title: Elf4 KO1 activated CD8 T cells

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

description: Elf4 KO1  activated CD8 T cells  FILE: pag_LA_3317_MA2_12535

hyb_protocol: Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0µL.  Fluidics Script: EukGE ws2v5

scan_protocol: GeneChiP® Scanner 3000, GCOS version 1.2

data_processing: Affymetrix MAS5.0

source_name: CD8+ cells isolated from spleen

label_protocol: Affymetrix One Cycle Target and Labeling Protocol, exactly as described in Affymetrix Expression Analysis Technical Manual

growth_protocol: CD8+ T cells were left untreated or activated in vitro by culturing on anti-CD3 coated plates and anti-CD28 in media (RPMI 10% FBS supplemented with 5% T-stim) for 3.5 days

extract_protocol: Total RNA extracted using RNeasy® kit from Qiagen

treatment_protocol: CD8+ cells were isolated and purified from the spleen of wild type (C57BL/6) or Elf-/-  knock out mice and cultured in vitro.  CD8 T cells were left untreated or activated in vitro by culturing on anti-CD3 coated plates and anti-CD28 in media (RPMI 10% FBS supplemented with 5% T-stim) for 3.5 days

tag: cells

value: CD8+ cells

value: spleen

tag: strain

value: Elf4-/- KO


title: WT2 activated CD8 T cells

status: Public on Mar 24 2009

type: RNA

country: USA

description:
WT2 activated CD8 T cells
FILE: pag_LA_3317_MA2_12534

hyb_protocol: Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0µL.  Fluidics Script: EukGE ws2v6

scan_protocol: GeneChip® Scanner 3000, GCOS version 1.2

label: Biotin

molecule: total RNA

organism: Mus musculus

extract_protocol: Total RNA was isolated using RNeasy® kit from Qiagen

tag: tissue


title: WT1 activated CD8 T cells

description:
WT1 activated CD8 T cells
FILE pag_LA_3317_MA2_12533

hyb_protocol: Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0ÂµL.  Fluidics Script: EukGE ws2v5

scan_protocol: GeneChipÂ® Scanner 3000, GCOS version 1.2

extract_protocol: Total RNA was isolated using RNeasyÂ® kit from Qiagen


title: Elf4 KO2 activated CD8 T cells

description: Elf4 KO2 activated CD8 T cells  File: pag_LA_3317_MA2_12536


title: Ube2m shRNA, biological replicate 3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description: Gene expression data from NIH 3T3 cells transduced with shRNA vector targeting Ube2m.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: NIH 3T3 cells

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: NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).

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

treatment_protocol: Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.

tag: NIH 3T3 transduced with retroviral shRNA vector targeting Ube2m


title: Ube2m shRNA, biological replicate 1


title: Elf4 KO2 naive CD8 T cells

description: Elf4 KO2 naive CD8 T cells	FILE hnl_LA_1977_MA2_8198


title: control shRNA, biological replicate 3

description: Gene expression data from NIH 3T3 cells transduced with vector containing control shRNA.

tag: NIH 3T3 transduced with control retroviral shRNA vector


title: WT2 naive CD8 T cells

description: WT2 naive CD8 T cells	FILE hnl_LA_1977_MA2_8194


title: Ube2f shRNA, biological replicate 1

description: Gene expression data from NIH 3T3 cells transduced with shRNA vector targeting Ube2f.

tag: NIH 3T3 transduced with retroviral shRNA vector targeting Ube2f


title: Elf4 KO1 naive CD8 T cells

description: KO1_DAY0	FILE hnl_LA_1977_MA2_8197

extract_protocol: Total RNA was extracted using RNeasy® kit from Qiagen


title: Ube2f shRNA, biological replicate 3


title: Ube2m shRNA, biological replicate 2


title: Ube2f shRNA, biological replicate 2


title: control shRNA, biological replicate 1


title: 36-65 hybridoma subclone H27

status: Public on Mar 23 2009

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description: RNA amplification, labeling, hybridization scanning and image analysis was performed at the Albert Einstein College of Medicine genomics Facility, using standardized procedures.

hyb_protocol: Hybridization of 15mg labeled cRNA to GeneChip Mouse Genome 430 2.0 arrays was conducted at the Albert Einstein College of Medicine genomics Facility following the recommendations of the array manufacturer (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 at the Albert Einstein College of Medicine genomics Facility.

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program.

source_name: 36-65 hybridoma subclone H27

label_protocol: The cDNA was prepared using the GeneChip One-Cycle cDNA Synthesis Kit with Eukaryotic Poly-A RNA Controls and biotin labeled cRNA was prepared using GeneChip IVT Labeling Kit at the Albert Einstein College of Medicine Genomics Facility following manufacturer's instructions.

growth_protocol: Dulbecco's modified Eagle's medium (DME) supplemented with 10% (vol/vol) fetal calf serum (FCS), 5% National Cancer Tissue Culture (NCTC) 109 (BioWhittaker), 1% nonessential amino acids (GIBCO), 1% penicillin, and 1% streptomycin.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit and genomic DNA digested with DNase I, according to manufacturer's instructions.

tag: hybridoma subclone

value: 36-65 hybridoma subclone H27

tag: isotype switching

value: Spontaneous high frequencies of switching in vitro


title: 36-65 hybridoma subclone L25

source_name: 36-65 hybridoma subclone L25

value: 36-65 hybridoma subclone L25

value: Low frequencies of switching in vitro


title: 36-65 hybridoma subclone L27

source_name: 36-65 hybridoma subclone L27

value: 36-65 hybridoma subclone L27


title: 36-65 hybridoma subclone H23

source_name: 36-65 hybridoma subclone H23

value: 36-65 hybridoma subclone H23


title: WT1 naive CD8 T cells

description: WT1 naive CD8 T cells hnl_LA_1977_MA2_8194

hyb_protocol: Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0µL.  Fluidics Script: EukGE ws2v5.


title: A/J CS-1.5mos-exposed-2

city: Baltimore

first: vikas

last: misra

state: MD

address: 615 N. Wolfe street, E6609

department: Environmental health sciences

institute: Johns Hopkins University School of public health

description: A/J CS Lung gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manual- Affymetrix)

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

data_processing: Data extraction was processed by Affy GeneChip« Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets A/J 1.5 mos CS x 3 sets A/J 1.5 mos Air comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons).

source_name: A/J CS-1.5mos-2 Lung

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

growth_protocol: no growth protocol

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

treatment_protocol: CS exposed

value: A/J mouse strain (Jackson Lab)

tag: gender

value: male

tag: age

value: 1.5 mos, n = 1, # of tissue = 1

value: Lung


title: A/J Air-6mos-exposed-3

description: A/J Air Lung gene expression

data_processing: Data extraction was processed by Affy GeneChip« Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets A/J 6 mos CS x 3 sets A/J 6 mos Air comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons).

label: ENZO BioArray HighYield RNA Transcript Labeling Kit

source_name: A/J Air-6mos-3 Lung

treatment_protocol: Air exposed

value: 6 mos, n = 1, # of tissue = 1


title: A/J Air-1.5mos-exposed-1

description: A/J Air Lung gene expression

source_name: A/J Air-1.5mos-1 Lung


title: A/J CS-1.5mos-exposed-3

description: A/J CS Lung gene expression

source_name: A/J CS-1.5mos-3 Lung


title: A/J CS-6mos-exposed-2

description: A/J CS Lung gene expression

source_name: A/J CS-6mos-2 Lung


title: A/J Air-6mos-exposed-2

description: A/J Air Lung gene expression

source_name: A/J Air-6mos-2 Lung


title: control shRNA, biological replicate 2


title: A/J CS-1.5mos-exposed-1

description: A/J CS Lung gene expression

source_name: A/J CS-1.5mos-1 Lung


title: A/J CS-6mos-exposed-1

description: A/J CS Lung gene expression

source_name: A/J CS-6mos-1 Lung


title: A/J Air-6mos-exposed-1

description: A/J Air Lung gene expression

source_name: A/J Air-6mos-1 Lung


title: A/J CS-6mos-exposed-3

description: A/J CS Lung gene expression

source_name: A/J CS-6mos-3 Lung


title: A/J CS-8day-exposed-3

description: A/J CS Lung gene expression

data_processing: Data extraction was processed by Affy GeneChip« Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets A/J 8 day CS x 3 sets A/J 8 day Air comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons).

source_name: A/J CS-8day-3 Lung

value: 8 days, n = 1, # of tissue = 1


title: A/J Air-1.5mos-exposed-2

description: A/J Air Lung gene expression

source_name: A/J Air-1.5mos-2 Lung


title: A/J Air-1.5mos-exposed-3

description: A/J Air Lung gene expression

source_name: A/J Air-1.5mos-3 Lung


title: A/J CS-8day-exposed-2

description: A/J CS Lung gene expression

source_name: A/J CS-8day-2 Lung


title: A/J Air-8day-exposed-3

description: A/J Air Lung gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip FluidiAir Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manual- Affymetrix)

source_name: A/J Air-8day-3 Lung


title: A/J Air-8day-exposed-2

description: A/J Air Lung gene expression

source_name: A/J Air-8day-2 Lung


title: A/J Air-8day-exposed-1

description: A/J Air Lung gene expression

source_name: A/J Air-8day-1 Lung


title: A/J CS-5hr-exposed-1

description: A/J CS Lung gene expression

data_processing: Data extraction was processed by Affy GeneChip« Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets A/J 1 day CS x 3 sets A/J 1 day Air comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons).

source_name: A/J CS-5hr-1 Lung

value: 5 hr, n = 1, # of tissue = 1


title: A/J Air-5hr-exposed-3

description: A/J Air Lung gene expression

source_name: A/J Air-5hr-3 Lung


title: A/J CS-8day-exposed-1

description: A/J CS Lung gene expression

source_name: A/J CS-8day-1 Lung


title: PMN_inflam+RO+F_30min

city: Quebec

first: Marc

last: Pouliot

state: Qc

address: 2705 boul Laurier

country: Canada

institute: CHUL Research center

description: Neutrophils were resuspended at a concentration of 25 x 106 cells/ml in Hank's balanced salt solution (HBSS; 37°C) containing 1% fetal bovine serum, 10 mM HEPES pH 7.4, 1,6 mM Ca2+ and no Mg2+. Adenosine deaminase (ADA; 0.1U/mL) was added to cell suspensions 20 min prior to stimulation. Where mentioned, PGE2, CGS 21680, RO 20-1724 and forskolin, dissolved in DMSO, were added to cell suspensions 10 min before stimulation. The final organic solvent concentration was identical in all samples and did not exceed 0.1% (v/v). Neutrophils were stimulated with a mixture of LPS (100 ng/mL), GM-CSF (1.4 nM), TNF-α (100 ng/mL), fMLP (100 nM) and IL-1β (30 nM) for 30 min at 37oC. These experiments were performed 5 times in identical conditions, each time with a different donor.

hyb_protocol: Fifteen µg of fragmented cRNA were hybridized for 16 h at 45°C with constant rotation, using a human oligonucleotide array U133 Plus 2.0 (Genechip, Affymetrix, Santa Clara, CA, USA). After hybridisation, chips were processed by using the Affymetrix GeneChip Fluidic Station 450 (protocol: EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE; Invitrogen, Burlington, ON, Canada), followed by amplification with a biotinylated anti-streptavidin antibody (Vector Laboratories, Burlingame, CA, USA), and by a second round of SAPE

scan_protocol: Chips were scanned using a GeneChip Scanner 3000 G7 (Affymetrix, Santa Clara, CA, USA) enabled for High-Resolution Scanning. Images were extracted with the GeneChip Operating Software (Affymetrix GCOS v1.4). Quality control of microarray chips was performed using the AffyQCReport software

organism: Homo sapiens

source_name: neutrophils, stimulated, 30min

label_protocol: cDNA was purified by phenol-chloroform extraction using phase lock gels (Brinkmann, Westbury, NY, USA), then transcribed in vitro for 16 h at 37°C by using the IVT Labelling Kit (Affymetrix, Santa Clara, CA, USA) to produce biotinylated cRNA. Labelled cRNA was isolated by using the RNeasy Mini Kit column (QIAGEN, Mississauga, ON, Canada).

extract_protocol: neutrophil total RNA was isolated using Trizol (Invitrogen, Burlington, ON, Canada) according to the manufacturer's protocol

tag: Neutrophils were isolated from blood provided by unknown donors.


title: PMN_inflam+PGE2_30min


title: PMN_ctrl_30min

description: Neutrophils were resuspended at a concentration of 25 x 106 cells/ml in Hank's balanced salt solution (HBSS; 37°C) containing 1% fetal bovine serum, 10 mM HEPES pH 7.4, 1,6 mM Ca2+ and no Mg2+. Adenosine deaminase (ADA; 0.1U/mL) was added to cell suspensions 20 min prior to stimulation. Neutrophils were stimulated for 30 min at 37oC. These experiments were performed 5 times in identical conditions, each time with a different donor.

source_name: neutrophils, non stimulated, 30min


title: PMN_inflam+CGS_30min


title: PMN_inflam_30min


title: A/J Air-5hr-exposed-1

description: A/J Air Lung gene expression

source_name: A/J Air-5hr-1 Lung


title: 301425

status: Public on Mar 22 2009

city: Nashville

first: Christine

middle: H.

last: Chung

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

description: Gene expression comparisons of head and neck squamous cell carcinoma in humans.

hyb_protocol: manufacturer’s recommendations

scan_protocol: manufacturer’s recommendations

data_processing: GC-RMA (Bioconductor) followed by distance weighted discrimination to eliminate variation due to protocol

label: ENZO BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA)

source_name: HNSCC from FFPE block

extract_protocol: Total RNA was purified from frozen tumors using Qiagen RNeasy Mini Kit according to the manufacturer’s recommendations (Qiagen, Valencia, CA) using approximately 10-20 milligram of wet tissue from each sample

tag: Head and Neck Squamous Cell Carcinoma from FFPE block

tag: recurrence censor

tag: recurrence date

tag: death censor (1 dead_0 alive)


title: 359050

label_protocol: ENZO BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA)


title: 301137


title: 359046


title: A/J Air-5hr-exposed-2

description: A/J Air Lung gene expression

source_name: A/J Air-5hr-2 Lung


title: SQ20B (Go6976 24hr Tx3)

description: NuGEN Ovation

data_processing: GC-RMA (Bioconductor)

source_name: SQ20B cells 24hr 100nm Gö6976

label_protocol: NuGEN Ovation Biotin RNA Amplification and Labeling Kit (NuGEN, San Carlos, CA)

growth_protocol: SQ20B (5 x 10e6) tumor cells were injected into the right hind limbs of female athymic nude mice

extract_protocol: Qiagen RNeasy Mini kit

treatment_protocol: control, 12 or 24hr 100nm Gö6976 exposure

tag: cells 24hr 100nm Gö6976


title: SQ20B (Go6976 24hr Tx1)

description: NuGEN Ovation


title: SQ20B (Go6976 24hr Tx2)

description: NuGEN Ovation


title: 301016


title: 359026


title: 359039


title: 359037


title: SQ20B (Go6976 12hr Tx1)

description: NuGEN Ovation

source_name: SQ20B cells 12hr 100nm Gö6976

tag: cells 12hr 100nm Gö6976


title: SQ20B (Go6976 12hr Tx3)

description: NuGEN Ovation


title: SQ20B (Go6976 NoTx2)

description: NuGEN Ovation

source_name: SQ20B cells control

tag: CONTROL


title: SQ20B (Go6976 12hr Tx2)

description: NuGEN Ovation


title: SQ20B (Go6976 NoTx3)

description: NuGEN Ovation


title: SQ20B (Go6976 NoTx1)

description: NuGEN Ovation


title: CCD-18Co CONTROL (contains only the mixture of enzymes + salts)_24h_biological rep2

status: Public on Mar 21 2009

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

description: Gene expression data from normal colon CCD-18Co cells exposed for 24h to a control mixture containing only the equivalent quantities of digestive enzymes and salts as those used in the in vitro gastro-duodenal digestion of the orange extract.

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

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

source_name: CCD-18Co fibroblasts, control mixture

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

growth_protocol: Human colon fibroblasts cells (CCD-18Co) were obtained from the American Type Culture Collection (ATCC) (Rockville, MD, USA). Cells were grown in Eagle´s minimum essential medium (EMEM) supplemented with 2 mM L-glutamine, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate, 100 U mL-1 penicillin, 100 μg mL-1 streptomycin (Gibco, Invitrogen S.A., Barcelona, Spain) and 10% v/v foetal bovine serum (FBS) at a final pH 7.2–7.4 and maintained at 37°C under a 5% CO2/95% air atmosphere at constant humidity. For the experiments, cells between passage number 13 and 14 (doubling population between 30 and 35) were seeded onto 6-wells plates at a density of 6000 cells cm-2, and used on day 5 after seeding (~90% confluent monolayers).

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

treatment_protocol: CCD-18Co cells were treated as follows: i) Control cells (C): treated for 24 h with the equivalent quantities of digestive enzymes and salts as those used in the treated group; ii) Treated cells (T): pre-digested orange bitter extract (final concentration of total flavanones in the culture medium, ~60 μM) for 24h.

tag: cell line

tag: cell type

value: Normal human colon fibroblasts cells

tag: confluency

value: ~90% confluent monolayer

tag: treatment

value: control mixture

tag: treatment time


title: CCD-18Co TREATED (digested orange extract, 60 μM total flavanones)_24h_biological rep2

description: Gene expression data from normal colon CCD-18Co cells exposed for 24h to a pre-digested orange extract containing a mixture of flavanones.

source_name: CCD-18Co fibroblasts, pre-digested orange extract rich in flavanones


title: KSUAP-DM mReissners Membrane F0hrB

city: Manhattan

first: Daniel

last: Marcus

state: KS

address: 228 Coles Hall

department: Anatomy & Physiology

institute: Kansas State University

description:
Absolute and comparison analysis are conducted using the following settings:
      Scaling - All Probe Sets: Target Signal = 500
      Normalization – User Defined: Scale Factor = 1

hyb_protocol: GENECHIP HYBRIDIZATION PROTOCOL: Hybridization cocktail composition: (for standard array format) Note: 10% DMSO is added for targets 								 Prepared using the GeneChip 								 Expression 3’-Amplificaton  IVT 								 Labeling Protocol.      30ul     fragmented cRNA 15ug                                                      (0.05ug/ul final conc.)        5ul     control Biotin labeled oligo B2 (3nM) (Affymetrix)          (50pM final conc.)      15ul     20x Eukaryotic Hybridization spike controls        (bioB, bioC, BioD, cre) (Affymetrix)                             (1.5, 5, 25 and 100pM final conc.                                                                                respectively)        3ul     Herring Sperm DNA (10mg/ml)(blocking reagent)            (0.1mg/ml final conc.)        3ul     Acetylated BSA (50mg/ml)(blocking reagent)                    (0.5mg/ml final conc.)    150ul     2x Hybridization Buffer        (Final 1x conc. is 100mM MES {12X stock: 70.4g MES free-acid monohydrate, 193.3g MES         sodium Salt/L pH 6.6}, 1M [Na+], 20mM EDTA, 0.01% Tween 20)   - DEPC H2O to 300ul.                  - Denatured at 99C 5min prior to applying to GeneChip Hybridization Conditions:        - GeneChip is prehybridized with 200ul 1x Hybridization buffer (see above) at 45C 10min at 60rpm        - 200ul denatured Hybridization cocktail is applied to GeneChip        - GeneChip is hybridized 16 hr at 45C and 60rpm in GeneChip Hybridization Oven 640. Washing and Staining: Automated process using the GeneChip Fluidics Station 400 with the Standard             Array Format. Enzo BioArray High Yield RNA Transcript Labeling Washing and Staining Protocol          Post Hyb wash #1 - 10 cycles of 2 mixes/ cycle with wash buffer A at 25C - non-stringent (6xSSPE, 0.01% Tween 20)          Post Hyb wash #2 - 4 cycles of 15 mixes/ cycle with wash buffer B at 50C - stringent   (100mM MES, 0.1M [Na+], 0.01% Tween 20)          1st Stain                 - 10 min. at 25C  (SAPE Stain: 300ul 2x MES stain buffer {41.7ml 12x MES,  92.5ml 5M NaCl, 2.5ml 10% Tween 20/ 250ml total vol. in DEPC H2O},                                             24ul 50mg/ml acetylated BSA, 6ul 1mg/ml Streptavidin-R-Phycoerythrin  conjugate, 270ul DEPC H2O, 600ul total vol.)          Post Stain Wash     - 10 cycles of 4 mixes/cycle with wash buffer A at 25C          2nd Stain                 - 10 min. at 25C   (Antibody Stain: 300ul 2x MES stain buffer {see above},              	  24ul 50 mg/ml acetylated BSA, 6ul 10mg/ml normal goat IgG,                                              3.6ul 0.5mg/ml biotinylated anti-streptavidine antibody, 266.4ul DEPC H2O,   600ul total vol.)          3rd Stain                  - 10 min at 25C   (SAPE stain: see above, 600ul total vol.)          Final Wash              - 15 cycles of 4 mixes/cycle with wash buffer A at 30C. The GeneChip remains   filled with wash buffer A for the scanning procedure. GeneChip Expression 3’-Amplification IVT Labeling Washing and Staining Protocol Post Hyb wash #1 - 10 cycles of  2 mixes/ cycle with wash buffer A at 30ºC - non-stringent (6xSSPE, 0.01% Tween 20)          Post Hyb wash #2 - 6 cycles of 15 mixes/ cycle with wash buffer B at 50ºC - stringent   (100mM MES, 0.1M [Na+], 0.01% Tween 20)          1st Stain                 - 5 min. at 30ºC  (SAPE Stain: 300ul 2x MES stain buffer {41.7ml 12x MES,  92.5ml 5M NaCl, 2.5ml 10% Tween 20/ 250ml total vol. in DEPC H2O},                                             24ul 50mg/ml acetylated BSA, 6ul 1mg/ml Streptavidin-R-Phycoerythrin  conjugate, 270ul DEPC H2O, 600ul total vol.)          Post Stain Wash     - 10 cycles of 4 mixes/cycle with wash buffer A at 30ºC          2nd Stain                 - 5 min. at 35ºC   (Antibody Stain: 300ul 2x MES stain buffer {see above},              	  24ul 50 mg/ml acetylated BSA, 6ul 10mg/ml normal goat IgG,                                              3.6ul 0.5mg/ml biotinylated anti-streptavidine antibody, 266.4ul DEPC H2O,   600ul total vol.)          3rd Stain                  - 5 min at 35ºC   (SAPE stain: see above, 600ul total vol.)          Final Wash              - 15 cycles of 4 mixes/cycle with wash buffer A at 35ºC. The GeneChip remains   filled with wash buffer A for the scanning procedure.

scan_protocol: Scanning: Automated process conducted using the Agilent GeneArray Scanner.         - 2x scans are conducted for the Enzo protocol and 1x scans are conducted for the GeneChip Expression protocol as follows:                       Pixel value = 3um                       Wavelength = 570nm

data_processing: Data was generated and calculated in GCOS1.2

label: Affymetrix Small Sample Labeling Protocol vII (2xIVT)

source_name: Fresh Reissner's Membrane (unincubated)

label_protocol:
First Cycle of Amplification
Step 1. First cycle, first strand cDNA synthesis
Note:  Use thermal cycler with a heated lid for incubations in this step. Use the 4C hold for the addition of reagents.  70C	6 minutes
	  4C	hold
	  42C	60 minutes
	  70C	10 minutes
	  4C	hold
a.	Mix 1ul of total RNA (50ng/ul) with 1ul of 5uM T7(dT)24 in 0.2ul PCR tube and incubate at 70C in thermal cycler with heated lid for 6 min.
(5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’)
b.	Cool to 4C for 2 min.
c.	Spin briefly.
d.	Add 3ul of RT-Premix-1 master mix using the following components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
1 rxn
	DEPC treated water			0.375ul
	5x first strand buffer			1ul
	DTT, 0.1M				0.5ul
	dNTP mix, 10mM			0.375ul
	Rnase inhibitor, 40 U/ul		0.25ul
	SuperScript II, 200 U/ul		0.5ul
	Total Volume			3ul
e.	Incubated at 42C 60 minutes.
f.	Heat sample at 70C for 10 minutes to inactivate SuperScript II.
g.	Spin briefly and cool sample to 4C.
Step 2. First cycle, second strand cDNA synthesis
Note:  Use thermal cycler without heated lid for incubations in this step. Use 4C hold for the addition of reagents.
16C	120 minutes
4C	hold
16C	10 minutes
4C	hold
a	Prepare the SS-Premix-1 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
					1 rxn
	DEPC treated water		22.75ul
	5x second strand buffer		7.5ul
	dNTP mix, 10mM		0.75ul
	DNA ligase, E. coli, 10U/ul	0.25ul
	DNA polymerase I, E. coli 10U/ul	1ul
	Rnase H, 2U/ul			0.25ul
	Total Volume			32.5ul
b.	Add 32.5ul of the SS-Premix-1 to each first strand reaction making a final volume of 37.5ul.
c.	Mix by pipetting and spin briefly.
d.	Incubate the samples at 16C for 2 hours.
e.	Add 1ul of T4 DNA polymerase (5U/ul) to the reaction and mix by pipetting.
f.	Continue incubation at 16C for 10 minutes.
Step 3. First cycle, double-stranded cDNA cleanup by ethanol precipitation.
a.	Transfer the reaction to a 1.5 ml centrifuge tube.
b.	Add 80ul of DEPC treated water to dilute reaction.
c.	Add 2ul of glycogen (5 mg/ml), 0.6 volumes (72ul) of 5M NH4OAc, and 2.5 volumes (480ul) of cold absolute ethanol. Mix by pipetting.
d.	Precipitate the double-stranded cDNA at -20C for 2 hours.
e.	Centrifuge at 14,000rpm for 20 minutes at 4C.
f.	Wash pellet with 800ul of 70% cold ethanol.
g.	Centrifuge at 14,000rpm for 5 minutes at 4C.
h.	Remove ethanol and dry pellet in speed vacuum for 10 minutes.
Step 4.  First cycle, IVT for cRNA amplification using MEGAscript T7 kit (Ambion).
a.	At room temperature, add the following reagents to the dried double-stranded cDNA pellet, in the order indicated.

						1rxn
DEPC treated water		4ul
Premixed NTPs, 18.75mM each	4ul
10x reaction buffer		1ul
10x enzyme mix			1ul
Total Volume			10ul
b.	Mix well by pipetting. Spin briefly.
c.	Incubate at 37C for 5 hours mixing every 30 minutes.
Step 5.  First cycle, cRNA cleanup with Qiagen RNeasy columns.
a.	Add 90ul of Rnase-free water to sample.
b.	Follow the RNeasy Mini Protocol for RNA Cleanup as directed in the RNeasy Mini Kit handbook.
c.	In the last step of the purification, elute the cRNA sample with 30ul of Rnase-free water first, and follow with an additional 20ul of water for the second elution.
d.	Determine the cRNA yield by conducting a 1/10 dilution in water and measuring the absorbance at 260nm.
e.	Transfer 400ng of cRNA to a new 1.5ml tube and use speed vacuum to concentrate sample to 4ul. Avoid drying the sample completely.  Note: If the yield is less that 400ng, use the entire sample for the second cycle of cDNA synthesis.
Second Cycle of Amplification and Labeling
Step 6.  Second cycle, first strand cDNA synthesis.
Note: Use heating blocks for incubation in this step.
a.	Add random primers to the cRNA sample and mix well.
cRNA, 400ng			4ul
Random primers, 0.2 ug/ul		1ul
Total Volume			5ul
b.	Incubate at 70C for 10 minutes to denature cRNA.
c.	Cool sample on ice for 2 minutes.
d.	Prepare the RT-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least two reactions to avoid pipetting small volumes.

					1rxn
5x first strand buffer			2ul
DTT, 0.1M				1ul
dNTP mix, 10mM			0.5ul
RNase Inhibitor, 40 U/ul			0.5ul
SuperScript II, 200 U/ul			1ul
Total Volume				5ul
e.	Add 5ul of the RT-Premix-2 to the denatured RNA and primer mixture, making a final volume 10ul. Mix well by pipetting. Spin briefly.
f.	Incubate the sample at 42C for 1 hour. Spin briefly.
g.	To remove the RNA template, add 1ul of RNase H (2 U/ul) and incubate the sample at 37C for 20 minutes.
h.	Heat the sample at 95C for 5 minutes to inactivate RNase H.
i.	Cool sample on ice 2 minutes. Spin briefly.
Step 7.  Second cycle, second strand cDNA synthesis
Note:  Transfer sample to a 0.2 ml PCR tube and perform the incubations in a thermal cycler without a heated lid. Use the 4C hold to add reagents.
70C		6 minutes
4C		hold
16C		120 minutes
4C		hold
16C		10 minutes
4C		hold
a.	Add 2.0ul of the 5uM T7(dT)24 promoter primer to the chilled sample from the previous step.
b.	Mix well. Spin briefly.
c.	Incubate sample at 70C for 6 minutes.
d.	Cool the sample to 4C and spin briefly.
e.	Prepare the SS-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen).
					1rxn
DEPC treated water			43.5ul
5x second strand buffer			15ul
dNTP mix, 10mM			1.5ul
DNA polymerase I, E. coli, 10 U/ul		2ul
Total Volume				62ul
f.	Add 62ul of the SS-Premix-2 to the sample making a total volume of 75ul. Mix well by pipetting. Spin briefly.
g.	Incubate at 16C for 2 hours.
h.	Add 2ul of T4 DNA polymerase (5 U/ul) to the reaction. Mix well.
i.	Incubate at 16C for 10 minutes.
Step 8.  Second cycle, double-strand cDNA cleanup by ethanol precipitation.
a.	Add 2ul of 5 mg/ml glycogen, 0.6 volume 5M NH4OAc, and 2.5 volumes of cold absolute ethanol.
b.	Mix well by pipetting.
c.	Precipitate the double-stranded cDNA at -20C for 30 minutes.
d.	Centrifuge the sample at 14,000 rpm for 20 minutes at 4C.
e.	Carefully remove supernatant and wash the cDNA pellet by adding 800ul of 70% cold ethanol.
f.	Centrifuge the tube at 14,000 rpm for 5 minutes at 4C.
g.	Carefully remove the ethanol. Dry pellet in a speed vacuum for 10 minutes.
h.	Store dry pellet at –20C or proceed to next step.
Step 9.  Second cycle, IVT for cRNA amplification and labeling with ENZO BioArray High Yield RNA Transcription
              Labeling Kit  (Affymetrix)  or GeneChip Expression 3’-Amplification IVT Labeling kit (Affymetrix).
a.	At room temperature, add the following reagents to the dried double-stranded cDNA pellet.
Enzo BioArray High Yield RNA Transcription Labeling kit
					1rxn
DEPC treated water		22ul
10X HY reaction buffer		4ul
10X Biotin labeled ribonucleotides	4ul
10X DTT			4ul
10X RNase inhibitor mix		4ul
20X T7 RNA polymerase		2ul
Total Volume			40ul
1. Mix the components well after adding each reagent; especially after adding water, ensuring the cDNA
    pellet is completely dissolved.
	2. Incubate at 37C for 5 hours mixing every 30 minutes.
GeneChip Expression 3’-Amplification IVT Labeling Kit
					1rxn
	DEPC treated water		20ul
	10x IVT Labeling Buffer		  4ul
	IVT Labeling NTP Mix		12ul
	IVT Labeling Enzyme Mix	  4ul
	Total Volume			40ul
	1. Mix components well after adding each reagent, especially after adding water, ensuring the cDNA pellet
	    is completely dissolved.
	2. Incubate at 37ºC for 16 hours in a hybridization oven or thermal cycler with a heated lid to prevent
	    condensation.
Step 10. Second cycle, labeled cRNA target cleanup with Qia

growth_protocol: Native tissue; no proliferation in organ culture

extract_protocol: RNA was extracted using a RNeasy Microkit following the manufacturer's protocol (no. 74004, Qiagen; Valencia, CA)

treatment_protocol: Reissner's Membrane explants unincubated

tag: Tissue

value: Reissner's Membrane

tag: Animal

value: Mouse

tag: Age

value: adult


title: CCD-18Co CONTROL (contains only the mixture of enzymes + salts)_24h_biological rep3


title: CCD-18Co TREATED (digested orange extract, 60 μM total flavanones)_24h_biological rep1

value: pre-digested orange extract containing a mixture of flavanones


title: KSUAP-DM mReissners Membrane I24hrB

source_name: Reissner's Membrane incubated for 24 hours

treatment_protocol: Reissner's Membrane explants incubated for 24 hours


title: CCD-18Co CONTROL (contains only the mixture of enzymes + salts)_24h_biological rep1


title: CCD-18Co TREATED (digested orange extract, 60 μM total flavanones)_24h_biological rep3


title: KSUAP-DM mReissners Membrane Dex24hrB

source_name: Reissner's Membrane treated with Dex for 24 hours

treatment_protocol: Reissner's Membrane explants treated with Dexamethasone (100mM) for 24 hours

value: adule


title: KSUAP-DM mReissners Membrane I24hrC

source_name: Reissner's membrane incubated for 24 hours


title: KSUAP-DM mReissners Membrane I24hrA


title: KSUAP-DM mReissners Membrane F0hrA


title: KSUAP-DM mReissners Membrane Dex24hrA

description:
- Absolute and comparison analysis are conducted using the following settings:
      Scaling - All Probe Sets: Target Signal = 500
      Normalization – User Defined: Scale Factor = 1

label_protocol:
Affymetrix Small Sample Labeling Protocol vII (2xIVT)
First Cycle of Amplification
Step 1. First cycle, first strand cDNA synthesis
Note:  Use thermal cycler with a heated lid for incubations in this step. Use the 4C hold for the addition of reagents.  70C	6 minutes
	  4C	hold
	  42C	60 minutes
	  70C	10 minutes
	  4C	hold
a.	Mix 1ul of total RNA (50ng/ul) with 1ul of 5uM T7(dT)24 in 0.2ul PCR tube and incubate at 70C in thermal cycler with heated lid for 6 min.
(5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’)
b.	Cool to 4C for 2 min.
c.	Spin briefly.
d.	Add 3ul of RT-Premix-1 master mix using the following components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
1 rxn
	DEPC treated water			0.375ul
	5x first strand buffer			1ul
	DTT, 0.1M				0.5ul
	dNTP mix, 10mM			0.375ul
	Rnase inhibitor, 40 U/ul		0.25ul
	SuperScript II, 200 U/ul		0.5ul
	Total Volume			3ul
e.	Incubated at 42C 60 minutes.
f.	Heat sample at 70C for 10 minutes to inactivate SuperScript II.
g.	Spin briefly and cool sample to 4C.
Step 2. First cycle, second strand cDNA synthesis
Note:  Use thermal cycler without heated lid for incubations in this step. Use 4C hold for the addition of reagents.
16C	120 minutes
4C	hold
16C	10 minutes
4C	hold
a	Prepare the SS-Premix-1 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
					1 rxn
	DEPC treated water		22.75ul
	5x second strand buffer		7.5ul
	dNTP mix, 10mM		0.75ul
	DNA ligase, E. coli, 10U/ul	0.25ul
	DNA polymerase I, E. coli 10U/ul	1ul
	Rnase H, 2U/ul			0.25ul
	Total Volume			32.5ul
b.	Add 32.5ul of the SS-Premix-1 to each first strand reaction making a final volume of 37.5ul.
c.	Mix by pipetting and spin briefly.
d.	Incubate the samples at 16C for 2 hours.
e.	Add 1ul of T4 DNA polymerase (5U/ul) to the reaction and mix by pipetting.
f.	Continue incubation at 16C for 10 minutes.
Step 3. First cycle, double-stranded cDNA cleanup by ethanol precipitation.
a.	Transfer the reaction to a 1.5 ml centrifuge tube.
b.	Add 80ul of DEPC treated water to dilute reaction.
c.	Add 2ul of glycogen (5 mg/ml), 0.6 volumes (72ul) of 5M NH4OAc, and 2.5 volumes (480ul) of cold absolute ethanol. Mix by pipetting.
d.	Precipitate the double-stranded cDNA at -20C for 2 hours.
e.	Centrifuge at 14,000rpm for 20 minutes at 4C.
f.	Wash pellet with 800ul of 70% cold ethanol.
g.	Centrifuge at 14,000rpm for 5 minutes at 4C.
h.	Remove ethanol and dry pellet in speed vacuum for 10 minutes.
Step 4.  First cycle, IVT for cRNA amplification using MEGAscript T7 kit (Ambion).
a.	At room temperature, add the following reagents to the dried double-stranded cDNA pellet, in the order indicated.

						1rxn
DEPC treated water		4ul
Premixed NTPs, 18.75mM each	4ul
10x reaction buffer		1ul
10x enzyme mix			1ul
Total Volume			10ul
b.	Mix well by pipetting. Spin briefly.
c.	Incubate at 37C for 5 hours mixing every 30 minutes.
Step 5.  First cycle, cRNA cleanup with Qiagen RNeasy columns.
a.	Add 90ul of Rnase-free water to sample.
b.	Follow the RNeasy Mini Protocol for RNA Cleanup as directed in the RNeasy Mini Kit handbook.
c.	In the last step of the purification, elute the cRNA sample with 30ul of Rnase-free water first, and follow with an additional 20ul of water for the second elution.
d.	Determine the cRNA yield by conducting a 1/10 dilution in water and measuring the absorbance at 260nm.
e.	Transfer 400ng of cRNA to a new 1.5ml tube and use speed vacuum to concentrate sample to 4ul. Avoid drying the sample completely.  Note: If the yield is less that 400ng, use the entire sample for the second cycle of cDNA synthesis.
Second Cycle of Amplification and Labeling
Step 6.  Second cycle, first strand cDNA synthesis.
Note: Use heating blocks for incubation in this step.
a.	Add random primers to the cRNA sample and mix well.
cRNA, 400ng			4ul
Random primers, 0.2 ug/ul		1ul
Total Volume			5ul
b.	Incubate at 70C for 10 minutes to denature cRNA.
c.	Cool sample on ice for 2 minutes.
d.	Prepare the RT-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least two reactions to avoid pipetting small volumes.

					1rxn
5x first strand buffer			2ul
DTT, 0.1M				1ul
dNTP mix, 10mM			0.5ul
RNase Inhibitor, 40 U/ul			0.5ul
SuperScript II, 200 U/ul			1ul
Total Volume				5ul
e.	Add 5ul of the RT-Premix-2 to the denatured RNA and primer mixture, making a final volume 10ul. Mix well by pipetting. Spin briefly.
f.	Incubate the sample at 42C for 1 hour. Spin briefly.
g.	To remove the RNA template, add 1ul of RNase H (2 U/ul) and incubate the sample at 37C for 20 minutes.
h.	Heat the sample at 95C for 5 minutes to inactivate RNase H.
i.	Cool sample on ice 2 minutes. Spin briefly.
Step 7.  Second cycle, second strand cDNA synthesis
Note:  Transfer sample to a 0.2 ml PCR tube and perform the incubations in a thermal cycler without a heated lid. Use the 4C hold to add reagents.
70C		6 minutes
4C		hold
16C		120 minutes
4C		hold
16C		10 minutes
4C		hold
a.	Add 2.0ul of the 5uM T7(dT)24 promoter primer to the chilled sample from the previous step.
b.	Mix well. Spin briefly.
c.	Incubate sample at 70C for 6 minutes.
d.	Cool the sample to 4C and spin briefly.
e.	Prepare the SS-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen).
					1rxn
DEPC treated water			43.5ul
5x second strand buffer			15ul
dNTP mix, 10mM			1.5ul
DNA polymerase I, E. coli, 10 U/ul		2ul
Total Volume				62ul
f.	Add 62ul of the SS-Premix-2 to the sample making a total volume of 75ul. Mix well by pipetting. Spin briefly.
g.	Incubate at 16C for 2 hours.
h.	Add 2ul of T4 DNA polymerase (5 U/ul) to the reaction. Mix well.
i.	Incubate at 16C for 10 minutes.
Step 8.  Second cycle, double-strand cDNA cleanup by ethanol precipitation.
a.	Add 2ul of 5 mg/ml glycogen, 0.6 volume 5M NH4OAc, and 2.5 volumes of cold absolute ethanol.
b.	Mix well by pipetting.
c.	Precipitate the double-stranded cDNA at -20C for 30 minutes.
d.	Centrifuge the sample at 14,000 rpm for 20 minutes at 4C.
e.	Carefully remove supernatant and wash the cDNA pellet by adding 800ul of 70% cold ethanol.
f.	Centrifuge the tube at 14,000 rpm for 5 minutes at 4C.
g.	Carefully remove the ethanol. Dry pellet in a speed vacuum for 10 minutes.
h.	Store dry pellet at –20C or proceed to next step.
Step 9.  Second cycle, IVT for cRNA amplification and labeling with ENZO BioArray High Yield RNA Transcription
              Labeling Kit  (Affymetrix)  or GeneChip Expression 3’-Amplification IVT Labeling kit (Affymetrix).
a.	At room temperature, add the following reagents to the dried double-stranded cDNA pellet.
Enzo BioArray High Yield RNA Transcription Labeling kit
					1rxn
DEPC treated water		22ul
10X HY reaction buffer		4ul
10X Biotin labeled ribonucleotides	4ul
10X DTT			4ul
10X RNase inhibitor mix		4ul
20X T7 RNA polymerase		2ul
Total Volume			40ul
1. Mix the components well after adding each reagent; especially after adding water, ensuring the cDNA
    pellet is completely dissolved.
	2. Incubate at 37C for 5 hours mixing every 30 minutes.
GeneChip Expression 3’-Amplification IVT Labeling Kit
					1rxn
	DEPC treated water		20ul
	10x IVT Labeling Buffer		  4ul
	IVT Labeling NTP Mix		12ul
	IVT Labeling Enzyme Mix	  4ul
	Total Volume			40ul
	1. Mix components well after adding each reagent, especially after adding water, ensuring the cDNA pellet
	    is completely dissolved.
	2. Incubate at 37ºC for 16 hours in a hybridization oven or thermal cycler with a heated lid to prevent
	    condensation.
Step

growth_protocol: Native tissue; no proliferation in organ culture.

extract_protocol: RNA was extracted using a RNeasy Micro Kit following the manufacturer's protocol (no.74004, Qiagen; Valencia, CA)

treatment_protocol: Reissner's Membrane explants treated with Dexamethasone (100 nM) for 24 hours


title: npr1-3_MOCK_48h_rep2

status: Public on Mar 20 2009

city: Riverside

first: Thomas

last: Eulgem

state: CA

address: University of California, Department of Botany and Plant Sciences

department: Botany and Plant Sciences

institute: University of California

description: The goal of this project was a comparative analysis of defense responses triggered by the synthetic elicitors 3,5-Dichloroanthranilic acid (DCA) or 2,6-Dichloroisonicotinic acid (INA) in Arabidopsis thaliana.

hyb_protocol: RNA was processed and hybridized to Affymetrix Arabidopsis ATH1 genome array GeneChip following manufacturer’s instructions (Affymetrix) by the University of California, Riverside Core Instrument Facility.  Three independent biological replicates were performed for each treatment.

data_processing: The data files were generated using the Affymetrix GCOS package.

organism: Arabidopsis thaliana

source_name: whole aerial tissue of Arabidopsis npr1-3 seedlings 48h after mock treatment

growth_protocol: Arabidopsis thaliana plants (accession Col-0) were grown on soil in a semi-sterile growth chamber under fluorescent lights (14 hours light, 10 hours dark, 21oC, 100 Einstein/m2/s). Wild type Col-0 plants and the npr1-3 mutant were used in this study.

extract_protocol: Total RNA was isolated from seedlings using TRIZOL (Invitrogen) follwing the manufacturer’s instructions.

treatment_protocol: Arabidopsis thaliana plants (accession Col-0) were grown on soil in a semi-sterile growth chamber under fluorescent lights (14 hours light, 10 hours dark, 21 centi grades, 100 Einstein/m2/s). Wild type Col-0 plants and the npr1-3 mutant were used in this study. Aerial tissues of 2 week old soil grown Arabidopsis seedlings were sprayed with 100uM 3,5-Dichloroanthranilic acid (DCA), or 100uM 2,6-Dichloroisonicotinic acid (INA) or mock solution and harvested 48h or 6 days after the treatment. Final DMSO concentrations never exceeded 0.002%.  Mock treatments were application of 0.002% DMSO in water. For harvesting the arial plant parts were shock-frozen in liquid nitrogen.

tag: aerial tissues of 2 week old soil grown wild type Arabidopsis seedlings (accession Col-0) weretreated  with 100uM 3,5-Dichloroanthranilic acid (DCA), or 100uM 2,6-Dichloroisonicotinic acid (INA) or mock solution and harvested 48h or 6 days after the treatment.


title: npr1-3_DCA_48h_rep3

scan_protocol: RNA was processed and hybridized to Affymetrix Arabidopsis ATH1 genome array GeneChip following manufacturer’s instructions (Affymetrix) by the University of California, Riverside Core Instrument Facility.  Three independent biological replicates were performed for each treatment.

source_name: whole aerial tissue of Arabidopsis npr1-3 seedlings 48h after DCA treatment


title: npr1-3_DCA_48h_rep1

label_protocol: RNA was processed and hybridized to Affymetrix Arabidopsis ATH1 genome array GeneChip following manufacturer’s instructions (Affymetrix) by the University of California, Riverside Core Instrument Facility.  Three independent biological replicates were performed for each treatment.


title: npr1-3_DCA_48h_rep2


title: npr1-3_MOCK_48h_rep1


title: Col-0_MOCK_48h_rep3

source_name: whole aerial tissue of Arabidopsis seedlings 48h after mock treatment


title: Col-0_MOCK_48h_rep1


title: Col-0_MOCK_48h_rep2


title: Col-0_INA_6d_rep2

source_name: whole aerial tissue of Arabidopsis seedlings 6d after INA


title: Col-0_INA_48h_rep3

source_name: whole aerial tissue of Arabidopsis seedlings 48h after INA treatment


title: npr1-3_MOCK_48h_rep3


title: Col-0_DCA_48h_rep1

source_name: whole aerial tissue of Arabidopsis seedlings 48h after DCA treatment


title: Col-0_INA_6d_rep3


title: Col-0_MOCK_6d_rep3

source_name: whole aerial tissue of Arabidopsis seedlings 6d after mock treatment


title: Col-0_MOCK_6d_rep1


title: Col-0_DCA_48h_rep3


title: Col-0_INA_48h_rep1


title: Col-0_INA_6d_rep1


title: Col-0_MOCK_6d_rep2


title: KSUAP-DM mReissners Membrane Dex24hrC


title: Col-0_DCA_48h_rep2


title: Col-0_DCA_6d_rep2

source_name: whole aerial tissue of Arabidopsis seedlings 6d after DCA

tag: aerial tissues of 2 week old soil grown wild type Arabidopsis seedlings (accession Col-0) weretreated  with 100uM 3,5-Dichloroanthranilic acid (DCA), or 100uM 2,6-Dichloroisonicotinic acid (INA) or mock solution and harvested 48h or 6 days after the treatment


title: Col-0_DCA_6d_rep3


title: Granulosa cells from ERK1/2 conditional KO ovary, eCG-treated 48h, hCG 4h

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

description: gene expression data

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using Affy package from Bioconductor with RMA method.

source_name: Granulosa cells, ERK1/2 conditional KO ovary, hCG 4h

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

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA).

tag: tissue

value: ovarian granulosa cells

tag: genotype

value: ERK1 knockout and ERK2 fl/fl;Cyp19CRE

tag: age

value: 23 days


title: Granulosa cells from wild type ovary, eCG-treated 48h, hCG 2.5h

description: gene expression data

source_name: Granulosa cells, wild type ovary, hCG 2.5h

value: wild type


title: Granulosa cells from wild type ovary, eCG-treated 48h, no hCG

description: gene expression data

source_name: Granulosa cells, wild type ovary, no hCG


title: 3F-serumfree iPS cell line S53C5

status: Public on Mar 18 2009

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G

data_processing: The data were analyzed with Robust Multichip Average（RMA) using ArrayAssist 5.5.1 (stratagene Co., Ltd).

source_name: induced pluripotent stem cell lines with Oct4/Sox2/Klf4 in gradual replacement strategy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cells were cultured in described medium at 37 ℃ with 5% CO2

treatment_protocol: Cells were cultured for 3-6 days to allowed them get a 90% consistency and then trypsinized with 0.05%Trypsin/EDTA. The cells were washed by PBS and then placed on ice in TRIZOL solution.

tag: strain

value: induced from MEF


title: Granulosa cells from wild type ovary, eCG-treated 48h, hCG 4h

description: gene expression data

source_name: Granulosa cells, wild type ovary, hCG 4h


title: Col-0_DCA_6d_rep1

tag: Aerial tissues of 2 week old soil grown wild type Arabidopsis seedlings (accession Col-0) were treated with 100uM 3,5-Dichloroanthranilic acid (DCA), or 100uM 2,6-Dichloroisonicotinic acid (INA) or mock solution and harvested 48h or 6 days after the treatment.


title: Granulosa cells from ERK1/2 conditional KO ovary, eCG-treated 48h, no hCG

description: gene expression data

source_name: Granulosa cells, ERK1/2 conditional KO ovary, no hCG


title: Normal_testis_cell_line_rep_2

city: Bethesda

first: Hoi Hung

last: Cheung

address: 49 Convent Dr, Rm.2C08 Bldg.49

institute: NICHD

description: Expression data was coupled with the differential methylation analysis by tiling arrays.

hyb_protocol: Standard Affymetrix Hybridization protocol

scan_protocol: Arrays were scanned with GeneChip Scanner GCS3000 (7G)

data_processing: Triplicate sets of hybridization were performed for cancer and normal cells. Raw data were normalized (CHP files) and analyzed in Partek Genomics Suite Software. Differential gene expression was evaluated using one-way ANOVA.

source_name: Cultured normal testis cell line (CRL-7002)

label_protocol: 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using GeneChip 3' IVT Expression Kit (Affymetrix) according to Affymetrix's protocol

extract_protocol: Total RNA was extracted from 90% confluent cells using Trizol Reagent. RNA was precipitated by isopropanol and resuspended in DEPC water. Total RNA was treated by DNaseI and purified by PureLink RNA Mini Kit (Invitrogen). RNA integrity and concentration was detected by BioAnalyzer (Agilent).

tag: gender

value: Male

value: testis


title: Col-0_INA_48h_rep2


title: Testicular_cancer_cell_line_rep_3

source_name: Cultured testicular cancer cell line (Ntera2)


title: 4F-serumfree iPS cell line S2C16

source_name: induced pluripotent stem cell lines with Oct4/Sox2/Klf4/c-Myc in gradual replacement strategy


title: MEF cultured in serum medium

source_name: mouse embryonic fibroblast cells cultured in serum-containing medium

value: d.p.c 13.5 embryo


title: Granulosa cells from ERK1/2 conditional KO ovary, eCG-treated 48h, hCG 2.5h

description: gene expression data

source_name: Granulosa cells, ERK1/2 conditional KO ovary, hCG 2.5h


title: embryonic stem cell line R1

source_name: embryonic stem cell line R1

value: d.p.c 3.5 embryo


title: 4F-serumfree iPS cell line S2C12


title: Normal_testis_cell_line_rep_3


title: MEF cultured in serum-free medium

source_name: mouse embryonic fibroblast cells cultured in serum-free medium


title: ES_HoxB4_on

city: Tokyo

first: Hideo

last: Ema

address: 4-6-1 Shirokanedai, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

description: co-culture with OP9 cells in the presence of  HOXB4

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GCOS was used with target intensity=100.

source_name: ES cell

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

value: HoxB4 on


title: 3F-serumfree iPS cell line S53C1


title: embryonic stem cell line CGR8

source_name: embryonic stem cell line CGR8


title: Testicular_cancer_cell_line_rep_2


title: EB6

description: ES cell differentiated into Embryonal body

value: ES cell control


title: Normal_testis_cell_line_rep_1


title: Testicular_cancer_cell_line_rep_1


title: Rex KO_plus LIF_rep4

status: Public on Mar 17 2009

city: New York

first: Kymora

last: Scotland

state: NY

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medical College

description: The differential expression of putative Rex-1 target genes in wild type vs. Rex-1-/- ES cells was examined according to the Affymetrix microchip array protocol (Affymetrix, Santa Clara, CA).

hyb_protocol: This mixture was hybridized to Mouse 430 2.0 microarray chips (cat# 900495, Affymetrix, San Diego, CA) for 16 h at 37 °C.  The hybridized microarray chips were washed and stained in a Fluidics station in the Microarray Core facility of the Weill Medical College of Cornell University.

scan_protocol: Scanning of the chips was performed by the microarray core facility at Weil Cornell Medical College.

data_processing: data from the chips were recorded as .cel files. Normalizaton was performed using the GC-RMA method.

source_name: J1 mouse embryonic stem cell

label_protocol: cRNA was prepared by in vitro transcription of double strand cDNA with biotinylated ribonucleotides (Enzo Diagnostics, Farmingdale, NY). The cRNA was then fragmented by heating at 95 °C for 35 min and mixed with control oligonucleotide, control cRNA (composed of biotin B, biotin C, biotin D, and Cre), and herring sperm DNA.

growth_protocol: J1 mouse ES cells were cultured in monolayer on gelatin-coated dishes containing ES medium (Dulbecco's Modified Eagle's Medium supplemented with 10% ES cell qualified fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM glutamine, 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 100 µM MEM nonessential amino acids, and 0.1 mM ß-mercaptoethanol). 1 x 103 units/ml of leukemia inhibitory factor (LIF, Esgro, Invitrogen) were added prior to use to maintain undifferentiated ES cell growth.

extract_protocol: Wild-type and Rex-1-/- ES cells were cultured for 12 hours in the absence of LIF, and total RNA was extracted using TRIzol (Invitrogen) as indicated by the manufacturer.

treatment_protocol: Cells were cultured in ES media in the presence of LIF

tag: Strain

value: J1 Cell type:mouse embryonic stem cell


title: ES_HoxB4_off

description: co-culture with OP9 cells in the absence of  HOXB4

value: HoxB4 off


title: Rex KO_minus LIF_rep3r

treatment_protocol: Cells were cultured in ES media in the absence of LIF


title: J1_plus LIF_rep2r

value: J1 Cell type:mouse embryonic stem culture


title: J1_plus LIF_rep2


title: J1_minus LIF_rep1r

growth_protocol: J1 mouse ES cells were cultured in monolayer on gelatin-coated dishes containing ES medium (Dulbecco's Modified Eagle's Medium supplemented with 10% ES cell qualified fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM glutamine, 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 100 µM MEM nonessential amino acids, and 0.1 mM ß-mercaptoethanol).

tag: Strain:J1 Cell type

value: mouse embryonic stem cell


title: Logjam HT_1

status: Public on Mar 16 2009

city: College Station

first: Ginger

middle: E.

last: Carney

address: 3258 TAMU

department: Biology

institute: Texas A&M University

description: Abdomen or Head/thorax tissue samples from females of the following genotypes: loj 00898/loj 04026, loj 00898/+, and loj 04026/+

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing:
Data were analyzed 3 different ways:
VALUE [dCHIP_PMMM]: All 6 chips were analyzed simultaneously in dCHIP, which uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-MM procedure under default parameters.
VALUE2 [dCHIP_PMonly]: All 6 chips were analyzed simultaneously in dCHIP, which uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM_only procedure under default parameters.
VALUE3 [GCOS]: Expression values were computed using the recommended settings in GCOS version 1.2. All probesets were scaled using a TGT value of 500, and no normalization was applied (i.e., the normalization factor was 1.0).

organism: Drosophila melanogaster

source_name: Logjam mutant, Head/thorax, 1

label_protocol: Standard Affymetrix

growth_protocol: Drosophila melanogaster stocks and cross progeny were maintained at 25ºC on a 12h light-dark cycle using a standard cornmeal, sugar, agar and yeast culture medium.

extract_protocol: Standard Trizol (Invitrogen) extraction.  Only females that mated within 30 min for 18-30 min were collected for subsequent RNA extractions. Female abdomens were dissected away from the head/thorax 3 hours after the end of the mating period and each of the two tissue types (abdomen or head with thorax) was quick-frozen in Trizol reagent (Invitrogen). Total RNA from abdomen or head/thorax tissue was extracted in Trizol using the manufacturer's protocol. Twelve female tissue samples were collected for each of 6 independent RNA extractions for loj 00898/loj 04026. Our control samples consisted of 6 loj 00898/+ and 6 loj 04026/+ samples combined together for each of 6 independent RNA extractions.

treatment_protocol: Females of the genotypes loj 00898/loj 04026, loj 00898/+, and loj 04026/+ were collected as virgins within 1-2 h of the beginning of the 12h lighted portion of the cycle, kept in glass vials in groups of 20 or fewer flies, and aspirated singly into new vials on day 3 after collection. On day 4, a single wild-type male was aspirated into a vial containing a single female and observed for mating.

tag: genotype/variation

value: Logjam

value: head to thorax

tag: other

value: loj 00898/loj 04026 mutants and control samples containing equal numbers of loj 00898/+ and loj 04026/+

value: Female

value: 4 days


title: Control HT_2

source_name: Control, Head/thorax, 2

value: Control


title: J1_minus LIF_rep1

value: J1 Cell type:mouse embryonis stem cell


title: Logjam HT_2

source_name: Logjam mutant, Head/thorax, 2


title: Logjam Abd_3

source_name: Logjam mutant, Abdomen, 3

value: abdomen


title: Control HT_1

source_name: Control, Head/thorax, 1


title: Control HT_3

source_name: Control, Head/thorax, 3


title: Control Abd_1

source_name: Control, Abdomen, 1


title: Logjam Abd_1

source_name: Logjam mutant, Abdomen, 1


title: Logjam HT_3

source_name: Logjam mutant, Head/thorax, 3


title: wt_3

status: Public on Mar 15 2009

city: Melbourne

first: Francois-Xavier

last: Hubert

state: Victoria

address: 1G Royal Parade

department: Immunology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: Gene expression data from wild type mTECs, third biological replicate

hyb_protocol: 15 micro-grams of labelled RNA were then fragmented as described in the Affymetrix manual. The mouse genome 430 2.0 arrays were hybridised overnight and washed.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The intensities for each probe set were normalized and summarized using the Robust Multi-array Analysis (RMA) algorithm in the software programme R.

source_name: Wild type mTEC

label_protocol:
100ng of total RNA was amplified using T7-oligo dT and the Megascript T7 kit (Ambion). A second round of cDNA synthesis was performed using first round amplified RNA.
Amplified RNA was biotin-labelled using the GeneChip IVT Labelling Kit.

extract_protocol: RNA extraction was performed using the RNeasy Micro Kit (Qiagen) according to manufacturer's instructions.


title: Control Abd_2

source_name: Control, Abdomen, 2


title: Aireko_2

description: Gene expression data from Aire-deficient mTECs, second biological replicate

source_name: Aire-deficient mTEC


title: wt_1

description: Gene expression data from wild type mTECs, first biological replicate


title: Aireko_1

description: Gene expression data from Aire-deficient mTECs, first biological replicate


title: Logjam Abd_2

source_name: Logjam mutant, Abdomen, 2


title: Control Abd_3

source_name: Control, Abdomen, 3


title: wt_2

description: Gene expression data from wild type mTECs, second biological replicate


title: CD11b+ CD27-_NK cells_rep1

city: Marseille

first: Thierry

last: Walzer

address: Case 906, Campus de Luminy

institute: Centre d'Immunologie de Marseille-Luminy, INSERM U631

description: Comparison of mouse NK cell subsets defined by CD27 and CD11b expression

hyb_protocol: manufacturer instruction (affymetrix)

scan_protocol: manufacturer instruction (affymetrix)

data_processing: Normalized using the RMA algorithm with "R" software

label: manufacturer instruction (affymetrix)

source_name: Mouse spleen

label_protocol: manufacturer instruction (affymetrix)

extract_protocol: Qiagen RNeasy micro

treatment_protocol: Flow cytometry sorted (NK1.1+ CD27+ CD11b-)

tag: RAG-/- spleen flow cytometry sorted


title: Arabidopsis iron minus 24 h biological rep1

status: Public on Mar 13 2009

city: Taipei

first: Wolfgang

last: Schmidt

address: No. 128, Sec 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: gene expression data from arabidopsis roots under iron deficiency medium

hyb_protocol: Ten microgram labeled samples were hybridized to the ATH1 Genome Array at 45℃ for 16.5 h. Washing and staining involved Fluidic Station-450 and the ATH1 Genome.

scan_protocol: Array was scanned with use of the Affymetrix GeneChip Scanner 7G.

data_processing: The results were quantified and analyzed by use of MicroArray Suite 5.0 software (Affymetrix Inc.).

source_name: Arabidopsis plants in iron minus medium, 24 h

label_protocol: Ten microgram of total RNA was used for cDNA synthesis, labeled by in vitro transcription, followed by fragmentation according to the manufacturer's suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix)

extract_protocol: Total RNA was extracted with Qiagen RNeasy mini kit.

value: root


title: CD11b+ CD27+_NK cells_rep2

treatment_protocol: Flow cytometry sorted (NK1.1+ CD27+ CD11b+)

tag: RAG-/- spleen, flow cytometry sorted


title: Arabidopsis iron plus 1 h biological rep3

description: gene expression data from arabidopsis roots under iron efficiency medium

source_name: Arabidopsis plants in iron plus medium, 1 h


title: Arabidopsis iron plus 0 h biological rep3

source_name: Arabidopsis plants in iron plus medium, 0 h


title: Arabidopsis iron plus 0 h biological rep1


title: Arabidopsis iron plus 0 h biological rep2


title: Arabidopsis iron plus 1 h biological rep2


title: Arabidopsis iron minus 6 h biological rep2

source_name: Arabidopsis plants in iron minus medium, 6 h


title: Arabidopsis iron plus 24 h biological rep1

source_name: Arabidopsis plants in iron plus medium, 24 h


title: Arabidopsis iron minus 0 h biological rep2

source_name: Arabidopsis plants in iron minus medium, 0 h


title: Arabidopsis iron minus 0 h biological rep3


title: Arabidopsis iron plus 6 h biological rep2

source_name: Arabidopsis plants in iron plus medium, 6 h


title: Arabidopsis iron minus 6 h biological rep1


title: Arabidopsis iron minus 24 h biological rep2


title: Arabidopsis iron minus 6 h biological rep3


title: CD11b-_NK cells_rep1

source_name: mouse spleen

tag: RAG-/- mouse spleen, flow-cytometry sorted


title: CD11b+ CD27+_NK cells_rep1

tag: RAG-/- mouse spleen NK cells flow cytometry sorted


title: CD11b+ CD27-_NK cells_rep2

treatment_protocol: Flow cytometry sorted (NK1.1+ CD11b+ CD27-)


title: Rex KO_plus LIF_rep4r

source_name: J1 mouse embryonic stem cell


title: Arabidopsis iron minus 1 h biological rep3

source_name: Arabidopsis plants in iron minus medium, 1 h


title: Arabidopsis iron plus 6 h biological rep3


title: CD11b-_NK cells_rep2


title: Arabidopsis iron minus 1 h biological rep1


title: Arabidopsis iron plus 1 h biological rep1


title: Arabidopsis iron minus 0 h biological rep1


title: Arabidopsis iron plus 24 h biological rep2


title: Arabidopsis iron plus 6 h biological rep1


title: Arabidopsis iron minus 1 h biological rep2


title: GliNS2

city: Cambridge

first: Steven

middle: Michael

last: Pollard

state: Cambs

address: Tennis Court Road

department: Centre for Stem Cell Research

country: United Kingdom

institute: University of Cambridge

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The data was pre-processed using the vsnrma method from the Bioconductor package vsn.

source_name: Glioblastoma derived cell line

label_protocol: Cy3 cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Cells were grown in standard human foetal NS cell expansion media. As described in detail in the Supplemental Methods of Pollard S., et al. Cell Stem Cell, 2009.

treatment_protocol: Cells were grown to near 70-90% confluence, washed using PBS and then treated with Accutase for 5mins to detach cells. Cells were harvested by centrifugation and immediately processed.

value: brain

tag: condition

value: Proliferating cultures in EGF and FGF-2

tag: cell type

value: malignant

value: cell line

value: glioblastoma


title: Rex-1 KO_minus LIF_rep3

value: J1 Cell type:mouse embryonic stem cell


title: Laser capture microdissected (LCM) seed coat at the mature green stage, biological replicate 1

status: Public on Mar 12 2009

city: Davis

first: John

middle: J

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California, Davis

description: Seed coat collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined using the LEICA LMD6000 system for microdissection.

hyb_protocol: Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.

source_name: Arabidopsis mature green stage seed coat captured by LCM

label_protocol: 5 to 6 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.

extract_protocol: Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.

treatment_protocol: Siliques between 1.8-2.0 cm long containing mature green-stage seeds were collected from 38-46 day old plants. Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on sections using a Leica LMD6000 system.

tag: development stage

value: mature green stage

value: seed coat captured by LCM


title: Laser capture microdissected (LCM) seed coat at the mature green stage, biological replicate 2

tag: tissue


title: hf240-NS-C

source_name: human foetal cortex derived NS cell line

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

value: non-malignant

value: neural stem


title: hf240-NS-B


title: G179-NS_A

source_name: Oligoastrocytoma derived cell line

value: oligoastrocytoma


title: Laser capture microdissected (LCM) whole seeds at the mature green stage, biological replicate 1

description: Serial sections of whole seeds collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis mature green whole seeds captured by LCM

value: whole seeds captured by LCM

tag: genotype


title: NORM#12

source_name: Non-malignant human cortex sample

value: Primary biopsy

value: primary tissue

value: normal cortex


title: Laser capture microdissected (LCM) chalazal endosperm at the mature green stage, biological replicate 1

description: Chalazal endosperm collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis mature green stage chalazal endosperm captured by LCM

value: chalazal endosperm captured by LCM


title: Laser capture microdissected (LCM) chalazal endosperm at the mature green stage, biological replicate 2


title: hf289-NS


title: Normal Brain #4


title: Laser capture microdissected (LCM) whole seeds at the mature green stage, biological replicate 2


title: G166-NS_A


title: hf286-NS


title: G144-ED (GliNS1)


title: G144-NS_A


title: Laser capture microdissected (LCM) chalazal seed coat at the mature green stage, biological replicate 2

description: Chalazal seed coat collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis mature green stage chalazal seed coat captured by LCM

value: chalazal seed coat captured by LCM


title: Norm Brain#36

value: brain


title: G166-NS_B

value: Proliferating cultures in EGF and FGF-2


title: Laser capture microdissected (LCM) peripheral endosperm at the mature green stage, biological replicate 2

description: Peripheral endosperm collected from seeds containing a mature green embryo proper as determined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis mature green stage peripheral endosperm captured by LCM

value: peripheral endosperm captured by LCM


title: Norm Brain#102


title: G144-NS_B

value: malignant

value: cell line


title: NORM#41


title: G179-NS_B


title: hf240-NS-A


title: Laser capture microdissected (LCM) chalazal seed coat at the mature green stage, biological replicate 1


title: NORM#31


title: G174-NS

source_name: Giant cell glioblastoma derived cell line

value: glioblastoma


title: Laser capture microdissected (LCM) peripherial endosperm at the mature green stage, biological replicate 1

description: Peripherial endosperm collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis mature green stage peripherial endosperm captured by LCM

value: mature green stage

value: peripherial endosperm captured by LCM


title: Laser capture microdissected (LCM) micropylar endosperm at the mature green stage, biological replicate 1

description: Micropylar endosperm collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis mature green stage micropylar endosperm captured by LCM

value: micropylar endosperm captured by LCM


title: Laser capture microdissected (LCM) chalazal seed coat at the heart stage, biological replicate 3

description: Chalazal seed coat collected from seeds containing a heart-shaped embryo proper measuring 52-85 microns in length as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis heart stage chalazal seed coat captured by LCM

treatment_protocol: Siliques between 1.2 and 1.5 cm long containing heart stage seeds were collected from 38-46 day old plants. Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on sections using a Leica LMD6000 system.

value: heart stage


title: Laser capture microdissected (LCM) seed coat at the heart stage, biological replicate 1

description: Seed coat collected from seeds containing a heart-shaped embryo proper measuring 52-85 microns in length as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis heart stage seed coat captured by LCM

value: seed coat captured by LCM


title: Laser capture microdissected (LCM) chalazal seed coat at the heart stage, biological replicate 1


title: Laser capture microdissected (LCM) chalazal endosperm at the heart stage, biological replicate 2

description: Chalazal endosperm collected from seeds containing a heart-shaped embryo proper measuring 52-85 microns in length as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis heart stage chalazal endosperm captured by LCM


title: Laser capture microdissected (LCM) micropylar endosperm at the mature green stage, biological replicate 2


title: Laser capture microdissected (LCM) seed coat at the heart stage, biological replicate 2


title: Laser capture microdissected (LCM) micropylar endosperm at the heart stage, biological replicate 1

description: Micropylar endosperm collected from seeds containing a heart-shaped embryo proper measuring 52-85 microns in length as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis heart stage micropylar endosperm captured by LCM


title: Laser capture microdissected (LCM) chalazal endosperm at the heart stage, biological replicate 3


title: Laser capture microdissected (LCM) peripheral endosperm at the heart stage, biological replicate 1

description: Peripheral endosperm collected from seeds containing a heart-shaped embryo proper measuring 52-85 microns in length as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis heart stage peripheral endosperm captured by LCM


title: Laser capture microdissected (LCM) embryo proper at the heart stage, biological replicate 1

description: Embryo proper collected from seeds containing a heart-shaped embryo proper measuring 52-85 microns in length as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis heart stage embryo proper captured by LCM

value: embryo proper captured by LCM


title: Laser capture microdissected (LCM) whole seeds at the heart stage, biological replicate 1

description: Serial sections of whole seeds collected from seeds containing a heart-shaped embryo proper measuring 52-85 microns in length as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis heart whole seeds captured by LCM

value: whole seeds captured by LCM


title: Laser capture microdissected (LCM) whole seeds at the heart stage, biological replicate 2


title: HepG2 cells quercetin 24h

status: Public on Mar 11 2009

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

description: This sample was part of a time course experiment of the effect of quercetin on HepG2 cells gene axpression

hyb_protocol: Hybridization was perfoermed according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual) by the Laboratoire Transcriptome of CHU Montpellier, France

scan_protocol: Signals were detected by an Affymetrix microarray chip reader.

data_processing: RMA normalization was performed with the raw data using Genespring GX V9.0 (Agilent, Foster City, CA).

source_name: HepG2 human hepatocellular carcinoma cell line

label_protocol: RNA was labeled according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual) by the Laboratoire Transcriptome of CHU Montpellier, France.

extract_protocol: Total RNA was isolated using NucleospinII columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions.

treatment_protocol: HepG2 cell cultures were incubated with quercetin (3μM) for 24 hours after overnight serum starvation.

tag: cell line


title: HepG2 cells control 2h

label: RNA was labeled according to the Affymetrix protocol

treatment_protocol: HepG2 cell cultures were incubated with serum free medioum for 2 hours after overnight serum starvation.


title: Laser capture microdissected (LCM) peripheral endosperm at the heart stage, biological replicate 2


title: HepG2 cells control 12h

treatment_protocol: HepG2 cell cultures were incubated with serum free medium for 12 hours after overnight serum starvation.


title: Laser capture microdissected (LCM) chalazal seed coat at the heart stage, biological replicate 2


title: Laser capture microdissected (LCM) embryo proper at the mature green stage, biological replicate 2

description: Embryo proper collected from seeds containing a mature green embryo proper as dermined by a medial embryo section showing cotyledons that have extended fully to the chalazal pole and possessing full and visible seed coat layers showing no collapse or senescence, when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis mature green stage embryo proper captured by LCM


title: Laser capture microdissected (LCM) embryo proper at the heart stage, biological replicate 2


title: Laser capture microdissected (LCM) chalazal endosperm at the heart stage, biological replicate 1


title: Laser capture microdissected (LCM) micropylar endosperm at the heart stage, biological replicate 2


title: HepG2 cells control 4h

treatment_protocol: HepG2 cell cultures were incubated with serum free medium for 4 hours after overnight serum starvation.


title: HepG2 cells quercetin 4h

treatment_protocol: HepG2 cell cultures were incubated with quercetin (3μM) for 4 hours after overnight serum starvation.


title: HepG2 cells quercetin 2h

treatment_protocol: HepG2 cell cultures were incubated with quercetin (3μM) for 2 hours after overnight serum starvation.


title: HepG2 cells quercetin 12h

treatment_protocol: HepG2 cell cultures were incubated with quercetin (3μM) for 12 hours after overnight serum starvation.


title: Laser capture microdissected (LCM) embryo proper at the mature green stage, biological replicate 1


title: HepG2 cells control 24h

treatment_protocol: HepG2 cell cultures were incubated with serum free medium for 24 hours after overnight serum starvation.


title: mouse progenitors_WT_MP sorted (rep1)

first: Iannis

last: Aifantis

address: 550 First Ave

department: Pathology

institute: NYU Sch of Medicine

hyb_protocol: 15 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

source_name: Lin-ckit+Sca1- myeloid progenitors (MP) sorted from total bone marrow

label_protocol: 20 ng total RNA converted to cRNA using Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: Rneasy (QIAGEN) according to manufacturer's protocol.

treatment_protocol: Animals were injected intra-peritoneally with 20 ug/g polyI:C 3 times on alternate days.  Six weeks post-treatment, total bone marrow was harvested and LSK and MP cells were sorted by FACS.

tag: strain

value: mixed male and female

tag: protocol

value: intraperitoneal injection of 20 ug/g polyI:C 3 times on alternate days

tag: agent

value: Smo flox/flox, Mx1Cre-


title: mouse progenitors_Smo deficient_LSK sorted (rep1)

description: Six weeks post-treatment, total bone marrow was harvested and LSK and MP cells were sorted by FACS.

source_name: Lin-ckit+Sca1+ (LSK) sorted from total bone marrow

tag: gender

value: Smo flox/flox, Mx1Cre+


title: mouse progenitors_WT_LSK sorted (rep1)


title: P493-6 MSCV-empty +tet (low Myc) sample #2

status: Public on Mar 09 2009

city: Baltimore

first: Joshua

middle: T

last: Mendell

address: 733 N. Broadway, BRB 471

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

description:
Gene expression data from P493-6 cells infected with empty vector with low Myc expression. Described in:
Chang TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT.  Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. Proc. Natl. Acad. Sci., In press.

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

scan_protocol: GeneChips were scanned using a Hewlett-Packard GeneArray Scanner 3000 G7 upgrade.

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 150.

source_name: P493-6 cells infected with MSCV-empty retrovirus with low Myc expression

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

growth_protocol: Cells were grown in RPMI 1640 media plus 0.1 ug/mL tetracycline, 10% fetal bovine serum, and antibiotics.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Cells were infected with empty MSCV retroviral vector and selected for 2 weeks in 2 ug/mL puromycin.

tag: Human B lymphocytes transformed with Epstein-Barr virus and Myc


title: P493-6 MSCV-Lin28B +tet (low Myc) sample #1

description:
Gene expression data from P493-6 cells infected with Lin28B retroviral vector with low Myc expression. Described in:
Chang TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT.  Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. Proc. Natl. Acad. Sci., In press.

source_name: P493-6 cells infected with MSCV-Lin28B retrovirus with low Myc expression

treatment_protocol: Cells were infected with MSCV-Lin28B retroviral vector and selected for 2 weeks in 2 ug/mL puromycin.


title: mouse progenitors_Smo deficient_MP sorted (rep1)

tag: genotype/variation


title: Adenocarcinoma, bone marrow positive AC 23

city: Hamburg

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Gene expression profile of lung tumor

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on hgu133plus2 Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Post Hyb Wash No.1: 10 cycles of of 2 mixes/cycle with Wash Buffer A at 25°C. Post Hyb Wash No.2: 4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C. Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C. Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C. 2nd Stain: Stain the probe array for 10 minutes in antibody solution at 25°C. 3rd Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C.  Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C. Hybridization Buffer: 100 mM MES 1 M [Na+] 20 mM EDTA 0.01% Tween 20. Wash Buffer A (Nonstringent): 6x SSPE 0.01% Tween 20. Wash Buffer B (Stringent): 100 mM MES 0.1 M [Na+] 0.01% Tween 20. Stain Buffer: 100 mM MES 1 M [Na+] 0.05% Tween 20. SAPE Solution: 100 mM MES 1 M [Na+] 0.05% Tween 20 2 mg/ml acetylated BSA 10 μg/ml Streptavidin Phycoerythrin. Antibody Solution: 100 mM MES 1 M [Na+] 0.05% Tween 20 2 mg/ml acetylated BSA 0.1 mg/ml Normal Goat IgG 3 μg/ml biotinylated Anti-Streptavidin.

scan_protocol: Affymetrix GeneChip Scanner 7G Pixel Size: 1.56 μ Filter: 570 nm Number of Scans: 1 Affymetrix GeneChip Operating Software 1.3

data_processing: Data preprocessing using the GC Robust Multi-array Average (GC-RMA) method. Signal scaling against the median probe signal of three normal patients and log2-transformation. Genes for which information about the physical location is not given in the Affymetrix annotations files or is ambiguous are removed.

source_name: Human pulmonary adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle protocol from 50 ng total RNA

extract_protocol: Rneasy Micro Kit (Qiagen)

tag: male pulmonary adenocarcinoma

tag: bone marrow positive


title: Adenocarcinoma, bone marrow negative AC 15

description: Gene expression profile of lung tumor

tag: female pulmonary adenocarcinoma

tag: bone marrow negative


title: Adenocarcinoma, bone marrow positive AC 22

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow negative AC 14

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow positive AC 34

description: Gene expression profile of lung tumor


title: P493-6 MSCV-Lin28B +tet (low Myc) sample #2


title: Adenocarcinoma, bone marrow negative AC 12

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow positive AC 30

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow negative AC 3

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow positive AC 33

description: Gene expression profile of lung tumor


title: P493-6 MSCV-Lin28B -tet (high Myc) sample #1

description:
Gene expression data from P493-6 cells infected with Lin28B retroviral vector with high Myc expression. Described in:
Chang TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT.  Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. Proc. Natl. Acad. Sci., In press.

source_name: P493-6 cells infected with MSCV-Lin28B retrovirus with high Myc expression

growth_protocol: Cells were grown in RPMI 1640 media plus 10% fetal bovine serum and antibiotics.


title: Adenocarcinoma, bone marrow negative AC 8

description: Gene expression profile of lung tumor


title: P493-6 MSCV-empty -tet (high Myc) sample #2

description:
Gene expression data from P493-6 cells infected with empty vector with high Myc expression. Described in:
Chang TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT.  Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. Proc. Natl. Acad. Sci., In press.

source_name: P493-6 cells infected with MSCV-empty retrovirus with high Myc expression

growth_protocol: Cells were grown in RPMI 1640 media plus 10% fetal bovine serum plus antibiotics.


title: Normal N3

description: Gene expression profile of lung tumor

source_name: Human pulmonary lung

tag: male pulmonary lung

tag: normal tissue


title: Normal N1

description: Gene expression profile of lung tumor


title: P493-6 MSCV-empty +tet (low Myc) sample #1


title: Adenocarcinoma, bone marrow positive AC 27

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow positive AC 25

description: Gene expression profile of lung tumor


title: Normal N2

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow negative AC 10

description: Gene expression profile of lung tumor


title: P493-6 MSCV-Lin28B -tet (high Myc) sample #2


title: Adenocarcinoma, bone marrow negative AC 2

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow negative AC 11

description: Gene expression profile of lung tumor


title: Adenocarcinoma, bone marrow negative AC 16

description: Gene expression profile of lung tumor


title: N11792A1: Unremarkable breast ducts (Normal)

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

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

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: N11732C4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: P493-6 MSCV-empty -tet (high Myc) sample #1


title: T11478C1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue

tag: Invasive ductal carcinoma (IDC)


title: N11464B3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11472B1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11464B1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11689D4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11478A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11580C3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11478C4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T11770A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T11455B1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T11688A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T11580C1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N11693B2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11732C5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11451A4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11732C2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11640A1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11472B3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11580C5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11580C4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11464A5: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11478A3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11545D4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11688A4: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: T11478C3: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N11472B4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11455B2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11354D3: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11451A2: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11123D4: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: T11286A1: Invasive ductal carcinoma (IDC)

description: frozen breast tissue


title: N11354D1: Unremarkable breast ducts (Normal)

description: frozen breast tissue


title: N11103G2: Unremarkable breast ducts (Normal)

description: frozen breast tissue