title: T11063A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N11147J1: Unremarkable breast ducts (Normal)

status: Public on Mar 09 2009

type: RNA

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

country: USA

institute: Moffitt Cancer Center

description: frozen breast tissue

hyb_protocol: Hybridization was carried out according to the standard Affymetrix protocol

scan_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

data_processing: Expression values were calculated using the robust multi-array average (RMA) algorithm

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: frozen breast tissue

label_protocol: Labeling was done according to the standard Affymetrix protocol

growth_protocol: Breast tissues (normal and malignant) from patients that underwent mastectomy for various stages of breast carcinoma were collected and frozen in liquid nitrogen.

extract_protocol: Total RNA was extracted from microdissected breast tissues using the Trizol method.

treatment_protocol: The tissues were embedded in Tissue-Tek® O.C.T., 5-um sections cut. The sections were stained using a standard H&E protocol, and tissue boundaries marked by a pathologist  Using the marked slide as a map, tissues were microdissected.  Adipose tissues were trimmed,  the tumor and normal tissues were separated and stored in liquid nitrogen.

tag: Unremarkable breast ducts (Normal)


title: N11354D4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11320G3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11209A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11103G4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11123D2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11196A5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11196A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11209A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T11365A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue

tag: Invasive ductal carcinoma (IDC)


title: T11147A3: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N11320G2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11003A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11063A5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11196A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11354D6: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11003A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11063A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11003A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11103G1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11123D3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11196A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11063A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10964A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10964A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10874A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T10928M1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T10918A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N10964A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T10962A5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10910A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T10957A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N10608K5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10650C3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10910A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T10739D1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N10608K3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10535A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10739D4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10584A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10496H2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10563D3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10608K2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10910A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T10686A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T10786D1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T10781D2: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T10781D1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N10608K4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T10496H1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N10559A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10481A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10475G1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10475G2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10443A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10180C2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T10180C1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N10180C3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10475G3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T10473B1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T10143A2: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T10143A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N10473B5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10176F4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N10176F2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T9740A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N10176F3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N9744A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N9740A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T9097C1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T9740A3: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N9112A5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8880I4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8803D4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8881D4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8862B1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N9100J1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8936B1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N9740A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N9100J3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8803K4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N9112A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8803D3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8514B4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8803K3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8803K1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8642A2: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N9393B3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8513C2: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N8721A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8735C2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8735A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8717B2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8642B1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N8514B5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8642A1.3: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T8642A1.1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T8642A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N8703A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8706L4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8703A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T8703A1.1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N8706A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8703A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8696B1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8696B2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8653D1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8669A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8672A1.1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T8636A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T8636A1.3: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N8696B3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8653E4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8626B1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8628A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8636A1.2: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N8671B5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8689A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8608A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8671B4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8615H4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8615A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8615A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8615H3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8463I2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8608A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8456B3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8463I3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8456B4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8463I4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8615H1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8463I1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8456B2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8607A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8542A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N8627A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8380A5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T8380A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N7397F3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N7397F5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8380A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N7954C3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N7619A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N7619A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N7397F1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N8456B1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N7369B5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: ribo deficient 48hr (EN 10)

status: Public on Mar 06 2009

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
Ribo deficient cells after 48 hour treatment
Gene expression data from human colonic epithelial cells.

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

growth_protocol: Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion.  After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted

extract_protocol: Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

tag: cell line


title: ribo deficient 72hr (EN 18)

description:
Ribo deficient cells after 72 hour treatment
Gene expression data from human colonic epithelial cells.


title: control 72hr (EN 11)

description:
Untreated cells after 72 hours
Gene expression data from human colonic epithelial cells.


title: control 72hr (EN 17)


title: N7369B4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: control 48hr (EN 15)

description:
Untreated cells after 48 hours
Gene expression data from human colonic epithelial cells.


title: control 48hr (EN 9-2)


title: N7369B3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: ribo deficient 24hr (EN 8-2)

description:
Ribo deficient cells after 24 hour treatment
Gene expression data from human colonic epithelial cells.


title: ribo deficient 48hr (EN 16)


title: control 24h (EN 7-2)

description:
Untreated cells after 24 hours
Gene expression data from human colonic epithelial cells.


title: control 24h (EN 13)


title: control 72hr (EN 5)


title: ribo deficient 72hr (EN 12)


title: ribo deficient 24hr (EN 14)


title: ribo deficient 48hr (EN 4)


title: ribo deficient 24hr (EN 2)


title: ribo deficient 72hr (EN 6)


title: control 24h (EN 1)


title: control 48hr (EN 3)


title: stomach infected Rg  5

status: Public on Mar 05 2009

city: Zurich

first: Anne

last: Müller

address: Winterthurerstr. 190

department: IMCR

country: Switzerland

institute: University of Zurich

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Standard Affymetrix procedures using a Hewlett-Packard scanner

data_processing: Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the Robust Multichip Average (RMA) method.

organism: Mus musculus

source_name: stomach epithelium

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

extract_protocol: Trizol ectraction followed by Rneasy Mini Kit (Qiagen)

tag: Infection

value: infected

tag: Pathology

tag: Treatment


title: stomach uninfected Rg  1

value: uninfected


title: stomach infected Rg  3


title: stomach infected metaplasia 2

value: metaplasia


title: stomach infected Rg  4


title: stomach uninfected Rg  2


title: stomach infected metaplasia 3


title: stomach infected Rg  2


title: stomach infected hyperplasia 1

value: hyperplasia


title: stomach infected gastritis 1

value: gastritis


title: stomach infected Rg  1


title: IMPGE IFNG 3

source_name: immortalized primary gastric epithelial cell line

extract_protocol: Rneasy Mini Kit (Qiagen)

value: 24h IFNG 10ug/ml


title: stomach infected metaplasia 1


title: stomach infected metaplasia 4


title: stomach infected hyperplasia 5


title: stomach uninfected 1


title: stomach infected hyperplasia 3


title: IMPGE IFNG 1

value: 24h IFNG 0.1ug/ml


title: IMPGE IFNG 2

value: 24h IFNG 1.0ug/ml


title: stomach infected hyperplasia 4


title: stomach infected gastritis 2


title: stomach infected gastritis 4


title: IMPGE untreated

value: untreated


title: stomach infected metaplasia 5


title: stomach infected hyperplasia 2


title: stomach infected gastritis 3


title: stomach uninfected 2


title: Differentiating P19CL6 cells at day 10 after DMSO treatment, replicate 1 (Affymetrix)

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: CL6 lines of P19 embryonal carcinoma cells were treated with 1% dimethyl sulfoxide (DMSO) to differentiate the cells into beating cardiomyocytes. On day 10, contracting cells were observed.

hyb_protocol: We followed the Affymetrix standard Eukaryotic samples preparation protocol (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

data_processing: PLIER algorithm

label: Biotin

source_name: P19CL6 cells treated with 1% DMSO, day 10

extract_protocol: Total RNA was extracted with TRIzol.

tag: Cell line

value: 1% DMSO

tag: Time

value: day 10


title: Differentiating P19CL6 cells at day 6 after DMSO treatment, replicate 3 (Affymetrix)

scan_protocol: We followed the Affymetrix standard Eukaryotic samples preparation protocol (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

source_name: P19CL6 cells treated with 1% DMSO, day 6

value: day 6


title: Differentiating P19CL6 cells at day 10 after DMSO treatment, replicate 3 (Affymetrix)

label_protocol: We followed the Affymetrix standard Eukaryotic samples preparation protocol (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).


title: Differentiating P19CL6 cells at day 10 after DMSO treatment, replicate 2 (Affymetrix)


title: Differentiating P19CL6 cells at day 6 after DMSO treatment, replicate 1 (Affymetrix)


title: Differentiating P19CL6 cells at day 6 after DMSO treatment, replicate 2 (Affymetrix)


title: Calcineurin Tg, biological replicate 4 (Affymetrix)

description:
MHCa-CN mice were a gift from Jeffery Molkentin. The mice were maintained by
crossing transgenic males with B6C3F1 females (Charles River Labs). Samples were collected from males at two months of age, unless otherwise noted. Intramyocardial adenoviral injections were performed in FVB/N mice (Charles River Labs) under ultrasound guidance (Visualsonic Vevo 770). Mice were anesthetized with 2% isoflurane, and injected via a 30 Ga needle with adenovirus, 2 x 109 infectious units/40 µl, divided equally between four independent locations.
 One week after injection, osmotic minipumps containing either isoproterenol (ISO; 30 mg/kg/d) or vehicle were implanted subcutaneously. Two weeks after implantation, mice were sacrificed and cardiomyocytes were dissociated by retrograde collagenase perfusion.

source_name: Cardiomyocytes dissociated by retrograde collagenase perfusion

tag: Genotype

value: Calcineurin-transgenic mice


title: NTg, biological replicate 3 (Affymetrix)

value: Nontransgenic control mice


title: Calcineurin Tg, biological replicate 3 (Affymetrix)


title: NTg, biological replicate 1 (Affymetrix)


title: Day_4 1a

city: Baltimore

first: John

middle: D.

last: Gearhart

state: MD

address: 733 North Broadway

department: School of Medicine

institute: Jons Hopkins University

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

source_name: Day 4 mESCs, 1a

label_protocol: TwoCycle amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol: Following primary mouse embryonic fibroblasts (PMEF) feeder subtraction, mESCs were dissociated and resuspended in differentiation medium at a density of 5x104 cells/ml.

extract_protocol: RNeasy Kit (QIAGEN)

treatment_protocol: The mouse enbryonic stem cells (MESCs) were differentiated through embryoid body formation (hanging droplet technique) as described in PMID:8155574 . Following primary mouse embryonic fibroblasts (PMEF) feeder subtraction, mESCs were dissociated and resuspended in differentiation medium at a density of 5x104 cells/mL. Cells at this time point were designated as day 0.  Following incubation for two days, the EBs were transferred, in suspension, to poly-HEMA coated tissue culture dishes to prevent cell attachment and grown in medium containing ascorbic acid (PMID:12668514) which was replenished every 3 days thereafter.  These cells were harvested at day 4 (D4).

tag: Transgenic mouse embryonic stem cell line (Nkx2-5-GFP, PMID:9834187) containing an Nkx2-5 cardiac-specific transcription factor driving expression of green fluorescent protein (GFP).


title: Day_6 GFPneg 1a

source_name: Day 6 GFP negative mESCs, 1a

treatment_protocol: The mouse enbryonic stem cells (MESCs) were differentiated through embryoid body formation (hanging droplet technique) as described in PMID:8155574 . Following primary mouse embryonic fibroblasts (PMEF) feeder subtraction, mESCs were dissociated and resuspended in differentiation medium at a density of 5x104 cells/mL. Cells at this time point were designated as day 0.  Following incubation for two days, the EBs were transferred, in suspension, to poly-HEMA coated tissue culture dishes to prevent cell attachment and grown in medium containing ascorbic acid (PMID:12668514) which was replenished every 3 days thereafter.  These cells were harvested at day 6 (D6), washed in PBS for 30 minutes at 37ºC then resuspended in 0.25% trypsin for 7 minutes. Cells were then sorted using the BD Biosciences FACSAria™ Cell sorting system into GFP+ and GFP- fractions into RLT buffer (RNeasy, Qiagen).  These cells are GFP negative.


title: NTg, biological replicate 4 (Affymetrix)


title: Day_6 GFPneg 2a

source_name: Day 6 GFP negative mESCs, 2a

growth_protocol: Following primary mouse embryonic fibroblasts (PMEF) feeder subtraction, mESCs were dissociated and resuspended in differentiation medium at a density of 5x104 cells/mL.


title: Day_0 1a

source_name: Day 0 mESCs, 1a

treatment_protocol: The mouse enbryonic stem cells (MESCs) were differentiated through embryoid body formation (hanging droplet technique) as described in PMID:8155574 . Following primary mouse embryonic fibroblasts (PMEF) feeder subtraction, mESCs were dissociated and resuspended in differentiation medium at a density of 5x104 cells/mL. Cells at this time point were designated as day 0 (Day 0).


title: Day_4 2a

source_name: Day 4 mESCs, 2a


title: NPC_CNE2 (U133 Plus 2.0 Array)

city: Guangzhou

first: Zhong-Xi

last: Huang

address: Tonghe

department: Cancer Institute

country: China

institute: Southern Medical University

description: gene expression analysis

hyb_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix HG U133 Plus 2.0 microarray.

scan_protocol: Microarray scanning and data acquisition was carried out at GeneTech Biotechnology Limited Company (Shanghai, China) using Affymetrix-recommended equipment and procedures.

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 250.

source_name: Nasopharyngeal carcinoma cell line CNE2

growth_protocol: Cells were grown in RPMI-1640 medium (Hyclone, Logan, UT) supplemented with 10% fetal calf serum (ExCell, Shanghai, China) and 1% L-glutamine. Cells were cultured at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was isolated by using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

value: nasopharyngeal carcinoma cell line CNE2


title: Calcineurin Tg, biological replicate 2 (Affymetrix)


title: Day_0 2a

source_name: Day 0 mESCs, 2a


title: Calcineurin Tg, biological replicate 1 (Affymetrix)


title: Day_6 GFPneg 3a

source_name: Day 6 GFP negative mESCs, 3a


title: NTg, biological replicate 2 (Affymetrix)


title: Day_0 3a

source_name: Day 0 mESCs, 3a


title: NPC_HONE1 (U133 Plus 2.0 Array)

description: gene expression analysis

source_name: Nasopharyngeal carcinoma cell line HONE1

label_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix HG U133 Plus 2.0 microarray.

value: nasopharyngeal carcinoma cell line HONE1


title: Day_6 GFPpos 2a

source_name: Day 6 GFP positive mESCs, 2a

treatment_protocol: The mouse enbryonic stem cells (MESCs) were differentiated through embryoid body formation (hanging droplet technique) as described in PMID:8155574 . Following primary mouse embryonic fibroblasts (PMEF) feeder subtraction, mESCs were dissociated and resuspended in differentiation medium at a density of 5x104 cells/mL. Cells at this time point were designated as day 0.  Following incubation for two days, the EBs were transferred, in suspension, to poly-HEMA coated tissue culture dishes to prevent cell attachment and grown in medium containing ascorbic acid (PMID:12668514) which was replenished every 3 days thereafter.  These cells were harvested at day 6 (D6), washed in PBS for 30 minutes at 37ºC then resuspended in 0.25% trypsin for 7 minutes. Cells were then sorted using the BD Biosciences FACSAria™ Cell sorting system into GFP+ and GFP- fractions into RLT buffer (RNeasy, Qiagen).  These cells are GFP positive.


title: NP_NP69 (U133 Plus 2.0 Array)

description: gene expression analysis

source_name: immortalized nasopharyngeal epithelial cell line NP69

growth_protocol: Cells were grown in defined-KSFM medium supplemented with EGF. Cells were cultured at 37°C in a humidified atmosphere of 5% CO2.


title: NPC_CNE1 (U133 Plus 2.0 Array)

description: gene expression analysis

source_name: Nasopharyngeal carcinoma cell line CNE1

value: nasopharyngeal carcinoma cell line CNE1


title: Day_6 GFPpos 1a

source_name: Day 6 GFP positive mESCs, 1a


title: Day_4 3a

source_name: Day 4 mESCs, 3a


title: PC3_Mock_rep2

status: Public on Mar 04 2009

city: Seattle

first: Biaoyang

last: Lin

state: WA

address: 550 17th Ave, James Tower suite 550

department: Swedish Neuroscience Institute

institute: Swedish Medical Center

hyb_protocol: Affymetrix's standard protocol

scan_protocol: Affymetrix's standard protocol

data_processing: GCRMA normalization

source_name: PC3 transfected with empty vector, without R1881

label_protocol: Affymetrix's standard protocol

growth_protocol: RPMI + %charcoal stripped FBS +1X L-glutamine.

extract_protocol: Qiagen RNA extraction kit

treatment_protocol: adding ethanol or R1881 (androgen)

value: PC3 cells


title: PC3_AR_1nM_R1881_replicate2

source_name: PC3 transfected with AR, treated with 1nM R1881


title: PC3_AR_ETOH_replicate 2

description: PC3_AR_ETOH_replicate 2

source_name: PC3 transfected with AR, treated with Ethanol


title: PC3_AR_1nM_R1881_replicate1


title: Subject 15, Family 5, Control

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

description: microarray hybridization data 07/11/2007

hyb_protocol: 15 micrograms of fragmented cRNA were hybridized to U133 Plus 2.0 chips for 16 hours at 45 °C, 60 rpm. The chips were washed and stained in the Affymetrix Fluidics Station 450, using instructions and reagents provided by Affymetrix.

scan_protocol: The probe arrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: MAS5 algorithm

source_name: human skeletal muscle

label_protocol: In vitro transcription (IVT) was performed using the GeneChip Expression Amplification Reagents kit following the standard Affymetrix protocols.

extract_protocol: Total RNA was isolated from muscle tissue using the TRIReagent method (Molecular Research Center, Inc.) following the manufacturer’s protocol. Concentrations were determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual.

tag: sex

value: Male

tag: family

tag: age

tag: disease status

value: Control

tag: tissue


title: PC3_AR_ETOH_replicate 1

description: PC3_AR_ETOH_replicate 1


title: Day_6 GFPpos 3a

source_name: Day 6 GFP positive mESCs, 3a


title: PC3_Mock_rep1


title: Subject 14, Family 5, Asymptomatic

value: Female

value: Asymptomatic


title: Subject 9, Family 3, Control

description: microarray hybridization data 07/10/2007


title: Subject 7, Family 3, Affected

value: Affected


title: Subject 3, Family 1, Control


title: Subject 4, Family 2, Affected


title: Subject 11, Family 4, Asymptomatic


title: Subject 5, Family 2, Asymptomatic


title: PC3_AR_R1881_10nM_replicate 1

description: PC3_AR_R1881_10nM_replicate 1

source_name: PC3 transfected with AR, treated with 10nM R1881


title: Subject 1, Family 1, Affected


title: Subject 12, Family 4, Control


title: Subject 10, Family 4, Affected


title: Subject 13, Family 5, Affected


title: Subject 6, Family 2, Control


title: PA80

city: London

first: Patricia

middle: Jean

last: Hunter

address: 30 Guilford Street

department: Rheumatology

institute: UCL Institute of Child Health

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Data was normalised using MAS5.0.

source_name: Synovial fluid mononuclear cells

label_protocol: RNA was coverted to cDNA (Roche) using an oligod(T) primer and converted to cRNA using In Vitro Triscription labelling kit (Affymetrix).

extract_protocol: Cell were thawed and RNA was extracted using Qiagen Rneasy

treatment_protocol: Synovial fluid was aspirated from patients' knees. Mononuclear cells were isolated using density centrifugation with Lymphoprep. Cells were preserved in liquid nitrogen

tag: outcome at one year

value: extended

tag: cell type

value: Synovial fluid mononuclear cells


title: Subject 2, Family 1, Asymptomatic


title: PA102


title: PA55


title: Subject 8, Family 3, Asymptomatic


title: PA92


title: PA215

value: persistent


title: PA94


title: PA224


title: PA203


title: PA184


title: PA195


title: PA207


title: dsPc/ph+PTIP3

city: Ann Arbor

first: Greg

last: Dressler

state: MI

address: 109 Zina Pitcher Drive

department: Pathology

institute: University of Michigan

hyb_protocol: 10 ug of cRNA was hybridized for 16h at 46oC to Drosophila 2.0 arrays.  Washing and staining used the Affymetrix fluidics staion 400.

scan_protocol: Affymetrix scanner 3000 was used to read arrays

data_processing: The data were analyzed using the limma and affy bioconductor  packages implemented in the R statistical programming environment. Normalization was done using RMA

organism: Drosophila melanogaster

source_name: cells with loss of PTIP, polycomb, and polyhomeotic

label_protocol: Biotinilated UTP and CTP were used as speficied by Affymetrix in their standard protocols.

growth_protocol: All cells were cultured in Schneiders Drosophila media and plated at 1e6 cells per well in 6 well plates ar room temperature in air.

extract_protocol: Cells were centrifuged and RNA was isolated with 1 ml of TRIZOL  according to manufacturer's protocol.

treatment_protocol: double stranded RNAs against the genes of interest were added at 15 ug per well.  After 1 hour fetal calf serumwas added to 5%.  Cells were cultured for 6 days.

value: K67 cell culture


title: PA192


title: dsPc/ph+PTIP2


title: dsPc/ph3

source_name: cells with loss of polycomb and polyhomeotic


title: control3

source_name: Kc167 cells alone


title: dsPc/ph1


title: dsPc/ph+PTIP1


title: dsPTIP1

source_name: Kc cells with loss of PTIP


title: dsPc/ph2


title: moDC_anti-miR-155-LNA_LPS_rep1

city: Marseille

first: Philippe

last: Pierre

address: Campus Luminy - case 906

country: France

institute: CIML - CNRS - INSERM

description: For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix).

hyb_protocol: Standard Affymetrix hybridization procedure.

scan_protocol: Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure.

data_processing: The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 9.0 software (Agilent).

source_name: monocyte-derived dendritic cells, transfected with anti-miR-155-LNA, activated with LPS

label_protocol: Standard Affymetrix labelling procedure.

growth_protocol: Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.

extract_protocol: Human monocyte-derived dendritic cells were grown in culture for 5 days. Total RNA was isolated from untreated (0h) and 4h or 16h LPS-treated dendritic cells, using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).

tag: Human peripheral blood mononuclear cells (PBMC) were enriched on the 12 october 2007 (donor

value: "JIJI").


title: dsPTIP3


title: moDC_anti-miR-155-LNA_rep1

source_name: monocyte-derived dendritic cells, transfected with anti-miR-155-LNA, NO LPS


title: moDC_scramble-LNA_LPS_rep1

source_name: monocyte-derived dendritic cells, transfected with scramble-LNA, activated with LPS


title: dsPTIP2


title: moDC_scrambleLNA_rep1

source_name: monocyte-derived dendritic cells, transfected with scramble-LNA, NO LPS


title: control2


title: Cav1KO 1761

city: Philadelphia

first: Michael

middle: P

last: Lisanti

state: PA

address: 233 S. 10th St BLSB 939

department: Cancer Biology

institute: Thomas Jefferson University

description: Gene expression data from mouse heart tissue at 5-6mos of age, male mice, 6 hours fasted

hyb_protocol: Fragmented and biotin-labeled 10 ug target in 200ul hybridization cocktail was used for each Affymetrix Mouse Genome 430 20. array

scan_protocol: GeneChips were scanned using the Affymetric Gene-Array scanner 3000

data_processing: The data were analyzed with Gene Chip Operating Software (GCOS v1.4) using Affymetrix default analysis settings

source_name: Cav1KO 1761

label_protocol: biotinylated cRNA was prepared from 2ug total RNA using Affymetrix One-Cycle Target Labeling Assays

extract_protocol: RNA extracted using Trizol, clean up using Qiagen Rneasy Cleanup kit

tag: Cav1 knockout


title: Cav1KO 1762

source_name: Cav1KO 1762


title: WT 2 1509

tag: wild type


title: control1

tag: cell line


title: WT 3 1782


title: myb5 mutant seed rep3

status: Public on Mar 02 2009

city: Melbourne

first: Song

middle: Feng

last: Li

state: Victoria

address: Plenty Rd

department: Botany

country: Australia

institute: La Trobe University

description: Wild-type plants (Col) and myb5-1 plants were grown at the same time. Developing seeds (globular to walking-stick stages) were collected from each group of plants, respectively.

hyb_protocol: The labeled cRNA was fragmented and then injected into the GeneChips containing the Arabidopsis ATH1 Genome array (four chips for four wild-type (Col) biological replicates and three for three myb5-1 biological replicates) (Affymetrix). After hybridization, the GeneChips were stained with streptavidin-phycoerythrin and biotinylated anti-streptavidin antibody.

scan_protocol: The array was scanned with an Affymetrix GeneChip Scanner 3000 (Victoria Agribiosciences Centre).

data_processing: The Arabidopsis gene annotation data set was imported from NetAffx (Affymetrix).  GeneChip operating software was used to produce cel files containing raw probe intensities for the arrays and to incorporate the annotation data set.

organism: Arabidopsis thaliana

source_name: myb5 mutant seed

label_protocol: Approximately 100 ng of RNAwas used as template for the synthesis of labeled cRNA probe using the Two Cycle Amplification Kit (Affymetrix). Briefly, the first cycle of cDNA synthesis was carried out using an oligo (dT) primer fused to a T7 RNA polymerase promoter and was followed by the first cycle of in vitro transcription using  T7 RNA polymerase to generate cRNA. The cRNA was used as a template for the second cycle of cDNA synthesis followed by the second cycle of in vitro transcription, to generate the biotin-labeled antisense cRNA.

growth_protocol: Plants were grown on soil under constant illumination.

extract_protocol: The seeds were dissected out from siliques in RNAlater solution (Ambion) and total RNAs were extracted using the RNeasy Plant Mini Kit (QIAGEN). RNA quality and integrity were determined using an Agilent 2100 Bioanalyzer (Agilent Technologies).


title: Cav3KO 1504

source_name: Cav3KO 1504

tag: Cav3 knockout


title: WT 1 1508


title: Cav1KO 1758

source_name: Cav1KO 1758


title: CD4+CD25- T cells_IL-6/TGFbeta

status: Public on Mar 03 2009

city: New York

first: Jiangnan

last: Xu

state: NY

address: 1425 Madison Ave

department: Gene and Cell Medicine

institute: Mount Sinai School of Medicine

description: CD4+CD25- T cells_IL-6/TGFbeta

hyb_protocol: Following fragmentation, 20ug cRNA were hybridized for 16hours at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GMS fluorescent microarray scanner.

data_processing: Data were normalized and analyzed using GeneChip Operating Software (Affymetrix).

source_name: Spleen and lymph node CD4+CD25- T cells

label_protocol: Biotinylated cRNA were prepared according to the standard protocol (Expression Analysis Technical Manual, Affymetrix) from 10 ug total RNA.

growth_protocol: Purified Stat6 and T-bet double deficient CD4+CD25- T cells were stimulated with plate-bound anti-CD3 (5 ug/ml), anti-CD28 (1 ug/ml) mAbs, and IL-6 (10 ng/ml) plus TGFbeta (5 ng/ml) for 2 days.

extract_protocol: Total RNAs were isolated using RNeasy Protect Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: genotype

value: Stat6/T-bet double knockout (BALB/c background)

tag: gender

value: female

value: 6-8 weeks

tag: celltype

value: Spleen and lymph node CD4+CD25- T cells


title: myb5 mutant seed rep2

tag: Wild-type plants (Col) and myb5-1 plants were grown at the same time. Developing seeds (globular to walking-stick stages) were collected from each group of plants, respectively.


title: Wild-type seed rep4

source_name: Wild-type seed


title: Cav3KO 1505

source_name: Cav3KO 1505


title: myb5 mutant seed rep1


title: Cav3KO 1506

source_name: Cav3KO 1506


title: CD4+CD25- T cells_TGFbeta

description: CD4+CD25- T cells_TGFbeta

growth_protocol: Purified Stat6 and T-bet double deficient CD4+CD25- T cells were stimulated with plate-bound anti-CD3 (5 ug/ml), anti-CD28 (1 ug/ml) mAbs, and TGFbeta (5 ng/ml) for 2 days.


title: CD4+CD25- T cells_IL-6/IL-23

description: CD4+CD25- T cells_IL-6/IL-23

growth_protocol: Purified Stat6 and T-bet double deficient CD4+CD25- T cells were stimulated with plate-bound anti-CD3 (5 ug/ml), anti-CD28 (1 ug/ml) mAbs, and IL-6 (10 ng/ml) plus IL-23 (10 ng/ml) for 2 days.


title: Wild-type seed rep2


title: Arabidopsis pGL3::GL3-GR with Dex treatment for 4 hours, sample 2

city: Columbus

first: Kengo

last: Morohashi

state: OH

address: 1060 Carmack Rd

department: Molecular Genetics

institute: The Ohio State University

description: This experiment was done to compare the gene expression between Dex and mock treatment plants

hyb_protocol: For each array, 2.2 µg of cDNA is hybridized onto Arabidopsis ATH1 Genome GeneChips® (Affymetrix Inc., USA), designed in collaboration with TIGR, containing more than 22,500 probe sets representing approximately 24,000 genes. The array is based on information from the international Arabidopsis sequencing project that was formally completed in December, 2000. In parallel and subsequent to the genome's completion, TIGR reannotated the entire genome in a project funded by the National Science Foundation and the resulting data was used in the design of this array. Hybridization is 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 are scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA) and CEL files are generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals are generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and are used to determine differential gene expression by pair-wise comparisons. The genes that are altered by two-fold either way are sorted and used for further interpretation of the microarray data.

data_processing: AffyGUI, normalized by GCRMA.

source_name: Arabidopsis green tissues, pGL3::GL3-GR with Dex treatment for 4 hours, sample 2

label_protocol: Following confirmation of RNA quality, Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) is used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA is 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 is 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 is purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content is measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

extract_protocol: RNA was extracted with Qiagen RNeasy Plant RNA extraction kit.

tag: GR inducible system using transgenic Arabidopsis carrying pGL3::GL3-GR


title: Arabidopsis pGL3::GL3-GR with Dex treatment for 4 hours, sample 1

source_name: Arabidopsis green tissues, pGL3::GL3-GR with Dex treatment for 4 hours, sample 1


title: Arabidopsis pGL3::GL3-GR with Dex treatment for 4 hours, sample 3

source_name: Arabidopsis green tissues, pGL3::GL3-GR with Dex treatment for 4 hours, sample 3


title: Arabidopsis pGL3::GL3-GR with Dex treatment for 24 hours, sample 2

source_name: Arabidopsis green tissues, pGL3::GL3-GR with Dex treatment for 24 hours, sample 2


title: Arabidopsis pGL3::GL3-GR with mock treatment for 24 hours, sample 2

source_name: Arabidopsis green tissues, pGL3::GL3-GR with mock treatment for 24 hours, sample 2


title: Wild-type seed rep3


title: Arabidopsis pGL3::GL3-GR with Dex treatment for 24 hours, sample 1

source_name: Arabidopsis green tissues, pGL3::GL3-GR with Dex treatment for 24 hours, sample 1


title: Arabidopsis pGL1::GL1-GR with Dex treatment for 24 hours, sample 1

source_name: Arabidopsis green tissues, pGL1::GL1-GR with Dex treatment for 24 hours, sample 1

tag: GR inducible system using transgenic Arabidopsis carrying pGL1::GL1-GR


title: Wild-type seed rep1


title: Arabidopsis pGL1::GL1-GR with mock treatment for 24 hours, sample 2

source_name: Arabidopsis green tissues, pGL1::GL1-GR with mock treatment for 24 hours, sample 2


title: Arabidopsis pGL1::GL1-GR with mock treatment for 24 hours, sample 1

source_name: Arabidopsis green tissues, pGL1::GL1-GR with mock treatment for 24 hours, sample 1


title: Arabidopsis pGL3::GL3-GR with mock treatment for 4 hours, sample 2

source_name: Arabidopsis green tissues, pGL3::GL3-GR with mock treatment for 4 hours, sample 2


title: Arabidopsis pGL1::GL1-GR with Dex treatment for 24 hours, sample 3

source_name: Arabidopsis green tissues, pGL1::GL1-GR with Dex treatment for 24 hours, sample 3


title: Arabidopsis pGL1::GL1-GR with Dex treatment for 4 hours, sample 3

source_name: Arabidopsis green tissues, pGL1::GL1-GR with Dex treatment for 4 hours, sample 3


title: Arabidopsis pGL3::GL3-GR with mock treatment for 4 hours, sample 3

source_name: Arabidopsis green tissues, pGL3::GL3-GR with mock treatment for 4 hours, sample 3


title: Arabidopsis pGL1::GL1-GR with Dex treatment for 24 hours, sample 2

source_name: Arabidopsis green tissues, pGL1::GL1-GR with Dex treatment for 24 hours, sample 2


title: Arabidopsis pGL1::GL1-GR with mock treatment for 4 hours, sample 1

source_name: Arabidopsis green tissues, pGL1::GL1-GR with mock treatment for 4 hours, sample 1


title: Arabidopsis pGL3::GL3-GR with mock treatment for 24 hours, sample 1

source_name: Arabidopsis green tissues, pGL3::GL3-GR with mock treatment for 24 hours, sample 1


title: Arabidopsis pGL1::GL1-GR with mock treatment for 24 hours, sample 3

source_name: Arabidopsis green tissues, pGL1::GL1-GR with mock treatment for 24 hours, sample 3


title: Arabidopsis pGL1::GL1-GR with Dex treatment for 4 hours, sample 2

source_name: Arabidopsis green tissues, pGL1::GL1-GR with Dex treatment for 4 hours, sample 2


title: Arabidopsis green tissue gl3 egl3 sample 1

description: This experiment was done to compare the gene expression between L.er wild type seedlings and gl3egl3 double mutants.

data_processing: Affy-GUI, normalized by GCRMA.

source_name: Arabidopsis green tissues 20 days old

tag: Arabidopsis L.er seedling, grown on MS medium for 20 days, and corrected only green tissues


title: Arabidopsis green tissue wild type L. er sample 2

description: This experiment was done to compare the gene expression between L.er wild type seedlings and gl3egl3 double mutants

tag: Arabidopsis L.er seedling, grown on MS medium for 20 days.


title: Arabidopsis pGL1::GL1-GR with mock treatment for 4 hours, sample 2

source_name: Arabidopsis green tissues, pGL1::GL1-GR with mock treatment for 4 hours, sample 2


title: Arabidopsis pGL1::GL1-GR with Dex treatment for 4 hours, sample 1

source_name: Arabidopsis green tissues, pGL1::GL1-GR with Dex treatment for 4 hours, sample 1


title: Arabidopsis green tissue wild type L. er sample 1


title: Arabidopsis green tissue gl3 egl3 sample 2


title: nmMLCK-/- -SB replicate 3

city: Charlottesville

first: Yong

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: nmMLCK-/- -SB replicate 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse320_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) for ABS_Call; Bioconductor GCRMA package for normalization

source_name: Lung; nmMLCK-/-; spontaneous breathing

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: standard conditions (12h light-dark cycle, 25-27ºC, ~40% humidity)

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

treatment_protocol: Spontaneous breathing

tag: strain

tag: Gender

value: male

tag: Age

value: 8-12 week

tag: nmMLCK-/-


title: nmMLCK-/- -VILI replicate 3

description: nmMLCK-/- -VILI replicate 3

source_name: Lung; nmMLCK-/-; VILI

treatment_protocol: VILI (40 ml/kg tidal volume, 65 breath/minute, positive expiratory pressure 0 cm H2O, 4 hours)


title: Arabidopsis pGL3::GL3-GR with mock treatment for 4 hours, sample 1

source_name: Arabidopsis green tissues, pGL3::GL3-GR with mock treatment for 4 hours, sample 1


title: nmMLCK-/- -SB replicate 1

description: nmMLCK-/- -SB replicate 1


title: nmMLCK-/- -VILI replicate 1

description: nmMLCK-/- -VILI replicate 1


title: Arabidopsis pGL1::GL1-GR with mock treatment for 4 hours, sample 3

source_name: Arabidopsis green tissues, pGL1::GL1-GR with mock treatment for 4 hours, sample 3


title: nmMLCK-/- -VILI replicate 2

description: nmMLCK-/- -VILI replicate 2


title: nmMLCK-/- -SB replicate 2

description: nmMLCK-/- -SB replicate 2


title: WT-VILI replicate 1

description: WT-VILI replicate 1

source_name: Lung; wild type; VILI

tag: Wild type


title: WT-SB replicate 1

description: WT-SB replicate 1

source_name: Lung; wild type; spontaneous breathing

tag: Weight


title: WT-VILI replicate 2

description: WT-VILI replicate 2


title: WT-SB replicate 2

description: WT-SB replicate 2


title: WT-VILI replicate 3

description: WT-VILI replicate 3


title: WT-SB replicate 3

description: WT-SB replicate 3


title: gene expression profile in sigmoid colon of UC patient

middle: H

last: Kwon

address: 720 Rutland Ave.

institute: Johns Hopkins Univ

description: no special addition

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

data_processing: Affymetrix GCOS software. Scaling TGT=150

source_name: sigmoid colon biopsy

label_protocol: Affymetrix standard protocol.

extract_protocol: Total RNA was isolated from sigmoid colon biopsy kept in TRIZOL.

tag: sigmoid colon biopsy from 6 patients with ulcerative colitis (UC).


title: SIMVA replicate1

description: Gene expression data from lung tissue of control animal

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) for ABS_Call; Bioconductor GCRMA package for normalization;

source_name: Lung

treatment_protocol: 10 mg/kg simvastatin via intraperitoneal injection three times a week pre and post irradiation for up to 6 weeks;

tag: Mouse C57BL/6J

tag: Mouse, male

value: Wild type


title: IAA7mII over-expressor_IAA treated_replicate 2

status: Public on Mar 01 2009

first: Kenneth

middle: David

last: Birnbaum

address: 12 Waverly Place

department: Biology

institute: New York University

description:
Roots grown horizontally on square plates, protoplasted, transformed and sorted by FACS.
Replicate 2 of 3.

hyb_protocol: Labeled cDNA was hybridized for 16 hr at 45C on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array in the Affymetrix Hybridization oven 640 following standard Affymetrix protocol. GeneChips were washed and stained using an Affymetrix Wash and Stain Kit and the FS450_001 protocol in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to standard Affymetrix protocols.

data_processing: The data was normalized using MAS5 with a target intensity of 250.

source_name: IAA7mII over-expressor, IAA treated

label_protocol: cDNA was produced, amplified, fragmented and labeled using NuGEN WT-Ovation Pico RNA Amplification System and FL-Ovation cDNA Biotin Module V2.

growth_protocol: Pwer::GFP plants were grown in vertically placed square 10x10 cm petri dishes for 7 days in long day (18hr light/6hr dark) 22C conditions in a Percival (Percival Scientific). Plants were grown on MS agar (0.5x MS, 1% sucrose, 1% agar, pH 5.7 with KOH) on top of a nylon mesh.

extract_protocol: Protoplasts were sorted into 350 microliters RLT exrtraction buffer from a QIAGEN Rneasy micro kit and RNA was extracted according to the manufacturer's instructions, including a DNase treatment.

treatment_protocol: The roots of the seedlings were harvested with a scalpel and incubated in protoplasting solution for 3 h. Protoplasts were filtered and PEG-transformed with an empty vector (pMON999_mRFP), an IAA7mII over-expressor (pBeaconRFP_IAA7mII) or an IAA19mII over-expressor (pBeaconRFP_IAA19mII). Protoplasts were left overnight and treated for 3 h with 5microM IAA or solvent alone. Dually labeled protoplasts were sorted directly into RNA extraction buffer by FACS.

tag: Genotype

tag: Pwer:GFP positive protoplasts


title: IAA19mII over-expressor_mock treated_replicate 3

description:
Roots grown horizontally on square plates, protoplasted, transformed and sorted by FACS.
Replicate 3 of 3.

source_name: IAA19mII over-expressor, mock treated


title: SIMVA replicate3

tag: genotype


title: SIMVA replicate2


title: Radiation replicate2

treatment_protocol: 6 week after one time of 25Gy radiation


title: IAA19mII over-expressor_mock treated_replicate 1

description:
Roots grown horizontally on square plates, protoplasted, transformed and sorted by FACS.
Replicate 1 of 3.


title: SIMVA-Radiation replicate1

treatment_protocol: 10 mg/kg simvastatin via intraperitoneal injection three times a week pre and post irradiation for up to 6 weeks; 6 week after one time of 25Gy radiation


title: IAA7mII over-expressor_IAA treated_replicate 1


title: IAA7mII over-expressor_mock treated_replicate 3

source_name: IAA7mII over-expressor, mock treated


title: Radiation replicate1


title: IAA19mII over-expressor_mock treated_replicate 2


title: IAA7mII over-expressor_IAA treated_replicate 3


title: IAA19mII over-expressor_IAA treated_replicate 3

source_name: IAA19mII over-expressor, IAA treated


title: IAA7mII over-expressor_mock treated_replicate 1


title: SIMVA-Radiation replicate2


title: IAA19mII over-expressor_IAA treated_replicate 1


title: Control replicate1

treatment_protocol: Vehicle

value: 8-10 week


title: IAA19mII over-expressor_IAA treated_replicate 2


title: Gene expression in colon from Healthy controls

description: no special addition

extract_protocol: total RNAs was isolated from sigmoid colon biopsy kept in TRIZOL.

tag: sigmoid colon biopsy from 5 normal healthy individuals


title: IAA7mII over-expressor_mock treated_replicate 2


title: Control replicate2


title: Radiation replicate3


title: Control replicate3


title: SIMVA-Radiation replicate3


title: empty vector_IAA treated_replicate 3

source_name: empty vector, IAA treated


title: IL-2-cultured induced CD4+Foxp3deltaEGFP+ cells 1

city: los angeles

first: Brian

last: O'Connor

state: CA

address: 2018 Griffith Park Blvd

institute: UCLA

description: Group 10

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

data_processing: The data was normalized using the justRMA algorithm from the Bioconductor group following the methods of the Celsius project.

source_name: Sorted CD4+Foxp3deltaEGFP+ cells isolated from anti-CD3+anti-CD28 mAbs+TGF-beta treated CD4+Foxp3deltaEGFP- peripheral T cells then cultured with IL-2 for one week

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Conventional CD4+Foxp3-EGFP- and natural CD4+Foxp3+EGFP+ regulatory T cells were isolated from secondary lymphoid tissues (spleens and lymph nodes) of bicistronic Foxp3/EGFP mice. Conventional CD4+Foxp3deltaEGFP- were isolated from Foxp3deltaEGFP mutant males, while CD4+Foxp3deltaEGFP+ regulatory T cell precursors were isolated from heterozygous Foxp3deltaEGFP females. The respective cell populations were isolated by cell sorting.

extract_protocol: Total RNA was isolated by Trizol extraction and was furher purified by Qiagen Rneasy spin columns following the manufacturer's specifications

treatment_protocol: Group 1: induced regulatory T cells, derived by treatment of CD4+Foxp3-EGFP– T cells of Foxp3EGFP bicistronic mice with anti-CD3+anti-CD28 monoclonal antibodies (mAbs) +TGF-beta for 3 days, then sorting for CD4+Foxp3+EGFP+ cells; Group 2: Failed induced regulatory T cells: CD4+Foxp3-EGFP– cells, derived from group 1 cultures that failed to express Foxp3EGFP following treatment with anti-CD3+anti-CD28 mAbs+TGF-beta; Group 3: induced CD4+Foxp3deltaEGFP+ cells, derived by treatment of CD4+Foxp3deltaEGFP– T cells of Foxp3deltaEGFP mutant mice with anti-CD3+anti-CD28 mAbs+TGF-beta for 3 days, then sorting for CD4+Foxp3deltaEGFP+ cells; Group 4: activated T cells, derived from conventional CD4+Foxp3-EGFP- T cells of Foxp3/EGFP bicistronic mice that were stimulated in vitro with anti-CD3+anti-CD28 mAbs but NO TGF-beta; Group 5: Activated natural regulatory T cells are CD4+Foxp3+EGFP+ T cells isolated from Foxp3/EGFP bicistronic mice and activated with anti-CD3+antiCD28 mAbs +TGF-beta to simulate treatment of groups  1-3; Group 6: native (not activated) CD4+Foxp3+EGFP+ natural regulatory T cells of Foxp3EGFP bicistronic mice; Group 7: Native (not activated) CD4+Foxp3deltaEGFP+ T cells isolated from heterozygos Foxp3deltaEGFP females; Group 8: Native (not activated) conventional CD4+T cells isolated from bicistonic Foxp3/EGFP mice; Group 9: IL-2-cultured induced regulatory T cells, derived by treatment of CD4+Foxp3-EGFP– T cells (from Foxp3EGFP bicistronic muce) with anti-CD3+anti-CD28 mAbs +TGF-beta for 3 days then sorting for CD4+Foxp3+EGFP+ cells and culturing those for one week with IL-2 at 100 units/ml; Group 10: IL-2-cultured induced CD4+Foxp3deltaEGFP+ cells, derived by treatment of CD4+Foxp3deltaEGFP– T cells (isolated from Foxp3deltaEGFP mice) with anti-CD3+anti-CD28 mAbs+TGF-beta for 3 days, then sorting for CD4+Foxp3deltaEGFP+ cells and culturing those for one week with IL-2 at 100 units/ml.

tag: Foxp3deltaEGFP mutant mice on BALB/c background


title: empty vector_IAA treated_replicate 2


title: empty vector_mock treated_replicate 1

source_name: empty vector, mock treated


title: empty vector_IAA treated_replicate 1


title: IL-2-cultured induced regulatory T cells 2

description: Group 9

source_name: Sorted CD4+Foxp3+EGFP+ cells isolated from anti-CD3+anti-CD28 mAbs+TGF-beta treated CD4+Foxp3-EGFP- peripheral T cells then cultured with IL-2 for one week

tag: Foxp3/EGFP bicistronic mice


title: empty vector_mock treated_replicate 2


title: IL-2-cultured induced CD4+Foxp3deltaEGFP+ cells 2

description: Group 10


title: Activated T cells 2

description: Group 4

source_name: Peripheral CD4+Foxp3-EGFP- T cells treated with anti-CD3+anti-CD28 mAbs

tag: Foxp3/EGFP bicistronic mice on BALB/c background


title: Activated T cells 3

description: Group 4


title: Native (not activated) conventional CD4+T cells 3

description: Group 8

source_name: Peripheral CD4+Foxp3-EGFP- T cells


title: empty vector_mock treated_replicate 3


title: Activated natural regulatory T cells 2

description: Group 5

source_name: Peripheral CD4+Foxp3+EGFP+ T cells treated with anti-CD3+anti-CD28 mAbs +TGF-beta


title: IL-2-cultured induced regulatory T cells 1

description: Group 9


title: Activated natural regulatory T cells 1

description: Group 5


title: Induced regulatory T cells 4

description: Group 1

source_name: Sorted CD4+Foxp3+EGFP+ cells isolated from anti-CD3+anti-CD28 mAbs+TGF-beta treated CD4+Foxp3-EGFP- peripheral T cells


title: Native (not activated) conventional CD4+T cells 2

description: Group 8


title: Native (not activated) natural regulatory T cells 1

description: Group 6

source_name: Peripheral CD4+Foxp3+EGFP+ T cells


title: Induced CD4+Foxp3deltaEGFP+ cells 1

description: Group 3

source_name: Sorted CD4+Foxp3deltaEGFP+ cells isolated from anti-CD3+anti-CD28 mAbs+TGF-beta treated CD4+Foxp3deltaEGFP- peripheral T cells

tag: Foxp3deltaEGFP mutant mice on BALB/c Background


title: Native (not activated) CD4+Foxp3deltaEGFP+ T cells 1

description: Group 7

source_name: Peripheral CD4+Foxp3deltaEGFP+ T cells

tag: Foxp3deltaEGFP heterozygos female mice on BALB/c background


title: Induced CD4+Foxp3deltaEGFP+ cells 3

description: Group 3


title: Failed induced regulatory T cells 2

description: Group 2

source_name: Sorted CD4+Foxp3-EGFP_ cells isolated from anti-CD3+anti-CD28 mAbs+TGF-beta treated CD4+Foxp3-EGFP- peripheral T cells


title: Induced CD4+Foxp3deltaEGFP+ cells 2

description: Group 3


title: Induced regulatory T cells 3

description: Group 1


title: Activated T cells 4

description: Group 4


title: Activated natural regulatory T cells 3

description: Group 5


title: Failed induced regulatory T cells 3

description: Group 2


title: Native (not activated) CD4+Foxp3deltaEGFP+ T cells 2

description: Group 7


title: Failed induced regulatory T cells 1

description: Group 2

source_name: Sorted CD4+Foxp3-EGFP- cells isolated from anti-CD3+anti-CD28 mAbs+TGF-beta treated CD4+Foxp3-EGFP- peripheral T cells


title: Induced regulatory T cells 5

description: Group 1


title: Activated T cells 1

description: Group 4


title: Srf mutant_3

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

description: Serum response factor (SRF) is a transcription factor that binds to the serum response element (SRE) of genes that are expressed in response to mitogens. SRF plays essential roles in muscle and nervous system development; however, little is known about the role of SRF during liver growth and function. To examine the function of SRF in the liver, we generated mice in which the Srf gene was specifically disrupted in hepatocytes. The survival of mice lacking hepatic SRF activity was lower than that of control mice; moreover, surviving mutant mice were smaller and had lower blood glucose and triglyceride levels compared with control mice. Srf-deficient livers were also smaller than control livers, hepatocyte morphology was abnormal, and liver-cell proliferation and viability was compromised. Gene array and quantitative RT-PCR analysis of SRF depleted livers revealed a reduction in mRNAs encoding components of the growth hormone/IGF1 pathway, cyclins, several metabolic regulators, and cytochrome p450 enzymes. Conclusion: SRF is essential for hepatocyte proliferation and survival, liver function, and control of postnatal body growth by regulating hepatocyte gene expression.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Standard GCOS data processing produced the values provided.

source_name: Srf loxP/loxP AlfpCre male liver; mutant sample

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Rneasy mini kit (qiagen)

tag: Srf loxP/loxP AlfpCre male liver

tag: 3 weeks old

tag: mutant sample


title: Srf control_2

source_name: Srf loxP/+ AlfpCre male liver; control sample

tag: Srf loxP/+ AlfpCre male liver

tag: control sample


title: Srf mutant_1


title: Gastrocnemius Muscle WT rep2

first: Paul

middle: T

last: Martin

address: 700 Children's Drive

institute: Columbus Children's Research Institute

description: Gene expression data from skeletal muscle of two months old mouse

hyb_protocol: For each array, 2.2 µg of fragmented and labeled cDNA was hybridized onto 430 2.0 GeneChips® (Affymetrix Inc., USA), 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) and probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene).

source_name: Gastrocnemius, 2 months old

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 25 ng of total RNA from gastrocnemius muscle following manufacturer’s instructions.

growth_protocol: All mice were maintained in the institute animal facility following the IACUC guidelines

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by further purification on a silica-gel-based membrane (RNeasy-Mini; Qiagen, Valencia, CA).

treatment_protocol: 1AAV-Galgt2 and 2AAV-Galgt2 were mdx mice whose gastrocnemius muscle was treated with AAV carrying the Galgt2 gene. 3mdxPBS and 4mdxPBS were contralateral muscles mock-treated with phosphate-buffered saline.

tag: Strain

value: C57BL/6J, Gender:Male, Age:2 months, Tissue:Gastrocnemius Muscle


title: Induced regulatory T cells 1

description: Group 1


title: Induced regulatory T cells 2

description: Group 1


title: Myoblast Cell Line Stably Transfected with Galgt2 rep1

description: Gene expression data from C2CT myoblasts - C2C12 myoblasts stably transfected with Galgt2

source_name: Skeletal Muscle

tag: Mouse Myoblast Cell Line Stably Transfected with Galgt2


title: Gastrocnemius Muscle Galgt2 Transgenic rep1

value: C57BL/6J, Gender:Male, Age:2 months, Tissue:Gastrocnemius Muscle, Galgt2 Transgenic


title: Myoblast Cell Line Stably Transfected with Galgt2 Differentiated rep1

description: Gene expression data from C2CT myotubes - C2C12 myoblasts stably transfected with Galgt2

tag: Mouse Myoblast Cell Line Stably Transfected with Galgt2, Differentiated


title: Myoblast Cell Line rep1

description: Gene expression data from C2C12 myoblasts

tag: Mouse Myoblast Cell Line


title: Srf control_1


title: Gastrocnemius Muscle Galgt2 Transgenic mdx rep2

value: C57BL/10J x C57BL/6J, Gender:Male, Age:2 months, Tissue:Gastrocnemius Muscle, Deficient in Dystrophin, Galgt2 Transgenic


title: Gastrocnemius Muscle WT rep1


title: Gastrocnemius Muscle mdx rep1

value: C57BL/10J, Gender:Male, Age:2 months, Tissue:Gastrocnemius Muscle, Deficient in Dystrophin


title: Gastrocnemius Muscle mdx PBS-Treated rep1

value: C57BL/10J, Gender:Male, Age:2 months, Tissue:Gastrocnemius Muscle Treated with Phosphate-Buffered Saline, Deficient in Dystrophin


title: Gastrocnemius Muscle Galgt2 Transgenic rep2

value: C57BL/6J, Gender:Male, Age:2 months, Tissue:Gastrocnemius Muscle. Galgt2 Transgenic


title: Gastrocnemius Muscle mdx AAV-Galgt2-Treated rep2

value: C57BL/10J, Gender:Male, Age:2 months, Tissue:Gastrocnemius Muscle Treated with AAV carrying Galgt2, Deficient in Dystrophin


title: GM cells, biological replicate 2 of 2

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

description: Gene expression of GM06990 (GM) cells using Affymetrix GeneChip Human Genome U133 Plus 2.0 Array

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: gcRMA normalization

label: Affymetrix protocol

source_name: total RNA from GM cells

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol

tag: GM06990 cells


title: Gastrocnemius Muscle Galgt2 Transgenic mdx rep1


title: Srf mutant_2


title: Gastrocnemius Muscle mdx rep2


title: Srf control_3


title: Myoblast Cell Line Differentiated rep1

description: Gene expression data from C2C12 myotubes

tag: Mouse Myoblast Cell Line, Differentiated


title: Gastrocnemius Muscle mdx PBS-Treated rep2


title: K562 cells, biological replicate 1 of 2

description: Gene expression of K562 cells using Affymetrix GeneChip Human Genome U133 Plus 2.0 Array

source_name: total RNA from K562 cells

tag: K562 cells


title: GM cells, biological replicate 1 of 2


title: K562 cells, biological replicate 2 of 2


title: T cell donor 4, rolipram

first: John

last: Meyers

address: 650 Albany St. Rm. X420

department: Hematology/Oncology

institute: Boston University School of Medicine

description: Cells treated with 20 uM rolipram

hyb_protocol: biotinylated cRNA + hybridization controls hybridized to U133 2.0 arrays, 16 hours at 45 degC at 60 rpm

scan_protocol: Scanned on Affymetrix GeneChip Scanner 3000 at 532 nm

data_processing: Background subtraction, quantiles normalization, RMA expression set generation, loess normalization using R

source_name: MACS purified T cells from healthy donor peripheral blood

label_protocol: Affymetrix IVT labeling kit per manufacturer's protocol

growth_protocol: Cultured at 37 degC at 5% CO2

extract_protocol: Ambion RiboPure RNA isolation, quality verified by Agilent 2100

treatment_protocol: Treated with 20 uM rolipram (Biomol) or DMSO (Sigma) vehicle control

tag: T cell donor 4, rolipram


title: T cell donor 3, control

description: Cells treated with DMSO vehicle control

tag: T cell donor 3, control


title: T cell donor 3, rolipram

description: Cells treated with 20 uM rolipram

tag: T cell donor 3, rolipram


title: T cell donor 2, rolipram

description: Cells treated with 20 uM rolipram

tag: T cell donor 2, rolipram


title: CLL donor 4, rolipram treated

description: Cells treated with 20 uM rolipram

source_name: PBMC from B-CLL patient

tag: CLL donor 4, rolipram treated


title: T cell donor 4, control

description: Cells treated with DMSO vehicle control

tag: T cell donor 4, control


title: T cell donor 2, control

description: Cells treated with DMSO vehicle control

tag: T cell donor 2, control


title: B cell donor 3, control

description: Cells treated with DMSO vehicle control

source_name: MACS purified resting B cells from healthy donor peripheral blood

tag: B cell donor 3, control


title: B cell donor 2, control

description: Cells treated with DMSO vehicle control

tag: B cell donor 2, control


title: T cell donor 1, rolipram

description: Cells treated with 20 uM rolipram

tag: T cell donor 1, rolipram


title: CLL donor 4, control

description: Cells treated with DMSO vehicle control

tag: CLL donor 4, control


title: CLL donor 3, control

description: Cells treated with DMSO vehicle control

tag: CLL donor 3, control


title: B cell donor 4, control

description: Cells treated with DMSO vehicle control

tag: B cell donor 4, control


title: CLL donor 3, rolipram treated

description: Cells treated with 20 uM rolipram

tag: CLL donor 3, rolipram treated


title: T cell donor 1, control

description: Cells treated with DMSO vehicle control

tag: T cell donor 1, control


title: CLL donor 2, rolipram treated

description: Cells treated with 20 uM rolipram

tag: CLL donor 2, rolipram treated


title: B cell donor 1, control

description: Cells treated with DMSO vehicle control

tag: B cell donor 1, control


title: B cell donor 2, rolipram

description: Cells treated with 20 uM rolipram

tag: B cell donor 2, rolipram


title: B cell donor 3, rolipram

description: Cells treated with 20 uM rolipram

tag: B cell donor 3, rolipram


title: B cell donor 1, rolipram

description: Cells treated with 20 uM rolipram

tag: B cell donor 1, rolipram


title: CLL donor 1, control

description: Cells treated with DMSO vehicle control

tag: CLL donor 1, control


title: B cell donor 4, rolipram

description: Cells treated with 20 uM rolipram

tag: B cell donor 4, rolipram


title: CLL donor 2, control

description: Cells treated with DMSO vehicle control

tag: CLL donor 2, control


title: CLL donor 1, rolipram treated

description: Cells treated with 20 uM rolipram

tag: CLL donor 1, rolipram treated


title: blood_cd34neg_D1

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

description: 3 samples CD34+ and 2 samples CD34-

hyb_protocol: affymetrix standard: GeneChip Eukaryotic Target Labelling Assays for Expression Analysis

data_processing: RMA, quantile normalization

source_name: periphereal blood

growth_protocol: 10dd cytokines

extract_protocol: phenol chloroform 5:1, acid-equilibrated PH 4.7

treatment_protocol: GCSF

tag: healty donor treated with GCSF isolated CD34+ cells and CD34+ after 10dd of differentiating medium.


title: blood_cd34pos_D3

description: 3 samples CD34+ and 2 samples CD34-

scan_protocol: affymetrix standard: GeneChip Eukaryotic Target Labelling Assays for Expression Analysis

tag: healty donors treated with GCSF isolated CD34+ cells and CD34+ after 10dd of differentiating medium.


title: blood_cd34pos_D2

description: 3 samples CD34+ and 2 samples CD34-

label_protocol:
affymetrix standard:
GeneChip Eukaryotic Target Labelling Assays for Expression Analysis


title: Foxo1KO CD4 T cell

status: Public on Feb 28 2009

first: Ming

address: 408 East 69th Street

department: Immunology

institute: Memorial Sloan-Kettering Cancer Center

description: Gene expression data for Foxo1-deficient T cells

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

data_processing: The data were analyzed with Genechip Operating System (GCOS1.4) 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: mouse spleen and lymph nodes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted by using miRNease kit from Qiagen according to the manufacturer's instructions.

tag: cell type

value: CD4 T cell

tag: genotype

tag: age


title: Foxo1KO CD8 T cell

value: CD8 T cell


title: Wild-type CD4 T cell

value: wild-type


title: blood_cd34pos_D1

description: 3 samples CD34+ and 2 samples CD34-


title: AJ-2-liver

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

institute: University of Lausanne

hyb_protocol: Twelve micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G and hybridization quality control were assessed using RACE (Psarros et al., 2005), a web service based on Bioconductor “affy” and “affyPLM” packages (Gautier et al., 2004).

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: A/J, liver, individual 2

label_protocol: Target preparations were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the DNA array facility of the University of Lausanne (Switzerland). 3 ug of each pool was used to perform the chiparray experiment according to the Affymetrix Gene Expression procedure.

extract_protocol: Mice were sacrificed by cervical dislocation. RNA from whole brain, testis, kidney, heart, liver and lung was isolated with TRIzol (Invitrogen) and purified on Qiagen RNeasy Mini columns (Qiagen), according to manufacturers' instructions.

tag: Strain

value: A/J, Gender:male, Age:11-14 weeks of age, Tissue:liver


title: blood_cd34neg_D2

description: 3 samples CD34+ and 2 samples CD34-


title: AK-1-liver

source_name: AKR/J, liver, individual 1

value: AKR/J, Gender:male, Age:11-14 weeks of age, Tissue:liver


title: D2-3-liver

source_name: DBA2/J, liver, individual 3

value: DBA2/J, Gender:male, Age:11-14 weeks of age, Tissue:liver


title: AK-3-liver

source_name: AKR/J, liver, individual 3


title: D2-2-liver

source_name: DBA2/J, liver, individual 2


title: S2-2-liver

source_name: 129S2, liver, individual 2

value: 129S2, Gender:male, Age:11-14 weeks of age, Tissue:liver


title: S2-3-liver

source_name: 129S2, liver, individual 3


title: B6-12-liver

source_name: C57BL/6J, liver, individual 12

value: C57BL/6J, Gender:male, Age:11-14 weeks of age, Tissue:liver


title: Gastrocnemius Muscle mdx AAV-Galgt2-Treated rep1

source_name: Gastrocnemius, 2 months old


title: AJ-3-liver

source_name: A/J, liver, individual 3


title: Wild-type CD8 T cell

value: 6-8 weeks


title: D2-1-liver

source_name: DBA2/J, liver, individual 1


title: S2-4-liver

source_name: 129S2, liver, individual 4


title: AJ-1-liver

source_name: A/J, liver, individual 1


title: C3H-1-liver

source_name: C3HeB/FeJ, liver, individual 1

value: C3HeB/FeJ, Gender:male, Age:11-14 weeks of age, Tissue:liver


title: C3H-3-liver

source_name: C3HeB/FeJ, liver, individual 3


title: AJ-2-testis

source_name: A/J, testis, individual 2

value: A/J, Gender:male, Age:11-14 weeks of age, Tissue:testis


title: C3H-2-liver

source_name: C3HeB/FeJ, liver, individual 2


title: D2-2-testis

source_name: DBA2/J, testis, individual 2

value: DBA2/J, Gender:male, Age:11-14 weeks of age, Tissue:testis


title: B6-10-liver

source_name: C57BL/6J, liver, individual 10


title: B6-11-liver

source_name: C57BL/6J, liver, individual 11


title: AK-2-liver

source_name: AKR/J, liver, individual 2


title: S2-2-testis

source_name: 129S2, testis, individual 2

value: 129S2, Gender:male, Age:11-14 weeks of age, Tissue:testis


title: C3H-2-testis

source_name: C3HeB/FeJ, testis, individual 2

value: C3HeB/FeJ, Gender:male, Age:11-14 weeks of age, Tissue:testis


title: B6-11-testis

source_name: C57BL/6J, testis, individual 11

value: C57BL/6J, Gender:male, Age:11-14 weeks of age, Tissue:testis


title: AK-2-testis

source_name: AKR/J, testis, individual 2

value: AKR/J, Gender:male, Age:11-14 weeks of age, Tissue:testis


title: AK-1-testis

source_name: AKR/J, testis, individual 1


title: AJ-1-testis

source_name: A/J, testis, individual 1


title: C3H-1-testis

source_name: C3HeB/FeJ, testis, individual 1


title: B6-12-testis

source_name: C57BL/6J, testis, individual 12


title: AK-3-testis

source_name: AKR/J, testis, individual 3


title: S2-3-testis

source_name: 129S2, testis, individual 3


title: D2-1-testis

source_name: DBA2/J, testis, individual 1


title: AK-1-heart

source_name: AKR/J, heart, individual 1

value: AKR/J, Gender:male, Age:11-14 weeks of age, Tissue:heart


title: B6-10-testis

source_name: C57BL/6J, testis, individual 10


title: D2-1-heart

source_name: DBA2/J, heart, individual 1

value: DBA2/J, Gender:male, Age:11-14 weeks of age, Tissue:heart


title: C3H-3-testis

source_name: C3HeB/FeJ, testis, individual 3


title: D2-3-testis

source_name: DBA2/J, testis, individual 3


title: B6-4-heart

source_name: C57BL/6J, heart, individual 4

value: C57BL/6J, Gender:male, Age:11-14 weeks of age, Tissue:heart


title: AK-2-heart

source_name: AKR/J, heart, individual 2


title: AJ-3-testis

source_name: A/J, testis, individual 3


title: AJ-3-heart

source_name: A/J, heart, individual 3

value: A/J, Gender:male, Age:11-14 weeks of age, Tissue:heart


title: S2-4-testis

source_name: 129S2, testis, individual 4


title: C3H-2-heart

source_name: C3HeB/FeJ, heart, individual 2

value: C3HeB/FeJ, Gender:male, Age:11-14 weeks of age, Tissue:heart


title: B6-2-heart

source_name: C57BL/6J, heart, individual 2


title: C3H-1-heart

source_name: C3HeB/FeJ, heart, individual 1


title: AK-3-heart

source_name: AKR/J, heart, individual 3


title: S2-1-heart

source_name: 129S2, heart, individual 1

value: 129S2, Gender:male, Age:11-14 weeks of age, Tissue:heart


title: AJ-1-heart

source_name: A/J, heart, individual 1


title: B6-3-brain

source_name: C57BL/6J, brain, individual 3

value: C57BL/6J, Gender:male, Age:11-14 weeks of age, Tissue:brain


title: B6-3-heart

source_name: C57BL/6J, heart, individual 3


title: AK-1-brain

source_name: AKR/J, brain, individual 1

value: AKR/J, Gender:male, Age:11-14 weeks of age, Tissue:brain


title: AJ-2-heart

source_name: A/J, heart, individual 2


title: D2-2-heart

source_name: DBA2/J, heart, individual 2


title: D2-3-heart

source_name: DBA2/J, heart, individual 3


title: S2-3-heart

source_name: 129S2, heart, individual 3


title: C3H-3-heart

source_name: C3HeB/FeJ, heart, individual 3


title: S2-2-heart

source_name: 129S2, heart, individual 2


title: C3H-1-brain

source_name: C3HeB/FeJ, brain, individual 1

value: C3HeB/FeJ, Gender:male, Age:11-14 weeks of age, Tissue:brain


title: S2-1-brain

source_name: 129S2, brain, individual 3

value: 129S2, Gender:male, Age:11-14 weeks of age, Tissue:brain


title: C3H-2-brain

source_name: C3HeB/FeJ, brain, individual 2


title: AJ-2-brain

source_name: A/J, brain, individual 2

value: A/J, Gender:male, Age:11-14 weeks of age, Tissue:brain


title: B6-4-brain

source_name: C57BL/6J, brain, individual 4


title: Blood_TD51282_Dayone_2pm

first: Emma

last: Meaburn

address: PO 82, Denmark Hill

department: SGDP

institute: Institute Of Psychiatry

description: Venous blood samples were collected using a standard phlebotomy protocol in conjunction with the PAXgene Blood RNA System (Becton & Dickinson, Oxford), which allows the collection, stabilization and transportation of a whole blood cellular RNA sample in a closed evacuated system.

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to Affymetrix U133 Plus 2.0 Arrays for 16 hours at 45°C in an Affymetrix hybridization oven 640. Arrays were then washed and stained on an Affymetrix fluidic station 450 (protocol FS450_0001).

scan_protocol: Each array was scanned using an Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software (GCOS) version 1.4 was used to obtain fluorescence intensities

data_processing: The arrays were processed together using Robust Multiarray Average (RMA; [Irizarry et al., 2003]), implemented in the ‘affy’ package in the statistical software environment R (http://www.r-project.org/), to produce normalized, background-adjusted, perfect-match, log-transformed probe set summaries.

source_name: Whole blood

label_protocol:
Expression profiles were generated by hybridizing cRNA derived from 5µg of total RNA to Affymetrix U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA) in accordance with the Affymetrix Eukaryote One-Cycle protocol with integrated globin reduction (see Affymetrix GeneChip Globin-reduction Kit Handbook and Affymetrix GeneChip Expression Analysis technical manual).
Total RNA was concentrated (GeneChip blood RNA concentration kit; PN 900585) and 5µg used to generate first-strand cDNA synthesis with integrated globin reduction using peptide nucleic acid (PNA) oligonucleotides in order to block reverse transcription of globin mRNA (GeneChip Globin-Reduction RNA controls; PN 900586, GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents; PN 900493). After second-strand cDNA synthesis, biotinylated cRNA was generated.

extract_protocol: Total RNA was isolated from the PAXgene blood samples using the PAXgene Blood RNA Kit protocol (PreAnalytiX GmbH, Feldbachstrasse, CH-8634 Hombrechtikon).

tag: gender

value: Female

tag: tissue

value: whole blood


title: D2-1-brain

source_name: DBA2/J, brain, individual 1

value: DBA2/J, Gender:male, Age:11-14 weeks of age, Tissue:brain


title: Blood_TD51282_Daytwo_2pm


title: AK-2-brain

source_name: AKR/J, brain, individual 2


title: AJ-3-brain

source_name: A/J, brain, individual 3


title: D2-2-brain

source_name: DBA2/J, brain, individual 2


title: Blood_TD51282_Dayone_10am


title: Blood_TD51282_Daytwo_10am


title: S2-2-brain

source_name: 129S2, brain, individual 1


title: B6-2-brain

source_name: C57BL/6J, brain, individual 2


title: Blood_TD51281_Daytwo_2pm


title: C3H-3-brain

source_name: C3HeB/FeJ, brain, individual 3


title: D2-3-brain

source_name: DBA2/J, brain, individual 3


title: Blood_TD51281_Daytwo_10am


title: Blood_TD51281_Dayone_10am


title: Blood_TD32681_Dayone_2pm

label_protocol:
Expression profiles were generated by hybridizing cRNA derived from 5μg of total RNA to Affymetrix U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA) in accordance with the Affymetrix Eukaryote One-Cycle protocol with integrated globin reduction (see Affymetrix GeneChip Globin-reduction Kit Handbook and Affymetrix GeneChip Expression Analysis technical manual).
Total RNA was concentrated (GeneChip blood RNA concentration kit; PN 900585) and 5μg used to generate first-strand cDNA synthesis with integrated globin reduction using peptide nucleic acid (PNA) oligonucleotides in order to block reverse transcription of globin mRNA (GeneChip Globin-Reduction RNA controls; PN 900586, GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents; PN 900493). After second-strand cDNA synthesis, biotinylated cRNA was generated.

value: Male


title: AJ-1-brain

source_name: A/J, brain, individual 1


title: Blood_TD32682_Dayone_10am


title: Blood_TD32682_Daytwo_2pm


title: Blood_TD32681_Daytwo_2pm


title: D2-3-kidney

source_name: DBA2/J, kidney, individual 3

value: DBA2/J, Gender:male, Age:11-14 weeks of age, Tissue:kidney


title: S2-3-brain

source_name: 129S2, brain, individual 2


title: AK-3-brain

source_name: AKR/J, brain, individual 3


title: Blood_TD32681_Daytwo_10am


title: Blood_TD51281_Dayone_2pm


title: S2-4-kidney

source_name: 129S2, kidney, individual 3

value: 129S2, Gender:male, Age:11-14 weeks of age, Tissue:kidney


title: Blood_TD32681_Dayone_10am


title: AJ-1-kidney

source_name: A/J, kidney, individual 1

value: A/J, Gender:male, Age:11-14 weeks of age, Tissue:kidney


title: AK-1-kidney

source_name: AKR/J, kidney, individual 1

value: AKR/J, Gender:male, Age:11-14 weeks of age, Tissue:kidney


title: Blood_TD23462_Dayone_2pm

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to Affymetrix U133 Plus 2.0 Arrays for 16 hours at 45°C in an Affymetrix hybridization oven 640.  Arrays were then washed and stained on an Affymetrix fluidic station 450 (protocol FS450_0001).


title: Blood_TD23462_Dayone_10am


title: AK-3-kidney

source_name: AKR/J, kidney, individual 3


title: D2-2-kidney

source_name: DBA2/J, kidney, individual 2


title: Blood_TD23461_Dayone_10am

source_name: Whole blood


title: B6-11-kidney

source_name: C57BL/6J, kidney, individual 11

value: C57BL/6J, Gender:male, Age:11-14 weeks of age, Tissue:kidney


title: Blood_TD23461_Dayone_2pm


title: S2-2-kidney

source_name: 129S2, kidney, individual 2


title: B6-12-kidney

source_name: C57BL/6J, kidney, individual 12


title: Blood_TD24112_Daytwo_2pm


title: C3H-1-kidney

source_name: C3HeB/FeJ, kidney, individual 1

value: C3HeB/FeJ, Gender:male, Age:11-14 weeks of age, Tissue:kidney


title: Blood_TD24111_Dayone_2pm


title: Blood_TD24111_Daytw0_10am


title: Blood_TD24112_Daytwo_10am


title: C3H-3-kidney

source_name: C3HeB/FeJ, kidney, individual 3


title: AK-2-kidney

source_name: AKR/J, kidney, individual 2


title: AJ-2-kidney

source_name: A/J, kidney, individual 2


title: Blood_TD24111_Dayone_10am


title: B6-2-lung

source_name: C57BL/6J, lung, individual 2

value: C57BL/6J, Gender:male, Age:11-14 weeks of age, Tissue:lung


title: B6-10-kidney

source_name: C57BL/6J, kidney, individual 10


title: S2-3-kidney


title: Blood_TD24111_Daytwo_2pm


title: D2-1-kidney

source_name: DBA2/J, kidney, individual 1


title: Blood_TD24112_Dayone_2pm


title: Blood_TD19902_Dayone_2pm


title: Blood_TD23461_Daytwo_10am


title: AK-1-lung

source_name: AKR/J, lung, individual 1

value: AKR/J, Gender:male, Age:11-14 weeks of age, Tissue:lung


title: C3H-3-lung

source_name: C3HeB/FeJ, lung, individual 3

value: C3HeB/FeJ, Gender:male, Age:11-14 weeks of age, Tissue:lung


title: AK-3-lung

source_name: AKR/J, lung, individual 3


title: AJ-3-kidney

source_name: A/J, kidney, individual 3


title: S2-1-lung

source_name: 129S2, lung, individual 1

value: 129S2, Gender:male, Age:11-14 weeks of age, Tissue:lung


title: Blood_TD24112_Dayone_10am


title: C3H-1-lung

source_name: C3HeB/FeJ, lung, individual 1


title: Blood_TD19902_Daytwo_2pm

source_name: Whole blood


title: Blood_TD23461_Daytwo_2pm


title: Blood_TD19902_Daytwo_10am


title: D2-3-lung

source_name: DBA2/J, lung, individual 3

value: DBA2/J, Gender:male, Age:11-14 weeks of age, Tissue:lung


title: Blood_TD19901_Dayone_10am


title: C3H-2-kidney

source_name: C3HeB/FeJ, kidney, individual 2


title: Blood_TD19901_Daytwo_2pm


title: Blood_TD19902_Dayone_10am


title: AK-2-lung

source_name: AKR/J, lung, individual 2


title: D2-1-lung

source_name: DBA2/J, lung, individual 1


title: AJ-2-lung

source_name: A/J, lung, individual 2

value: A/J, Gender:male, Age:11-14 weeks of age, Tissue:lung


title: Blood_TD19901_Dayone_2pm


title: AJ-3-lung

source_name: A/J, lung, individual 3


title: S2-3-lung

source_name: 129S2, lung, individual 3


title: C3H-2-lung

source_name: C3HeB/FeJ, lung, individual 2


title: S2-2-lung

source_name: 129S2, lung, individual 2


title: B6-3-lung

source_name: C57BL/6J, lung, individual 3


title: D2-2-lung

source_name: DBA2/J, lung, individual 2


title: TGFB KO2 liver

city: Hanover

first: Jennifer

middle: L

last: Sargent

state: NH

address: Dartmouth College; HB7400

department: Genetics

institute: Dartmouth Medical School

description: Following RNA preparation, all microarray procedures were carried out at the Dartmouth Genomics and Microarray Laboratory (Lebanon, NH)

hyb_protocol: Standard hybridization protocols as per Affymetrix directions.  Hybe for 16 hours, at 45oC, 60 rpm

scan_protocol: washed, stained and scanned according to standard Affymetrix protocols.

data_processing: Initial data processing and normalizations were carried out at the Dartmouth Genomics and Microarray Laboratory (Lebanon, NH).

source_name: TGFB KO2 (balb/c)

label_protocol: standard Affymetrix one-cycle labelling protocol

extract_protocol: Trizol extraction

tag: 11 day old, balb/c TGFB KO mouse liver (replicate 2)


title: Blood_TD23462_Daytwo_2pm


title: AJ-1-lung

source_name: A/J, lung, individual 1


title: B6-4-lung

source_name: C57BL/6J, lung, individual 4


title: TGFB KO1 liver

source_name: TGFB KO1 (balb/c)

tag: 11 day old, balb/c TGFB KO mouse liver (replicate 1)


title: INFko TGFB+  2 liver

hyb_protocol: Standard hybridization protocols as per Affymetrix directions. Hybe for 16 hours, at 45oC, 60 rpm

source_name: INFko TGBF+ 2 (balb/c)

tag: 11 day old balb/c INF knock out, TGFB+(wt) mouse liver (replicate 2)


title: IFNko TGFB1 KO1 liver

source_name: IFNko TGFB1 KO1 (balb/c)

tag: 11 day old balb/c INF knockout, TGFB1 knockout mouse liver (replicate 1)


title: TGFB KO3 liver

source_name: TGFB KO3 (balb/c)

tag: 11 day old balb/c TGFB KO mouse liver (replicate 3)


title: Balb/c WT3 liver

source_name: Balb/c wildtype control 3

tag: 11 day old balb/c wildtype mouse liver (replicate 3)


title: Aged C57-52, chip

status: Public on Feb 26 2009

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by System Administrator (OGCInfo@ohri.ca; ) for analysis.
Stembase Experiment ID:			E246
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=246
SCGP Sample ID:				S405
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=246#SAMPLE_406
Short description:			Gastrocnemius from normal C57b1/6 mice.
Estimated purity:				95-99%
RNA concentration:			0.05 ug/ul
Sample volume:				5 ul

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

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

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

source_name: Total Muscle, Seletal Muscle Gastrocnemius

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

extract_protocol: RNA prep method:				RNeasy

tag: strain

tag: karyotype

value: Normal


title: Balb/c WT1 liver

source_name: Balb/c wildtype control 1

label_protocol: standard affymetrix one-cycle labeling protocol.

tag: 11 day old balb/c wildtype mouse liver (replicate 1)


title: INFko TGFB+ 3 liver

source_name: INFko TGBF+ 3 (balb/c)

tag: 11 day old balb/c INF knock out, TGFB+(wt) mouse liver (replicate 3)


title: Aged C57-53, chip


title: dexrazoxane 2

status: Public on Feb 24 2009

city: Mainz

first: Shiwei

last: Deng

address: Obere Zahlbacher Str. 67

country: Germany

institute: Uni Mainz

description:
>99.5% TOP2A expression can be silenced in HTETOP cells by the addition of tetracycline
pooled RNA from three cell passages was used for hybridization

hyb_protocol: Following fragmentation, cRNA were hybridized to Human Genome U133 Plus 2.0 GeneChips from Affymetrix.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000.

data_processing: The images were processed by GeneChip Operating Software 1.3 and the raw data were normalized by Robust Multiarray Analysis (RMA).

source_name: dexrazoxane-treated HTETOP cells

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

extract_protocol: Total RNA was extracted using peqGOLD Total RNA Kit according to the manufacturer’s instructions.

treatment_protocol: HTETOP cells were treated with 100 µM dexrazoxane or vehicle for 24 hours.

tag: cell line

value: HTETOP


title: Aged C57-51, chip