title: UET-13TR-EWS/FLI1 0hr

description: Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the absence of tetracycline for 0 hours

source_name: UET-13TR-EWS/FLI1 0hr

tag: UET-13TR-EWS/FLI1 cells were cultured in the absence of tetracycline for 0 hours


title: Unfertilized Egg_3wk. FVB

status: Public on Aug 02 2007

type: RNA

city: Dallas

first: Diego

middle: H

last: Castrillon

state: TX

address: 6000 Harry Hines Blvd. NB6.126

department: Pathology

country: USA

institute: U.T. Southwestern Medical Center

description: Gene expression data on Affymetrix Mouse Genome 430 2.0 chip.

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array in the Affymetrix Hybridization oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 per manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner (Affymetrix).

data_processing: GCOS v1.4.0.036 with probe sets scaled to a target signal of 250.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Unfertilized eggs from superovulated 3wk. FVB mice

label_protocol: Biotinylated cRNA was prepared (ENZO BioArray IVT kit) following two rounds of RNA amplification using the Eberwine method of amplification (Phillips and Eberwine, 1996).

growth_protocol: All experiments used Foxo3 littermates or FVB wild-type mice from our own breeding colony. Animals were maintained in a pathogenfree facility administered by U.T. Southwestern Medical Center in accordance with the institutional guidelines of Charles River Laboratories. A maximum of five minutes was allowed to elapse between sacrifice and tissue harvest to prevent RNA degradation and transcriptional changes

extract_protocol: Total RNA extraction was performed using 1ml of Tripure (Roche) and 20mg of glycogen per manufacturer's instructions.

treatment_protocol: FVB mice were treated with pregnant mare serum (5IU/mouse) followed by a single dose 42 hours later of human chorionic gonadotropin (5IU/mouse). Adult mice were sacrificed by CO2 asphyxiation followed by cervical dislocation 24 hours after last injection. Complexes were collected in HEPES buffer, washed, and digested with hyaluronidase. Oocytes were seperated from somatice cells, washed and total RNA prepared using 1ml of Tripure (Roche) and 20mg glycogen as per manufacturer's instructions

tag: Unfertilized eggs were seperated from cumulus cells from 3wk. FVB mice.


title: UET-13TR-EWS/ERG 0hr

status: Public on Aug 03 2007

city: Okura

first: Yoshitaka

last: Miyagawa

address: Setagaya-ku

country: Japan

institute: National Research Institute for Child Health and Development

description: Gene expression data from UET-13TR-EWS/ERG cells incubated in the absence of tetracycline for 0 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000.

data_processing: The arrays were analyzed using GeneChip Operating Software 1.2 (GCOS 1.2) (Affymetrix).  Background subtraction and normalization were performed by GeneSpring GX 7.3 software (Agilent Technologies, Inc., Santa Clara, CA).

organism: Homo sapiens

source_name: UET-13TR-EWS/ERG 0hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: UET-13 transfectants (UET-13TR-EWS/FLI1 and UET-13TR-EWS/ERG ) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% Tet System Approved Fetal Bovine Serum (T-FBS)(Takara, Shiga, Japan) at 37°C under a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from cells using RNeasy kit (QIAGEN, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: UET-13 transfectants were treated with or without 3 μg/ml of tetracycline for the indicated periods.

tag: UET-13TR-EWS/ERG cells were cultured in the absence of tetracycline for 0 hours


title: Tg77

city: Chicago

first: Yugang

last: Wang

state: IL

address: 5841 S. Maryland

institute: University of Chicago

description: Gene expression data from wt B6 mice liver HFD 2 weeks.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array.

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

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

label: biotin

source_name: LIGHT Tg, HFD 2wks

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

extract_protocol: Trizol extraction and Qiagen Column.

treatment_protocol: Mice were feed high-fat diet(TD88137) for 2 weeks

tag: Lck LIGHT Tg

tag: Age

value: 4-8 wks


title: WT31

source_name: B6, HFD 2wks

tag: B6 wild type


title: WT30


title: Embryo_E11.5_Foxo3 Null_Female

source_name: Whole E11.5 female embryo Foxo3 null

label_protocol: Biotinylated cRNA was prepared (ENZO BioArray IVT kit) from 5 micrograms of total RNA per manufacturer's instructions.

extract_protocol: Total RNA extraction was performed using Tripure (Roche) per manufacturer's instructions.

treatment_protocol: Adult mice were sacrificed by CO2 asphyxiation followed by cervical dislocation and tissues were immediately transferred to Tripure for homogenization.

tag: Foxo3 -/- E11.5 female embryo


title: LCM oocytes_3wk ovary_FVB

source_name: Primary and secondary oocytes collected by LCM from 3wk. FVB ovaries

extract_protocol: Total RNA extraction was performed using Picopure RNA Isolation kit per manufacturer's instructions (Arcturus).

treatment_protocol: Adult mice were sacrificed by CO2 asphyxiation followed by cervical dislocation. Ovaries were dissected and frozen in OCT. Sections were prepared on neutral slides per methods from Arcturus to use in laser capture microdissection.

tag: Oocytes from 3wk. FVB female


title: LCM Somatic_3wk. ovary_FVB

source_name: Granulosa and stromal cell collected from 3wk. FVB ovary

tag: Somatic cells from 3wk. FVB ovary


title: Cumulus Granulosa Cells_FVB

source_name: Cumulus Granulosa cells collected from superovulated unfertilized female.

tag: Cumulus Granulosa cells collected from superovulated unfertilized FVB female.


title: Embryo_E11.5_Foxo3 Wt_Female

source_name: Whole E11.5 female embryo Foxo3 wild-type

tag: Foxo3 +/+ E11.5 female embryo


title: Lung_6wk_FVB_Female

source_name: Lung sample from 6wk FVB female

tag: 6wk. FVB lung


title: UET-13TR-EWS/FLI1 24hr tet+

description: Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the presence of tetracycline for 24 hours

source_name: UET-13TR-EWS/FLI1 24hr tet+

tag: UET-13TR-EWS/FLI1 cells were cultured in the presence of tetracycline for 24 hours


title: Intestine_6wk_FVB_Female

source_name: Intestine sample from 6wk FVB female

tag: 6wk. FVB intestine


title: Kidney_6wk_FVB_Female

source_name: Kidney sample from 6wk FVB female

tag: 6wk. FVB kidney


title: Liver_6wk_FVB_Female

source_name: Liver sample from 6wk FVB female

tag: 6wk. FVB liver


title: Testis_16wk._Kitl(Sl)/Kitl(Sl-d)

source_name: Testis sample from 16wk Kitl(Sl)/Kitl(Sl-d) (Shinohara et al.; 2000)

tag: 16wk Kitl(Sl)/Kitl(Sl-d) testis


title: Brain_6wk_FVB_Male

source_name: Brain sample from 6wk FVB male

tag: 6wk. FVB brain


title: Heart_6wk_FVB_Female

source_name: Heart sample from 6wk FVB female

tag: 6wk. FVB heart


title: Eye_6wk_FVB_Male

source_name: Eye sample from 6wk FVB male

tag: 6wk. FVB eye


title: Bone Marrow_6wk_FVB_Female

source_name: Bone Marrow sample from 6wk FVB female

tag: 6wk. FVB bone marrow


title: Spleen_6wk_FVB_Female

source_name: Spleen sample from 6wk FVB female

tag: 6wk. FVB spleen


title: Skeletal Muscle_6wk_FVB_Female

source_name: Skeletal muscle from hind leg of 6wk FVB female

tag: 6wk. FVB skeletal muscle


title: Ovary_PD3_Foxo3 Wt_Replica 2

description: Gene expression data from PD3 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip.

source_name: Ovary sample from PD3 Foxo3 wild-type

label_protocol: Biotinylated cRNA was prepared (ENZO BioArray IVT kit) following two rounds of RNA amplification from a single pair of ovaries using the Eberwine method of amplification (Phillips and Eberwine, 1996).

treatment_protocol: Female pups were sacrificed by decapitation and ovaries were immediately removed to RNase-free PBS. Bursa and oviduct material was removed and the ovaries were transferred to Tripure for homogenization

tag: PD3 Foxo3 +/+ ovary


title: Ovary_PD3_Foxo3 Null_Replica 1

description: Gene expression data from PD3 Foxo3 Null ovary sample on Affymetrix Mouse Genome 430 2.0 chip.

source_name: Ovary sample from PD3 Foxo3 Null

tag: PD3 Foxo3 -/- ovary


title: Ovary_PD3_Foxo3 Null_Replica 2


title: Ovary_PD1_Foxo3 Null_Replica 3

description: Gene expression data from PD1 Foxo3 Null ovary sample on Affymetrix Mouse Genome 430 2.0 chip.

source_name: Ovary sample from PD1 Foxo3 Null

tag: PD1 Foxo3 -/- ovary


title: Ovary_PD3_Foxo3 Null_Replica 3


title: Ovary_PD1_Foxo3 Wt_Replica 2

description: Gene expression data from PD1 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip.

source_name: Ovary sample from PD1 Foxo3 wild-type

tag: PD1 Foxo3 +/+ ovary


title: Ovary_PD3_Foxo3 Wt_Replica 1


title: Testis_6wk_FVB Wt

source_name: Testis sample from 6wk FVB wild-type

tag: 6wk. FVB testis


title: Adrenal Gland_6wk_FVB_Female

source_name: Adrenal gland sample from 6wk FVB Female

tag: 6wk. FVB adrenal gland


title: Ovary_PD3_Foxo3 Wt_Replica 3


title: Ovary_PD1_Foxo3 Null_Replica 1


title: Uterus_6wk_FVB Wt

source_name: Uterus sample from 6wk FVB wild-type

tag: 6wk. FVB uterus


title: Ovary_PD1_Foxo3 Wt_Replica 3


title: Ovary_6wk_FVB Wt

source_name: Ovary sample from 6wk FVB wild-type

tag: 6wk. FVB ovary


title: Ovary_PD1_Foxo3 Null_Replica 2


title: Ovary_PD14_Foxo3 Wt_Replica 2

description: Gene expression data from PD14 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip.

source_name: Ovary sample from PD14 Foxo3 wild-type

tag: PD14 Foxo3 +/+ ovary


title: Ovary_PD14_Foxo3 Null_Replica 3

description: Gene expression data from PD14 Foxo3 Null ovary sample on Affymetrix Mouse Genome 430 2.0 chip.

source_name: Ovary sample from PD14 Foxo3 Null

tag: PD14 Foxo3 -/- ovary


title: Placenta_9wk_FVB Wt

source_name: Placenta sample from 9wk FVB wild-type

tag: 9wk. FVB placenta


title: Ovary_PD14_Foxo3 Null_Replica 2


title: Ovary_PD14_Foxo3 Null_Replica 1

tag: PD14 Foxo3 Null ovary


title: Ovary_PD7_Foxo3 Null_Replica 3

description: Gene expression data from PD7 Foxo3 null ovary sample on Affymetrix Mouse Genome 430 2.0 chip.

source_name: Ovary sample from PD7 Foxo3 Null

tag: PD7 Foxo3 -/- ovary


title: Ovary_PD1_Foxo3 Wt_Replica 1


title: Ovary_PD14_Foxo3 Wt_Replica 3


title: Ovary_PD14_Foxo3 Wt_Replica 1


title: Ovary_PD7_Foxo3 Null_Replica 1

source_name: Ovary sample from PD7 Foxo3 null


title: Ovary_PD7_Foxo3 Null_Replica 2


title: TAp63 alpha 24h without induction s2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

hyb_protocol: Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided by the manufacturer (Affymetrix Inc.).

scan_protocol: GeneChip Fluidics station 400 (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.

data_processing:
DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
Probe set intensities were obtained by means of GCRMA, a robust
multiarray analysis method.
The full data set was normalized according to the
quantiles method.

molecule: cytoplasmic RNA

source_name: TET-on Human lung carcinoma H1299

label_protocol: cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).

extract_protocol:
Total RNA (ttlRNA) was extracted and
purified from stably transfected H1299 cell lines with the Concert
Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
with a Bioanalyzer (Agilent Technologies).

tag: Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on


title: TAp63 alpha 24h without induction s3


title: Ovary_PD7_Foxo3 Wt_Replica 3

description: Gene expression data from PD7 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip.

source_name: Ovary sample from PD7 Foxo3 wild-type

tag: PD7 Foxo3 +/+ ovary


title: TAp63 alpha 24h without induction s1


title: TAp63 alpha Q540L 24h without induction s3


title: TAp63 alpha Q540L 24h without induction s2


title: TAp63 alpha Q540L 24h induction s1

treatment_protocol: 1 μg/ml doxycycline for 24 hours


title: TAp63 alpha 24h induction s1


title: TAp63 alpha Q540L 24h induction s2


title: TAp63 alpha 24h induction s2


title: Ovary_PD7_Foxo3 Wt_Replica 1

growth_protocol: All experiments used Foxo3 littermates or FVB wild-type mice from our own breeding colony. Animals were maintained in a pathogenfree facility administered by U.T. Southwestern Medical Center in accordance with the institutional guidelines of Charles River Laboratories. A maximum of five minutes was allowed to elapse between sacrifice and tissue harvest to prevent RNA degradation and transcriptional changes.

treatment_protocol: Female pups were sacrificed by decapitation and ovaries were immediately removed to RNase-free PBS. Bursa and oviduct material was removed and the ovaries were transferred to Tripure for homogenization.


title: TAp63 alpha 24h induction s3


title: Ovary_PD7_Foxo3 Wt_Replica 2

extract_protocol: Total RNA extraction was performed using 1ml of Tripure (Roche) and 20mg of glycogen per manufacturer's instructions


title: Errb mutant stria vascularis replicate 3

status: Public on Aug 01 2007

city: Stanford

first: Jichao

last: Chen

state: CA

address: 279 Campus Drive, B461

institute: Stanford University

description: contact Jichao Chen (jchen35@stanford.edu) for details

hyb_protocol: Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/

data_processing: RMA (bioconductor)

source_name: Errb mutant mouse stria vascularis

extract_protocol: Trizol + RNeasy

tag: postnatal 3~5 days, mixed gender, C57BL6/129 mixed background


title: wild type stria vascularis replicate 3

scan_protocol: Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/

source_name: wild type mouse stria vascularis


title: TAp63 alpha Q540L 24h without induction s1


title: wild type stria vascularis replicate 2

label_protocol:
Johns Hopkins Microarray Core Facility
http://www.microarray.jhmi.edu/


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 4

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

country: Sweden

institute: Lund University

description: Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM

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

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

data_processing: Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: Adult murine BM from 10-14 weeks old mice

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix(TM); GeneChip Expression Analysis Technical Manual

extract_protocol: Cells were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

tag: Wild type C57bl/6


title: Errb mutant stria vascularis replicate 2


title: Adult murine BM, Lin-Sca1-Kit+Itga2b+Slamf1+ 1


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1-Englow 3


title: Adult murine BM, Lin-Sca1-Kit+Itga2b+Slamf1+ 2


title: Errb mutant stria vascularis replicate 1


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 3


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 1


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 5


title: Adult murine BM, Lin-Sca1lowKitlowIL7r+Flk2+ 3


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1-Englow 1


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Enghigh 2


title: wild type stria vascularis replicate 1

source_name: wild type mouse stria vascularis postnatal 3~5 days


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1-Englow 2


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Enghigh 3


title: Adult murine BM, Lin-Sca1-Kit+Itga2b+Slamf1+ 3


title: Adult murine BM, Lin-Sca1lowKitlowIL7r+Flk2+ 2


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Enghigh 1


title: Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 2


title: Adult murine BM, Lin-Sca1lowKitlowIL7r+Flk2+ 1


title: Embryoid body EB9

city: Berkeley

first: Alex

middle: S

last: Nord

address: 1 Cyclotron Road, Mail Stop 84-171

department: Genomics Divsion

institute: Lawrence Berkeley National Laboratory

description: no additional information

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: gcRMA signal

source_name: E14 cells

label_protocol: Standard Affymetrix procedure

growth_protocol: ES cells grown as per protocol on described at the UCSF Bay Genomics website

extract_protocol: Rneasy

treatment_protocol: no treatment

tag: E14 ES cells


title: Embryonic stem cell ES8

description: no additional information


title: Embryonic stem cell ES6

description: no additional information


title: Embryoid body EB3

description: no additional information


title: Embryonic stem cell ES10

description: no additional information


title: Embryoid body EB5

description: no additional information


title: Embryoid body EB1

description: no additional information


title: Embryoid body EB7

description: no additional information


title: Embryonic stem cell ES2

description: no additional information


title: TGF-beta24h_DMSO

city: Kyoto

first: shin

last: yonehara

address: Yoshida Konoe-cho, Sakyo-ku

institute: Graduate School of Biostudies, Kyoto University

description: Gene expression data from A20 cells stimulated with TGF-beta for 24 h

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS v.1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA.

growth_protocol: A20 cells were cultured in RPMI medium supplemented with 10 % fetal bovine serum, 20 mM Hepes, 50 microM beta-mercaptoethanol, 50 units/ml penicillin and 50 microg/ml streptomycin at 37C.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: A20 cells were left untreated or treated for 12 h or 24 h with TGF-beta in the absence or presence of SP600125

tag: Cell line

value: BALB/c mouse B lymphoma


title: TGF-beta12h_DMSO

description: Gene expression data from A20 cells stimulated with TGF-beta for 12 h


title: TGF-beta12h_SP600125

description: Gene expression data from A20 cells stimulated with TGF-beta in the presence of SP600125 for 12 h


title: TGF-beta24h_SP600125

description: Gene expression data from A20 cells stimulated with TGF-beta in the presence of SP600125 for 24 h


title: siRNA 2

city: Amsterdam

first: Olaf

last: Mook

address: Meibergdreef 9

department: Neurogenetics

country: Netherlands

institute: AMC

description: Expression data from MiaPaca II tumors treated systhemically with siRNA solution

hyb_protocol: following fragmentation, 10 ug of cRNA wre hybridized for 16 hr at 45C on Human Genome U133plus2 GeneChip. Genechips were washed and stained in a Affymetrix Fluidics Station 400

scan_protocol: GeneChips wer scanned using an Affymetrix GC 3000 6G scanner

data_processing: The data were analyzed as calculated ration profiles with Benjamini-Hochberg FDR correction using Rosetta Resolver.

source_name: In vivo siRNA treatment biol. repl. 2

label_protocol: Biotinylated cRNA wre prepared according to standard one cycle target protocol from 10 ug total RNA(Expression Analysis Technical Manual,2001, Affymetrix)

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

treatment_protocol: siRNA treatment via osmotic minipump (0.25 mg/kg/day) for one weeks

tag: Human pancreatic xenograft (MiaPaca II)


title: non-stimulated_SP600125

description: Gene expression data from A20 cells cultured in the presence of SP600125 for 24 h


title: siLNA 1

description: Expression data from MiaPaca II tumors treated systhemically with siLNA solution

source_name: In vivo siLNA treatment biol. repl. 1

treatment_protocol: siLNA treatment via osmotic minipump (0.25 mg/kg/day) for one weeks


title: non-stimulated_DMSO

description: Gene expression data from A20 cells cultured with normal growth medium


title: empty vector

city: London

first: Masahiro

last: Ono

address: 30 Guilford Street

department: Immunobiology Unit

country: United Kingdom

institute: Institute of Child Health

description: Refer to Ono, M. et al, Nature 2007 (Supplementary Figure S7).

hyb_protocol: Labelled cRNA (15ug) were hybridized with Mouse Genome 430 2.0 Array for 16 hours, washed, and stained by streptavidin-phycoerthrin.

scan_protocol: The arrays were scanned and aquired data were analyzed by Gene chip operating software (GCOS).

data_processing: Gene chip operating software (GCOS).

source_name: CD4+ T cells gene-transduced with empty vector

label_protocol: One cycle target labelling according to the protocol provided by Affymetrix

growth_protocol: Naive CD4+ T cells were activated by soluble anti-CD3 Ab [0.5ug/ml], IL-2 [20u/ml] and antigen presenting cells (T cell-depleted, mitomycin-C-treated splenocytes). Twenty-four hours after transfection, retroviral supernatant and polybrene were added and centrifuged for one hour at 3200 rpm. Cells were kept at 37 C, 5% CO2 until they were sorted.

extract_protocol: We performed RNA extraction using QIAGEN's RNeasy micro columns. according to the manufacteur's protocol.

treatment_protocol: CD4+ naive T cells were activated and retrovirally gene transduced with either empty vector (pMCsIg) or AML1-, wild type Foxp3-, or an AML1-non binding mutant Foxp3. Sixty hours after transfection, GFP+ cells were sorted and lysed for RNA samples.

tag: T cells were obtained from BALB/c mice and purified into CD4+ naive T cells (GITRlowCD25-CD4+) and retrovirally gene transduced.


title: Foxp3 mutant

source_name: CD4+ T cells gene-transduced with a Foxp3 mutant defective in binding to AML1.

treatment_protocol: CD4+ naive T cells were activated and retrovirally gene transducedwith either empty vector (pMCsIg) or AML1-, wild type Foxp3-, or an AML1-non binding mutant Foxp3. Sixty hours after transfection, GFP+ cells were sorted and lysed for RNA samples.

tag: T cells were obtained from BALB/c mice and puridied to CD4+ naive T cells (GITRlowCD25-CD4+) and retrovirally gene transduced


title: AML1

source_name: CD4+ T cells gene-transduced with AML1


title: Saline 3

description: Expression data from MiaPaca II tumors treated systhemically with saline solution

source_name: In vivo saline treatment biol. repl. 3

treatment_protocol: Saline treatment via osmotic minipump for one weeks


title: wild type Foxp3

source_name: CD4+ T cells gene-transduced with wild type Foxp3


title: siRNA 1

source_name: In vivo siRNA treatment biol. repl. 1


title: siLNA 2

source_name: In vivo siLNA treatment biol. repl. 2


title: siRNA 3

source_name: In vivo siRNA treatment biol. repl. 3


title: siLNA 3

source_name: In vivo siLNA treatment biol. repl. 3


title: Saline 1

source_name: In vivo saline treatment biol. repl. 1


title: R6/1 18 week transgenic_BC91

status: Public on Jul 31 2007

city: Cardiff

first: Lesley

last: Jones

address: Heath Park

department: Psychological Medicine

institute: Cardiff University School of Medicine

description: R6/1 transgenic, brain hemisphere

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: Brain hemisphere

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

extract_protocol: Three sex-matched mice from each genotype (R6/1 and wild-type) were sacrificed at 18, 22 and 27 weeks of age. Brain samples were collected, snap frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from one hemisphere for microarray analysis, as described previously (Morton et al., 2005). Microarray analysis of global gene expression was carried out using 10µg of total RNA and murine genome 430 2.0 Arrays

tag: Transgenic, brain hemisphere


title: R6/1 18 week transgenic_5D42

description: R6/1 transgenic, brain hemisphere


title: R6/1 18 week transgenic_C627

description: R6/1 transgenic, brain hemisphere


title: R6/1 18 week wildtype_F272

description: R6/1 wildtype, brain hemisphere

tag: Wild type, brain hemisphere


title: R6/1 22 week transgenic_BD1Bv1

description: R6/1 transgenic, brain hemisphere


title: Dental Molar Tooth (DMT) replicate 3

city: Ann Arbor

first: Trevor

middle: J

last: Pemberton

state: MI

address: 100 Washtenaw Ave

department: Human Genetics

institute: University of Michigan

description: Global gene expression in the developing mouse molar tooth between post-natal days 1 to 10. Replicate 1.

hyb_protocol: Affymetrix recommended protocol and reagents.

scan_protocol: Affymetrix recommended protocol.

label: Biotin-dUTP

source_name: Molar Teeth, collected 1 to 10 days post-natal

extract_protocol: Molar teeth were manually extracted from 60 Swiss Webster mouse pups between 1 and 10 days post-natal (USC IACUC Protocol # 7225). The teeth were pooled and ground in the presence of liquid nitrogen using a pestle and mortar and the RNA extracted using the RNeasy RNA purification kit (Qiagen, Valencia, CA) following the manufacturer’s recommended protocol.

tag: Strain

value: Swiss-Webster

tag: Gender

value: Pool of male and female

tag: Age

value: Post-natal days 1 to 10

tag: Tissue

value: Molar Teeth


title: Dental Molar Tooth (DMT) replicate 4

label_protocol: Affymetrix recommended protocol and reagents.


title: R6/1 27 week wildtype_D494

description: R6/1 wildtype, brain hemisphere


title: R6/1 22 week wildtype_O7A2

description: R6/1 wildtype, brain hemisphere


title: R6/1 22 week wildtype_OAD3

description: R6/1 wildtype, brain hemisphere


title: R6/1 22 week wildtype_C835

description: R6/1 wildtype, brain hemisphere


title: R6/1 27 week transgenic_OE41

description: R6/1 transgenic, brain hemisphere


title: R6/1 27 week transgenic_O8AE

description: R6/1 transgenic, brain hemisphere


title: Dental Molar Tooth (DMT) replicate 2


title: R6/1 22 week transgenic_BBB4

description: R6/1 transgenic, brain hemisphere


title: Saline 2

source_name: In vivo saline treatment biol. repl. 2


title: R6/1 18 week wildtype_DFFC

description: R6/1 wildtype, brain hemisphere


title: R6/1 27 week transgenic_75F3

description: R6/1 transgenic, brain hemisphere


title: R6/1 27 week wildtype_1338

description: R6/1 wildtype, brain hemisphere


title: SEG1_vehicle pretreated_acid pulsed

status: Public on Jul 30 2007

city: Columbus

first: Laura

last: Kresty

state: OH

address: CCC Building, Rm 302B

department: Internal Medicine

institute: The Ohio State University

description: Gene expression data from acid-pulsed cells pretreated with vehicle

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the human genoma gene chip U133 2.0 Plus. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.

source_name: Derived from human esophageal cancer

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: SEG-1 esophageal adenocarcinoma cells were plated at 2 x 10^6 cells/T75 flask.

extract_protocol: Trizol extraction of total RNA was performed per the manufacterer's instructions.

treatment_protocol: Cells were pretreated with vehicle or HDAC-42 (1.6 uM) in DMEM phenol red-free medium containing 5% FBS for 24 hours.  Cells were then rinsed and pulsed with serum-free acidified medium (pH 3.5) or vehicle for 20 mins in a humidified chamber (37C).  Cells were rinsed again and replenished with serum-free media or HDAC-42 (1.6 uM) in serum-free media.  Cells were harvested 6 hours post vehicle or acid exposure.

tag: Human esophageal cancer cell line SEG-1


title: SEG1_HDAC42 pretreated_acid pulsed

description: Gene expression data from acid-pulsed cells pretreated with HDAC-42


title: R6/1 27 week wildtype_B9F2

description: R6/1 wildtype, brain hemisphere


title: Dental Molar Tooth (DMT) replicate 1


title: R6/1 27 week transgenic_2C4C

description: R6/1 transgenic, brain hemisphere


title: BALB/cJ strain, brain hemisphere,  biological rep2

city: Orangeburg

first: Csaba

last: Vadasz

state: NY

address: 140 Old Orangeburg Road

department: Center for Neurobehavior Genetics

institute: New York University NKI

description: Gene expression data from brain hemispheres of experimentally naive male mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChipR Scanner

data_processing: We used .CEL files produced by GCOS for probe (cell) level Robust Multi-Array Average (RMA)-based normalization of data as implemented in GeneTraffic ver. 3.0

source_name: Brain hemisphere of adult male mouse, cerebellum not included

label_protocol: Fragmented cRNA probes were prepared from 7 µg of total RNA according to the protocol of Affymetrix using Superscript Choice System (Invitrogen) and a RNA Transcript Labeling Kit (Enzo, Farmingdale, NY).

treatment_protocol: Animals were killed by cervical dislocation, brains were quickly removed, hemisectioned, and alternate left or right hemispheres were collected in RNA-Later.  After processing each hemisphere separately, 10 hemispheres were pooled for one high-density oligonucleotide microarray

tag: Inbred strain

value: BALB/cJ; Gender:male; Age:11-week-old (+/- 1 week)


title: B6By.C.132.54 strain, brain hemisphere,  biological rep2

value: B6By.C.132.54; Gender:male; Age:11-week-old (+/- 1 week)


title: BALB/cJ strain, brain hemisphere,  biological rep1


title: B6By.C.132.54 strain, brain hemisphere,  biological rep1


title: B6By.C.132.54 strain, brain hemisphere,  biological rep3


title: C57BL/6ByJ strain, brain hemisphere,  biological rep3

value: C57BL/6ByJ; Gender:male; Age:11-week-old (+/- 1 week)


title: BALB/cJ strain, brain hemisphere,  biological rep3


title: Affymetrix Gene Expression profiling of mouse ES cells (R1)

status: Public on Jul 28 2007

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: R1 ES cells (a gift from Dr. Don Cleveland, Ludwig institute for cancer research, San Diego) were maintained on top of feeder cells in cell culture dish with DMEM high glucose medium supplemented with 15% FBS, 0.1mM non-essential amino acid, 1mM sodium pyruvate, 15M _-mercaptoethanol, 2mM L-glutamine, 50g/ml pen/strep and LIF. ES Cells were passed once on 0.1% gelatin without feeder cells before harvested

hyb_protocol: Affymetrix total RNA hybridization protocol

scan_protocol: Affymetrix scan protocol

data_processing: Data processed using Affymetrix GCOS Software

source_name: Total RNA from mouse ES cells (R1)

label_protocol: Purified total RNA was submitted to UCSD Cancer Center Microarray Resource for GeneChip RNA Expression Analysis. Biotin labeling protocol.

extract_protocol: Total RNA from each mouse tissue was extracted using Trizol. reagent (Invitrogen, Carlsbad, CA) and further purified using RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer recommendations

tag: R1 ES cells


title: Affymetrix Gene Expression profiling of adult mouse brain

description: Total RNA from adult mouse brain, 10-12 weeks

data_processing: Affymetrix GCOS software

source_name: Total RNA from adult mouse brain cells

label_protocol: biotinylation

tag: Sample of mouse adult tissue was dissected out from 10-12 week old wild-type BL6 female mouse


title: Affymetrix Gene Expression profiling of adult mouse liver

description: Total RNA from adult mouse  10-12 weeks

source_name: Total RNA from adult mouse liver cells

tag: sample of mouse adult tissue was dissected out from 10-12 week old wild-type BL6 female mouse


title: NCR-EW2

status: Public on Jul 27 2007

description: Gene expression data from a EFT cell line expressing EWS/FLI1 typeII

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: EFT cells and NB cells  were cultured in RPMI 1640 with 10% fetal bovine serum (FBS) at 37°C under a humidified 5% CO2 atmosphere.  RMS cells were cultured in MEMa with 10% FBS.  UET-13 cells werecultured in Dulbeccoﾕs modified Eagleﾕs medium (DMEM)  with 10% FBS.

tag: EFT cell line expressing EWS/FLI1


title: Affymetrix Gene Expression profiling of adult mouse kidney

description: Total RNA from adult mouse  10-12 weeks

source_name: Total RNA from adult mouse kidney cells


title: NRS-1

description: Gene expression data from a RMS cell line

tag: RMS cell line


title: Affymetrix Gene Expression profiling of adult mouse heart

description: Total RNA from adult mouse  10-12 weeks

source_name: Total RNA from adult mouse heart cells


title: C57BL/6ByJ strain, brain hemisphere,  biological rep2


title: GOTO

description: Gene expression data from a NB cell line

source_name: GOTO

tag: NB cell line


title: W-ES

description: Gene expression data from a EFT cell line expressing EWS/ERG

source_name: W-ES

tag: EFT cell line expressing EWS/ERG


title: NB69


title: UET-13

description: Gene expression data from UET-13 cells

tag: UET-13 cells are derived from human bone marrow stromal cells by prolonging the life span by retroviral transgenes, hTERT and E7


title: SK-ES1


title: NCR-EW3

description: Gene expression data from a EFT cell line expressing EWS/E1AF

tag: EFT cell line expressing EWS/E1AF


title: C57BL/6ByJ strain, brain hemisphere,  biological rep1


title: RD-ES

source_name: RD-ES


title: NB9


title: SCCH196

description: Gene expression data from a EFT cell line expressing EWS/FLI1 typeI


title: EES-1


title: umbilical cord_bpd: 9I

status: Public on Jul 26 2007

city: Boston

first: Jennifer

middle: N

last: Cohen

state: MA

address: 75 Francis Street

department: Newborn Medicine

institute: Brigham and Women's Hospital

description: low gestational age

hyb_protocol: Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols

scan_protocol: Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols

data_processing: MAS_5.0 scaled to 1500

source_name: umbilical cord tissue; low gestational age

label_protocol: GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols

extract_protocol: initial step used Trizol extraction of RNA, following manufacturer's recommended protocols, followed by Qiagen RNeasy Mini Kit per manufacturer's recommended protocols

tag: 23 weeks male


title: umbilical cord_nobpd: 5I

description: low gestational age

tag: 26 weeks male


title: umbilical cord_bpd: 2I

description: low gestational age

tag: 26 weeks female


title: umbilical cord_bpd: 4I

description: low gestational age


title: umbilical cord_nobpd: 8D

description: high gestational age

source_name: umbilical cord tissue; high gestational age

tag: 27 weeks male


title: umbilical cord_bpd: 7F

description: high gestational age

tag: 27 weeks female


title: umbilical cord_bpd: 6H

description: low gestational age


title: umbilical cord_nobpd: 7I

description: high gestational age


title: umbilical cord_nobpd: 4F

description: low gestational age


title: umbilical cord_bpd: 8I

description: high gestational age


title: umbilical cord_nobpd: 9B

description: high gestational age


title: umbilical cord_nobpd: 8C

description: high gestational age


title: umbilical cord_bpd: 7H

description: low gestational age

tag: 25 weeks female


title: umbilical cord_nobpd: 8F

description: high gestational age


title: umbilical cord_nobpd: 3I

description: low gestational age

tag: 23 weeks female


title: umbilical cord_bpd: 9F

description: low gestational age

tag: 25 weeks male


title: umbilical cord_bpd: 7C

description: low gestational age

tag: 24 weeks male


title: umbilical cord_bpd: 9C

description: low gestational age


title: umbilical cord_nobpd: 8B

description: low gestational age


title: umbilical cord_bpd: 8A

description: low gestational age


title: umbilical cord_bpd: 6F

description: low gestational age


title: umbilical cord_bpd: 5H

description: high gestational age


title: R6/1 18 week wildtype_15E8

description: R6/1 wildtype, brain hemisphere

tag: Wild type, brain hemisphere


title: umbilical cord_nobpd: 9D

description: high gestational age


title: umbilical cord_nobpd: 6D

description: low gestational age


title: umbilical cord_nobpd: 6E/2F

description: high gestational age


title: umbilical cord_nobpd: 7D

description: high gestational age


title: umbilical cord_nobpd: 6A

description: high gestational age


title: umbilical cord_nobpd: 9A

description: low gestational age


title: umbilical cord_nobpd: 5F

description: high gestational age


title: umbilical cord_nobpd: 4D

description: low gestational age


title: umbilical cord_nobpd: 4A

description: high gestational age


title: umbilical cord_bpd: 5B

description: low gestational age


title: umbilical cord_nobpd: 3D

description: low gestational age


title: umbilical cord_nobpd: 5A

description: high gestational age


title: umbilical cord_bpd: 3E

description: high gestational age


title: umbilical cord_nobpd: 2G

description: high gestational age


title: umbilical cord_nobpd: 3C

description: high gestational age


title: umbilical cord_nobpd: 5D

description: low gestational age


title: umbilical cord_nobpd: 3F

description: high gestational age


title: umbilical cord_bpd: 5C

description: low gestational age


title: umbilical cord_nobpd: 4B

description: high gestational age


title: umbilical cord_bpd: 3B

description: low gestational age

tag: 24 weeks female


title: umbilical cord_nobpd: 3A

description: low gestational age


title: umbilical cord_nobpd: 4C

description: low gestational age


title: umbilical cord_nobpd: 2D

description: high gestational age


title: umbilical cord_nobpd: 2C

description: low gestational age


title: umbilical cord_nobpd: 3G

description: low gestational age


title: umbilical cord_nobpd: 2E

description: high gestational age


title: umbilical cord_nobpd: 1E

description: high gestational age


title: umbilical cord_nobpd: 2A

description: high gestational age


title: umbilical cord_bpd: 1C

description: high gestational age


title: umbilical cord_bpd: 1D

description: low gestational age


title: umbilical cord_bpd: 2B

description: low gestational age


title: umbilical cord_nobpd: 1A

description: high gestational age


title: Gene expression profiling of Phgdh knockout embryo KO3

status: Public on Jul 25 2007

city: Fukuoka

first: Shigeki

last: Furuya

state: Fukuoka

address: 6-10-1 Hakozaki, Higashiku

department: Bio-Architecture Center

institute: Kyushu University

description: Affymetrix GeneChip® Mouse Genome 430 2.0 Array

hyb_protocol: Hybridization was carried out for 16 hr at 45 ºC according the Affymetrix GeneChip® Manual.

scan_protocol: Scanning was carried out using Affymetrix® GeneChip® Scanner with GCOS software according to manufactuer's protocol.

data_processing: Fluorescent data were processed using the Microarray Suite (MAS) 5.0 software (Affymetrix) and then were transferred to GeneSpring 7.0 software (Agilent).

source_name: Head RNA of Phgdh Knockout@E13.5 No.3

label_protocol: Labeling was carried out using Affymetrix GeneChip® One-Cycle Target Labeling kit, according to manufactuer's protocol.

extract_protocol: Total RNA from embryo heads was extracted and purified using RNeasy Lipid Tissue kit (Qiagen Inc) according to the manufacturer’s instructions.

treatment_protocol: Targeted disruption of D-3-Phosphoglycerate dehydrogenase (Phgdh; EC 1.1.1.95) in mice.

tag: ES cells

value: E14 (129P2/OlaHsd background), Genotype:Knockout (Phgdh-/-), C57BL/6J background, Gestation:13.5 days, Tissue:head


title: Gene expression profiling of Phgdh knockout embryo KO1

source_name: Head RNA of Phgdh KO@E13.5 No.1


title: Gene expression profiling of Phgdh knockout embryo KO4

source_name: Head RNA of Phgdh Knockout@E13.5 No.4


title: Gene expression profiling of Phgdh knockout embryo KO2

source_name: Head RNA of Phgdh Knockout@E13.5 No.2


title: Gene expression profiling of Phgdh knockout embryo wild2

source_name: Head RNA of littermate wild@E13.5 No.2

value: E14 (129P2/OlaHsd background), Genotype:Wild (Phgdh+/+), C57BL/6J background, Gestation:13.5 days, Tissue:head


title: Gene expression profiling of Phgdh knockout embryo wild3

source_name: Head RNA of littermate wild@E13.5 No.3


title: liver_PPARa-knockout_control_5d_rep2

status: Public on Jul 24 2007

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: liver, PPARa-null mice, control conditions

hyb_protocol: According to standard Affymetrix protocols.

data_processing: GCRMA version 2.20, empirical Bayes

extract_protocol: TRIzol reagent (Invitrogen), according to manufacturer's instructions

tag: Strain

value: 129S4/SvJae (PPARα-null)

tag: Gender

value: male

tag: Age

value: 12-20 weeks

tag: Tissue

value: liver


title: liver_wildtype_control_5d_rep2

description: liver, wild-type mice, control conditions

scan_protocol: According to standard Affymetrix protocols.

value: 129S1/SvImJ (wildtype)


title: liver_PPARa-knockout_control_5d_rep3

label_protocol: According to standard Affymetrix protocols.


title: mouse_hepatocytes_WY24h_pooled

description: primary hepatocytes, mouse, treatment with WY14643 for 24h

extract_protocol: TRIzol reagent (Invitrogen), according to manufacturer's instructions.

tag: Material

value: primary hepatocytes, mouse


title: liver_PPARa-knockout_WY14643_5d_rep3

description: liver, PPARa-null mice, treatment with WY14643 for 5d


title: mouse_hepatocytes_control_pooled

description: primary hepatocytes, mouse, control condition


title: liver_PPARa-knockout_WY14643_5d_rep2


title: liver_wildtype_control_5d_rep4

description: liver, wild type mice, control conditions


title: liver_wildtype_control_5d_rep1


title: liver_PPARa-knockout_WY14643_5d_rep4


title: liver_wildtype_control_5d_rep3


title: liver_PPARa-knockout_WY14643_5d_rep1


title: Gene expression profiling of Phgdh knockout embryo wild4

source_name: Head RNA of littermate wild@E13.5 No.4


title: liver_PPARa-knockout_control_5d_rep4


title: liver_wildtype_WY14643_5d_rep2

description: liver, wild type mice, treatment with WY14643 for 5d


title: liver_wildtype_WY14643_5d_rep1


title: liver_wildtype_WY14643_5d_rep3


title: liver_PPARa-knockout_control_5d_rep1


title: Uterus_Gravid_d18_WT-rep4

city: Indianapolis

first: Kathleen

last: Bethin

state: IN

address: 702 Barnhill Dr.

department: Pediatrics

institute: Indiana University

description: The Center for Medical Genomics Core at Indiana University School of Medicine analyzed the RNA using Affymetrix 430 2.0 GeneChips.

hyb_protocol: Fifteen micrograms of biotinylated cRNA was added to a total hybridization cocktail of 300 microliters and 200 microliters was hybridized to a 430 2.0 GeneChip at 45º for 17 h with constant rotation.   The GeneChips were washed, stained with phycoerythrin-labeled streptavidin, washed, incubated with biotinylated anti-streptavidin and then restained with phycoerythrin-lableled streptavidin to amplify the signals, all following the standard Affymetrix protocol.

scan_protocol: GeneChips were then scanned using a dedicated scanner controlled by Affymetrix GCOS software.  The images were examined for defects and the hybridization intensity data was analyzed with the Affymetrix Microarray Suite version 5 (MAS5).

data_processing: The images were examined for defects and the hybridization intensity data was analyzed with the Affymetrix Microarray Suite version 5 (MAS5).  MAS5 calculated a set of metrics that describe probe performance.  The average intensity on each array was normalized by global scaling to a target intensity of 1000.  Data were imported into the MicroArray Data Portal for further analysis.  All genes included in the analysis had to have a “present” call in at least 50% of the samples.

label: Biotinylated

source_name: Gravid day 18.0 Wild-type Uterus

label_protocol: Five micrograms of total RNA was labeled following single cycle protocols recommended in the GeneChip Expression Analysis Technical Manual.  The cDNA was synthesized from RNA using a T7 promoter-dT24 oligonucleotide primer with the Invitrogen Life Technologies SuperScript Choice system.  After the second strand synthesis and incubation with T4 DNA polymerase the products were purified using an Affymetrix Cleanup Module.  Biotynylated cRNA was made using the Affymetrix IVT kit.  The cRNA was purified with Qiagen RNeasy columns, quantitated and then fragmented at high temperature with magnesium.

extract_protocol: Trizol extracted, followed by RNeasy

treatment_protocol: Rinsed in PBS in DEPC, Snap frozen

value: C57BL/6, Gender:female, Age 6-16 weeks, Tissue:Gravid day 18.0 Uterus


title: human_hepatocytes_WY12h_pooled

description: primary hepatocytes, human, treatment with WY14643 (12h)

tag: Primary hepatocytes, human


title: Uterus_Gravid_d18_WT-rep3


title: RNA from G0 arrested T98G cells

status: Public on Jul 21 2007

first: Subhashini

last: Sadasivam

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Insitute

description: RNA from G0 arrested T98G cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

source_name: T98G cells

label_protocol: RNA from each sample is converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA. The cRNA is hybridized to a microarray chip. The bound cRNA is stained with fluorescent streptavidin.

growth_protocol: RNA was purified from T98G cells that were either cycling, G0 arrested, or released into S phase for 10 hr and 16 hr. For each experimental condition, 15 μg of RNA was processed and hybridized against Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

extract_protocol: Trizol method of RNA isolation and purification by Rneasy mini kit vy Qiagen

tag: human glioblastoma cell line


title: Uterus_Gravid_d18_Cox-1 KO-rep3

source_name: Gravid day 18.0 Cox-1 KO Uterus

value: C57BL/6 x Sv129, Gender:female, Age 6-16 weeks, Tissue:Gravid day 18.0 Cox-1 KO Uterus


title: Uterus_Gravid_d18_WT-rep1


title: Uterus_Gravid_d18_Cox-1 KO-rep4


title: RNA from T98G cells in S phase of the cell cycle


title: Uterus_Gravid_d18_Cox-1 KO-rep2


title: Uterus_Gravid_d18_Cox-1 KO-rep1


title: Uterus_Gravid_d18_WT-rep2


title: Macrophage smi54

status: Public on Jul 19 2007

city: Cleveland

first: Jonathan

middle: David

last: Smith

address: 9500 Euclid Avenue

department: Cell Biology

institute: Cleveland Clinic

description: Gene expression data from mouse bone marrow macrophages

hyb_protocol: Following fragmentation, 12 ug of cRNA was hybridized to Affymetrix 430v2 arrays according to Affymetric protocols

scan_protocol: Arrays were scanned using the Hewlet-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed with Affymetrix Microarray Suite version 5.0 (MAS 5.0) using Refiner software (Genedata) using default settings. The normalization target was set to 500.

source_name: 16 week old apoE-deficient F2 female mouse from an AKRxDBA/2 intercross

label_protocol: Biotin labeled cRNA was prepared from 1 ug RNA using the BioARray High Yield RNA Transcript labeling kit (Enzo)

growth_protocol: Cells were cultured for 2 weeks in DMEM containing 10% FBS and 20% L-cell conditioned medium

extract_protocol: RNA extracted with RNAeasy minikit (Qiagen)

tag: Female


title: liver_wildtype_WY14643_5d_rep4


title: human_hepatocytes_control_pooled

description: primary hepatocytes, human, control condition

value: primary hepatocytes, human


title: RNA from actively growing T98G cells

description: RNA from actively growing T98G cells


title: RNA from T98G cells in G1 stage of the cell cycle


title: D1 aggregate culture, 9A1, rep 1 (430)

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Gene expression data from 9A1 BMEL cells cultured 1 day under aggregate conditions.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Array 430a . GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (non-upgraded).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 (non-upgraded).

data_processing: The data were analyzed with the Bioconductor affy (Gautier L, Cope L, Bolstad BM, et al. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (Oxford, England). 2004;20(3):307-315) package using R 2.3.1 and RMA (Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (Oxford, England). 2003;4(2):249-264) as the normalization method.

source_name: bipotential mouse embryonic liver cell line 9A1, aggregate culture 1 day

extract_protocol: RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.  RNA had an 18S/28S ratio greater than 1.7, a 260/230 ratio greater than 1.5, and a lack of visual RNA degradation on Agilent 2100 Bioanalyzer electropherograms (Agilent Technologies Inc.).

treatment_protocol: aggregate culture (Strick-Marchand H, Weiss MC. Inducible differentiation and morphogenesis of bipotential liver cell lines from wild-type mouse embryos. Hepatology. 2002;36:794-804)

value: embryos were derived from a CBA/J x C57Bl/6J cross.

value: cell lines derived from dpc14 embryonic mouse liver

tag: Cell line

tag: Culture condition

value: aggregate 1 day


title: D5 aggregate culture, 9A1, rep 1 (430)

description: Gene expression data from 9A1 BMEL cells cultured 5 days under aggregate conditions.

source_name: bipotential mouse embryonic liver cell line 9A1, aggregate culture 5 days

value: aggregate 5 days


title: D1 aggregate culture, 14B3, rep 2 (430)

description: Gene expression data from 14B3 BMEL cells cultured 1 day under aggregate conditions.

source_name: bipotential mouse embryonic liver cell line 14B3, aggregate culture 1 day


title: basal culture, 14B3, rep 1 (430)

description: Gene expression data from 14B3 BMEL cells cultured under basal conditions.

source_name: bipotential mouse embryonic liver cell line 14B3, basal culture

treatment_protocol: basal culture (Strick-Marchand H, Weiss MC. Inducible differentiation and morphogenesis of bipotential liver cell lines from wild-type mouse embryos. Hepatology. 2002;36:794-804)

value: basal


title: basal culture, 14B3, rep 2 (430)


title: D5 aggregate culture, 14B3, rep 2 (430)

description: Gene expression data from 14B3 BMEL cells cultured 5 days under aggregate conditions.

source_name: bipotential mouse embryonic liver cell line 14B3, aggregate culture 5 days


title: D5 aggregate culture, 9A1, rep 2 (430)

tag: Culture condition :aggregate 5 days


title: D1 aggregate culture, 14B3, rep 1 (430)


title: Aldosterone-producing adenoma (APA1)

status: Public on Jul 18 2007

city: Augusta

first: Ping

last: Ye

state: GA

address: 1120 15th Street

department: Physiology

institute: Medical College of Georgia

description: Gene expression data from aldosterone-producing adenoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics

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

data_processing: The data were analyzed with GeneSpring 7.3 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1.

source_name: Aldosterone-producing adenoma

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

extract_protocol: The tissue was pulverized in liquid nitrogen to a powder. Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA). The purity and integrity of the RNA were assessed by the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and its quantity was determined by NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE).

tag: Genotype

value: Homo sapiens


title: Aldosterone-producing adenoma (APA7)


title: basal culture, 9A1, rep 1 (430)

description: Gene expression data from 9A1 BMEL cells cultured under basal conditions.

source_name: bipotential mouse embryonic liver cell line 9A1, basal culture


title: D5 aggregate culture, 14B3, rep 1 (430)

treatment_protocol: aggregate (Strick-Marchand H, Weiss MC. Inducible differentiation and morphogenesis of bipotential liver cell lines from wild-type mouse embryos. Hepatology. 2002;36:794-804)


title: Aldosterone-producing adenoma (APA12)


title: Aldosterone-producing adenoma (APA13)


title: Aldosterone-producing adenoma (APA15)


title: Normal Adrenal Gland (AN18)

description: Gene expression data from normal adrenal gland

source_name: Normal Adrenal Gland


title: basal culture, 9A1, rep 2 (430)


title: Aldosterone-producing adenoma (APA19)


title: Normal Adrenal Gland (AN14)


title: Normal Adrenal Gland (AN15)


title: Aldosterone-producing adenoma (APA11)


title: Normal Adrenal Gland (AN11)


title: Aldosterone-producing adenoma (APA6)


title: Aldosterone-producing adenoma (APA4)


title: Normal Adrenal Gland (AN26)


title: Aldosterone-producing adenoma (APA5)


title: Angiotensin II Sample 2

first: Edson

middle: da Fonseca

last: Nogueira

description:
Quality control steps taken:
Sample from treated cells were compared to untreated (control) using different arrays. 3 replicates were used for human array. No dye-swap was used in any experiment.

hyb_protocol: HYBRIDIZATION Sample Fragmented cRNA 		40	40 Control oligo B2		3.9	3.9 Control cRNA from Affy	12	12 Herring Sperm DNA		2.4	2.4 Acetylated BSA		2.4	2.4 2XMES Hybrid buffer	120	120 Water to final volume 	59.3	59.3 The control RNA must be heated at 65o C for 5 minutes before adding to mix (use Affymetrix kit)   Warm chips to room temperature Set up the experiment in GCOS Experiment name Project- name of the PI Sample name could be same as experiment. Read the bar code on chip and all the other information is filled up. Add 1X MES to chip and incubate at 45o C for 10 minutes Heat hybridization cocktail to 99o C for 5 min and then 45o C for 5 minutes Spin for 5 min Remove buffer solution from the chip and add 200ul of hybridization cocktail. Hybridize for 16 hours Prepare buffer A and B Non-stringent Wash Buffer A For 1000 mL 300 ml of 20X SSPE 1.0 mL of 10% Tween-20 698 water Filter through 0.2um filter Stringent Wash Buffer B For 1000 ml 83.3 mL of 12X MES stock buffer (refer chapter 5 of the manual to prepare 12X MES) 5.2 mL of 5M NaCl 1.0ml of 10%tween 20 910.5 mL of water Filter through 0.2um filter Next day Prepare the stains and antibody solution for x number of samples according to the chart on the desk. Switch on fuidics and scanner and then click on GCOS. Change water bottles on fuidics to buffer A and B at the designated places. Prime fuidics by choosing Prime_450 in the protocol dropdown list Remove cocktail from the chip and fill with buffer A. In the Fluidics Station dialog box on the workstation, select the correct experiment in the dropdown Experiment list. In the protocol dropdown list, select the specific satin protocol which is in most cases FlexGE WS3. Choose run in the fluidics Station dialog box to begin the washing and staining and follow the instruction on the LCD window of the fuidics. When the wash is complete the LCD window will display EJECT CARTIDGE. Remove the cartridge and follow the instruction on LCD window again. Run the shutdown protocol replacing water bottles with buffer. There should not be any air bubble in the chip.

scan_protocol: The scanner is also controlled by GCOS.  Put the chips in the scanner.  You can scan as many as 48 chips at the same time.  Click the start icon in GCOS and the follow the direction there on.  After all the chips are scanned, data can be analyzed. Analysis Open the data files.  Check the grid corners by pressing F5, F6, F7 and F8.  Then press the analyze icon.  Choose target signal 150 then proceed for analysis.  Analyzed data is presented as excel spreadsheet and present as .CHP file.  Check for GAPDH5’/3’ signal intensity.  The ratio should be less then 4.

data_processing:
Software: GeneSpring (Agilent)
Data (.chip files) were inserted into the program and RMA normalization was selected. Then we used a protocol on GeneSpring to create an experiment. The parameters were: Basal versus Angiotensin II
Normalization order: Data Transformation: set measurements less than 0.01 to 0.01; Normalization to the 50th percentile
Error model for one-color data was selected
Base error model on deviation from one selected
Experiment interpretation:
Analysis mode: ration (signal/control); Use measurements flagged: flags present in both arrays.

label: ENZO LABELING KIT

source_name: Human H295R Cells (NCI-H295R) cell line originated from a human adrenocortical carcinoma (Gazdar et al 1990; Bird et al 1993; Holland et al 1993; Bird et al 1994; Rainey et al 2004).

label_protocol: Mix 20ul of cDNA from above (from 5ug of RNA), Xul Water (Final volume should be 40 ul), 3ul of 10X HY, 3ul Labeled ribonucleotides, 3ul 10XDTT, 3ul 10XRNase Inhibitor, 1.5ul	20X T7 RNA polymerase. Add above at RT to tube in order listed. Mix by centrifugation 5 sec. Place at 37 oC for 5hrs. Remove and mix about every 30-45 minutes.Place in freezer at –20 overnight

growth_protocol: DMEM/Ham’s F12 medium (Invitrogen, Grand Island, NY) supplemented with 10 % Cosmic Calf Serum (Hyclone, Logan, UT), 1 % penicillin/streptomycin (Invitrogen) and 0.01 % gentamicin (Invitrogen). Cells were maintained in a 37ºC humidified atmosphere (5 % CO2).

extract_protocol: Total RNA was extracted from cells plates using Trizol (Invitrogen) according to the manufacturer’s directions.

treatment_protocol: Prior to treatments, adrenal cells were maintained overnight in low serum medium (DMEM/Ham’s F12 medium supplemented with 0.1 % cosmic calf serum medium, 1 % penicillin/streptomycin and 0.01 % gentamicin). Then cells were treated without or with 10 nM angiotensin II for 1 hour.

tag: This file represents the second repeat of a set of experiments treating H295R adrenortical carcinoma cells with Angiotensin II for 1 hour.


title: Cycloheximide

hyb_protocol: HYBRIDIZATION Sample + Fragmented cRNA 		40	40 Control oligo B2		3.9	3.9 Control cRNA from Affy	12	12 Herring Sperm DNA		2.4	2.4 Acetylated BSA		2.4	2.4 2XMES Hybrid buffer	120	120 Water to final volume 	59.3	59.3 The control RNA must be heated at 65o C for 5 minutes before adding to mix (use Affymetrix kit)   Warm chips to room temperature Set up the experiment in GCOS Experiment name Project- name of the PI Sample name could be same as experiment. Read the bar code on chip and all the other information is filled up. Add 1X MES to chip and incubate at 45o C for 10 minutes Heat hybridization cocktail to 99o C for 5 min and then 45o C for 5 minutes Spin for 5 min Remove buffer solution from the chip and add 200ul of hybridization cocktail. Hybridize for 16 hours Prepare buffer A and B Non-stringent Wash Buffer A For 1000 mL 300 ml of 20X SSPE 1.0 mL of 10% Tween-20 698 water Filter through 0.2um filter Stringent Wash Buffer B For 1000 ml 83.3 mL of 12X MES stock buffer (refer chapter 5 of the manual to prepare 12X MES) 5.2 mL of 5M NaCl 1.0ml of 10%tween 20 910.5 mL of water Filter through 0.2um filter Next day Prepare the stains and antibody solution for x number of samples according to the chart on the desk. Switch on fuidics and scanner and then click on GCOS. Change water bottles on fuidics to buffer A and B at the designated places. Prime fuidics by choosing Prime_450 in the protocol dropdown list Remove cocktail from the chip and fill with buffer A. In the Fluidics Station dialog box on the workstation, select the correct experiment in the dropdown Experiment list. In the protocol dropdown list, select the specific satin protocol which is in most cases FlexGE WS3. Choose run in the fluidics Station dialog box to begin the washing and staining and follow the instruction on the LCD window of the fuidics. When the wash is complete the LCD window will display EJECT CARTIDGE. Remove the cartridge and follow the instruction on LCD window again. Run the shutdown protocol replacing water bottles with buffer. There should not be any air bubble in the chip.

treatment_protocol: Cells were incubated for 1 hour with no treatment or treated with 10 nM Ang II, 35 uM cycloheximide, or 10 nM Ang II + 35 uM cycloheximide. Treatment with cycloheximide was done 15 min prior to treatment with Ang II.

tag: This file represents H295R cells incubated with Cycloheximide to be used as controls for Angiotensin II + Cycloheximide treatment.


title: Angiotensin II Sample 3

tag: This file represents the third repeat of a set of experiments treating H295R adrenortical carcinoma cells with Angiotensin II for 1 hour.


title: Angiotensin II Sample 1

treatment_protocol: Prior to treatments, adrenal cells were maintained overnight in low serum medium (DMEM/Ham’s F12 medium supplemented with 0.1 % cosmic calf serum medium, 1 % penicillin/streptomycin and 0.01 % gentamicin). Then cells were then incubated without or with 10 nM angiotensin II for 1 hour.

tag: This file represents the first repeat of a set of experiments treating H295R adrenortical carcinoma cells with Angiotensin II for 1 hour. The suplementary table lists the top 50 genes up-regulated by angiotensin II treatment in H295R cells. Data was obtained by pooling the 3 repeat experiments together into GeneSpring Software.


title: Basal 1 (control 1)

tag: This file represents the first repeat used as a control for a set of experiments.


title: Seedling_ConstantWhiteLight_64hr

status: Public on Jul 15 2007

city: Davis

first: Michael

middle: F

last: Covington

address: One Shields Avenue, LS 1002

department: Plant Biology

institute: University of California-Davis

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Absence Calls were calculated using MAS5.0.  The data were further analyzed with dChip using the following parameters: Version=1.3 Test; BaselineArray=Arabidopsis-LL24.CEL; ModelMethod=PM-only model; CheckOutlier=Single,Array,Probe; ImageSpikeAsSingleOutlier=Yes; Exclude5PrimeProbes=0; ReplicateNotAllOutlier=No; LogTransformed=No (with base 2); TruncateLowValue=No (to value 0); TruncateToAbsentPercent=No (to percent 10); OutputArrayOutlierAsBlank=No

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings after 64 h in constant white light

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

growth_protocol: Seeds sown on  filter paper on media (1x MS, 3% sucrose, 0.8% agar); stratified at 4C for 4 d; grown for 7 d at 22C in 12-h  light (cool white fluorescence tubes, ~120 µmol m-2 s-1)/12-h dark cycles before being released into free-running conditions of constant white light, 22C; sample collection initiated at subjective dawn of day 9

extract_protocol: Qiagen's RNeasy Plant Mini Kit was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Samples were collected at 4-h intervals (by freezing in liquid nitrogen) while growing in constant light conditions

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:64 h


title: Angiotensin II + Cycloheximide

tag: This file represents data from H295R adrenortical carcinoma cells pre-incubated with angiotensin II for 15 min and then treated with 10 nM Angiotensin II for 1 hour.


title: D1 aggregate culture, 9A1, rep 2 (430)

tag: Strain


title: Basal 2 (Control 2)

treatment_protocol: Prior to treatments, adrenal cells were maintained overnight in low serum medium (DMEM/Ham’s F12 medium supplemented with 0.1 % cosmic calf serum medium, 1 % penicillin/streptomycin and 0.01 % gentamicin). Then cells were treated with or without 10 nM angiotensin II for 1 hour.

tag: This file represents the second repeat used as control sample for a set of experiments.


title: Seedling_ConstantWhiteLight_56hr

source_name: Arabidopsis seedlings after 56 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:56 h


title: Basal 3 (control 3)

tag: This file represents the third repeat of  Control samples usef for a set of experiments.


title: Seedling_ConstantWhiteLight_68hr

source_name: Arabidopsis seedlings after 68 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:68 h


title: C57BL6J mice infected peritoneal lavage day 3pi, biological repeat 2

city: Memphis

first: Lorne

last: Rose

state: TN

address: 854 Madision Ave

department: Molecular Sciences

institute: University of Tennessee

description: Transcription profile of  peritoneal lavage cells 3 days post infection with Chlamydia psittaci

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

data_processing: The data were analyzed with Robust multiple array average using default analysis settings and global scaling as normalization method.  RMA data normalized to 8 with SD of 2 units.

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: 6 week old male C57BL6J and DBA2J mice were purchased from Jackson Laboratories and maintained  in our animal care facility for 1 week prior to use

extract_protocol: Peritoneal lavage was collected sterily by injection and collection of PBS into the peritoneal cavity. Extracted lavage was centrifuged and supernatent was discarded. Cell pellets were treated with Trizol. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Chlamydia psittaci (10,000 IFU) was suspended in 200 microL  of PBS and injected intraperitoneally

tag: C57BL6J 7 wk old Male


title: DBA2J mice infected peritoneal lavage day 3pi, biological repeat 3

tag: DBA2J 7 wkold Male


title: C57BL6J mice infected peritoneal lavage day 3pi, biological repeat 5


title: Seedling_ConstantWhiteLight_60hr

source_name: Arabidopsis seedlings after 60 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:60 h


title: Seedling_ConstantWhiteLight_52hr

source_name: Arabidopsis seedlings after 52 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:52 h


title: Seedling_ConstantWhiteLight_32hr

source_name: Arabidopsis seedlings after 32 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:32 h


title: Seedling_ConstantWhiteLight_28hr

source_name: Arabidopsis seedlings after 28 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:28 h


title: Seedling_ConstantWhiteLight_44hr

source_name: Arabidopsis seedlings after 44 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:44 h


title: DBA2J mice infected peritoneal lavage day 3pi, biological repeat 2


title: Seedling_ConstantWhiteLight_36hr

source_name: Arabidopsis seedlings after 36 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:36 h


title: DBA2J mice infected peritoneal lavage day 3pi, biological repeat 1


title: Seedling_ConstantWhiteLight_24hr

source_name: Arabidopsis seedlings after 24 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:24 h


title: C57BL6J mice infected peritoneal lavage day 3pi, biological repeat 3


title: Seedling_ConstantWhiteLight_40hr

source_name: Arabidopsis seedlings after 40 h in constant white light

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:40 h


title: Arabidopsis roots, mock treatment, replica 1

status: Public on Jul 13 2007

city: Raleigh

first: Jose

middle: M

last: Alonso

state: NC

department: Genetics

institute: North Carolina State University

description:
Wild-type Col-0 seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC.
Seedlings were then sprayed with a 0.01% EtOH solution (mock treatment) under safe green light and incubated in the dark for four hours. 50 ml of RNAlater solution were then poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.

hyb_protocol: Hybridization and washes were performed according to Affymetrix recommendations. Affymetrix GeneChip Fluidics Station and Afymetrix GeneChip hybridization Oven 640 were used.

scan_protocol: The Affymetrix GeneChip Scanner was used according to the manufactirers' recommendations.

data_processing: Data from Cel files were normalized using the gcRMA package from Bioconductor.

source_name: Arabidopsis roots. Control for the IAA treatment.

label_protocol:
cRNA synthesis and labeling were performed according to manufacturers' (Affymetrix)
recommendations, except that the labeling reactions were scaled down 50%.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogene Life Technologies) and then further purified using RNasy Mini Kit (QIAGEN)

tag: Wild-type Arabidopsis seeds (Col-0) were germinated in the dark for 72 hours in sterile vertical plates. Seedlings were sprayed with 0.01% EtOH (mock treatment) under safe green light and incubated for 4 additional hours in the dark.


title: Arabidopsis ein2 mutant roots, mock treatment, replica 2

description: ein2-5 mutant seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC. Seedlings were then sprayed with a 0.01% EtOH solution (mock treatment) under safe green light and incubated in the dark for four hours. 50 ml of RNAlater solution were then poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.

source_name: Arabidopsis ein2 mutant roots. Control for the IAA treatment.

tag: Arabidopsis ein2 mutant seeds (ein2-5) were germinated in the dark for 72 hours in sterile vertical plates. Seedlings were sprayed with 0.01% EtOH (mock treatment) under safe green light and incubated for 4 additional hours in the dark.


title: Arabidopsis ein2 mutant roots, IAA treatment, replica 1

description: ein2-5 mutant seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC. Seedlings were then sprayed with 1 microMolar IAA in a 0.01% EtOH solution under safe green light and incubated in the dark for four hours. 50 ml of RNAlater solution were then poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.

source_name: Arabidopsis ein2 mutant roots. IAA treatment.

tag: Arabidopsis ein2 mutant seeds (ein2-5) were germinated in the dark for 72 hours. Seedlings were grown in sterile vertical plates. Seedlings were sprayed with 1 microMolar IAA in a 0.01% EtOH solution under safe green light and incibated for 4 additional hours in the dark.


title: Arabidopsis aux1 mutant roots, air treatment, replica 2

description:
aux1 mutant seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC.
Hydrocarbon-free air was flushed through the plates with seedlings for four hours. 50 ml of RNAlater solution were then poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.

source_name: Arabidopsis aux1 mutant roots. Air treatment control

tag: Arabidopsis aux1 mutant seeds (aux1-7) were germinated in the dark for 72 hours in sterile vertical plates. Hydrocarbon-free air was flushed for 4 additional hours.


title: Arabidopsis roots, mock treatment, replica 2


title: Arabidopsis aux1 mutant roots, ethylene treatment, replica 2

description:
aux1 mutant seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC.
Hydrocarbon-free air supplemented with 10ppm of ethylene was flushed through the plates with seedlings for four hours. 50 ml of RNAlater solution were then poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.

source_name: Arabidopsis aux1 mutant roots. Ethylene treatment.

tag: Arabidopsis aux1 mutant seeds (aux1-7) were germinated in the dark for 72 hours in sterile vertical plates. Hydrocarbon-free air supplemented with 10ppm of ethylene was flushed through the plates with seedlings for four additional hours.


title: Arabidopsis roots, IAA treatment, replica 2

description:
Wild-type Col-0 seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC.
Seedlings were then sprayed with 1 microMolar IAA in a 0.01% EtOH solution under safe green light and incubated in the dark for four hours. 50 ml of RNAlater solution were then poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.

source_name: Arabidopsis roots. IAA treatment.

tag: Wild-type Arabidopsis seeds (Col-0) were germinated in the dark for 72 hours in sterile vertical plates. Seedlings were sprayed with 1 microMolar IAA in a 0.01% EtOH solution under safe green light and incubated for 4 additional hours in the dark.


title: Arabidopsis ein2 mutant roots, mock treatment, replica 1

tag: Arabidopsis ein2 mutant seeds (ein2-5) were germinated in the dark for 72 hours in sterile vertical plates. Seedlings were sprayed with 0.01% EtOH (mock treatment) under safe green light four hours and incubated for 4 hours in the dark.


title: Arabidopsis aux1 mutant roots, ethylene treatment, replica 1


title: Arabidopsis ein2 mutant roots, IAA treatment, replica 2

tag: Arabidopsis ein2 mutant seeds (ein2-5) were germinated in the dark for 72 hours in sterile vertical plates. Seedlings were sprayed with 1 microMolar IAA in a 0.01% EtOH solution under safe green light and incubated for 4 additional hours in the dark.


title: Arabidopsis roots, ethylene treatment, replica 2

description:
Wild-type Col-0 seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC.
Hydrocarbon-free air supplemented with 10ppm of ethylene was flushed through the plates with seedlings for four hours. 50 ml of RNAlater solution was poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.

source_name: Arabidopsis roots. Ethylene treatment.

tag: Wild-type Arabidopsis seeds (Col-0) were germinated in the dark for 72 hours in sterile vertical plates. Hydrocarbone-free air supplemented with 10 ppm of ethylene was flushed through the plates with seedlings for four additional hours.


title: Seedling_ConstantWhiteLight_48hr

source_name: Arabidopsis seedlings after 48 h in constant white light

tag: Genotype

value: Wild-type with CCR2::LUCIFERASE; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:48 h


title: Arabidopsis roots, ethylene treatment, replica 1

tag: Wild-type Arabidopsis seeds (Col-0) were germinated in the dark for 72 hours in sterile vertical plates. Hydrocarbone-free air supplementeed with 10 ppm of ethylene was flushed through the plates with seedlings for four additional hours.


title: Arabidopsis roots, air treatment, replica 1

description:
Wild-type Col-0 seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC.
Hydrocarbon-free air was flushed through the plates with seedlings for four hours. 50 ml of RNAlater solution was poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.

source_name: Arabidopsis roots. Air treatment control.

tag: Wild-type Arabidopsis seeds (Col-0) were germinated in the dark for 72 hours in sterile vertical plates. Hydrocarbone free air was flushed through the plates with seedlings for four additional hours.


title: Arabidopsis roots, air treatment, replica 2

tag: Wild-type Arabidopsis seeds (Col-0) were germinated in the dark for 72 hours in sterile vertical plates. Hydrocarbon-free air was flushed through the plates with seedlings for four additional hours.


title: Arabidopsis aux1 mutant roots, air treatment, replica 1

source_name: Arabidopsis aux1 mutant roots. Air treatment control.

tag: Arabidopsis aux1 mutant seeds (aux1-7) were germinated in the dark for 72 hours. Seedlings were grown in sterile vertical plates. Hydrocarbon-free air was flushed through the plates with seedlings for four additional hours.


title: E18.5 ERRg +/- heart, biological rep 1

status: Public on Jul 10 2007

first: Ronald

last: Evans

address: 10010 North Torrey Pines

department: Howard Hughes Medical Institute

institute: The Salk Institute for Biological Studies

description:
Title: ERRγ Directs and Maintains the Transition to Oxidative Metabolism in the Post-Natal Heart
Abstract: At birth the heart undergoes a critical metabolic switch to transition from a predominant dependence on carbohydrates during fetal life to a greater dependence on postnatal oxidative metabolism.  This remains the principle metabolic state throughout life; although pathologic conditions such as heart failure and cardiac hypertrophy reactivate components of the fetal genetic program to increase carbohydrate utilization. Disruption of the ERRγ gene, which is expressed at high levels in the fetal and postnatal mouse heart, blocks this switch resulting in lactatemia, electrocardiographic (ECG) abnormalities and death during the first week of life. Genomic ChIP-on-chip and expression analysis at E18.5 clearly identifies ERRγ as both a direct and indirect regulator of a nuclear-encoded mitochondrial genetic network that coordinates the postnatal metabolic transition. These findings reveal an unexpected and essential molecular genetic component of the oxidative metabolic gene program in the heart and highlight ERRγ in the study of cardiac hypertrophy and failure.
Key Words: ChIP-on-chip, electrocardiography, fetal gene program, OXPHOS, PGC-1α, sodium current

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

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

source_name: 3 ERRg HET E18.5 male cadiac ventricles

growth_protocol: E18.5 male mouse cardiac ventricle

extract_protocol: RNeasy of total RNA was performed according to the manufacturer's instructions (Qiagen). Disrupted by passage through hypedermic needle.

treatment_protocol: Stored -20degrees C in RNALater (Qiagen)

tag: mixed background e18.5 male cardiac ventricle


title: E18.5 ERRg +/- heart, biological rep 3


title: Arabidopsis roots, IAA treatment, replica 1

tag: Wild-type Arabidopsis seeds (Col-0) were germinated in the dark for 72 hours. Seedlings were grown in sterile vertical plates. Seedlings were sprayed with 1 microMolar IAA in a 0.01% EtOH solution under safe green light and incubated for 4 additional hours in the dark.


title: E18.5 ERRg -/- heart, biological rep 1

source_name: 3 ERRg KO E18.5 male cadiac ventricles


title: E18.5 ERRg +/+ heart, biological rep 2

source_name: 3 ERRg WT E18.5 male cadiac ventricles


title: E18.5 ERRg -/- heart, biological rep 2


title: E18.5 ERRg -/- heart, biological rep 3


title: E18.5 ERRg +/+ heart, biological rep 1

description: no additional information


title: SN:1022965;Fetal Cartilage, biological rep2 validation

status: Public on Jul 06 2007

city: Los Angeles

first: Vincent

middle: Anthony

last: Funari

address: 8700 Beverly Drive

department: Medical Genetics

institute: Cedars Sinai

description: Normal human fetal cartilage from 18-22 weeks.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed using R 2.2.1 and RMA as normalization method with PM model.

source_name: RNA isolated from Fetal Cartilage 18-22 weeks - rep2 validation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Distal fetal cartilage from femur of Homo sapiens at 18-22 weeks was dissected from non cartilage tissue using a dissecting scope. RNA was isolated from Cartilage using the Trizol solution (GibcoBRL).

tag: Normal Fetal Cartilage from Distal Femur


title: SN:1022993;Fetal Cartilage, biological rep2 validation


title: E18.5 ERRg +/- heart, biological rep 2


title: SN:1022995;Fetal Cartilage, biological rep1

source_name: RNA isolated from Fetal Cartilage 18-22 weeks - rep1


title: SN:1022996;Fetal Cartilage, biological rep1


title: SN:1029731;Fetal Cartilage, biological rep2 validation


title: SN:1022994;Fetal Cartilage, biological rep2 validation


title: SN:1022992;Fetal Cartilage, biological rep1


title: SN:1022905;Fetal Cartilage, biological rep1


title: SN:1022991;Fetal Cartilage, biological rep1


title: E18.5 ERRg +/+ heart, biological rep 3


title: EP-4HRS

status: Public on Jul 05 2007

city: Hellerup

first: John

middle: R.

last: Zibert

address: Niels Andersens Vej 65, KA-1502

department: Dep. of Dermatology

country: Denmark

institute: Copenhagen University Hospital Gentofte

description: Nothing in line.

hyb_protocol: The biotinlabelled antisense cRNA was fragmentated at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM MgOAc,10 mM KOAc), the labelled cRNA were hybridised for 16 hrs to Affymetrix MOE 430 2.0 arrays (Affymetrix, Santa Clara, CA, USA).The arrays were washed and stained with phycoerythrin conjugated streptavidin using the Affymetrix Fluidics Station® 400.

scan_protocol: The arrays were scanned in the Affymetrix GeneArray® scanner to generate fluorescent images, as described in the Affymetrix GeneChip protocol.

data_processing:
The cel image files (Affymetrix) were imported, pre-processed and analysed in DNA-Chip Analyser 2006 (http://www.dchip.org). The array files were normalised using the non-linear invariant set normalisation
method, choosing array (DNA-EP-48HRS) as baseline. Normalisation curves were visually inspected and none of the arrays were critical. In order to interpret the probe signal, model-based gene expression indexes
(MBEI) gene expression modelling was calculated using the PM/MM perfect match/ miss match) method. During the analysis array outliers were detected. None of the arrays exceeded 1.4% of array outliers
and the probe presence call was between 36.6% and 50.3%.

molecule: polyA RNA

label_protocol: 5 μg aRNA was used to synthesize double stranded cDNA using Superscript® Choice System (Invitrogen, Denmark) with an oligo(dT) primer containing a T7 RNA polymerase promoter (GenSet, Evry, France). The cDNA was used as template for an IVT reaction to generate biotinlabelled antisense cRNA (BioArrayTM High Yield RNA Transcript Labelling Kit; Enzo Diagnostics, Farmingdale, NY, USA).

growth_protocol: Six to eight weeks old female C57Black/C mice (average weight 22 g, Taconic, Denmark) were kept under pathogen-free conditions at 22 °C in a 14/10 hrs light/dark cycle with food and water ad libitum. All animal experiments were conducted in accordance with the recommendations of the European Convention for the Protection of Vertebrate Animals used for Experimentation and after permission from the Danish Animal Welfare Committee.

extract_protocol: Four hrs, 48 hrs and 3 weeks after treatment the mice were euthanized and the muscles were removed and placed in 1 ml solution D (guandinium thiocyanat, sodium citrate, sarcosyl and mercaptoethanol) on ice. Muscle extracts were prepared by homogenising the muscles with a rotor-stator homogeniser, and RNA were extracted using the Chomczynski and Sacchi method and digested with DNase. Due to low yield of total RNA, mRNA were amplified yielding antisense RNA (aRNA) using the MessageAMP II aRNA kit (Ambion, Europe).

treatment_protocol:
Electroporation:
Plate electrodes with 4-mm gap were fitted around the hind legs and an electric field was applied. The muscle was pulsed with a combination of a high voltage pulse (100 μsec, 1000V/cm) followed by a long low voltage pulse (400 ms, 100V/cm) with 1s lag between the pulses.
tibialis cranialis muscle, exercised 4 hrs after electroporation.

tag: Strain

value: C57Bl/6, gender:female, 8 weeks old.


title: EP-3W

description: Nothing in line.

treatment_protocol:
Electroporation:
Plate electrodes with 4-mm gap were fitted around the hind legs and an electric field was applied. The muscle was pulsed with a combination of a high voltage pulse (100 μsec, 1000V/cm) followed by a long low voltage pulse (400 ms, 100V/cm) with 1s lag between the pulses.
tibialis cranialis muscle, exercised 3 weeks after electroporation.


title: DNA-EP-48HRS

description: Nothing in line.

treatment_protocol:
Plasmid DNA and in vivo Electro gene transfer:
Five micrograms of the plasmid phGFP-S65T, encoding the green fluorescent protein (GFP), plasmid was dissolved in 20 μl PBS and injected intramuscularly along the fibres into the tibialis cranialis muscle of anaesthetised C57Bl/6 mice using an insulin syringe. Plate electrodes with 4-mm gap were fitted around the hind legs and an electric field was applied. The muscle was pulsed with a combination of a high voltage pulse (100 μsec, 1000V/cm) followed by a long low voltage pulse (400 ms, 100V/cm) with 1s lag between the pulses.
The tibialis cranialis muscle, exercised 48 hrs after plasmid DNA and in vivo electro gene transfer.


title: DNA-EP-4HRS_1

description: Nothing in line.

source_name: tibialis cranialis muscle, exercised 4 hrs after plasmid DNA and in vivo electro gene transfer. Replicate one.

treatment_protocol:
Plasmid DNA and in vivo Electro gene transfer:
Five micrograms of the plasmid phGFP-S65T, encoding the green fluorescent protein (GFP), plasmid was dissolved in 20 μl PBS and injected intramuscularly along the fibres into the tibialis cranialis muscle of anaesthetised C57Bl/6 mice using an insulin syringe. Plate electrodes with 4-mm gap were fitted around the hind legs and an electric field was applied. The muscle was pulsed with a combination of a high voltage pulse (100 μsec, 1000V/cm) followed by a long low voltage pulse (400 ms, 100V/cm) with 1s lag between the pulses.
The tibialis cranialis muscle, exercised 4 hrs after plasmid DNA and in vivo electro gene transfer.


title: EP-48HRS

description: Nothing in line.

source_name: tibialis cranialis muscle, exercised 48 hrs after electroporation.

treatment_protocol:
Electroporation:
Plate electrodes with 4-mm gap were fitted around the hind legs and an electric field was applied. The muscle was pulsed with a combination of a high voltage pulse (100 μsec, 1000V/cm) followed by a long low voltage pulse (400 ms, 100V/cm) with 1s lag between the pulses. The
tibialis cranialis muscle was exercised 48 hrs after electroporation.


title: DNA-EP-3W

description: Nothing in line.

source_name: tibialis cranialis muscle, exercised 3 weeks after plasmid DNA and in vivo electro gene transfer.

treatment_protocol:
Plasmid DNA and in vivo Electro gene transfer:
Five micrograms of the plasmid phGFP-S65T, encoding the green fluorescent protein (GFP), plasmid was dissolved in 20 μl PBS and injected intramuscularly along the fibres into the tibialis cranialis muscle of anaesthetised C57Bl/6 mice using an insulin syringe. Plate electrodes with 4-mm gap were fitted around the hind legs and an electric field was applied. The muscle was pulsed with a combination of a high voltage pulse (100 μsec, 1000V/cm) followed by a long low voltage pulse (400 ms, 100V/cm) with 1s lag between the pulses. The tibialis cranialis muscle was exercised 3 weeks after plasmid DNA and in vivo electro gene transfer.


title: DNA-4HRS

description: Nothing in line.

source_name: tibialis cranialis muscle, exercised 4 hrs after DNA was injected

treatment_protocol:
Plasmid injection:
Five micrograms of the plasmid phGFP-S65T, encoding the green fluorescent protein (GFP), plasmid was dissolved in 20 μl PBS and injected intramuscularly along the fibres into the tibialis cranialis muscle of anaesthetised C57Bl/6 mice using an insulin syringe.
The muscle was exercised 4 hrs after DNA was injected


title: CONTROL_3

description: Nothing in line.

source_name: tibialis cranialis muscle, exercised, control 3

treatment_protocol: A negative control muscle. No treatment at all.