cDNA kit (incorporating a T7-oligo(dT) primer) and the GeneChip IVT labeling kit.  In vitro
transcribed cRNA was fragmented (20ug) and analyzed for quality control purposes by spectrophotometry and gel electrophoresis prior to hybridization.

extract_protocol:
Frozen samples were processed by the authors using standard protocols and commercially available kits.  Briefly, frozen tissues were homogenized using a carbide bead mill (Mixer Mill MM 300, Qiagen, Melbourne, Australia) in the presence of chilled Promega SV RNA Lysis Buffer (Promega, Sydney, Australia) to neutralize RNase activity.  Homogenized tissue lysates for each tissue were aliquoted to convenient volumes and stored -80degC.  Total RNA was extracted from tissue lysates using the Promega SV Total RNA system according to manufacturers instructions and integrity
was assessed visually by gel electrophoresis.

treatment_protocol:
The colorectal specimens in this set were collected from a tertiary referral
hospital tissue bank in metropolitan Adelaide, Australia (Repatriation General Hospital and Flinders Medical Centre). The tissue bank and this project were approved by the Research and Ethics Committee of the Repatriation General Hospital and patient consent was received for each tissue studied.  Following surgical resection, specimens were placed in a sterile receptacle and collected from theatre.  The time from operative resection to collection from theatre was variable but not more than 30 minutes.  Samples, approximately 125mm3 (5x5x5mm) in size, were taken from the macroscopically normal tissue as far from pathology as possible, defined both by colonic region as well as by distance either proximal or distal to the pathology. Tissues were placed in cryovials, then immediately immersed in liquid nitrogen and stored at -150degC until processing.

tag: Tissue

value: Colorectal mucosa

tag: Location

value: (as per 'SOURCE')


title: HUVEC vs SC5314 3hr exposure 3rd expt

growth_protocol: grown in M199 culture medium supplemented with human serum at 37 degrees Celsius for 3 hours in 5% CO2

treatment_protocol: 3hr co-culture of confluent culture of HUVECs with SC5314 strain of Candida albicans in M199 culture medium

tag: HUVECs co-cultured with SC5314 strain (Candida albicans) for 3hrs in M199 culture medium


title: Normal_colon_01_20April05

hyb_protocol: An hybridization cocktail was prepared with 15ug of cRNA (0.5 ug/uL) and hybridized to HG U133 Plus 2.0 microarrays for 16h at 45degC in an Affymetrix Hybridization Chamber 640.  Each cRNA sample was spiked with standard prokaryotic hybridization controls for

source_name: colorectum, sigmoid

label_protocol: To measure relative expression of mRNA transcripts, tissue RNA samples were analyzed using Affymetrix HG U133 Plus 2.0 GeneChips (Affymetrix, Santa Clara, CA USA) according to the manufacturers protocols.  Biotin labeled cRNA was prepared using 5ug (1.0 ug/uL) total RNA


title: HUVEC vs SC5314 8hr 3rd expt

treatment_protocol: 8hr co-culture of confluent culture of HUVECs with SC5314 strain of Candida albicans in M199 culture medium

tag: HUVECs co-cultured with SC5314 strain (Candida albicans) for 8hrs in M199 culture medium


title: HUVEC vs M199 8hr exposure 3rd expt

treatment_protocol: 8hr culture of HUVECs in M199 culture medium

tag: HUVECs cultured in M199 culture medium alone (reference sample)


title: Normal_colon_40_20April05

source_name: colorectum, rectum


title: Normal_colon_39_20April05


title: Normal_colon_36_13April05


title: Normal_colon_33_20April05


title: Normal_colon_35_13April05


title: Normal_colon_29_20April05

source_name: colorectum, transverse


title: Normal_colon_27_13April05


title: HUVEC vs TNF-alpha 3hr

treatment_protocol: 3hr culture of confluent culture of HUVECs  in M199 culture medium containing 1ng/ml human TNF-alpha

tag: HUVECs cultured in M199 culture medium containing 1ng/ml human TNF-alpha for 3hrs


title: Normal_colon_25_13April05


title: HUVEC vs CAN34 8hr exposure 3rd expt

treatment_protocol: 8hr co-culture of confluent culture with CAN34 strain of Candida albicans in M199 culture medium

tag: HUVECs co-cultured with CAN34 strain (Candida albicans) for 8hrs in M199 culture medium


title: Normal_colon_23_13April05


title: Normal_colon_22_13April05

source_name: colorectum, cecum


title: Normal_colon_20_13April05


title: Normal_colon_19_12April05


title: Normal_colon_08_12April05


title: Normal_colon_31_13April05


title: Healthy volunteer_V

status: Public on Nov 29 2007

city: boston

first: sonia

last: vallet

address: 44 binney street

department: medical oncology

institute: dana-farber cancer institute

description: Healthy volunteer

hyb_protocol: The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidic station 400 (Affymetrix, Santa Clara, CA, USA) that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe.

scan_protocol: The DNA chips were then analyzed using a Gene Array Scanner (Affymetrix).

data_processing: CEL files were obtained using Affymetrix Microarray Suite 5.0 software; a DNA Chip Analyzer (DChip) normalized all CEL files to a baseline array with overall median intensity, and the model-based expression (perfect match only) was used to compute expression values.

source_name: Healthy volunteer

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.

extract_protocol: Total RNA was isolated from PBMCs using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA), followed by additional purification using RNeasy from Qiagen.

tag: Healthy volunteer


title: Normal_colon_16_12April05


title: Normal_colon_12_12April05


title: HUVEC vs CAN34 3hr exposure 3rd expt

source_name: HUVECs co-cultured with CAN34 strain (Candida albicans)

treatment_protocol: 3hr co-culture of confluent culture with CAN34 strain of Candida albicans in M199 culture medium

tag: human umbilical vascular endothelial cells (primary culture)


title: Healthy volunteer_IV

description: Healthy volunteer


title: Healthy volunteer_III

description: Healthy volunteer


title: Normal_colon_03_12April05


title: Healthy volunteer_II

description: Healthy volunteer


title: Peripheralbloodmononuclearcells_MM_9

description: Multiple Myeloma patient on bisphosphonate therapy without osteonecrosis of the jaw

source_name: Peripheral blood mononuclear cells, MM patient without ONJ


title: Peripheralbloodmononuclearcells_MM_10

tag: Multiple Myeloma patient on bisphosphonate therapy without osteonecrosis of the jaw


title: Peripheralbloodmononuclearcells_MM_6


title: Peripheralbloodmononuclearcells_MM_2


title: Peripheralbloodmononuclearcells_MM_1


title: Peripheralbloodmononuclearcells_MM_3


title: Healthy volunteer_Ia

description: Healthy volunteer


title: Peripheralbloodmononuclearcells_MM_5


title: Peripheralbloodmononuclearcells_MM_8


title: Peripheralbloodmononuclearcells_MM_7


title: Peripheralbloodmononuclearcells_MM_4


title: Peripheralbloodmononuclearcells_ONJ_k

source_name: Peripheral blood mononuclear cells, MM patient with ONJ

tag: Multiple Myeloma patient with osteonecrosis of the jaw, patient data will be provided in the manuscript


title: Peripheralbloodmononuclearcells_ONJ_j

description: Multiple Myeloma patient with osteonecrosis of the jaw


title: Peripheralbloodmononuclearcells_ONJ_i


title: ICC-DMP, biological rep2

city: Reno

first: Hui

last: Chen

state: NV

address: 1664 N Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

description: Gene expression data from ICC-DMP cells

hyb_protocol: Target cDNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip 3000 System  Spike controls were added to 15 µg fragmented cRNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin.

scan_protocol: The sample was scanned on an Affymetrix GeneChip 3000 system.

data_processing: Analysis was performed using publicly available software Bioconductor. Simpleaffy was used to preprocess individual probe intensities from CEL files into expression values from which fold changes were derived using Limma.  Robust MultiArray Analysis (RMA), which uses quantile normalization for cross-chip normalization, was used to preprocess the data.

source_name: BALB/c mice aged 6-9-days, small intestine

label_protocol: Total RNA from each sample was used to prepare biotinylated target RNA, according to the manufacturers' instructions.  Briefly, about 50 ng of total RNA was used to generate first strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with unlabelled ribonucleotides (Ambion, PN AM1333).  A second round of cDNA synthesis was then performed with random primers, followed by in vitro transcription with biotinylated UTP and CTP resulting in a final yield of more than 40ug cRNA.

extract_protocol: Total RNA was isolated and purified using Trizol (Invitrogen, Carlsbad, CA) and the RNeasy Mini kit (Qiagen, Valencia, CA) respectively per manufacturers' instructions.  RNA was quantified and its quality was tested by Agilent Bioanalyser (Agilent Technologies, Palo Alto, CA).

tag: ICC-DMP cells were isolated from the tunica muscularis tissues by fluorescence-activated cell sorting .


title: ICC-MY, biological rep2

description: Gene expression data from ICC-MY cells

tag: ICC-MY cells were isolated from the tunica muscularis tissues by fluorescence-activated cell sorting .


title: Peripheralbloodmononuclearcells_ONJ_f


title: ICC-MY, biological rep1

description: Gene expression data from ICC-MY cells


title: ICC-DMP, biological rep3

description: Gene expression data from ICC-DMP cells


title: tunica muscularis, biological rep2

description: Gene expression data from tunica muscularis tissues

tag: The mucosa and submucosa were removed by peeling and the tunica muscularis of the entire jejunum and ileum was used.


title: tunica muscularis, biological rep1


title: Peripheralbloodmononuclearcells_ONJ_e


title: ICC-MY, biological rep3

description: Gene expression data from ICC-MY cells


title: Peripheralbloodmononuclearcells_ONJ_c


title: Peripheralbloodmononuclearcells_ONJ_h


title: Peripheralbloodmononuclearcells_ONJ_b


title: Peripheralbloodmononuclearcells_ONJ_d


title: Peripheralbloodmononuclearcells_ONJ_g


title: 4hr MOCK Replicate 1

status: Public on Nov 28 2007

city: New Haven

first: Chloe

last: Mara

state: CT

address: 160 Prospect Street

department: MCDB

institute: Yale University

description: 4hr MOCK Replicate 1

hyb_protocol: cRNA is fragmented in the presence of heat and Mg+2 before hybridization to the array. The sample is hybridized to the standard array for 16 hours at 45°C.  The standard array is then washed and stained using the fluidics station and then scanned. (information from the Affymetrix Gene Expression website of the W.M. Keck Foundation Biotechnology Resource Laboratory)

scan_protocol: The scanner is a 16-bit sophisticated opto-mechanical confocal scanner which measures fluorescence intensity emitted by the labeled cRNA bound to the probe arrays.  The scanner uses a high-quality, solid state 532nm Diode-Pumped, Frequency Doubled Nd:YAG (Neodymium-doped Yttrium Aluminum Garnet) Green Laser.  The scanner optics are designed to condition the laser beam to deliver an excitation spot size of 3.5  μm and can detect as few as 400 phycoerythrin molecules in a 20 x 20 μm probe site. (information from the Affymetrix Gene Expression website of the W.M. Keck Foundation Biotechnology Resource Laboratory)

data_processing: The computer workstation with GeneChip Operating software controls the fluidics station and the scanner.  GeneChip Operating software can control up to eight fluidics stations using preprogrammed hybridization, wash, and stain protocols for the probe array.  The software also acquires and converts hybridization intensity data into a presence/absence call for each gene using appropriate algorithms. Finally, the software detects changes in gene expression between experiments by comparison analysis and formats the output into .txt files which can be used with other software programs for further data analysis. (information from the Affymetrix Gene Expression website of the W.M. Keck Foundation Biotechnology Resource Laboratory)

source_name: 35S::AP3-GR, ap3-3, 35S::PI, MOCK treated, 4hr

label_protocol: Single stranded cDNA is synthesized by reverse transcription using the poly (A) RNA present in the starting total RNA sample.  Single stranded cDNA is then converted into double stranded cDNA and purified using the Affymetrix Cleanup Module.  An in vitro transcription (IVT) reaction is then carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA. (information from keck.med.yale.edu/affymetrix/analysis.html)

extract_protocol: Flower buds were snap frozen in liquid nitrogen. Total RNA was extracted using the Trizol (GibcoBRL, Fredrick, MD, USA) reagent and protocol. RNA was cleaned using the Qiagen RNeasy Mini Kit (GmbH, Hamburg, Germany).

tag: Flower buds from 35S::AP3-GR, ap3-3, 35S::PI transgenic plants, MOCK treated, collected at 4hr.


title: 4hr DEX Replicate 2

description: 4hr DEX Replicate 2

source_name: 35S::AP3-GR, ap3-3, 35S::PI, DEX treated, 4hr

tag: Flower buds from 35S::AP3-GR, ap3-3, 35S::PI transgenic plants, DEX treated, collected at 4hr.


title: ICC-DMP, biological rep1

description: Gene expression data from ICC-DMP cells


title: 4hr MOCK Replicate 2

description: 4hr MOCK Replicate 2


title: 4hr DEX Replicate 1

description: 4hr DEX Replicate 1


title: 4hr MOCK Replicate 3

description: 4hr MOCK Replicate 3


title: HUVEC vs M199 3hr exposure 3rd expt

treatment_protocol: 3hr culture of HUVECs in M199 culture medium

tag: HUVECs cultured in M199 alone (reference sample)


title: normal with no hydrocortisone treatment-2

status: Public on Nov 26 2007

city: Nashville

first: Shirley

middle: Brody

last: Russell

address: 519 Light Hall

department: Medicine

institute: Vanderbilt University

description: Cell cultures were initiated from human biopsy material from normal dermal scars and keloids of adult males and females and frozen at first or second passage, in liquid nitrogen.  Experimental cultures were derived from the first passage of cells thawed from liquid nitrogen.

hyb_protocol: Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples

data_processing: For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).

source_name: Primary culture of dermal fibroblasts from normal scar, no hydrocortisone treatment

label_protocol: Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).  Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter.  In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.

growth_protocol: Five strains each of cultured low-passage fibroblasts from keloids and normal scars were thawed from liquid nitrogen, subcultured and triplicate cultures grown to confluency (10 days) under standard culture conditions (daily feeding with Ham’s Nutrient Mixture F10 + 10% FBS) with and without 1.5 micromolar hydrocortisone.

extract_protocol: Total RNA was isolated using a standard Trizol method with DNase treatment followed by a second Trizol extraction.

tag: strain

tag: Disorder

value: normal

tag: Condition

value: no hydrocortisone


title: normal with no hydrocortisone treatment-5

treatment_protocol: Five strains each of cultured low-passage fibroblasts from keloids and normal scars were thawed from liquid nitrogen, subcultured and triplicate cultures grown to confluency (10 days) under standard culture conditions (daily feeding with Ham’s Nutrient Mixture F10 + 10% FBS) with and without 1.5 micromolar hydrocortisone.


title: Peripheralbloodmononuclearcells_ONJ_a

source_name: Peripheral blood mononuclear cells, MM patients with ONJ


title: 4hr DEX Replicate 3

description: 4hr DEX Replicate 3


title: normal with no hydrocortisone treatment-4


title: normal scar treated with hydrocortisone-3

source_name: Primary culture of dermal fibroblasts from normal scar, treated with 1.5uM hydrocortisone

value: normal scar

value: +hydrocortisone


title: 0hr DEX Replicate 1

description: 0hr DEX Replicate 1

source_name: 35S::AP3-GR, ap3-3, 35S::PI, DEX treated, 0hr

tag: Flower buds from 35S::AP3-GR, ap3-3, 35S::PI transgenic plants, DEX treated, collected at 0hr.


title: normal with no hydrocortisone treatment-3


title: 0hr DEX Replicate 2

description: 0hr DEX Replicate 2


title: normal scar treated with hydrocortisone-4


title: 0hr DEX Replicate 3

description: 0hr DEX Replicate 3


title: normal with no hydrocortisone treatment-1


title: keloid treated with hydrocortisone-5

source_name: Primary culture of dermal fibroblasts from keloid, treated with 1.5uM hydrocortisone

value: keloid


title: keloid treated with hydrocortisone-2


title: normal scar treated with hydrocortisone-2


title: keloid treated with hydrocortisone-4


title: keloid with no hydrocortisone treatment-5

source_name: Primary culture of dermal fibroblasts from keloid, no hydrocortisone treatment


title: keloid treated with hydrocortisone-3


title: keloid with no hydrocortisone treatment-1


title: keloid with no hydrocortisone treatment-2


title: keloid with no hydrocortisone treatment-3


title: normal scar treated with hydrocortisone-1


title: keloid with no hydrocortisone treatment-4


title: Dex-rga(delta17)_shoots_4h_GA4+DEX_repl2

status: Public on Nov 21 2007

city: Durham

first: Rodolfo

last: Zentella

state: NC

address: Box 90338, Science Dr

department: Biology

institute: Duke University

description: The aim of this study is to identify early DELLA protein-responsive genes that are also regulated by gibberellins using a DEX-inducible system. Two transgenic lines were used: one induces the expression of a dominant, gibberellin non-responsive DELLA protein (rga-delta17); the other is a control line that carries the same vector, but lacks the rga-delta17 transgene. A time course study on the accumulation the inducible DELLA protein as well as quantitative PCR for transcripts of early gibberellin responsive genes indicated that 2h and 4h were optimal to look at DELLA-regulated genes that are also responsive to gibberellins

hyb_protocol: Standard protocol from Affymetrix

scan_protocol: Standard protocol from Affymetrix

source_name: shoots, 4h GA4+DEX

label_protocol: Standard protocol from Affymetrix

growth_protocol: Seeds were germinated on MS agar plates supplemented with 2% sucrose on a piece of nylon mesh as support. Seedlings were grown vertically for 8 days under continuous light at 22C. On day 7, seedlings were pretreated with 2 micromolar GA4 in maximize gibberellin responses. On day 8, seedlings were sprayed with either 2 uM GA4 (mock) or a combination of 2 uM GA and 10 uM DEX. Tissue was collected after 2h and 4h.

extract_protocol: Qiagen RNeasy Plant minikit was used to extract RNA from 100 mg of tissue

treatment_protocol: Whole seedlings were sprayed with 2 uM GA4 with a fine mister, 16 h prior to the experiment. On the day of the experiment, the seedlings were resprayed with 2 uM GA4 plus 10 uM DEX and shoots were collected 4h after treatment by cutting with a razor blade.

tag: Strain

value: Transgenic line carrying a dexamethasone (DEX)-inducible construct that induces the expression of a dominant form of a DELLA protein (rga-delta17) when treated with DEX. Ecotype:Ler, Age:8 days, Tissue:shoots


title: Vector_shoots_4h_GA4_repl2

source_name: shoots, 4h GA4

treatment_protocol: Whole seedlings were sprayed with 2 uM GA4 with a fine mister, 16 h prior to the experiment. On the day of the experiment, the seedlings were resprayed with 2 uM GA4 and shoots were collected 4h after treatment by cutting with a razor blade.

value: Transgenic line carrying a dexamethasone (DEX)-inducible construct with an empty cassette, used as control. Ecotype:Ler, Age:8 days, Tissue:shoots


title: Vector_shoots_4h_GA4+DEX_repl2


title: Vector_shoots_4h_GA4_repl1


title: Dex-rga(delta17)_shoots_2h_GA4+DEX_repl2

source_name: shoots, 2h GA4+DEX

treatment_protocol: Whole seedlings were sprayed with 2 uM GA4 with a fine mister, 16 h prior to the experiment. On the day of the experiment, the seedlings were resprayed with 2 uM GA4 plus 10 uM DEX and shoots were collected 2h after treatment by cutting with a razor blade.


title: Dex-rga(delta17)_shoots_4h_GA4+DEX_repl3


title: Dex-rga(delta17)_shoots_2h_GA4_repl1

source_name: shoots, 2h GA4

treatment_protocol: Whole seedlings were sprayed with 2 uM GA4 with a fine mister, 16 h prior to the experiment. On the day of the experiment, the seedlings were resprayed with 2 uM GA4 and shoots were collected 2h after treatment by cutting with a razor blade.


title: Dex-rga(delta17)_shoots_2h_GA4+DEX_repl1


title: ga1-3_shoots_1h_GA4_repl4

description: The aim is to identify early gibberellin responsive genes in a gibberellin deficient strain such as ga1-3. A 1h time point was selected based on quantitative PCR analysis of known gibbrellin responsive genes, which showed a response only after 60 min of treatment. A concentration of 2 micromolar GA4 was used, and water as a mock treatment.

source_name: shoots, 1h GA4

label_protocol: Standard protocol from Affymetrix for One-Cycle cDNA Synthesis

growth_protocol: Seeds were germinated on MS agar plates supplemented with 2% sucrose on a piece of nylon mesh as support. Seedlings were grown vertically for 8 days under continuous light at 22C.

treatment_protocol: Whole seedlings were sprayed with 2 uM GA4 with a fine mister and shoots were collected 1h after treatment by cutting with a razor blade.

value: ga1-3 in Ler, Age:8 days, Tissue:shoots


title: keloid treated with hydrocortisone-1


title: Dex-rga(delta17)_shoots_2h_GA4+DEX_repl3


title: Dex-rga(delta17)_shoots_2h_GA4_repl2


title: Dex-rga(delta17)_shoots_4h_GA4_repl2


title: ga1-3_shoots_1h_GA4_repl3


title: Dex-rga(delta17)_shoots_4h_GA4_repl1


title: Dex-rga(delta17)_shoots_4h_GA4_repl3


title: ga1-3_shoots_1h_GA4_repl2


title: ga1-3_shoots_1h_water_repl4

source_name: shoots, 1h water

treatment_protocol: Whole seedlings were sprayed with water with a fine mister and shoots were collected 1h after treatment by cutting with a razor blade.


title: ga1-3_shoots_1h_GA4_repl1


title: Dex-rga(delta17)_shoots_4h_GA4+DEX_repl1


title: ga1-3_shoots_1h_water_repl3


title: ga1-3_shoots_1h_water_repl2


title: Nucleated Erythrocytes 2

city: Houston

first: Nathan

last: Boles

state: TX

address: One Baylor Plaza, N1030

department: Pediatrics

institute: Baylor College of Medicine

description: not applicable

hyb_protocol: Standard protocol from manufacturer

scan_protocol: Hardware: GeneChip¨ Scanner 3000

data_processing: Normalization was done with the GCRMA package from Bioconductor

molecule: polyA RNA

source_name: Nucleated Erythrocytes isolated via Flow cytometry

label_protocol: Second round of MessageAmp(Ambion) amplification was biotinylated with bio-CTP and bio-UTP per manufature's protocol.

extract_protocol: 25,000- 50,000 cells were FACS sorted, RNA was isolated with RNAqueous Kit (Ambion) per manufacture's protocol, DNAse treated with DNAse1, phenol:chloroform:isoamyl alcohol extracted, and amplified through two rounds of in vitro transcription using MessageAmp (Ambion) per manufacture's protocol

value: C57Bl/6, Gender:female, Age:12-14 weeks, Pooled samples:4


title: Granulocytes 1

description: not applicable

source_name: Granulocytes isolated via Flow cytometry


title: Granulocytes 2

description: not applicable


title: Nucleated Erythrocytes 1

description: not applicable


title: Monocyte 2

description: not applicable

source_name: Monocytes isolated via Flow cytometry


title: CD4+ naive T-cells t4n_1

description: not applicable

source_name: CD4+ T-cell naive isolated via Flow cytometry


title: B-Cell 1

description: not applicable

source_name: B-Cells isolated via Flow cytometry


title: ga1-3_shoots_1h_water_repl1


title: NK cells NK_2

description: not applicable

source_name: NK cell isolated via Flow cytometry


title: B-Cell 2

description: not applicable


title: Dex-rga(delta17)_shoots_2h_GA4_repl3


title: CD8+ activated T-cells t8a_1

description: not applicable

source_name: CD8+ T-cell activated with an LPS treatment and isolated via Flow cytometry


title: CD8+ naive T-cells t8n_2

description: not applicable

source_name: CD8+ T-cell naive isolated via Flow cytometry


title: Monocyte 1

description: not applicable


title: CD8+ activated T-cells  t8a_2

description: not applicable


title: Vector_shoots_4h_GA4+DEX_repl1


title: CD4+ activated T-cells t4a_2

description: not applicable

source_name: CD4+ T-cell activated with an LPS treatment and isolated via Flow cytometry


title: NK cells NK_1

description: not applicable


title: Long-term hematopoietic stem cells LT-HSC_SPKSL_2

description: not applicable

source_name: LT-HSC isolated via Flow cytometry


title: CD48+ naive T-cells t8n_1

description: not applicable


title: CD4+ activated T-cells t4a_1

description: not applicable


title: CD4+ naive T-cells t4n_2

description: not applicable


title: Long-term hematopoietic stem cells LT-HSC_SPKSL_1

description: not applicable


title: HUVEC_DMSO+TNF-α_6h_biological rep3

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

description: Gene expression data from unstimulated HUVEC exposed to DMSO and TNF-α for 6h

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Robust Multichip Average (RMA), using CEL files obtained from GCOS software (Affymetrix).

source_name: Confluent monolayers of HUVEC exposed to DMSO (final concentration in the culture medium <0.1%) for 45 min followed by addition of TNF-α (10 ng mL-1) for 6h.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were obtained from Cambrex Bio Science (Wokingham, England), grown in EGM2 Bullet Kit (Lonza-Cambrex) and maintained at 37°C under a 5% CO2/95% air atmosphere at constant humidity. For the experiments, cells between passage number 2 and 4 (doubling population ≤ 10) were seeded onto 6-wells plates at a density of 3500 cells cm-2, and used on day 5 after seeding (confluent monolayers).

extract_protocol: Total RNA was isolated using an RNeasy ® Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in RNAse free water, aliquoted and stored at –80ºC.

treatment_protocol: HUVEC cells were treated as follows: i) direct treatment with dp3.9 apple procyanidins extract (final concentration in the culture medium, 10 μg mL-1) for 4h. As controls, cells were treated with DMSO (<0.1% in the culture medium) for 4h; ii) induction of inflammation with TNF-α: cells were treated with DMSO followed by TNF-α (10 ng mL-1) for 6 h. As controls, cells were treated with DMSO for 6h; iii) pre-co-treatment: cells were treated with dp3.9 (final concentration in the culture medium, 10 μg mL-1) for 45 min followed by treatment with TNF-α (10 ng/mL) for 6 h. As controls, cells were treated with DMSO for 45 min prior to TNF-a for 6 h. Treatments were all done in triplicate.

tag: Normal human umbilical vein endothelial cells (HUVEC) under inflammatory conditions induced by cytokine TNF-α


title: HUVEC_DMSO+TNF-α_6h_biological rep1


title: HUVEC_DMSO+TNF-α_6h_biological rep2


title: HUVEC_DMSO_4h_biological rep2

description: Gene expression data from unstimulated HUVEC exposed to DMSO for 4h

source_name: Confluent monolayers of unstimulated HUVEC exposed to DMSO (final concentration in the culture medium <0.1%) for 4h.

tag: Normal human umbilical vein endothelial cells (HUVEC)


title: HUVEC_DMSO_4h_biological rep1


title: HUVEC_dp3.9 (10μg mL-1)+TNF-α_6h_biological rep2

description: Gene expression data from unstimulated HUVEC exposed to dp3.9 apple procyanidins extract and TNF-α for 6h

source_name: Confluent monolayers of HUVEC exposed to dp3.9 apple procyanidins extract (final concentration in the culture medium, 10 μg mL-1) and dissolved in DMSO for 45 min followed by addition of TNF-α (10 ng mL-1) for 6h.


title: HUVEC_dp3.9 (10μg mL-1)+TNF-α_6h_biological rep1


title: HUVEC_dp3.9 (10 μg mL-1)_4h_biological rep1

description: Gene expression data from unstimulated HUVEC exposed to dp3.9 apple procyanidins extract for 4h

source_name: Confluent monolayers of unstimulated HUVEC exposed to dp3.9 apple procyanidins extract (final concentration in the culture medium, 10 μg mL-1) and dissolved in DMSO for 4h.


title: HUVEC_dp3.9 (10 μg mL-1)_4h_biological rep3


title: HUVEC_DMSO_4h_biological rep3


title: HUVEC_dp3.9 (10 μg mL-1)_4h_biological rep2


title: HUVEC_dp3.9 (10μg mL-1)+TNF-α_6h_biological rep3


title: resistant2m2

status: Public on Nov 20 2007

city: Raleigh

first: Tatiana

middle: V

last: Morozova

address: campus box 7617

department: zoology

institute: NCSU

description:
Overall design: we performed 35 generations of artificial selection from a genetically heterogeneous base population to derive replicate lines that are sensitive or resistant to ethanol exposure, as well as unselected control lines.
At generation 25, two replicates of 15 3-5 day old virgin males and females were collected from each selection line.

hyb_protocol: Following fragmentation, 10 mkg 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 500. Scale factor is 2.036

label: Biotinylated cRNA

organism: Drosophila melanogaster

source_name: whole body of 3-5 day old males, resistant line 2 replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: under standard conditions 25C, 12:12 light/dark cycle

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

treatment_protocol: flies have been exposed to ethanol vapor prior to RNA extraction


title: sensitive2f2

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. Scale factor is 1.705

source_name: whole body of 3-5 day old females, sensitive line 2 replicate 2


title: resistant2f1

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. Scale factor is 1.692

source_name: whole body of 3-5 day old females, resistant line 2 replicate 1


title: resistant2m1

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. Scale factor is 2.084

source_name: whole body of 3-5 day old males, resistant line 2 replicate 1


title: resistant2f2

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. Scale factor is 2.175

source_name: whole body of 3-5 day old females, resistant line 2 replicate 2


title: resistant1f1

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. Scale factor is 1.919

source_name: whole body of 3-5 day old females, resistant line 1 replicate 1


title: sensitive1f2

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. Scale factor is 2.443

source_name: whole body of 3-5 day old females, sensitive line 1 replicate 2


title: sensitive2f1

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. Scale factor is 1.634

source_name: whole body of 3-5 day old females, sensitive line 2 replicate 1


title: control2f2

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. Scale factor is 2.137

source_name: whole body of 3-5 day old females, unselected control line 2 replicate 2


title: sensitive1f1

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. Scale factor is 2.082

source_name: whole body of 3-5 day old females, sensitive line 1 replicate 1


title: resistant1m2

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. Scale factor is 2.617

source_name: whole body of 3-5 day old males, resistant line 1 replicate 2


title: sensitive2m1

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. Scale factor is 1.567

source_name: whole body of 3-5 day old males, sensitive line 2 replicate 1


title: sensitive2m2

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. Scale factor is 2.196

source_name: whole body of 3-5 day old males, sensitive line 2 replicate 2


title: resistant1f2

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. Scale factor is 1.797

source_name: whole body of 3-5 day old females, resistant line 1 replicate 2


title: control2f1

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. Scale factor is 2.363

source_name: whole body of 3-5 day old females, unselected control line 2 replicate 1


title: control2m1

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. Scale factor is 1.801

source_name: whole body of 3-5 day old males, unselected control line 2 replicate 1


title: control2m2

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. Scale factor is 2.054

source_name: whole body of 3-5 day old males, unselected control line 2 replicate 2


title: resistant1m1

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. Scale factor is 2.104

source_name: whole body of 3-5 day old males, resistant line 1 replicate 1


title: control1m1

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. Scaling factor is 1.424

source_name: whole body of 3-5 day old males, unselected control line 1 replicate 1


title: sensitive1m2

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. Scale factor is 2.341

source_name: whole body of 3-5 day old males, sensitive line 1 replicate 2


title: control1m2

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. Scaling factor is 1.979

source_name: whole body of 3-5 day old males, unselected control line 1 replicate 2


title: Neutrophils before exercise 12

status: Public on Nov 19 2007

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

institute: University of California, Irvine

description: no additional

hyb_protocol: 10 µg of  fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix U133+2 arrays.

scan_protocol: The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip® Scanner 3000.

data_processing: The results were quantified and analyzed using GCOS 1.4 software (Affymetrix, Inc.) using default values (Scaling Target Signal Intensity=500; Normalization, All probe sets; Parameters, all set at default values). The microarray data was analyzed using ArrayAssistÒ version 4.0.3 (STRATAGENEÒ ). We normalized the data using GC-RMA.

source_name: Human netrophils before exercise

label_protocol: 2 μg total RNA was used as a template for double‑stranded cDNA synthesis. Single-stranded then double-stranded cDNA was synthesized from the poly A spike-in controls, and mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA), and a T-7-oligo(dT) primer (Integrated DNA Technologies Inc.,Coralville,IA) that contains a T7 RNA polymerase promoter site added to it’s 3' end. A portion of the resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Affymetrix GeneChip® IVT Labeling Kit.

extract_protocol: Neutrophils were isolated using OptiPrepÒ Density Gradient Medium (SIGMA).  Using hematoxylin staining, we determined that this approach to neutrophil isolation consistently yielded ≥ 98% purification. Total RNA was extracted using TRIzol®  reagent and purified using the RNeasy Midi columns method (Qiagen, Valencia, CA)

tag: neutrophil, healthy male, age 24

tag: before-exercise


title: human_intracranial_artery_aneurysm_pool_5

city: Detroit

first: Gerard

last: Tromp

state: MI

address: 3309 Scott Hall, 540 East Canfield Ave

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

description: Intracranial arteries obtained from autopsy for mRNA expression analysis

hyb_protocol: 1. 300 ul of hybridization cocktail (all 15 ug cRNA) is assembled for each sample as per the protocol detailed in the Affymetrix GeneChip  Expression Analysis Technical Manual, rev. 2, 2004, Section 2.2. 2. 200 ul of each cocktail (10 ug cRNA) is hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 array  for 16 h at 45oC, rotating at 60 rpm in the GeneChip  Hybridization Oven 640 (Affymetrix, #800138). 3. Samples are washed and stained on the Genechip  Fluidics Station 450 (Affymetrix, #00-0079), wash protocol EukGE-WS2v5. Stringent/non-stringent buffers and stains prepared as described in the Affymetrix GeneChip  Expression Analysis Technical Manual, rev. 2, 2004, Section 2.3 &2.4

scan_protocol: Arrays were scanned by the GeneChip Scanner 3000 with Auto Loader (Affymetrix, #00-0090) Expression analysis settings at _All Probe Sets_ Scale Factor 500, Normalization = 1.0, No Masking.

data_processing: GCRMA

label: biotin, streptavidin phycoerythrin

source_name: Total RNA from human intracranial artery, non-aneurysm

label_protocol:
300 ng of each RNA pool was amplified (one round) using the MessageAmpTM II aRNA Kit according to the Manual Version 0404 (Ambion Inc., Austin, Texas).
1) Subsequent sample processing strictly adhered to the standard protocols as described in the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 2, 2004, Section 2, chapters 1-3.
2) Synthesis of cDNA was performed using the GeneChip Expression 3'-Amplification One-Cycle cDNA Synthesis Kit (Affymetrix, #900431). A starting amount of 5 ug total RNA was used for each sample, synthesis reactions are assembled in MicroAmp PCR tubes (PE Biosystems, #N801-0540) employing master mixes of reaction components to accommodate all samples, and performed in a Peltier Thermal Cycler (PTC)-200 DNA Engine (MJ Research).
3) Purification of double-stranded cDNA was performed using the GeneChip Sample Clean-up Module (Affymetrix, #900371).
4) 100% of the cDNA product was carried forward to synthesize biotin labeled cRNA using the GeneChip IVT Labeling Kit (Affymetrix, #900449). A master mix of IVT reaction components was assembled and appropriate aliquots added to each cDNA sample in MicroAmp PCR tubes, and incubated at 37oC for 16 h in the MJ Research PTC-200 DNA Engine.
5) cRNA products are purified using the GeneChip Sample Clean-up Module (Affymetrix, #900371), and OD readings are performed as described in step 2 to assess purity (260/280) and determine the concentration and yield of biotin labeled cRNA.
6)  The final concentration of labeled cRNA was corrected based on the starting amount of total RNA (5 ug) and the amount of cDNA product (100%) utilized in the synthesis reaction, as described in the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 2, 2004, Section 2.1.
7) Using the corrected cRNA concentration (ug/ul), 15 ug of labeled cRNA was fragmented using 5x Fragmentation Buffer included with GeneChip Sample Clean-up Module (Affymetrix, #900371) at 94oC for 35 minutes.

extract_protocol: Guanidinium isothiocyanate, cesium chloride centrifugation (Sambrook Molecular Cloning:  a laboratory manual)

tag: Tissue

value: Intracranial artery, non-aneurysm (contralateral vessel to aneurysm)

tag: Source Disease Status

value: aneurysm, ruptured

tag: Individual/Pool

value: Pool, n=5

tag: Age

value: mean = 59.2 years

tag: Gender

value: Female

tag: Vessel

value: middle cerebral artery

tag: Ethnicity

value: Caucasian


title: sensitive1m1

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. Scale factor is 2.436

source_name: whole body of 3-5 day old males, sensitive line 1

tag: 3-5 day old males, sensitive line 1


title: control1f2

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. Scale factor is 2.165

source_name: whole body of 3-5 day old females, unselected control line 1

tag: 3-5 day old females, unselected control line 1 replicate 2


title: Neutrophils before exercise 09

description: no additional

tag: neutrophil, healthy male, age 20


title: control1f1

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. Scaling factor 1.896

tag: 3-5 day old females, unselected control line 1 replicate 1


title: Neutrophils after exercise 12

description: no additional

source_name: Human netrophils after 30 min bout of exercise

tag: after-exercise


title: Neutrophils after exercise 09

description: no additional


title: Neutrophils after exercise 08

description: no additional

tag: neutrophil, healthy male, age 22


title: human_intracranial_artery_aneurysm_1

source_name: Total RNA from human intracranial artery, aneurysm

value: Intracranial artery (aneurysm)

value: Aneurysm, ruptured

value: Pool, n=3

value: mean = 53.7 years

value: Male

value: anterior communicating artery


title: human_intracranial_artery_aneurysm_pool_3

label_protocol:
300 ng of each RNA pool was amplified (one round) using the MessageAmpTM II aRNA Kit according to the Manual Version 0404 (Ambion Inc., Austin, Texas).
1) Subsequent sample processing strictly adhered to the standard protocols as described in the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 2, 2004, Section 2, chapters 1-3.
2) Synthesis of cDNA was performed using the GeneChip Expression 3'-Amplification One-Cycle cDNA Synthesis Kit (Affymetrix, #900431). A starting amount of 5 ug total RNA was used for each sample, synthesis reactions are assembled in MicroAmp PCR tubes (PE Biosystems, #N801-0540) employing master mixes of reaction components to accommodate all samples, and performed in a Pelletier Thermal Cycler (PTC)-200 DNA Engine (MJ Research).
3) Purification of double-stranded cDNA was performed using the GeneChip Sample Clean-up Module (Affymetrix, #900371).
4) 100% of the cDNA product was carried forward to synthesize biotin labeled cRNA using the GeneChip IVT Labeling Kit (Affymetrix, #900449). A master mix of IVT reaction components was assembled and appropriate aliquots added to each cDNA sample in MicroAmp PCR tubes, and incubated at 37oC for 16 h in the MJ Research PTC-200 DNA Engine.
5) cRNA products are purified using the GeneChip Sample Clean-up Module (Affymetrix, #900371), and OD readings are performed as described in step 2 to assess purity (260/280) and determine the concentration and yield of biotin labeled cRNA.
6)  The final concentration of labeled cRNA was corrected based on the starting amount of total RNA (5 ug) and the amount of cDNA product (100%) utilized in the synthesis reaction, as described in the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 2, 2004, Section 2.1.
7) Using the corrected cRNA concentration (ug/ul), 15 ug of labeled cRNA was fragmented using 5x Fragmentation Buffer included with GeneChip Sample Clean-up Module (Affymetrix, #900371) at 94oC for 35 minutes.


title: Neutrophils after exercise 11

description: no additional

tag: neutrophil, healthy male, age 29


title: Neutrophils before exercise 10

description: no additional

tag: neutrophil, healthy male, age 19


title: human_intracranial_artery_aneurysm_pool_4

value: aneurysm, unruptured

value: Pool, n=4

value: mean = 62.8 years


title: human_intracranial_artery_aneurysm_2

value: Intracranial aneursym (aneurysm)


title: Neutrophils before exercise 11

description: no additional


title: Neutrophils after exercise 06

description: no additional


title: Neutrophils after exercise 10

description: no additional


title: Neutrophils before exercise 06

description: no additional


title: Neutrophils before exercise 08

description: no additional


title: Neutrophils after exercise 05

description: no additional


title: Neutrophils before exercise 07

description: no additional

tag: neutrophil, healthy male, age 27


title: Neutrophils after exercise 07

description: no additional


title: Neutrophils before exercise 04

description: no additional

tag: before-exercise


title: Neutrophils before exercise 05

description: no additional


title: Neutrophils after exercise 04

description: no additional


title: Neutrophils before exercise 03

description: no additional

tag: neutrophil, healthy male, age 26


title: Neutrophils after exercise 02

description: no additional

tag: neutrophil, healthy male, age 23


title: Neutrophils before exercise 02

description: no additional


title: Neutrophils after exercise 01

description: no additional

tag: neutrophil, healthy male, age 24


title: Neutrophils before exercise 01

description: no additional


title: HCC_KO_rep5

city: ILLKIRCH CEDEX

first: Régine

last: Losson

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description: Gene expression data from liver tumors of Trim24 KO mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner GCS3000

data_processing: The data were analyzed with Affymetrix GCOS software version 1.1 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: HCC of Trim24 KO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were bred and housed in the Clinical Mouse Institute, ICS (Strasbourg, France) according to guidelines in compliance with the European legislation on care and use of laboratory anaimals.

extract_protocol: Total RNA was isolated using the RNeasy Kit from QIAGEN.

tag: Male

tag: Age

value: 20 months


title: tumorigenic population of MMTV-Wnt-1 breast tumor, Mouse TG3

city: Redwood City

first: Xinhao

last: Wang

address: 800 Chesapeake

institute: OncoMed Pharmaceuticals Inc

description: tumorigenic population (CD24+Thy+CD45-) of MMTV-Wnt-1 tumor isolated using fluorescence activated cell sorting

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the manufacturer's instructions.

scan_protocol: standard Affymetrix procedures

data_processing: RMA

source_name: breast tumor

label_protocol: Total RNA was first amplified. Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Using RNAqueous-Micro (Ambion #1931).


title: tumorigenic population of MMTV-Wnt-1 breast tumor, Mouse TG1

tag: tumorigenic population (CD24+Thy+CD45-) of MMTV-Wnt-1 tumor isolated using fluorescence activated cell sorting


title: HCC_KO_rep1


title: HCC_KO_rep2


title: Normal liver_WT-rep2

description: Gene expression data from livers of adult wild-type mice

source_name: Normal liver of WT


title: Normal liver_WT-rep4


title: Normal liver_WT-rep5


title: Neutrophils after exercise 03

description: no additional


title: nontumorigenic population of MMTV-Wnt-1 breast tumor, Mouse TG3

description: nontumorigenic population (Not CD24+Thy+CD45-) of MMTV-Wnt-1 tumor isolated using fluorescence activated cell sorting


title: Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate A

status: Public on Nov 17 2007

city: Hanover

first: Thomas

middle: H

last: Hampton

state: NH

address: North College Street

department: Microbiology Immunology

institute: Geisel School of Medicine at Dartmouth

description: Gene expression data from liver

hyb_protocol: The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. Biotinylated cRNA (15 ug) targets were then cleaned up, fragmented, and hybridized to GeneChip® array during the overnight incubation at 45oC in rotating hybridization oven.

scan_protocol: After hybridization, the arrays were stained with streptavidin-phycoerythrin in the GeneChip Fluidics station and then scanned using Affymetrix GeneChip Scanner (laser filter set at 570 nm; pixel size 2.5 um). The array image data were acquired, and the fluorescent signal intensities were quantified using Affymetrix® GCOS v. 1.2 software with following settings of quantitation parameters: Alpha1=0.05, Alpha2=0.065, Tau=0.015, Gamma1H=0.0045, Gamma1L=0.0045, Gamma2H=0.006, Gamma2L=0.006, Perturbation=1.1, Target Intensity=150.

data_processing: CEL file data were normalized using RMA as implented in Bioconductor simpleaffy. Genes were selected by  Rank Product (Breitling, R., 2004, FEBS Letter, 57383-92) implemented in Bioconductor RankProd at  p < .05 and by ANOVA.

source_name: Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: 10 ppb, 5wk

label_protocol: Total RNA was first reverse-transcribed using T7-oligo(dT) promoter primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction.

growth_protocol: 6wk male C57BL/6 male mice were acclimated to their respective diets for 2 wk prior to treatments.

extract_protocol:
RNA was extracted from frozen liver samples and homogenized using QiashredderTM and RNeasy® Mini Kits (Qiagen, Valencia, CA) per manufacturer's protocol. Contaminating genomic DNA was removed using DNA-free kits
(Ambion, Austin, TX) and total RNA was quantified with a NanoDrop®ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). RNA quality was determined with the RNA 6000 LabChip kit Nano Assay (Agilent Technologies, Inc., Santa Clara, CA).

treatment_protocol: Sodium arsenite at prescribed concentrations was added to food, which was repelleted, or sodium arsenite was added to water. Injections were intraperitoneal in a normal saline solution.

tag: C57BL/6 male, age 8wk


title: HCC_KO_rep4


title: Normal liver_WT-rep1


title: Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate C

description: Gene expression data from liver

source_name: Sodium arsenite added to food: 10 ppb, 5wk; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: None


title: Normal liver_WT-rep3


title: Mouse Liver AIN Diet 5wk 10ppb As Food Exposure, biological replicate A

description: Gene expression data from liver

source_name: Sodium arsenite added to food: 10 ppb, 5wk; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: HCC_KO_rep3


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate D

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg sodium arsenite, 1 mg/kg Dexamethasone in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: Mouse Liver AIN Diet 5wk Control, biological replicate B

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: nontumorigenic population of MMTV-Wnt-1 breast tumor, Mouse TG1

tag: nontumorigenic population (Not CD24+Thy+CD45-) of MMTV-Wnt-1 tumor isolated using fluorescence activated cell sorting


title: tumorigenic population of MMTV-Wnt-1 breast tumor, Mouse TG2


title: nontumorigenic population of MMTV-Wnt-1 breast tumor, Mouse TG2


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate F

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate C

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex Injection, biological replicate D

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg Dexamethasone in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate D

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate D

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate F

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk Control, biological replicate E

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr Saline Injection, biological replicate C

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: IP 8hr saline only; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: Mouse Liver LRD Diet 5wk Control, biological replicate F

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: None


title: Mouse Liver AIN Diet 8hr Saline Injection, biological replicate F

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex Injection, biological replicate F

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate B

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg sodium arsenite in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: Mouse Liver AIN Diet 5wk Control, biological replicate C

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 10ppb As Food Exposure, biological replicate F

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 100ppb Drinking Water Exposure, biological replicate D

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: 100 ppb, 5wk


title: Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate B

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate A

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: 10 ppb, 5wk


title: Mouse Liver LRD Diet 5wk Control, biological replicate B

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 100ppb Drinking Water Exposure, biological replicate F

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr Saline Injection, biological replicate E

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate F

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate F

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk Control, biological replicate E

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex Injection, biological replicate E

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 100ppb Drinking Water Exposure, biological replicate E

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate A

description: Gene expression data from liver

source_name: Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: 100 ppb, 5wk


title: Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate C

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate F

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex Injection, biological replicate A

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk Control, biological replicate D

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate E

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate D

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk Control, biological replicate D

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate D

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate B

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr Saline Injection, biological replicate A

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate C

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate E

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 10ppb As Food Exposure, biological replicate E

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate A

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate E

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex Injection, biological replicate C

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate A

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate E

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate C

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 10ppb As Food Exposure, biological replicate C

description: Gene expression data from liver


title: Mouse Liver AIN Diet 8hr Saline Injection, biological replicate B

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 100ppb Drinking Water Exposure, biological replicate B

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate D

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk Control, biological replicate C

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate E

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk Control, biological replicate F

description: Gene expression data from liver


title: Mouse Liver LRD Diet 5wk 100ppb Drinking Water Exposure, biological replicate A

description: Gene expression data from liver


title: Mouse Liver AIN Diet 5wk 10ppb As Food Exposure, biological replicate D

description: Gene expression data from liver


title: Mock day 3 (day3E2)

status: Public on Nov 15 2007

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

country: United Kingdom

institute: JIC

description: mock treatment was ethanol 0.1%, Silwet L-77 0.015%

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 50C on GeneChip Arabidopsis ATH1 arrays. 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. To calculate p-values for expression changes after steroid treatmen at each time point, the Wilcoxon signed-rank test was applied to each of the four pairwise combinations of steroid-treated X control sample, using MAS 5.0.

source_name: inflorescence tips, 3 days after mock-treatment

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: Plants were grown on a mix of vermiculite:soil:sand at 18°C with 16 hours light/8 hours dark cycles.

extract_protocol: Total RNA was extracted using TRI reagent (Sigma) according to the manufacturer’s instructions. For array hybridisation, the RNA was cleaned up with RNeasy columns (Qiagen) and precipitated to increase final concentration.

treatment_protocol: Dexamethasone (Sigma, stock solution 10 mM in ethanol) was used at a final concentration of 10 μM in Silwet L-77 0.015%, applied directly on the inflorescence tips; for mock treatments, the solution contained the same amount of ethanol (0.1%) and Silwet L-77. After treatment, RNA was extracted from inflorescence apices and stored at -70 C until activation of AGGR was confirmed (2 weeks later).

tag: ap1-1 and cal-1, 35S:AGGR background, L-er accession, grown in controlled environment room at 18 C, 16h light/8h dark


title: Steroid day 1 (day1D2)

description: steroid treatment was dexamethasone 10 micromolar, ethanol 0.1%, Silwet L-77 0.015%

source_name: inflorescence tips, 1 day after steroid treatment


title: Steroid day 3 (day3D2)

source_name: inflorescence tips, 3 days after steroid treatment


title: Mock day 1 (day1E2)

source_name: inflorescence tips, 1 day after mock-treatment


title: Steroid day 7 (day7D1)

source_name: inflorescence tips, 7 days after steroid treatment


title: Mock day 7 (day7E2)

source_name: inflorescence tips, 7 days after mock-treatment


title: Steroid day 7 (day7D2)


title: Steroid day 1 (day1D1)


title: Mock day 3 (day3E1)


title: Mock day 7 (day7E1)


title: Mock day 1 (day1E1)


title: Liver fenofibrate feeding mouse wild type

status: Public on Nov 16 2007

city: Bronx

first: David

middle: L

last: Silver

address: 1300 Morris Park Ave.

department: Biochemistry

institute: Albert Einstein College of Medicine

description:
Comments:	standard format array hybridization with amplification  New 20x Euk ctl lot#3004405 exp 111004 DMSO lot # 103K2311
Algorithm:	Statistical
Corner+	Avg:115, Count:32
Corner-	Avg:10337, Count:32
Background	Avg:57.41,Stdev:1.91,Max:62.8,Min:54.7
Noise	Avg:3.36,Stdev:0.21,Max:4.0,Min:3.0
RawQ	1.81
BF
Alpha1	0.05
Alpha2	0.065
Tau	0.015
Gamma1H	0.002
Gamma1L	0.002
Gamma2H	0.002667
Gamma2L	0.002667
Perturbation	1.1
TGT	1000
NF	1
SF	22.8590126
SFGene	All

data_processing: standard Affymetrix protocols

label: standard affymetrix protocol

source_name: liver, 7 days 0.2% fenofibrate feeding

tag: liver from 8 week old male wild-type 129SvEJ mice


title: Steroid day 3 (day3D1)


title: CD45-negative SP cell fraction, biological rep2

status: Public on Nov 12 2007

city: Chapel Hill

first: Ajay

last: Gulati

address: 130 Mason Farm Road, CD#7220

department: Pediatric Gastroenterology

institute: University of North Carolina at Chapel Hill

description: Gene expression data from mouse CD45-/SP cells isolated via SP sorting

hyb_protocol: Following fragmentation, 15 mcg of biotinylated cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix Mouse Genome 430 2.0 GeneChips.  GeneChips were washed and stained using the Affymetrix Fluidics station 400 according to standard Affymetirx protocols.

scan_protocol: Laser scanning of the chips was performed using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed using the dChip software platform (v2005).

source_name: Mouse CD45-/SP cells isolated via SP sorting

label_protocol: 50 ng of total RNA was amplified using the Affymetrix Two Cycle Target Labeling Kit according to standard Affymetrix protocols (Expression Analysis Technical Manual, 2004, Affymetrix).  Biotinylated cRNA were prepared from 5 mcg of total RNA.

growth_protocol: All mice for this study were housed in our animal facility under a 12-hour light/dark cycle, and all had unrestricted access to rodent Lab Chow #5001 (PMI Nutrition International, Brentwood, MO) as well as acidified tap water.  The Institutional Animal Care and Use Committee of Baylor College of Medicine approved all experimental procedures.

extract_protocol: Total cellular RNA was extracted using an RNeasy Mini Kit (Qiagen, Valencia, CA) per the manufacturer’s instructions.

treatment_protocol: Mice were sacrificed at 8-10 weeks of age, and the jejunum was harvested.  Mucosal digests were prepared using collagenase and dispase.  These were then subject to SP sorting via Hoechst 33342 dye exclusion.  Cells were also stained with fluorescein isothiocyanate (FITC) labeled anti-CD45 antibody (BD Pharmingen, San Diego, CA) to eliminate bone-marrow derived cells from the populations to be analyzed.  Propidium iodide (PI) was used to exclude dead cells.

tag: Adult, male, C57Bl/6


title: Intact jejunum, biological rep4

description: Gene expression data from mouse jejunum prior to processing

source_name: Mouse jejunum


title: CD45-negative SP cell fraction, biological rep4


title: Intact jejunum, biological rep2


title: CD45-negative nSP cell fraction, biological rep4

description: Gene expression data from mouse CD45-/nSP cells isolated via SP sorting

source_name: Mouse CD45-/nSP cells isolated via SP sorting


title: Liver fenofibrate feeding mouse pparalpha-/-

tag: liver, 8 week old male 129SvEJ pparalpha -/- mice (pool of 3)


title: CD45-negative nSP cell fraction, biological rep2


title: Intact jejunum, biological rep1


title: CD45-negative nSP cell fraction, biological rep1


title: CD45-negative SP cell fraction, biological rep1


title: CD45-negative nSP cell fraction, biological rep3


title: vervet magnocellular layer 2 (human array)

city: Montreal

first: Pascal

last: Lachance

state: QC

address: 1205 Ave. Dr. Penfield

department: Psychology

country: Canada

institute: McGill University

description: Vervet monkey samples cross-species hybridized to the human HG-U133plus2 array. Split sample hybridized concurrently to the Rhesus Macaque Genome Array for comparison.

hyb_protocol: Standard Affymetrix protocol, processed at the McGill University and Genome Quebec Innovation Center.

data_processing: CHP file obtained from MAS 5.0

organism: Chlorocebus aethiops vervet

source_name: lateral geniculate nucleus magnocellular neuronal cell body

extract_protocol:
Laser-capture microdissected neuronal cell bodies from the magnocellular layer of the Lateral Geniculate Nucleus. Cells identified by cresyl violet staining.
Sample consists of roughly 3000 pulses from LCM, total RNA amplified through two rounds using the Affymetrix system.

treatment_protocol: normal animals

tag: Adult male vervet monkey (Cercopithecus aethipos), internal identifier number 05-1-2.


title: CD45-negative SP cell fraction, biological rep3


title: Intact jejunum, biological rep3


title: Untreated 0612_Dm_S2_untreated_1

status: Public on Nov 11 2007

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression analysis was conducted using Drosophila Genome 2.0 Genechip® arrays (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.  For each array, 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 6.0).  This system performs data pre-processing and error modeling as described in Weng (2004).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

source_name: Drosophila melanogaster S2 cells (no treatment control)

growth_protocol: Cells were grown in Shields and Sang medium, supplemented with bactopeptone and yeast extract, plus 10% Fetal Bovine Serum, as recommended by the Drosophila Genomics Resource Center

extract_protocol: The RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen) was used, according to manufacturer’s protocol.

treatment_protocol: Cells were untreated, or treated with dsRNA for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-73

tag: Drosophila melanogaster S2 cells, male, largely tetraploid


title: NELF-depleted 0612_Dm_S2_NELF-depleted_1

hyb_protocol: 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

source_name: Drosophila melanogaster S2 cells that have been depleted of the NELF complex using dsRNA targeting NELF-B and NELF-E, 96 hour treatment

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.

treatment_protocol: Cells were untreated, or treated with dsRNA for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-79


title: NELF-depleted 0612_Dm_S2_NELF-depleted_2

treatment_protocol: Cells were untreated, or treated with dsRNA for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-80


title: Untreated 0612_Dm_S2_untreated_

treatment_protocol: Cells were untreated, or treated with dsRNA for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-74


title: LacZ-treated 0612_Dm_S2_LacZ-treated_1

source_name: Drosophila melanogaster S2 cells that have been treated for 96 hours with dsRNA targeting Beta-galactosidase (mock-treated control)

treatment_protocol: Cells were untreated, or treated with dsRNA for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-76


title: vervet magnocellular layer 1 (human array)

scan_protocol: Standard Affymetrix protocol, processed at the McGill University and Genome Quebec Innovation Center.

tag: Adult male vervet monkey (Cercopithecus aethipos), internal identifier number 03-1-2.


title: cumulus cells-late cleavage-rep6a

status: Public on Nov 10 2007

city: maastricht

first: Aafke

last: van Montfoort

department: Obstetrics & Gynaecology

country: Netherlands

institute: Academic hospital Maastricht

description: Comparison of cumulus cells from eight oocytes resulting in an early cleavage embryo (EC-CC; n=8) and from eight oocytes resulting in a non-EC embryo  (NEC-CC; n=8).

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix GCOS, TGT value: 500, Norm Factor: 1

source_name: cumulus cells from oocyte resulting in a late cleavage embryo from patient 6

label_protocol: Fifty ng total RNA was amplified using the two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, USA) in combination with the MEGAscript T7 in vitro transcription system (Ambion) and biotin labeled with GeneChip IVT labeling kit (Affymetrix).

growth_protocol: In consenting IVF patients, immediately following ultrasound-guided cumulus-oocyte-complex (COC) retrieval, a proportion of the cumulus cells surrounding a single oocyte were removed using a sharp needle.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, USA) according to the manufacturers’ instructions with some adaptations for the small quantity of RNA. RNA was precipitated with isopropyl alcohol for 2h and the RNA pellet was washed three times with 75% ethanol. To be able to track the small RNA pellet, 5 mg glycogen (Ambion, Woodward, USA) was added to the sample before RNA precipitation.

treatment_protocol: Cumulus cells were immediately lysed in 100 ml Trizol reagent (Invitrogen, Carlsbad, USA) supplemented with 1% (v/v) 2-mercapto-ethanol (Merck, Darmstadt, Germany), snap-frozen in liquid nitrogen and stored at -80°C (cumulus cells from one oocyte per vial).

tag: The oocyte enclosed by these cumulus cells was fertilized normally (2PN) and developed into a 4-cell embryo with good morphology on day 2 and no multinucleated blastomeres present.


title: LacZ-treated 0612_Dm_S2_LacZ-treated_2

treatment_protocol: Cells were untreated, or treated with dsRNA for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-77


title: cumulus cells-late cleavage-rep4

source_name: cumulus cells from oocyte resulting in a late cleavage embryo from patient 4


title: cumulus cells-late cleavage-rep1b

source_name: cumulus cells from oocyte resulting in a late cleavage embryo from patient 1


title: cumulus cells-late cleavage-rep3

source_name: cumulus cells from oocyte resulting in a late cleavage embryo from patient 3


title: cumulus cells-late cleavage-rep6b


title: cumulus cells-early cleavage-rep6b

source_name: cumulus cells from oocyte resulting in an early cleavage embryo (i.e. cleaved between 23-26h post-injection or 25-28h post-insemination) from patient 6


title: cumulus cells-late cleavage-rep1a


title: cumulus cells-late cleavage-rep2

source_name: cumulus cells from oocyte resulting in a late cleavage embryo from patient 2


title: cumulus cells-late cleavage-rep5

source_name: cumulus cells from oocyte resulting in a late cleavage embryo from patient 5


title: cumulus cells-early cleavage-rep5

source_name: cumulus cells from oocyte resulting in an early cleavage embryo (i.e. cleaved between 23-26h post-injection or 25-28h post-insemination) from patient 5


title: cumulus cells-early cleavage-rep1b

source_name: cumulus cells from oocyte resulting in an early cleavage embryo (i.e. cleaved between 23-26h post-injection or 25-28h post-insemination) from patient 1


title: cumulus cells-early cleavage-rep3

source_name: cumulus cells from oocyte resulting in an early cleavage embryo (i.e. cleaved between 23-26h post-injection or 25-28h post-insemination) from patient 3


title: cumulus cells-early cleavage-rep1a


title: cumulus cells-early cleavage-rep6a


title: cumulus cells-early cleavage-rep4

source_name: cumulus cells from oocyte resulting in an early cleavage embryo (i.e. cleaved between 23-26h post-injection or 25-28h post-insemination) from patient 4