title: Saline ip saline ILI 4hrs post ILI sample A

description: gene expression data from melanoma xenografts following ILI with saline

source_name: human-derived melanoma cells grown in rat as xenograft


title: HaCaT_siETS1_0h

status: Public on Oct 29 2008

type: RNA

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: Gene expression data from HaCaT cells transfected with ETS1 siRNA, without TGF-beta stimulation

hyb_protocol: Array hybridization was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

scan_protocol: Array scanning was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

data_processing: Microarray Suite software 5.0 (Affymetrix) was used to calculate the average difference (AD) for each gene probe set, which was shown as an intensity value of the gene expression (Ishii et al, Genomics 68:136-143, 2000).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HaCaT cells, ETS1 siRNA transfected, without TGF-beta3 stimulation

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and a T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeled cRNA by using a BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to the manufacturer’s instructions (Ishii et al, Genomics 68:136-143, 2000).

growth_protocol: HaCaT cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM #11965, GIBCO/Invitrogen, CA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml of penicillin G, and 100 microgram/ml of streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37 oC.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen).

treatment_protocol: Cells were stimulated with 3ng/ml (120pM) of TGF-beta3 in growth medium for the indicated times.

tag: immmortalized keratinocyte cell line


title: Scraped off mucosal layer, S2

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Gene expression data from scrapped off mucosa normal cells, replicate 2

hyb_protocol: Affymetrix standard protocol

scan_protocol: GCOS

data_processing: GCOS; SAM analyses; binary indexing algorithm

label: Biotin

source_name: Scraped off mucosal layer

label_protocol: Affymetrix standard protocol

growth_protocol: Snap-frozen tissue blocks from 8 individual patients were included in the study.

extract_protocol: RNeasy Mini Kit

treatment_protocol: We used three frozen specimens from normal ileum (N) and three from scraped off normal mucosa layer of the ileum (S), which is enriched for neuroendocrine cells as normal tissue references.

tag: Cell type

value: Normal cells

tag: Tumor stage

value: Non tumor


title: Normal Ileum Mucosa, N3

description: Gene expression data from normal ileum mucosa normal cells, replicate 3

source_name: Normal ileum mucosa


title: Saline ip LPAM ILI 24hrs post ILI sample A

status: Public on Oct 30 2008

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

country: USA

institute: Duke University Medical Center

description: gene expression data from melanoma xenografts following ILI with melphalan

hyb_protocol: Cleaned and fragmented cRNA was hybridized to the Affymetrix Human U133 plus 2 genechip for 16 hrs at 45C followed by washing and staining according to Affymetrix instructions

scan_protocol: Hybridized probe arrays were stained according to Affymetrix protocols (streptavidin phycoerythrin conjugate) and scanned with the GeneChip Scanner

data_processing: The amount of light emitted is directly proportional to the amount of target bound to each location on the probe array.  Expression values were generated by calculating the difference between the perfect match signal and the mismatch signal for each probe using the Affymetrix GeneChip Operating System.

label_protocol: cDNA was synthesized from the total RNA and, using an Affymetrix recommended IVT protocol, biotin-labeled cRNA was generated from the cDNA.  Prior to hybridization the cRNA was fragmented.

growth_protocol: Cells used to generate xenograft in rat were grown in Iscove MEM with 10%FBS, 1% Pen/Strep and 2mM L-glutamine added;  37C, 5% CO2; Cells were prepared in PBS plus matrigel at a ratio of 2:1 and 4 million cells were injected per rat.

extract_protocol: RNA was isolated using Qiagen Rneasy plus kit.  RNA quality was assessed using Agilent bioanalyzer prior to labeling and hybridization.

treatment_protocol: When tumors had reached ~1cm diameter treatment started.  Animals were given either ADH-1 (100mg/kg) or saline via ip injection 1 hour prior to start of Isolated Limb Infusion (ILI) with either melphalan (LPAM) or saline.  4 hour time point samples were harvested 4 hours after the completion of ILI.  All other animals were given a second dose of ADH-1 (100mg/kg) 24hrs after the first.  24 hour time point tissue was harvested 1 hour later.  Remaining animals were given 2 more doses of ADH-1 (100mg/kg) over next 24hrs and tumor was harvested 1hr following final dose.  Rats were anesthetized for tumor harvest and were humanely euthanized at the end of the study following an IACUC approved protocol.  Harvested tumor was frozen immediately in liquid nitrogen and stored at -80C until ready for processing.

tag: human melanoma-derived cell lines injected into hind limb of Crl:NIH Rnu Nude Rat


title: Normal Ileum Mucosa, N1

description: Gene expression data from normal ileum mucosa normal cells, replicate 1


title: HaCaT_1.5h

description: Gene expression data from HaCaT cells treated with TGF-beta for 1.5 hours

source_name: HaCaT cells stimulated with TGF-beta3 for 1.5 hours


title: Midgut carinoid primary tumor, P1

description: Gene expression data from primary midgut carcinoid cells, replicate 1

source_name: Midgut carinoid primary tumor

value: Tumor cells

value: Primary


title: Normal Ileum Mucosa, N2

description: Gene expression data from normal ileum mucosa normal cells, replicate 2


title: HaCaT_24h

description: Gene expression data from HaCaT cells treated with TGF-beta for 24 hours

source_name: HaCaT cells stimulated with TGF-beta3 for 24 hours


title: Midgut carinoid primary tumor, P3

description: Gene expression data from primary midgut carcinoid cells, replicate 3


title: Scraped off mucosal layer, S3

description: Gene expression data from scrapped off mucosa normal cells, replicate 3


title: Midgut carinoid primary tumor, P2

description: Gene expression data from primary midgut carcinoid cells, replicate 2


title: Midgut carinoid Liver Metastasis, L3

description: Gene expression data from midgut carcinoids metastasis cells in the liver, replicate 3

source_name: Midgut carinoid liver metastasis

value: Metastasis


title: Midgut carinoid Liver Metastasis, L2

description: Gene expression data from midgut carcinoids metastasis cells in the liver, replicate 2


title: Scraped off mucosal layer, S1

description: Gene expression data from scrapped off mucosa normal cells, replicate 1


title: Ovarian cancer, IFN-alpha treated Side Population, rep2

city: Padova

first: Alberto

last: Corradin

state: PD

address: via Tiepolo

department: Dipertimento di Ingegneria dell'Informazione

country: Italy

institute: Università degli Studi di Padova

description: Aim of the study: To determine the IFN-alpha signature in Side Population of ovarian cancer

hyb_protocol: Affymetrix's manufacturer's protocol: hybridization onto Affymetrix Human Genome U133 Plus 2.0 array

scan_protocol: Affymetrix GCOS

data_processing: Data were loaded and filtered using the software package BRB Array Tools ver. 3.6.0-beta 3. Genes were excluded if the percentage of missing expression values was greater than 49%. Data were normalized following the RMA procedure of Bioconductor 2.1.

source_name: ascitic fluid

label_protocol: GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA)

growth_protocol: Sorted Side Population subset cells were immediately seeded in P24 plate at the concentration of 100,000 cells/well in a volume of 1 ml of RPMI medium, with or without interferon-alpha (IFN-alpha2b; 1000 IU/ml; IntronA, Schering-Ploug Europe, Bruxelles, Belgium). After 5h the cells were collected and centrifuged. The pellet was store at -80°C for the extraction of RNA. Pellets of sorted cells obtained from 3 different sorting were pooled and analysed by micro-arrays analysis.

extract_protocol: Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol:
Ovarian cancer cells were derived from the malignant effusion developed in mice injected with cells obtained from ascitic fluid of ovarian cancer bearing-patient. Ascites cells were centrifuged at 1200 rpm for 5 min; red blood cells were lysed by ammonium chloride and the tumor cells were resuspended in RPMI 1640 medium (Euroclone, Pero, Italy) supplemented with 10% FCS (Life Technologies, Gaithersburg, MD), 1% hepes (10 mM, Cambrex Bioscience, Verviers, Belgium), 1% L-glutamine 2 mM, and 1% antibiotics-antimycotic mix (Life Technologies). One day later, the cells were harvested cells (106 cells/ml) were and incubated in DMEM containing 2% FCS, 10 mM hepes and 5 microg/ml Hoechst 33342 dye (Sigma-Aldrich, St. Louis, MO) for 90 min at 37°C, either alone or in the presence of 50 microM verapamil (Sigma). At the end of incubation, cells were washed and then incubated in PBS supplemented with 2% FCS, 10 mM HEPES and 1 microg/ml propidium iodide (PI) (Sigma) at 4°C for 10 min, to discriminate dead cells. The cells were then analysed in a FACSVantage fluorescence-activated cell sorter (Becton Dickinson, San Diego, CA) by using a dual wavelength analysis (blue: 424-444 nm; red: 675 nm) after excitation with 350 nm UV light.
To dissociate multi-cellular aggregates obtained from ascitic fluid, before staining with Hoechst buffer cells were incubated with Accumax solution (Chemicon International, Temecula, CA) for approximately 45 minutes at 37°C with intermittent mixing, until a single cell suspension was obtained.
The labelled cells were sorted for the collection of Hoechst low cells, named Side Population subset.

tag: Side population subset of ovarian cancer cells


title: Midgut carinoid Liver Metastasis, L1

description: Gene expression data from midgut carcinoids metastasis cells in the liver, replicate 1


title: Ovarian cancer, IFN-alpha treated Side Population, rep1


title: Ovarian cancer, untreated Side Population, rep1


title: Ovarian cancer, untreated Side Population, rep2


title: GFP2

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: transduced with GFP siRNA clone 2

hyb_protocol: Following fragmentation, 10 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 GeneChip Fluidics Station FS 4500.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: The data were analyzed with Affymetrix dCHIP using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: transduced with lentivirus containing siRNA agaisnt GFP  clone 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix).

growth_protocol: A549 cells cultured in RPMI 1640 medium containing 10% FBS

extract_protocol: Total RNA was harvested using the RNeasy RNA Isolation kit  standard protocol (Qiagen, Valencia, CA)

treatment_protocol: A549 cells transduced with lentiviral vectors containing specific siRNA sequences against ALDH1A1+ALDH3A1 (Lenti 1+3 cells)

tag: transduced with GFP siRNA clone 2


title: WT2

description: wild type #2

source_name: wild type, clone 2

tag: wild type


title: GFP3

description: transduced with GFP siRNA clone 3

source_name: transduced with lentivirus containing siRNA agaisnt GFP  clone 3

tag: transduced with GFP siRNA clone 3


title: Clone 1B

description: transduced with lenti 1+3 clone 2

source_name: transduced with lenti 1+3 clone 2

tag: transduced with lenti 1+3 clone 2


title: WBC pCONS

status: Public on Oct 28 2008

city: Los Angeles

first: Ram

middle: Pyare

last: Singh

state: CA

address: 1000 Veteran Ave

department: Rheumatology/Medicine

institute: David Geffen School of Medicine at UCLA

description: Gene expression data from BWF1 mice (10-15 weeks) spleenocytes

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

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

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

organism: Mus musculus

source_name: BWF1 mice spleenocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: BWF1 mice were treated with 1 mg of pCONs (an artifical peptide) intravenously.

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

treatment_protocol: CD4, CD8, and WBC cell subsets were collected from control and pCONS treated mice spleens one week after treatment.

tag: NZB/NZW BWF1 mice treated with pCONS peptide intravenously


title: GFP4

description: transduced with GFP siRNA clone 4

source_name: transduced with lentivirus containing siRNA agaisnt GFP  clone 4

tag: transduced with GFP siRNA clone 4


title: CD8 pCONS


title: Clone 2

description: transduced with lenti 1+3 clone 3

source_name: transduced with lenti 1+3 clone 3

tag: transduced with lenti 1+3 clone 3


title: WT4

description: wild type #4

source_name: wild type, clone 4


title: WBC Naïve

tag: NZB/NZW BWF1 control


title: Clone 1A

description: transduced with lenti 1+3 clone 1

source_name: transduced with lenti 1+3 clone 1

tag: transduced with lenti 1+3 clone 1


title: WT1

description: wild type #1

source_name: wild type, clone 1


title: Clone 5

description: transduced with lenti 1+3 clone 4

source_name: transduced with lenti 1+3 clone 4

tag: transduced with lenti 1+3 clone 4


title: CD8 Naïve


title: CD4 pCONS


title: WT3

description: wild type #3

source_name: wild type, clone 3


title: Control 1

status: Public on Oct 27 2008

city: Houston

first: Alexei

last: Protopopov

state: TX

address: 1901 East Rd

department: IACS

institute: UT MD Anderson Cancer Center

description: standard processing performed by Microarray Core of DFCI

hyb_protocol: Purified cRNA is  processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).

source_name: Control

label_protocol: The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).

extract_protocol: Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.

tag: nonmalignant T cells


title: NIC Tumor 3

source_name: NIC Tumor

tag: T-ALL


title: NIC Tumor 1


title: Control 3


title: CD4 Naïve


title: Control 2


title: NIC Tumor 2


title: GFP1

description: transduced with GFP siRNA clone 1

source_name: transduced with lentivirus containing siRNA agaisnt GFP  clone 1

tag: transduced with GFP protein clone 1


title: Abnormal non-malignant 2

source_name: Abnormal non-malignant


title: Abnormal non-malignant 1


title: Abnormal non-malignant 3


title: KiPS obtained from reprogramming human keratinocytes with 4 factors (Oct4, Sox2, Klf4, cmyc) 2

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

description: Human pluripotent KiPS4F2 cell line

hyb_protocol: Standard affymetrix protocol

scan_protocol: Default settings for the Affymetrix GeneChip Scanner (7G upgrade)

data_processing: Data extraction is done by the Affymetrix GCOS software v1.4. Raw data were imported in R and normalized using the GCRMA algorithm.

label_protocol: Labeling of 3.75 ug ssDNA following the Nugen protocol FL-Ovation cDNA Biotin Module V2.

growth_protocol:
KiPS4F1 cells were cultured on top of irradiated
human fibroblasts and picked mechanically. Knockout DMEM
ES media was supplemented with 20% knockout serum replacement,
non-essential amino acids, 2-Mercaptoethanol, Penicillin/Streptomycin,
GlutaMAX, bFGF (all Gibco) and Human albumin (Grifols). Feeder cells
used: HFF-1: Human Foreskin Fibroblasts, ATCC Number SCRC-1041.

extract_protocol: Total RNA was isolated from KiPS4F2 cells using trizol (Invitrogen). The amplification was done following the Nugen protocol (Ovation RNA Amplification System V2) with 25ng starting material.

treatment_protocol: KiPS were obtained after infection of human foreskin keratinocytes with 4 retroviruses (Oct4, Sox2, Klf4, cmyc).

tag: Pluripotent KiPS cell line obtained from reprogramming human foreskin keratinocytes with 4 factors (Oct4, Sox2, Klf4, cmyc), cultured on feeders.


title: Human ES4 cell line

description: Human ES4 cell line

source_name: Human ES4 cell line

growth_protocol:
ES4 cells were cultured on matrigel by
trypsinization (using mouse fibroblast conditioned media). Knockout DMEM
ES media was supplemented with 20% knockout serum replacement,
non-essential amino acids, 2-Mercaptoethanol, Penicillin/Streptomycin,
GlutaMAX, bFGF (all Gibco) and Human albumin (Grifols). Feeder cells
used: HFF-1: Human Foreskin Fibroblasts, ATCC Number SCRC-1041.

extract_protocol: Total RNA was isolated from ES4 cells using trizol (Invitrogen). The amplification was done following the Nugen protocol (Ovation RNA Amplification System V2) with 25ng starting material.

tag: Human ES4 cell line


title: Human foreskin keratinocyte 1

description: Gene expression of human foreskin keratinocytes

scan_protocol: settings for the Affymetrix GeneChip Scanner (7G upgrade)

data_processing: Data extraction was done by the Affymetrix GCOS software v1.4. Raw data were imported in R and normalized using the GCRMA algorithm.

source_name: Human foreskin keratinocyte - 16 years old patient

growth_protocol: culture in serum free low calcium medium (Epilife, Invitrogen). Used at passage 4 growing on uncoated dishes.

extract_protocol: Total RNA was isolated from fibroblasts from individual 1 using Trizol (Invitrogen). The amplification was done following the Nugen protocol (Ovation RNA Amplification System V2) with 25ng starting material.

treatment_protocol: Keratinocytes were isolated from juvenile foreskins using dispase to remove the dermis from the epidermis followed by trypsinization.

tag: Human foreskin keratinocyte from a 16-year-old male


title: KiPS obtained from reprogramming human keratinocytes with 3 factors (Oct4, Sox2, Klf4)

description: Human pluripotent KiPS3F1 cell line

growth_protocol:
KiPS3F1 cells were cultured on matrigel by
trypsinization (using mouse fibroblast conditioned media). Knockout DMEM
ES media was supplemented with 20% knockout serum replacement,
non-essential amino acids, 2-Mercaptoethanol, Penicillin/Streptomycin,
GlutaMAX, bFGF (all Gibco) and Human albumin (Grifols). Feeder cells
used: HFF-1: Human Foreskin Fibroblasts, ATCC Number SCRC-1041.

extract_protocol: Total RNA was isolated from KiPS3F1 cells using trizol (Invitrogen). The amplification was done following the Nugen protocol (Ovation RNA Amplification System V2) with 25ng starting material.

treatment_protocol: KiPS were obtained after infection of human foreskin keratinocytes with 3 retroviruses (Oct4, Sox2, Klf4).

tag: KiPS obtained from reprogramming keratinocytes with 3 factors (Oct4, Sox2, Klf4)


title: Human foreskin fibroblast 2

description: Gene expression of human foreskin fibroblasts

source_name: Human foreskin fibroblast 2

treatment_protocol: Fibroblasts were isolated by explant outgrowth from dermis of foreskin biopsy using DMEM, 10% bovine serum, Pen/Strep, 1% Glutamax. Passage 4 growing on uncoated dishes.

tag: Human foreskin fibroblast


title: KiPS obtained from reprogramming human keratinocytes with 4 factors (Oct4, Sox2, Klf4, cmyc) 1

description: Human pluripotent KiPS4F1 cell line

growth_protocol:
KiPS4F1 cells were cultured on matrigel by
trypsinization (using mouse fibroblast conditioned media). Knockout DMEM
ES media was supplemented with 20% knockout serum replacement,
non-essential amino acids, 2-Mercaptoethanol, Penicillin/Streptomycin,
GlutaMAX, bFGF (all Gibco) and Human albumin (Grifols). Feeder cells
used: HFF-1: Human Foreskin Fibroblasts, ATCC Number SCRC-1041.

extract_protocol: Total RNA was isolated from KiPS4F1 cells using trizol (Invitrogen). The amplification was done following the Nugen protocol (Ovation RNA Amplification System V2) with 25ng starting material.

tag: Pluripotent KiPS cell lines obtained from reprogramming human foreskin keratinocytes with 4 factors (Oct4, Sox2, Klf4, cmyc)


title: Human ES2 cell line

description: Human ES2 cell line

source_name: Human ES2 cell line

growth_protocol:
ES2 cells were cultured on top of irradiated
human fibroblasts and picked mechanically. Knockout DMEM
ES media was supplemented with 20% knockout serum replacement,
non-essential amino acids, 2-Mercaptoethanol, Penicillin/Streptomycin,
GlutaMAX, bFGF (all Gibco) and Human albumin (Grifols). Feeder cells
used: HFF-1: Human Foreskin Fibroblasts, ATCC Number SCRC-1041.

extract_protocol: Total RNA was isolated from ES2 cells using Trizol (Invitrogen). The amplification was done following the Nugen protocol (Ovation RNA Amplification System V2) with 25ng starting material.

tag: human ES2 cells


title: Human foreskin keratinocyte 2

source_name: Human foreskin keratinocyte - 4 years old male

tag: Human foreskin keratinocyte from a 4-year-old male


title: Human foreskin fibroblast 1

source_name: Fibroblast 1


title: hES-T3 derived embryoid bodies, biological rep1

status: Public on Oct 25 2008

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: The mRNA profiles from the undifferentiated human embryonic stem cell line hES-T3 (T3ES), hES-T3 derived embryoid bodies (T3EB) and hES-T3 differentiated fibroblast-like cells (T3DF) were quantitatively determined.

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

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring software version 7.2 GC-RMA preprocessor to use on the CEL files

source_name: The T3EB embryoid bodies were formed in 7 days from hES-T3 by mechanically dissection , and they resembled early embryo development to some extent

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

growth_protocol: The formation of embryoid bodies (EBs) was induced by mechanically dissecting undifferentiated hES-T3 colonies into pieces that were transferred and grown with very slow shaking (20 rpm) in the EB medium containing 80% knockout DMEM, 20% ES-qualified FBS (GIBCO), 1% non-essential amino acids, and 1 mM L-glutamine without MEF feeder layer in bacterial Petri dish plate(£\-plus, 10 cm) under 5% CO2 at 37oC for 7 days with change of medium every two days. These embryoid bodies are designated as T3EB.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

treatment_protocol: Non

tag: gender

value: female

tag: passage

tag: sample type

value: embryoid bodies derived from T3ES


title: Human fibroblast-like cells, biological rep1

source_name: The T3DF fibroblast-like cells were derived from hES-T3 cell line and they appeared as flat cells with elongated nucleus and branching pseudopodia.

growth_protocol: hES-T3 cells were transferred into feeder-free and noncoated plate (10 cm) in DMEM supplemented with 10% FBS (GIBCO) under 5% CO2 at 37oC. After 10 Days, cells appeared as fibroblast-like morphology, that is, flat cells with elongated nucleus and branching pseudopodia, and these differentiated fibroblast-like cells are designated as T3DF. These T3DF cells were passaged using trypsin (0.05%, GIBCO) every 4 days or cryopreserved.

tag: Gender

tag: Passage


title: iliac_MSC_rep2

city: Hiroshima

first: Masakazu

last: SHIMIZU

state: Hiroshima

address: 1-2-3 Kasumi-cho, Minami-ku

department: Departments of Dental and Medical Biochemistry

institute: Hiroshima University

description: DNA microarray analysis was performed by KURABO (Osaka, Japan) GeneChip Custom Analysis Service with Human Genome U133 Plus 2.0 chips.

hyb_protocol: The hybridization was performed (Hybridization Oven 640 110V, Affymetrix 800138) according to the manufacturer's instructions (Expression Analysis Technical Manual, 701021 Rev. 5, Section2 Eukaryotic Sample and Array Processing, Chapter2 Eukaryotic Target Hybridization, Affymetrix). GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix 00-0079).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix 00-0074).

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 (Scaling Factor = 1, Normalization Value = 1, Detection Call a1 = 0.05, a2 = 0.065, Tau = 0.015).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

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

tag: Human iliac mesenchymal stem cells (MSC) were purchased from BioWhittaker Inc (Walkersville, MD) or obtained from iliac crest according to protocol approved by ethical authorities at Hiroshima University. Culture of MSC were performed as described. (Matsubara T, Suardita K, Ishii M, Sugiyama M, Igarashi A, et al. (2005) Alveolar bone marrow as a cell source for regenerative medicine

value: differences between alveolar and iliac bone marrow stromal cells. J Bone Miner Res 20:399-409.)


title: Human fibroblast-like cells, biological rep3


title: hES-T3 derived embryoid bodies, biological rep2


title: fibroblast_rep2

tag: Human skin fibroblasts were purchased from KURABO (Osaka, Japan), and human gingival fibroblasts were isolated as described previously. (Kawahara K, Shimazu A (2003) Expression and intracellular localization of progesterone receptors in cultured human gingival fibroblasts. J Periodontal Res 38


title: iliac_MSC_rep3


title: iliac_MSC_rep1


title: Human embryonic stem cell line T3ES, biological rep3

source_name: Human embryonic stem cell line hES-T3 (T3ES) with normal female karyotype (46, XX) was derived from preimplantation embryos

growth_protocol: hES-T3 was continuously cultured on mitotically inactivated mouse embryonic fibroblast (MEF) feeder layer in hES medium under 5% CO2 at 37oC and underwent freezing/thawing processes. The hES culture medium consisted of DMEM/F12 (1:1, GIBCO) supplemented with 20% KSR, 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM £]-mercaptoethanol, and 4 ng/ml basic fibroblast growth factor (bFGF; Life Technologies). Routine passages of hES-T3 line every 5-7 days were done with collagenase ( type IV, 1 mg/ml, Invitrogen) treatment and mechanical scrape. The undifferentiated state of hES-T3 cells (passage 36) grown on MEF feeder layer was indicated by expression of OCT4 and NANOG

tag: cell line


title: Human fibroblast-like cells, biological rep2


title: Human embryonic stem cell line T3ES, biological rep2


title: fibroblast_rep3

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 (Scaling Factor = 1, Normalization Value = 1, Detection Call a1 = 0.05, a2 = 0.065, Tau = 0.015).


title: Human embryonic stem cell line T3ES, biological rep1

source_name: Human embryonic stem cell line T3ES (hES-T3) with normal female karyotype (46, XX) was derived from preimplantation embryos


title: Kidney_400 mg/kg VCM ip_mouse #107

status: Public on Oct 23 2008

city: Menlo Park

first: Hanna

middle: Hongchin

last: Ng

address: 333 Ravenswood Avenue

institute: SRI International

description: Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 400 mg/kg administered via the intraperitoneal route (ip)

hyb_protocol: The cRNA was fragmented before hybridizing to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Hybridization was performed according to the manufacturer’s instructions, as described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

scan_protocol: Scaning was performed using a TGT value = 500 using the protocol described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

data_processing: The Affymetrix CEL files were loaded into GeneSpring GX version 7.3.1 (Agilent technologies, Santa Clara, CA, USA) and preprocessed using GenChip Robust Multi-Array analysis (GC-RMA).

source_name: Kidney from mice treated with 7 daily ip injections of vancomycin at 400 mg/kg

label_protocol: cDNA was prepared and cleaned from 10 µg total RNA using the One-Cycle cDNA Synthesis and Clean-up module kits (Affymetrix, Santa Clara, CA, USA). The cDNA was further processed to biotin-labeled cRNA using the IVT labeling kit (Affymetrix). Labeling protocol was performed according to the manufacturer’s instructions, as described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

growth_protocol: BALB/c mice were maintained on Purina Certified Rodent Chow 5002 (Richmond, IN, USA) and purified tap water ad libitum in microisolator cages under controlled lighting (12 h light/dark cycle).

extract_protocol: Approximately 15-20 mg of each kidney to analyze was transferred into 1 ml Trizol reagent (Invitrogen, Carlsbad, CA, USA) along with a stainless steel bead (Qiagen, Valencia, CA, USA) and homogenized with a TissueLyser (Qiagen). Total RNA was extracted with 200 µl chloroform, precipitated with 500 µl 100% ethanol, and transferred to a RNeasy mini spin column (Qiagen) for purification according to the manufacturer’s instructions. Total RNA was subsequently precipitated with ethanol, resuspended in water and stored at –70°C.

treatment_protocol: Groups of 6 mice were administered, daily for 7 consecutive days, with 50, 200, and 400 mg/kg vancomycin, delivered via the iv and ip routes. Six control mice were administered a similar volume of 0.9% saline solution using both routes.

tag: tissue

value: kidney

tag: protocol

value: intraperitoneal

tag: agent

value: vancomycin

tag: dose

value: 400 mg/kg


title: Kidney_400 mg/kg VCM ip_mouse #106


title: Retinal pigment epithelium (RPE)

status: Public on Oct 24 2008

first: Yuri

last: Futagami

address: 1-5-45 Yushima Bunkyoku

department: Ophthalmology

institute: Tokyo Medical and Dental University

description: Primary cultures of pigmented epithelial cells from retinal PE (RPE) cells were cultured in DMEM complete medium, composed of DMEM and 20% FBS for two weeks. The medium of ocular PE was changed to serum free medium, with a cellular RNA extraction then performed after an overnight culture. The RPE were also found to be 95% cytokeratin positive after 14 days of incubation.

hyb_protocol: 10 migro grams of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression  Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

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

data_processing: The data analysis were performed using the Affymetrix GeneChip Operating Software v1.3. using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of array was arbitrarily set to 100.

source_name: Primary cultured cells of retinal pigment epithelium

label_protocol: 1 micro gram of total RNA was reverse transcribed using the cDNA synthesis system of MessageAmp aRNA Kit (Ambion). The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3. Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf). In vitro transcription was performed using the 3'-Amplification Reagents for IVT Labeling (Affymetrix). The cRNA was cleaned using RNeasy 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 RNA was isolated using TRIZOL Reagent(Invitrogen) and used as starting material for the cDNA preparation. RNA was purified from total cellular RNA by Nucleospin RNA II (Macherey-Nagel, Inc, Germany) as outlined by the manufacturer. Integrity of total RNA was assessed qualitatively on the Agilent 2100 Bioanalizer (Agilent Technologies).

tag: Retinal pigment epithelium (Primary cultured cell)


title: Kidney_400 mg/kg VCM ip_mouse #103


title: Kidney_400 mg/kg VCM ip_mouse #108


title: fibroblast_rep1

tag: Human skin fibroblasts were purchased from KURABO (Osaka, Japan), and human gingival fibroblasts were isolated as described previously.

tag: (Kawahara K, Shimazu A (2003) Expression and intracellular localization of progesterone receptors in cultured human gingival fibroblasts. J Periodontal Res 38


title: Kidney_400 mg/kg VCM ip_mouse #105


title: Kidney_400 mg/kg VCM ip_mouse #104


title: Retinal pigment epithelium with INFg stimulation

description: Primary cultures of pigmented epithelial cells from retinal PE (RPE) cells were cultured in DMEM complete medium, composed of DMEM and 20% FBS for two weeks. RPE cells were stimulated with IFNg (final 100 U/ml) for 24hrs. The medium of ocular PE was changed to serum free medium, with a cellular RNA extraction then performed after an overnight culture. The RPE were also found to be 95% cytokeratin positive after 14 days of incubation.

tag: Retinal pigment epithelium stimulated by IFNg


title: Kidney_200 mg/kg VCM ip_mouse #090

description: Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 200 mg/kg administered via the intraperitoneal route (ip)

source_name: Kidney from mice treated with 7 daily ip injections of vancomycin at 200 mg/kg

value: 200 mg/kg


title: Kidney_200 mg/kg VCM ip_mouse #086


title: Kidney_200 mg/kg VCM ip_mouse #087


title: Kidney_200 mg/kg VCM ip_mouse #088


title: Kidney_saline ip_mouse #066

description: Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of saline, administered via the intraperitoneal route (ip)

source_name: Kidney from mice treated with 7 daily ip injections of saline

value: saline

value: 0 mg/kg


title: Kidney_200 mg/kg VCM ip_mouse #089


title: Kidney_50 mg/kg VCM ip_mouse #071

description: Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 50 mg/kg administered via the intraperitoneal route (ip)

source_name: Kidney from mice treated with 7 daily ip injections of vancomycin at 50 mg/kg

value: 50 mg/kg


title: Kidney_50 mg/kg VCM ip_mouse #072


title: Kidney_200 mg/kg VCM ip_mouse #085


title: Kidney_400 mg/kg VCM iv_mouse #048

description: Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 400 mg/kg administered via the intravenous route (iv)

source_name: Kidney from mice treated with 7 daily iv injections of vancomycin at 400 mg/kg

value: intravenous


title: Kidney_saline ip_mouse #061


title: Kidney_200 mg/kg VCM iv_mouse #026

description: Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 200 mg/kg administered via the intravenous route (iv)

source_name: Kidney from mice treated with 7 daily iv injections of vancomycin at 200 mg/kg


title: Kidney_50 mg/kg VCM ip_mouse #070


title: Kidney_50 mg/kg VCM ip_mouse #069


title: Kidney_200 mg/kg VCM iv_mouse #029


title: Kidney_50 mg/kg VCM ip_mouse #067


title: Kidney_400 mg/kg VCM iv_mouse #047


title: Kidney_50 mg/kg VCM ip_mouse #068


title: Kidney_200 mg/kg VCM iv_mouse #028


title: Kidney_saline ip_mouse #065


title: Kidney_200 mg/kg VCM iv_mouse #027


title: Kidney_400 mg/kg VCM iv_mouse #046


title: Kidney_saline ip_mouse #064


title: Kidney_200 mg/kg VCM iv_mouse #025


title: Kidney_saline ip_mouse #063


title: Kidney_50 mg/kg VCM iv_mouse #012

description: Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 50 mg/kg administered via the intravenous route (iv)

source_name: Kidney from mice treated with 7 daily iv injections of vancomycin at 50 mg/kg


title: Kidney_400 mg/kg VCM iv_mouse #045


title: Kidney_saline ip_mouse #062


title: Kidney_50 mg/kg VCM iv_mouse #009


title: Kidney_50 mg/kg VCM iv_mouse #011


title: Kidney_50 mg/kg VCM iv_mouse #010


title: Kidney_400 mg/kg VCM iv_mouse #043


title: Kidney_200 mg/kg VCM iv_mouse #030


title: Kidney_50 mg/kg VCM iv_mouse #0078


title: Kidney_400 mg/kg VCM iv_mouse #044


title: Kidney_50 mg/kg VCM iv_mouse #007


title: new_emigrant_EG

city: New York

first: Isabelle

last: Isnardi

state: NY

address: 535E 70th Street

institute: Hospital for Special Surgery

description: The labelling, hybridizing, scanning and data processing steps were performed by the Cornell Microarray Core Facility, supervised by Dr. Jenny Xiang.

hyb_protocol: Targets were prepared for array hybridization according to Affymetrix Expression Analysis Technical manual except for some modifications. Hybridization conditions, array washing and staining (with GeneChip Fluidics Station 450) were carried out according to the Affymetrix Expression Analysis technical Manual.

scan_protocol: Scanning (with GeneChip Scanner 3000 7G) was carried out according to the Affymetrix Expression Analysis technical Manual.

data_processing: Affymetrix GeneChip Operating Software was used as the image acquisition software for the U133A 2.0 chips. The signal, which represents the intensity of each gene, was extracted from the image. The target intensity value from each chip was scaled to 500.

source_name: new emigrant B cells, non stimulated

label_protocol: 50 ng total RNA samples were amplified and labeled with biotin using the Ovation Biotin system (NuGEN Technologies, Inc., San Carlos, CA). Amplification of starting total RNA yielded on average 7 μg of amplified single stranded cDNA. This material was then fragmented and labeled with biotin.

extract_protocol: Total RNA was extracted from 230,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

treatment_protocol: Peripheral B cells were purified from the blood of the donor by negative selection using RosetteSepTM procedure (StemCell Technologies, Vancouver, BC, Canada).  Enriched B cells were stained with fluorescein isothiocyanate (FITC) anti-human CD27, phycoerythrin (PE) anti-human CD10, anti-human IgM biotin, and allophycocyanin (APC) anti-human CD19. Biotinylated antibodies were revealed using streptavidin-PECy7. Single CD19+CD10+IgM+CD27- new emigrant from the donor were sorted on a FACSVantage (Becton Deckinson).

tag: Woman 58 y.o.

tag: CD19+CD10+IgM+CD27- new emigrant B cells.


title: mature_naive_JAS

source_name: mature naive B cells, non stimulated

label_protocol: Total RNA was extracted from 100,000 cells and purified using the 50 ng total RNA samples were amplified and labeled with biotin using the Ovation Biotin system (NuGEN Technologies, Inc., San Carlos, CA). Amplification of starting total RNA yielded on average 7 μg of amplified single stranded cDNA. This material was then fragmented and labeled with biotin.

extract_protocol: Total RNA was extracted from 250,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

treatment_protocol: Peripheral B cells were purified from the blood of the donor by negative selection using RosetteSepTM procedure (StemCell Technologies, Vancouver, BC, Canada). Enriched B cells were stained with fluorescein isothiocyanate (FITC) anti-human CD27, phycoerythrin (PE) anti-human CD10, anti-human IgM biotin, and allophycocyanin (APC) anti-human CD19. Biotinylated antibodies were revealed using streptavidin-PECy7. Single CD19+CD10-IgM+CD27- mature naive from the donor were sorted on a FACSVantage (Becton Deckinson).

tag: Woman 49 y.o.

tag: CD19+CD10-IgM+CD27- mature naive B cells.


title: SY5Y_siRNAControl_1

status: Public on Oct 22 2008

city: Essen

first: Johannes

middle: Hubertus

last: Schulte

state: NRW

department: Peadiatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Essen

hyb_protocol: according to manufacturer (Affy)

scan_protocol: according to manufacturer (Affy)

data_processing: JustMas Algorithm used with SimpleAffy (R)

source_name: neuroblastoma cell line SY5Y

label_protocol: according to manufacturer (Affy)

extract_protocol: RNeasy according to Qiagen protocol

tag: treated with siRNA Control


title: Kidney_saline iv_mouse #006

description: Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of saline, administered via the intravenous route (iv)

source_name: Kidney from mice treated with 7 daily iv injections of saline


title: SY5Y_siRNAvsLSD_2

tag: treated with siRNA against LSD1


title: Kidney_saline iv_mouse #004


title: SY5Y_siRNAvsLSD1_1


title: Kidney_saline iv_mouse #001


title: Kidney_saline iv_mouse #003


title: SY5Y_siRNAControl_2


title: Kidney_saline iv_mouse #005


title: mature_naive_EG

extract_protocol: Total RNA was extracted from 720,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

treatment_protocol: Peripheral B cells were purified from the blood of the donor by negative selection using RosetteSepTM procedure (StemCell Technologies, Vancouver, BC, Canada).  Enriched B cells were stained with fluorescein isothiocyanate (FITC) anti-human CD27, phycoerythrin (PE) anti-human CD10, anti-human IgM biotin, and allophycocyanin (APC) anti-human CD19. Biotinylated antibodies were revealed using streptavidin-PECy7. Single CD19+CD10-IgM+CD27- mature naive from the donor were sorted on a FACSVantage (Becton Deckinson).


title: mature_naive_EM

extract_protocol: Total RNA was extracted from 150,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

tag: Man 37 y.o.


title: mature_naive_II

tag: Woman 27 y.o.


title: Kidney_saline iv_mouse #002


title: osteoblast_rep1

tag: Human iliac mesenchymal stem cells (MSC) were purchased from BioWhittaker Inc (Walkersville, MD) or obtained from iliac crest according to protocol approved by ethical authorities at Hiroshima University. Culture of MSC and their differentiation from the osteoblast lineage were performed as described. (Matsubara T, Suardita K, Ishii M, Sugiyama M, Igarashi A, et al. (2005) Alveolar bone marrow as a cell source for regenerative medicine


title: chondrocyte_rep3

tag: Human iliac mesenchymal stem cells (MSC) were purchased from BioWhittaker Inc (Walkersville, MD) or obtained from iliac crest according to protocol approved by ethical authorities at Hiroshima University. Culture of MSC and their differentiation from the chondrocyte lineage were performed as described. (Matsubara T, Suardita K, Ishii M, Sugiyama M, Igarashi A, et al. (2005) Alveolar bone marrow as a cell source for regenerative medicine


title: H1 hESC_4% O2 rep2

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

description: Gene expression data from human embronic stem cell cultured under 4% oxygen condition

hyb_protocol: The biotin-labeled aRNA (10 ug) was then hybridized to the Affymetrix Human U133 Plus 2.0 gene chip (Affymetrix). Each sample was hybridized to an individual chip, for a total of 6 chips.

scan_protocol: The image data were acquired on an Affymetrix Genechip Scanner 3000.

data_processing: An absolute analysis of the resulting output was performed with Affymetrix Data Mining Tool, Version 3.0 software.

source_name: H1p50 hESC under 4% O2

label_protocol: RNA (5 ug) was used to prepare the biotin-labeled anti-sense RNA (aRNA) target by using the GeneChip® one-cycle target labeling and control reagents (#900493, Affymetrix, Santa Clara, CA).

growth_protocol: Human ESC H1 (WA01) at passage 23 and H9 (WA09) at passage 19 were purchased from WiCell Research Institute (Madison, WI) and cultured in six-well tissue culture plates on a monolayer of γ-irradiated (8,000 cGy) mouse embryonic fibroblast (MEF) feeder cells until passage number 33 and 30, respectively. Thereafter, cells were cultured on a substratum of 1:30 dilutions of Matrigel™ in medium conditioned by MEF.

extract_protocol: RNA was isolated from hESCs by using RNA STAT-60 reagent (Tel-Test Inc, Friendswood, TX) according to the manufacturer's instructions.

treatment_protocol: hESC were cultured in either a standard humidified tissue culture CO2 incubator, set at 5% CO2 in air, or a tri-gas incubator (Heraeus HERAcell 150) at a 4% O2, 5% CO2 setting. Oxygen levels, measured by using a Bacharach CO2/O2 Analyzer (Bacharach, Model 2830), were ~19% in the standard incubator and 3.5–4.5% in the low O2 incubator. To minimize differences unrelated to O2 tension, experimental groups within replicates were cultured in the same medium and passaged at approximately the same time. The H1 and H9 hESC lines had been maintained in a physiological O2 (3-5% O2) atmosphere since passage 26 and 23, respectively. RNA was isolated from H1 cells after 7 days of culture at two independent passage numbers (p37 and p50) and had been maintained on Matrigel™ for 3 and 16 passages, respectively. RNA from H9 cells was isolated at passage 32 and had been grown on Matrigel™ for 3 passages.

tag: human embronic stem cell, NIH code:WA01


title: chondrocyte_rep2


title: H9 hESC_20% O2 rep1

description: Gene expression data from human embronic stem cell cultured under 20% oxygen condition for 7days

source_name: H9p32 hESC under 20% O2 for 7days

tag: human embronic stem cell, NIH code:WA09


title: H1 hESC_20% O2 rep1

source_name: H1p37 hESC under 20% O2 for 7days


title: H1 hESC_20% O2 rep2

source_name: H1p50 hESC under 20% O2 for 7days


title: adipocyte_rep3

tag: Human iliac mesenchymal stem cells (MSC) were purchased from BioWhittaker Inc (Walkersville, MD) or obtained from iliac crest according to protocol approved by ethical authorities at Hiroshima University. Culture of MSC and their differentiation from the adipocyte lineage were performed as described. (Matsubara T, Suardita K, Ishii M, Sugiyama M, Igarashi A, et al. (2005) Alveolar bone marrow as a cell source for regenerative medicine


title: osteoblast_rep2


title: H9 hESC_4% O2 rep1

source_name: H9p32 hESC under 4% O2


title: midbrain mptp, biological rep3

status: Public on Oct 21 2008

city: Fairfax

first: Daniel

middle: M

last: Sforza

state: VA

address: 4400 University Drive

department: Computational and Data Sciences

institute: George Mason University

description: Gene expression data from midbrain, MPTP i.p.

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Robust Microarray Analysis (RMA)

source_name: Mus musculus midbrain, MPTP i.p.

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen Inc., Chatsworth, USA) was used for extraction of total RNA and performed according to the manufacturer's instructions.

treatment_protocol: Animals were randomly assigned to either the MPTP (n = 3) or saline (n = 3) groups. The MPTP treatment consisted of 30 mg/kg MPTP, i.p., calculated as the free base (MPTP-HCl, Sigma) administered once daily for 5 days. At four days after the last MPTP injection, the animals were briefly anaesthetized and immediately sacrificed by decapitation.

tag: Strain

tag: Gender

value: male

tag: Age

value: 14 weeks

tag: Tissue

value: midbrain

tag: Treatment

value: MPTP i.p.


title: frontal cortex mptp, biological rep2

description: Gene expression data from frontal cortex, MPTP i.p.

source_name: Mus musculus frontal cortex, MPTP i.p.

value: frontal cortex


title: striatum mptp, biological rep2

description: Gene expression data from striatum, MPTP i.p.

source_name: Mus musculus striatum, MPTP i.p.

value: striatum


title: striatum mptp, biological rep3


title: striatum control, biological rep3

description: Gene expression data from striatum, saline i.p.

source_name: Mus musculus striatum, saline i.p.

value: saline i.p.


title: frontal cortex mptp, biological rep1


title: striatum mptp, biological rep1


title: chondrocyte_rep1

description: DNA microarray analysis was performed by KURABO (Osaka, Japan) GeneChip Custom Analysis Service with Human Genome U133 Plus 2.0 chips.

hyb_protocol: The hybridization was performed (Hybridization Oven 640 110V, Affymetrix 800138) according to the manufacturer's instructions (Expression Analysis Technical Manual, 701021 Rev. 5, Section2 Eukaryotic Sample and Array Processing, Chapter2 Eukaryotic Target Hybridization, Affymetrix). GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix 00-0079)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix 00-0074)

value: differences between alveolar and iliac bone marrow stromal cells. J Bone Miner Res 20:399-409.)


title: adipocyte_rep2


title: midbrain control, biological rep3

description: Gene expression data from midbrain, saline i.p.

source_name: Mus musculus midbrain, saline i.p.


title: midbrain mptp, biological rep1


title: midbrain mptp, biological rep2


title: striatum control, biological rep2


title: midbrain control, biological rep2


title: frontal cortex mptp, biological rep3


title: striatum control, biological rep1


title: frontal cortex control, biological rep1

description: Gene expression data from frontal cortex, saline i.p.

source_name: Mus musculus frontal cortex, saline i.p.


title: frontal cortex control, biological rep3


title: midbrain control, biological rep1


title: adipocyte_rep1

tag: Human iliac mesenchymal stem cells (MSC) were purchased from BioWhittaker Inc (Walkersville, MD) or obtained from iliac crest according to protocol approved by ethical authorities at Hiroshima University. Culture of MSC and their differentiation from the adipocyte lineage were performed as described.

tag: (Matsubara T, Suardita K, Ishii M, Sugiyama M, Igarashi A, et al. (2005)

tag: Alveolar bone marrow as a cell source for regenerative medicine:

tag: differences between alveolar and iliac bone marrow stromal cells. J Bone Miner Res 20


title: HeLa_rep2

status: Public on Oct 20 2008

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

hyb_protocol: 20 micrograms of biotin labeled RNA was fragmented to ~200 bp fragments by incubating in a buffer containing 200 mM Tris-Acetate pH 8.2, 500 mM Potassium Acetate and 500 Magnesium Acetate for 35 minutes at 95C. Fragments were hybridized to Affymetrix U133A plus 2.0 chips for 16 hrs, washed and stained on an Affymetrix fluidics station.

scan_protocol: Scanning was performed with the Affymetrix GeneChip scanner using default settings.

data_processing: Raw signal values were normalized using RMA.

source_name: HeLa

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

extract_protocol: Total RNA extraction was performed using a Qiagen RNeasy mini kit following the manufacturer's directions.

tag: HeLa


title: HeLa_rep1


title: D3-pOct4 (pass 33) without LIF

status: Public on Oct 17 2008

city: Seville

first: Rafael

middle: A.

last: Tapia Limonchi

state: Seville

address: Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93

department: Department of Cell Therapy and Regenerative Medicine

institute: Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)

description:
D3-pOct4 cells cultured in the absence of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 2

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: D3-pOct4 mouse embryonic stem cells without LIF

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.

growth_protocol: The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2

extract_protocol: Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer

treatment_protocol: For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.

tag: D3-pOct4 treated without LIF, replicate 2


title: frontal cortex control, biological rep2


title: D3-pOct4 (pass 31) without LIF plus NO

description:
D3-pOct4 cells cultured in the absence of LIF with 2µM of DETA/NO were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 1

source_name: D3-pOct4 mouse embryonic stem cells without LIF plus NO

tag: D3-pOct4 treated without LIF adding NO, replicate 1


title: D3-pOct4 (pass 34) without LIF

description:
D3-pOct4 cells cultured in the absence of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 3

tag: D3-pOct4 treated without LIF, replicate 3


title: D3-pOct4 (pass 33) without LIF plus NO

description:
D3-pOct4 cells cultured in the absence of LIF with 2µM of DETA/NO were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 2

tag: D3-pOct4 treated without LIF adding NO, replicate 2


title: D3-pOct4 (pass 31) without LIF

description:
D3-pOct4 cells cultured in the absence of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 1

tag: D3-pOct4 treated without LIF, replicate 1


title: D3-pOct4 (pass 33) with LIF

description:
D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 2

source_name: D3-pOct4 mouse embryonic stem cells with LIF

tag: D3-pOct4 treated with LIF, replicate 2


title: NB tumor NBAF98

status: Public on Oct 16 2008

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

department: Genetics

country: France

institute: Institut Curie

hyb_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.

data_processing: GC-RMA normalization

source_name: neuroblastic tumor

extract_protocol: Total RNAs were isolated using the Trizol Reagent

tag: stage 4, neuroblastoma


title: NB tumor NBAF100

scan_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.

tag: stage not available, neuroblastoma


title: D3-pOct4 (pass 34) with LIF

description:
D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 3

tag: D3-pOct4 treated with LIF, replicate 3


title: D3-pOct4 (pass 34) without LIF plus NO

description:
D3-pOct4 cells cultured in the absence of LIF with 2µM of DETA/NO were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 3

tag: D3-pOct4 treated without LIF adding NO, replicate 3


title: NB tumor NBAF63

label_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.

tag: stage 3, neuroblastoma, localized, MYCN amplified


title: NB tumor NBAF90

tag: stage 2, ganglioneuroblastoma, tumor 89, nodule 2


title: NB tumor NBAF56

tag: neuroblastoma tumor, stage 4s, MYCN non amplified


title: NB tumor NBAF99

tag: stage 2, neuroblastoma


title: NB tumor NBAF65

tag: neuroblastoma, stage 1 or 2, MYCN nonamplified


title: NB tumor NBAF66

tag: neuroblastoma, stage 4, MYCN nonamplified


title: NB tumor NBAF55

tag: neuroblastoma, stage 1, MYCN nonamplified


title: NB tumor NBAF64


title: NB tumor NBAF59

tag: neuroblastoma, stage 2, MYCN nonamplified


title: NB tumor NBAF60


title: NB tumor NBAF88


title: NB tumor NBAF91

tag: stage 2, ganglioneuroblastoma, tumor 89, nodule3


title: NB tumor NBAF57

tag: neuroblastoma, stage 4, MYCN amplified


title: NB tumor NBAF86

tag: stage stage 1, neuroblastoma


title: NB tumor NBAF61

tag: neuroblastoma, stage 4s, MYCN nonamplified


title: NB tumor NBAF54


title: NB tumor NBAF51


title: NB tumor NBAF53


title: NB tumor NBAF50


title: NB tumor NBAF89

tag: stage 2, ganglioneuroblastoma, tumor 89, nodule 1


title: NB tumor NBAF48


title: NB tumor NBAF87

tag: stage stage 2B, neuroblastoma


title: NB tumor NBAF49


title: D3-pOct4 (pass 31) with LIF

description:
D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 1

growth_protocol: The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM of sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2.

treatment_protocol: The undifferentiated state of the cells was maintained by adding of 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding of 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were cultured as basal condition. All the cultures were maintained for 7 days.

tag: D3-pOct4 treated with LIF, replicate 1


title: osteoblast_rep3

tag: Human iliac mesenchymal stem cells (MSC) were purchased from BioWhittaker Inc (Walkersville, MD) or obtained from iliac crest according to protocol approved by ethical authorities at Hiroshima University. Culture of MSC and their differentiation from the osteoblast lineage were performed as described. (Matsubara T, Suardita K, Ishii M, Sugiyama M, Igarashi A, et al. (2005) Alveolar bone marrow as a cell source for regenerative medicine


title: NB tumor NBAF44

tag: neuroblastoma, stage 4, MYCN amplified, post-chemotherapy


title: NB tumor NBAF45

tag: neuroblastoma, stage 1, MYCN amplified


title: NB tumor 43

tag: neuroblastoma, stage 2, MYCN amplified


title: GN NBAF46

tag: stage 2, ganglioneuroma


title: NB tumor NBAF41


title: NB tumor NBAF42


title: NB tumor NBAF47

tag: neuroblastoma, multifocal, MYCN nonamplified


title: NB tumor NBAF17

data_processing: GC-RMA

tag: neuroblastoma, stage 3, MYCN amplified


title: NB tumor NBAF34


title: NB tumor NBAF29

tag: neuroblastoma, stage 3,MYCN nonamplified


title: NB tumor NBAF20

tag: stage 1, neuroblastoma, localized, MYCN amplified


title: NB tumor NBAF40


title: NB tumor NBAF28

tag: neuroblastoma, stage 3, MYCN nonamplified


title: GN NBAF21

tag: stage 1, ganglioneuroma


title: GGNB NBAF32

tag: localized tumor, ganglioneuroblastoma


title: GGNB NBAF24

tag: stage 2, ganglioneuroblastoma, tumor 89, nodule 4


title: GGNB NBAF30

tag: stage 2, ganglioneuroblastoma


title: NB tumor NBAF23


title: NB tumor NBAF22

tag: neuroblastoma, stage 1, MYCN nonamplified


title: NB tumor NBAF26

tag: neuroblastoma, stage 4s, MYCN nonamplified


title: NB tumor NBAF27

tag: neuroblastoma, stage 4, MYCN amplified


title: GGNB NBAF38


title: NB tumor NBAF25


title: NB tumor NBAF19

tag: neuroblastoma, stage 4, MYCN nonamplified


title: NB tumor NBAF11

tag: neuroblastoma, stage 4, post-chemotherapy


title: NB tumor NBAF15

tag: neuroblastoma, stage 2, MYCN nonamplified


title: NB tumor NBAF18

tag: stage 2, neuroblastoma, localized, MYCN nonamplified


title: GGNB tumor NBAF16

tag: stage 4, Ganglioneuroblastoma, MYCN nonamplified


title: NB tumor NBAF12


title: NB tumor NBAF7

tag: Neuroblastoma, stage 4, MYCN amplified


title: NB tumor NBAF8

tag: stage 1, neuroblastoma, localized, MYCN nonamplified


title: NB tumor NBAF4

tag: NB, stage 3, MYCN nonamplified, poorly differentiated


title: NB tumor NBAF14

tag: neuroblastoma tumor, stage 1, MYCN nonamplified


title: NB tumor NBAF6


title: SJNB8-MSX1 clone K5, t = 192 hrs

status: Public on Oct 15 2008

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.

hyb_protocol: 10 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer’s protocol (Affymetrix).

data_processing: Expression data (.cel files) were normalized with the MAS5 algorithm (target 	signal = 100) using GCOS software (Affymetrix).

source_name: SJNB8-MSX1 cells at 192hrs

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer both before and after fragmentation.

growth_protocol: SJNB8-MSX1 cells were grown in high-glucose DMEM without sodium-pyruvate with pyridoxine-HCl (Gibco 41965-039), supplemented with 10 % heat-inactivated foetal calf serum (Gibco 10106), 	2 mM L-Glutamine (ICN 1680149),1 x MEM (Minimal Non-Essential Amino Acids, Gibco 11140-035) and 10 U penicillin/10 μg streptomycin (Sigma P0781) per ml. Cells were maintained at 37 °C, in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy (Qiagen) according to the manufacturer's protocol.

treatment_protocol: To activate MSX1 in SJNB8 cells, doxycycline was added to the medium to a 	final concentration of 100 ng/ml.

tag: SJNB8, a human neuroblastoma tumor cell line, was stably transfected with the pcDNA6/TR expression vector (Invitrogen V1025-20) for constitutive expression of the TetR tetracycline repressor gene, and with the MSX1 gene in the pcDNA4/TO vector (Invitrogen V1030-20) for tetracycline/doxycycline-responsive expression of MSX1.


title: SJNB8-MSX1 clone K5, t = 48 hrs

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.

source_name: SJNB8-MSX1 cells at 48 hrs


title: NB tumor NBAF1

source_name: neuroblastoma tumor

extract_protocol: Total RNAs were isolated using the Trizol reagent

tag: Stage 4, MYCN nonamplified


title: NB tumor NBAF13

tag: neuroblastoma, stage 3, MYCN amplified


title: GN NBAF5

tag: stage 1, Ganglioneuroma


title: Rag-IgH_224

status: Public on Oct 12 2008

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression analysis was conducted using Mouse 430v2 GenechipÆ arrays (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3í Amplification One-Cycle Target labeling kit according to manufacturerís protocol.  For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the GenechipÆ Operating Software (Version 1.2.0.037).

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 7.1).  This system performs data pre-processing and error modeling as described in Weng (2006).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

source_name: Pre-B cells from RAG-1-deficient mice with an IgH transgene

growth_protocol: RNA harvested immediately after purification of cells from bone marrow

extract_protocol: RNA was isolated using Qiagen RNeasy technology following the manufacturer?s instructions.

treatment_protocol: RNA from purified bone marrow B cells

tag: Purified whole cell RNA


title: Rag-IgH_232

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

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

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


title: FoxD3-VP16-transfected B16-F10 cells (rep 3)

city: Davis

first: Aaron

last: Thomas

address: One Shields Ave.

department: MCB

institute: University of California, Davis

description: Analyzed in dChip

hyb_protocol: Hybridization was done by the microarray core facility at UC Davis, using the standard Affymetrix protocol on a Fluidics Station 450.

scan_protocol: Scanned on a 3000 GeneChip Scanner according to the instructions provided by Affymetrix

data_processing: MAS5 algorithm

source_name: B16-F10 mouse melanoma cells, FoxD3-VP16-pMES transfection

label_protocol: RNA was labeled using the TargetAmp™ 1-Round Biotin-aRNA Amplification kit from Epicentre Biotechnologies according to the manufacturer's protocol.  The resulting amino-allyl aRNA was biotinylated using Biotin-X-X-NHS, also from Epicentre, according to the manufacturer's protocol.

growth_protocol: grown in DMEM with 10% Hyclone Bovine Growth Serum supplemented with pen/strep

extract_protocol: 24 hours after transfection, cells were sorted and EGFP-postive cells were collected by FACS.   RNA was isolated using Trizol.

treatment_protocol: transfected with FoxD3-VP16-pMES vector (expresses chicken FoxD3-VP16 and EGFP under control the chick beta-actin promoter.  FoxD3-VP16 has the C-terminal repression domain replaced by the VP16 transactivation domain)

tag: B16-F10 mouse melanoma cells

tag: ATCC


title: FoxD3-VP16-transfected B16-F10 cells (rep 4)

description: Analyzed in dChip


title: FoxD3-VP16-transfected B16-F10 cells (rep 2)

description: Analyzed in dChip


title: control transfected B16-F10 cells (rep 4)

description: Analyzed in dChip

source_name: B16-F10 mouse melanoma cells, control tranfsection

label_protocol: RNA was labeled using the TargetAmp™ 1-Round Biotin-aRNA Amplification kit from Epicentre Biotechnologies according to the manufacturer's protocol.  The resulting amino-allyl aRNA was biotinylated using Biotin-X-X-NHS, also from Epicentre, according to the manufacturer's protocl.

treatment_protocol: transfected with empty pMES vector


title: Artemis-IgH_186

source_name: Pre-B cells from Artemis-deficient mice with an IgH transgene


title: FoxD3-transfected B16-F10 cells (rep 4)

description: Analyzed in dChip

source_name: B16-F10 mouse melanoma cells, FoxD3-pMES transfection

treatment_protocol: transfected with FoxD3-pMES vector (expresses chicken FoxD3 and EGFP under control the chick beta-actin promoter)


title: NB tumor NBAF2

tag: NB, stage 1, MYCN amplified


title: FoxD3-transfected B16-F10 cells (rep 2)

description: Analyzed in dChip


title: FoxD3-VP16-transfected B16-F10 cells (rep 1)

description: Analyzed in dChip


title: SJNB8-MSX1 clone K5, t = 0 hrs

description: SJNB8-MSX1 cells were grown under standard conditions and harvested at 		diferent timepoints after the addition of doxycycline. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 arrays.

source_name: SJNB8-MSX1 cells at 0 hrs

growth_protocol: SJNB8-MSX1 cells were grown in high-glucose DMEM without sodium-pyruvate with pyridoxine-HCl (Gibco 41965-039), supplemented with 10 % heat-inactivated foetal calf serum (Gibco 10106), 2 mM L-Glutamine (ICN 1680149), 1 x MEM (Minimal Non-Essential Amino Acids, Gibco 11140-035) and 10 U penicillin/10 μg streptomycin (Sigma P0781) per ml. Cells were maintained at 37 °C, in a humidified atmosphere containing 5% CO2


title: Artemis-IgH_143


title: SJNB8-MSX1 clone k2, t = 0 hrs


title: FoxD3-transfected B16-F10 cells (rep 3)

description: Analyzed in dChip


title: control transfected B16-F10 cells (rep 3)

description: Analyzed in dChip


title: control transfected B16-F10 cells (rep 1)

description: Analyzed in dChip


title: SJNB8-MSX1 clone K2, t = 48 hrs

tag: SJNB8, a human neuroblastoma tumor cell line, was stably transfected with the pcDNA6/TR expression vector (Invitrogen V1025-20) for constitutive expression  of the TetR tetracycline repressor gene, and with the MSX1 gene in the  pcDNA4/TO vector (Invitrogen V1030-20) for tetracycline/ doxycycline-responsive expression of MSX1.


title: FoxD3-transfected B16-F10 cells (rep 1)

description: Analyzed in dChip


title: control transfected B16-F10 cells (rep 2)

description: Analyzed in dChip


title: NB tumor NBAF39

tag: neuroblastoma, stage 2, MYCN non amplified


title: SJNB8-MSX1 clone K5, t = 24 hrs

source_name: SJNB8-MSX1 cells at 24 hrs


title: AA2 CJ31 b

description: Gene expression analysis was conducted using Mouse 430v2 Genechip® arrays (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.  For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 6.0).  This system performs data pre-processing and error modeling as described in Weng (2006).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

source_name: Artemis- and ATM- deficient v-abl-transformed pre-B cell

growth_protocol: Treated at 1 million cells per ml in DMEM 10% FCS

extract_protocol: RNA was isolated using Qiagen RNeasy technology following the manufacturer¹s instructions.

treatment_protocol: 3um STI571 for 48 hours

tag: G1-phase pre-B cells


title: IkB DN #3

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

source_name: Artemis-deficient v-abl-transformed pre-B cells expressing dominant negative IkB

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


title: Art 5.1

source_name: Artemis-deficient v-abl-transformed pre-B cell


title: IkB DN #6


title: IkB DN #4 b


title: AA2 CJ31


title: Art 2.1


title: R2K Bcl.3

source_name: RAG-2-deficient v-abl-transformed pre-B cell


title: ATM-2A

source_name: Wild type v-abl-transformed pre-B cell


title: Art.1 INV4


title: AA1 CJ46 b


title: AA1 CJ 46a


title: A70.1 b


title: R2K Bcl.2


title: A70.2


title: Mouse PUER 0h-3

status: Public on Oct 11 2008

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

institute: Institute of Human Genetics

description: Gene expression data from PU-ER cells without expression of PU.1.

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays (expression arrays) according to manufacturer’s protocols at the KFB Regensburg

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 Blank7G (Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression Console and Genomatix Software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: PU-ER cells without expression of PU.1

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix expression arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using 300ng total RNA and standard method according to the manufacturer’s protocols (Affymetrix, GeneChip WT terminal labelling kit 900671).

growth_protocol: PUER cells were cultivated in IMDM supplemented with penicillin/streptomycin (10,000 U/ml), glutamin (200 mM),  ß-ME (50  M), mouse IL-3 (5 ng/ml, Biosource, Camarillo, CA, USA), puromycin (1  g/ml), and 10% FCS.

extract_protocol: Total RNA from the PUER cells was extracted according to the manufacter's instructions using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA)

treatment_protocol: To activate the PU.1-ER fusion protein, PUER cells were centrifuged and resuspended in medium containing 100nM tamoxifen [4-hydroxytamoxifen (OHT)]

tag: PU.1 -/- deficient myeloid progenitors with PU-ER fusion protein


title: R2K Bcl.1


title: Mouse PUER 24h-1

description: Gene expression data from PUER cells 24h after induction of PU.1 expression with 100nM OHT


title: Mouse PUER 24h-2

source_name: PUER cells 24h after induction of PU.1 expression with 100nM OHT


title: Mouse PUER 0h-1


title: Mouse PUER 24h-3


title: FNR1 mutation in Wassilewskija ecotype

city: suita

first: Guy

middle: Thomas

last: Hanke

state: Osaka

address: 3-2 Yamadaoka

department: Institute for Protein Research

institute: Osaka University

description: gene expression data from fnr1 mutant Wassilewskija ecotype 31 day old plants

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Single Array Analysis and comparison analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting.

organism: Arabidopsis thaliana

source_name: above ground tissues 31 day old. 4 hours into light period

label_protocol: cDNA were synthesized by GeneChip T7-Oligo(dT) Promoter Primer Kit（Affymetrix) and TaKaRa cDNA Synthesis Kit （TaKaRa Bio） from 3ug total RNA. Biotinylated cRNA were synthesized by IVT Labeling Kit(Affymetrix)

growth_protocol: plants were grown on peat based soil (pH 6.5) under approximately 100 μmol quanta  m-2 s-1 in an 8 h light/16 h dark cycle at 21 °C.

extract_protocol: RNAiso(TaKaRa Bio) extraction of total RNA was performed according to the manufacturer's instructions.


title: Mouse PUER 0h-2


title: Wild Type Wassilewskija ecotype

description: gene expression data from wild type Wassilewskija ecotype 31 day old plants


title: m718 rhabdomyosarcoma

status: Public on Oct 10 2008

first: Ou

last: Ma

address: One Baylor Plaza

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

description: Gene expression in mc3T3 mouse osteoblast without treatment.

hyb_protocol: Standard Affymetrix hybridization protocol. The exact protocol is not available, but standard procedure can be found at: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: GeneChips were scanned with GeneChip® Scanner 3000 following standard Affymetrix procedure.

data_processing: Data was analyzed with GeneChip® Operating Software, or GCOS (Affymetrix).

source_name: m718 rhabdomyosarcoma

label_protocol: Standard Affymetrix label protocol from 5ug total RNA. The exact protocol is not available, but standard procedure can be found at: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

extract_protocol: RNA extracted with Qiagen RNeasy Mini Kit, following manufacturer's instructions.

tag: Rhabdomyosarcoma arisen from p53+/- mouse. Non-treated.


title: FNR1 mutation in columbia ecotype

description: gene expression data from fnr1 mutant columbia ecotype 31 day old above ground tissue

tag: fnr1 mutation columbia ecotype 31 day old plants


title: m520 osteosarcoma

source_name: m520 osteosarcoma

tag: Osteosarcoma arisen from p53+/- mouse. Non-treated.


title: c3261 osteosarcoma

source_name: c3261 osteosarcoma


title: m824 osteosarcoma

source_name: m824 osteosarcoma


title: Wild type columbia

description: gene expression in Wild type columbia Arabidopsis 31 day old above ground tissues 4 hours into the light period

data_processing: Single Array Analysis and comparison analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting.

tag: wild type columbia ecotype 31 day old plants


title: G105-3

city: Phoenix

first: Brock

last: Armstrong

state: AZ

address: 445 N. 5th Street

department: Cancer and Cell Biology

institute: TGen

description: This tumor has biological replicates G105-1, G105-2, and G105-4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133A 2.0 arrrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix protocols were followed using GS300.

organism:
Homo sapiens
Mus musculus

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

extract_protocol: Total RNA was extracted from Trizol solution, according to manufacturer's instructions and followed with purification through RNeasy mini kit (Qiagen, Valencia, Ca). Total RNA quality and quantity were assessed by Bioanalyzer RNA 6000 Nano LabChip Kit (Agilent Technologies, Palo Alto, CA). Samples selected for the study contained intact RNA as determined by visual inspection of electropherograms for distinct 18S and 28S ribosomal peaks.

tag: Mouse brain with human GBM cells in jected

tag: exposed to cilengitide for 8 hour


title: G105-1

description: This tumor has biological replicates G105-2, G105-3, and G105-4

scan_protocol: Standard Affmetrix protocols were followed using GS300.

tag: Mouse brain with human GBM 105 cells injected


title: m825 osteosarcoma

city: Houston

source_name: m825 osteosarcoma


title: m525 osteosarcoma

source_name: m525 osteosarcoma


title: G105-4

description: This tumor has biological replicates G105-1, G105-2, and G105-3

tag: Mouse brain with human GBM cells injected


title: m849 osteosarcoma

source_name: m849 osteosarcoma


title: G105-2

description: This tumor has biological replicates G105-1, G105-3, and G105-4

tag: Mouse brain with human GBM tumor 105 injected


title: G104-1

description: This tumor has biological replicates G104-2, G104-3, and G104-4

tag: Mouse brain injected with human GBM tumor 104

tag: exposed to cilengitide for 1 hour


title: G104-2

description: This tumor has biological replicates G104-1, G104-3, and G104-4

tag: Mouse brain injected with GBM 104


title: G103-4

description: This tumor has biological replicates G103-1, G103-2, and G103-3

tag: Mouse brain injected with human GBM G103

tag: control; no cilengtide exposure


title: c3193 osteosarcoma

source_name: c3193 osteosarcoma


title: m710 osteosarcoma

source_name: m710 osteosarcoma


title: o7-1 osteosarcoma

source_name: o7-1 osteosarcoma


title: o19 osteosarcoma

source_name: o19 osteosarcoma


title: G103-2

description: This tumor has biological replicates G103-1, G103-3, and G103-4

tag: Fresh frozen mouse brain injected with human GBM 103


title: c2984 osteosracoma

source_name: c2984 osteosarcoma

tag: c2984, osteosarcoma from p53+/- mouse. Non-treated.

tag: Chromosome 9A1 amplicon positive.


title: G104-3

description: This tumor has biological replicates G104-1, G104-2, and G104-4

tag: Mouse brain with human GBM tumor G104


title: G103-1

description: This tumor has biological replicates G103-2, G103-3, and G103-4

tag: Fresh frozen brain from a mouse injected with tumor G103.


title: G103-3

description: This tumor has biological replicates G103-1, G103-2, and G103-4

tag: Mouse brain injected with G103 GBM cells


title: G104-4

description: This tumor has biological replicates G104-1, G104-2, and G104-3

tag: Mouse brain injected with human GBM 104


title: mc3T3 osteoblast control

source_name: mc3T3 osteoblast RNA

growth_protocol: Cells were cultured in alpha-MEM with 10% FBS and 1%Pen-Strep at 37oC with 5% CO2.

tag: Cell type

value: mc3T3 mouse osteoblast, non-tumorigenic. Non-treated.


title: L591 HL Cell Line_rep1

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: total RNA from cultivated cells

hyb_protocol: Affymetrix hybridization protocol onto Human Genome U133 Plus 2.0 Array

scan_protocol: Affymetrix Standard protocol

data_processing: GCOS, RMA

source_name: HRS cell, L591 HL Cell line, rep1

label_protocol: Affymetrix labelling protocol

growth_protocol: cells were seeded out at 3E5/ml grown over night in RPMI containing 10% FCS and antibiotics.

extract_protocol: Total cellular RNA was isolated using RNeasy Mini Kit (Qiagen)

tag: cultivated HRS cells


title: L428 HL Cell Line_rep3

description: total RNA from cultivated cells

source_name: HRS cell, L428 HL Cell line, rep3

treatment_protocol: cells were seeded out at 3E5/ml grown over night in RPMI containing 10% FCS and antibiotics


title: L591 HL Cell Line_rep3

description: total RNA from cultivated cells

source_name: HRS cell, L591 HL Cell line, rep3


title: KMH2 HL Cell Line_rep2

description: total RNA from cultivated cells

source_name: HRS cell, KMH2 HL Cell line, rep2


title: c2846-(1) osteosarcoma

source_name: c2846-(1) osteosarcoma

tag: Osteosarcoma arisen from p53+/- mouse. Non-treated.

tag: Chromosome 9A amplicon positive.


title: L591 HL Cell Line_rep2

description: total RNA from cultivated cells

source_name: HRS cell, L591 HL Cell line, rep2


title: L428 HL Cell Line_rep2

description: total RNA from cultivated cells

source_name: HRS cell, L428 HL Cell line, rep2


title: L1236 HL Cell Line_rep3

description: total RNA from cultivated cells

source_name: HRS cell, L1236 HL Cell line, rep3


title: KMH2 HL Cell Line_rep1

description: total RNA from cultivated cells

source_name: HRS cell, KMH2 HL Cell line, rep1


title: L428 HL Cell Line_rep1

description: total RNA from cultivated cells

source_name: HRS cell, L428 HL Cell line, rep1


title: KMH2 HL Cell Line_rep3

description: total RNA from cultivated cells

source_name: HRS cell, KMH2 HL Cell line, rep3


title: GC B cell_rep3

description: total RNA from MACS sorted GC Bells

source_name: GC B cell, rep3

growth_protocol: cells were snap frozen after isolation.

treatment_protocol: Mononuclear cells were isolated by Ficoll-Isopaque centrifugation of tonsils from pediatric patients under informed consent and with ethical approval. Briefly, CD10+ GC B cells were isolated by magnetic separation at 4oC with anti-CD10-Phycoerythrin (PE) and anti-PE microbeads with LS columns (Miltenyi Biotec).

tag: B cells sorted using CD10 MACS from reactive human tonsils


title: GC B cell_rep1

description: total RNA from MACS sorted GC Bells

source_name: GC B cell, rep1


title: GC B cell_rep2

description: total RNA from MACS sorted GC Bells

source_name: GC B cell, rep2


title: L1236 HL Cell Line_rep1

description: total RNA from cultivated cells

source_name: HRS cell, L1236 HL Cell line, rep1


title: GC B cell_pSG5_rep2

description: Amplified total RNA from transfected and FACS sorted GC Bells

source_name: GC B cell transfected with empty vector (pSG5), rep2

growth_protocol: GC B cells were cultivated for 16 hours post-transfection in RPMI supplemented with 10% FCS and antibiotics.

extract_protocol: Total cellular RNA was isolated using RNeasy Micro Kit, Qiagen, and RNA was amplified with ExpressArt mRNA Amplification kit protocol (Amptech).

treatment_protocol: 4 x E6 CD10+ cells in 100 ul B cell solution were nucleofected with 7ug pSG5 or pSG5-LMP1 expression vector with 3ug pMACSLNFGR using program U15 on the Nucleofector I (Amaxa); cultivated for 16h and stained with anti-LNGRF-FITC or anti-LNGRF- Allophycocyanin and propidium iodide. FITC-labeled and PI-negative cells were collected by FACS on a MoFlo sorter

tag: GC B cells sorted using CD10 MACS from reactive human tonsils


title: GC B cell_LMP1_rep2

source_name: GC B cell transfected with LMP1 expression vector (pSG5-LMP1), rep2


title: GC B cell_pSG5_rep1

source_name: GC B cell transfected with empty vector (pSG5), rep1


title: GC B cell_pSG5_rep3

source_name: GC B cell transfected with empty vector (pSG5), rep3


title: GC B cell_LMP1_rep3

source_name: GC B cell transfected with LMP1 expression vector (pSG5-LMP1), rep3


title: GC B cell_LMP1_rep1

source_name: GC B cell transfected with LMP1 expression vector (pSG5-LMP1), rep1


title: Sample 25  primary neuroblastoma

status: Public on Oct 09 2008

city: Newcastle upon Tyne

first: Michael

middle: Stewart

last: Jackson

address: Central Parkway

department: Institute of Genetic Medicine

institute: Newcastle University

hyb_protocol: Biotinylated and fragmented cRNA (15 ug) was hybridised to the GeneChip arrays at 45oC for 16 hours, washed, and stained with streptavidin phycoerythrin using an Affymetrix FS-450 fluidics station.

scan_protocol: Scanned using Genechip Scanner 3000

data_processing: Raw data were firstly scaled using GCOS 1.1.1 software to a target signal of 500. Data were then imported into GeneSpring GX (Agilent Technologies, Santa Clara, CA, USA) when a ‘per gene normalisation’ to the median expression level of the gene across all samples was performed.

source_name: primary tumour

label_protocol: Standard Affymetrix Protocol

extract_protocol: Total RNA was extracted using the RNeasy Micro kit (Qiagen, Hilden, Germany).

treatment_protocol: Tumour samples were snap frozen and stored at -80oC prior to RNA extraction.

tag: Gender

tag: Age

value: 1.5 year

tag: Stage

tag: MYCN amp.:yes

tag: 1p del

value: yes

tag: 11q del

value: no

tag: 17q gain


title: Sample 28  primary neuroblastoma

value: 4 years

tag: MYCN amp.:no


title: Sample 33  primary neuroblastoma

value: <1 year

tag: 11q del:not known


title: L1236 HL Cell Line_rep2

description: total RNA from cultivated cells

source_name: HRS cell, L1236 HL Cell line, rep2


title: Sample 27  primary neuroblastoma

value: 2 years


title: Sample 34  primary neuroblastoma

value: mixed


title: Sample 30  primary neuroblastoma


title: Sample 31  primary neuroblastoma

value: female

tag: 17q gain yes


title: Sample 16  primary neuroblastoma


title: Sample 29  primary neuroblastoma

value: male

value: 2.5 years


title: Sample 32  primary neuroblastoma

value: 1 year


title: Sample 19  primary neuroblastoma


title: Sample 26  primary neuroblastoma


title: Sample 24  primary neuroblastoma


title: Sample 23  primary neuroblastoma


title: Sample 13  primary neuroblastoma

value: 8 years


title: Sample 17  primary neuroblastoma


title: Sample 20  primary neuroblastoma


title: Sample 18  primary neuroblastoma


title: Sample 9  primary neuroblastoma


title: Sample 10  primary neuroblastoma

tag: 11q del:no


title: Sample 6 primary neuroblastoma


title: Sample 7  primary neuroblastoma


title: Sample 5  primary neuroblastoma

value: 10 years


title: Sample 11  primary neuroblastoma


title: Sample 14  primary neuroblastoma


title: Sample 8  primary neuroblastoma


title: Sample 3  primary neuroblastoma


title: Sample 4  primary neuroblastoma


title: Sample 2  primary neuroblastoma


title: Ta side population 6Tsp

city: Philadelphia

first: Murat

middle: T

last: Budak

state: PA

institute: University of Pennsylvania

description:
SP cell preparations were washed, pelleted and resuspended in 20µl of PBS and stored at –80oC until processing for microarray analysis using manufacturers instructions and previously described methods from our laboratory . Total RNA was isolated using RNeasy micro kit (Qiagen, Valencia, CA). The purity, concentration and integrity of RNA was determined using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). RNAs were subjected to linear amplification using the GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).
Six independently separated EOM and six TA SP cell preparations were used for microarray analysis using the Affymetrix® Mouse 430 ver 2.0 GeneChip arrays.  Raw intensities for each probe set were stored in electronic formats by expression summaries calculated using Microarray Suite version 5.0 (MAS5) algorithms.

hyb_protocol: The GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: Agilent model G2500A GeneArray scanner used.

data_processing: MAS5 normalized data

source_name: Side population cells of TA

tag: C57BL/10ScSnJ mice were used to have SP cells of TA muscle


title: TA side population 0Tsp

label_protocol: RNAs were subjected to linear amplification using the GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using RNeasy micro kit (Qiagen, Valencia, CA).


title: Optic fissure_mouse_E11.5_B

status: Public on Oct 08 2008

city: Bethesda

first: Jacob

last: Brown

state: MD

address: 10 Center Drive

institute: NEI

description: Expression data were gathered in biological triplicate at E10.5, E11.5 and duplicate at E12.5, each array representing pooled optic fissure tissue from three embryos from a single litter.

hyb_protocol: Labeled samples from each timepoint were then hybridized to Affymetrix MOE 430 2.0 expression microarrays according to manufacturer’s protocol and scanned using GeneChip Scanner 3000 (Affymetrix).

data_processing: Raw expression signals and present/absent calls were made using Affymetrix GCOS 1.4.

source_name: Mouse embryo, optic fissure tissue, embryonic day 11.5

label_protocol: Biotin labeling of transcripts was performed in the final round of in vitro transcription using GeneChip IVT Labeling Kit (Affymetrix).

growth_protocol: A Veritas laser capture microdissection instrument (Molecular Devices) was used to collect optic fissure tissue from frozen sections through staged, wild-type C57BL6/J mouse embryos.

extract_protocol: Tissue lysates from three embryos from separate litters and the same embryonic stage were pooled and total RNA was extracted using Absolutely RNA Microprep Kit (Stratagene). Pooled RNA was amplified linearly with two rounds of T7 polymerase-mediated in vitro transcription as per instructions in RiboAmp OA kit (Molecular Devices).

treatment_protocol: Wild type embryos dissected in Rnase free 1X PBS.

tag: Strain

value: C57BL/6,  Age:Embryonic day 11.5, Tissue:Optic fissure


title: TA side population 1Tsp


title: EOM side population 5Esp

source_name: Side population cells of EOM

tag: C57BL/10ScSnJ mice were used to have SP cells of EOM muscle


title: TA side population 3Tsp


title: EOM side population 6Esp


title: EOM side population 1Esp


title: Optic fissure_mouse_E10.5_A

scan_protocol: Labeled samples from each timepoint were then hybridized to Affymetrix MOE 430 2.0 expression microarrays according to manufacturer’s protocol and scanned using GeneChip Scanner 3000 (Affymetrix).

source_name: Mouse embryo, optic fissure tissue, embryonic day 10.5

value: C57BL/6,  Age:Embryonic day 10.5, Tissue:Optic fissure


title: TA side population 5Tsp


title: Sample 1  primary neuroblastoma