title: Egg rep1

description: gene expression data from adult fly heads from individuals with a mutation in egg

data_processing: Data analysis was carried out using the Bioconductor packages affy and limma in R on the log2-transformed signal intensities.  The RMA method was employed to carry out background correction, quantile normalization, and summarization of gene expression levels.

source_name: D.m. adult heads egg

value: mutation in egg


title: Egg rep2

status: Public on Feb 10 2009

type: RNA

city: St. Louis

first: Nicole

middle: Christina

last: Riddle

state: MO

address: 1 Brookings Dr.; CB1137

department: Biology

country: USA

institute: Washington University

hyb_protocol: Hybridization was carried out according to the protocols recommended by Affymetrix (see 3' IVT manual available at www.affymetrix.com) on a SS450 fluidics station.

scan_protocol: Scanning was carried out according to the protocols recommended by Affymetrix (see 3' IVT manual available at www.affymetrix.com) with a 7G3000 scanner.

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

label_protocol: Preparation of the samples for hybridization was carried out following the protocols recommended by Affymetrix (see 3' IVT manual available at www.affymetrix.com).

growth_protocol: Flies were raised at 25C with 70% humidity on standard corn meal food.

extract_protocol: RNA was isolated using Trizol (Invitrogen) according to the manufacturer's recommendations.

tag: developmental stage

value: adult

tag: tissue

value: heads

tag: genotype


title: Egg rep3


title: yw rep3

description: gene expression data from adult fly heads with the yw control genotype

source_name: D.m. adult heads yw

value: yw control genotype


title: Egg+Su(var)3-9 rep3

description: gene expression data from adult fly heads from individuals with mutations in Su(var)3-9 and in egg

source_name: D.m. adult heads egg+Su(var)3-9

value: mutations in Su(var)3-9 and in egg


title: Su(var)3-9 rep1

description: gene expression data from adult fly heads carrying a mutation in Su(var)3-9

source_name: D.m. adult heads Su(var)3-9

value: mutation in Su(var)3-9


title: Su(var)3-9 rep2


title: Su(var)3-9 rep3


title: Egg+Su(var)3-9 rep2


title: Egg+Su(var)3-9 rep1


title: yw rep1A


title: yw rep2


title: Cl8-RNA-3

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

description: polydT-primed cDNA from total RNA

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

scan_protocol: GeneChips were scanned on an Affymetrix Scanner 3000 7G.

data_processing: Signal values for Affymetrix expression arrays were estimated using the GC-RMA module from Genedata’s Refiner 4.5 package (Genedata, Basel, Switzerland). Expression data analysis was performed in Genedata’s Analyst 4.5 package. Only those genes which had an Affymetrix detection p-value < 0.05 and signal values > 4 were assumed to be expressed.

source_name: Cl8 (Clone 8) cells

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

growth_protocol: Drosophila Kc cells were kept in HyQ-SFX (Hyclone). Clone8 (Cl.8+) cells were kept in Shields and Sang medium (Sigma), supplemented with 12.5IU/100ml insulin, 2% heat inactivated FCS and 2.5% fly extract.

extract_protocol: Trizol extraction of total RNA.

treatment_protocol: no treatment


title: Cl8-RNA-4

description: polydT-primed cDNA from total RNA


title: Cl8-RNA-5

description: polydT-primed cDNA from total RNA


title: Kc-RNA-5

description: polydT-primed cDNA from total RNA

source_name: Kc cells


title: Cl8-RNA-1

description: polydT-primed cDNA from total RNA


title: gapcp1gapcp2, biological rep1

city: Burjassot

first: Roc

last: Ros

state: valencia

address: Vicent Andres Estelles

department: Biologia Vegetal

country: Spain

institute: Universitat de Valencia

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Fragmented cRNA (15 μg) was added to 300 μL of hybridization solution, and 200 μL of this mixture was used for hybridization on Arabidopsis ATH1 Genome Arrays for 16 h at 45°C. The standard wash and double-stain protocols (EukGE-WS2v5-450) were applied using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays (three replicates of each treatment) were scanned on an Affymetrix GeneChip scanner 3000.

data_processing: Fluorescence images were normalized with the software GCOS from Affymetrix. Data were analyzed and compared using the dChip software  ( http://www.hsph.harvard.edu/~cli/complab/dchip/). A threshold criteria of 2 fold; P value <0.05 was used.

organism: Arabidopsis thaliana

source_name: 15 day old whole seedling

label_protocol: The cRNA was labeled with biotin, and 20 μg of the labeled cRNA was fragmented. The size distribution of the cRNAs and fragmented cRNAs was assessed using an Eppendorf Biophotometer and electrophoresis.

growth_protocol: Seeds were germinated and grown vertically in MS 1/5 with Gamborg vitamins. Light condicitions: 16 hours light, 8 hours dark. Temperature: 22ºC. Light 100 μmol m−2 s−1.

extract_protocol: Total RNA was extracted using the RNeasy plant mini kit (Qiagen).RNA was extracted from three sets of gapcp double mutants and wild type plants grown at the same time. RNA integrity was determined using RNA 6000 Nano Labchips® in an Agilent 2100 Bioanalyzer following the manufactures protocol. The purified RNA (8 μg) was used to generate first-strand cDNA in a reverse transcription reaction (One-Cycle Target Labeling and Control Reagents; Affymetrix). After second-strand synthesis, the double-stranded cDNAs were used to generate cRNA via an in vitro transcriptional reaction.

tag: mutant


title: KG_03

status: Public on Feb 13 2009

city: Zurich

first: Stefanie

last: Tiefenboeck

address: Schafmattstrasse 18

country: Switzerland

institute: ETH Zurich

hyb_protocol: Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Drosophila Genome 2.0 Arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the polyA spike in controls and the prokaryotic control.

label: Biotin

source_name: Larval fat body, srl1/srl1

label_protocol: The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using an IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.

extract_protocol: 20 fat bodies of 5d old mutant larvae were dissected into RNAlater. The RNA was isolated using Macherey-Nagel NucleoSpin RNA II isolation Kit following the manufacturer’s protocol.

tag: Larval fat body, srl1/srl1


title: Kc-RNA-4

description: polydT-primed cDNA from total RNA


title: Cl8-RNA-2

description: polydT-primed cDNA from total RNA


title: wild type, biological rep1

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

tag: wild type control


title: wild type, biological rep3


title: wild type, biological rep2


title: gapcp1gapcp2, biological rep3


title: gapcp1gapcp2, biological rep2


title: cerebellum: cd15 negative math-1GFP tumor cells 6_e1_le2

status: Public on Feb 09 2009

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: primary tumor cells  isolated from conventional Patched medulloblastomas

organism: Mus musculus

source_name: cerebellum


title: cerebellum: cd15 negative math-1GFP tumor cells 4_e1_le2


title: Kc-RNA-3

description: polydT-primed cDNA from total RNA


title: Kc-RNA-2

description: polydT-primed cDNA from total RNA


title: cerebellum: cd15 negative math-1GFP tumor cells 2_le2


title: Kc-RNA-1

description: polydT-primed cDNA from total RNA


title: cerebellum: cd15 positive math-1GFP tumor cells 9_e1_le2


title: cerebellum: cd15 negative math-1GFP tumor cells 8_e1_le2


title: cerebellum: cd15 positive math-1GFP tumor cells 5_e1_le2


title: cerebellum: cd15 negative math-1GFP tumor cells 10_e1_le2


title: cerebellum: CD15 positive Conventional patched medulloblastomas 6_e1_le1


title: cerebellum: CD 15 negative Conventional Patched medulloblastomas 4_e1_le1


title: cerebellum: CD 15 negative Conventional Patched medulloblastomas 5_e1_le1


title: cerebellum: CD 15 positive Conventional Patched medulloblastomas 5_e1_le1


title: cerebellum: CD 15 negative Conventional Patched medulloblastomas 3_e1_le1


title: cerebellum: CD 15 negative Conventional Patched medulloblastomas 2_e1_le1


title: Df_plus_03

first: Claudia

last: Baltzer

state: Zurich

department: Cell biology

institute: ETH Zürich

hyb_protocol: Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Drosophila Genome 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.

data_processing: Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.

source_name: Larval fat body, +/Df(3R)ro80b

label_protocol: The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.

extract_protocol: 60 fat bodies of 6d old mutant larvae were dissected into RNAlater. The RNA was isolated using Macherey-Nagel NucleoSpin RNA II isolation Kit following the manufacturers protocol.

tag: Larval fat body, +/Df(3R)ro80b


title: cerebellum: cd15 positive math-1GFP tumor cells 7_e1_le2


title: M12-Ctrl-1

city: San Diego

first: Yipeng

last: Wang

state: CA

institute: Vaccine Research Institute of San Diego

description: prostate cancer cell line M12

hyb_protocol: Affymetrix Standard Hybridization Protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The intensity data was generated with MAS5.

organism: Homo sapiens

source_name: prostate cancer cell line

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

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

tag: control cells


title: delg_mut_03

source_name: Larval fat body, delg613/Df(3R)ro80b

tag: Larval fat body, delg613/Df(3R)ro80b


title: M12-Test-2

description: prostate cancer cell line M12

tag: UV treated cells


title: Df_plus_02


title: M12-Test-1

description: prostate cancer cell line M12


title: delg_mut_01


title: Df_plus_01


title: cerebellum: CD 15 positive Conventional Patched medulloblastomas 4_e1_le1


title: delg_mut_02


title: M12-Ctrl-2

description: prostate cancer cell line M12


title: cerebellum: CD 15 positive Conventional Patched medulloblastomas 2_e1_le1


title: cerebellum: RNA extraction from conventional patched CD15 negative tumor cells_le1


title: R1=HeLa_M13_Aug5_2008

status: Public on Feb 08 2009

city: Piscataway

first: Samuel

middle: I

last: Gunderson

state: NJ

address: 604 Allison Road

department: Molecular Biology & Biochemistry

institute: Rutgers University

hyb_protocol: The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.

data_processing:
Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.
The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.

source_name: HeLa cell line (human cervical carcinoma)

label_protocol: Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.

growth_protocol: DMEM + 10% fetal calf serum at 37 degrees 5% CO2

extract_protocol: Total RNA was extracted using the RNeasy kit including Dnase 1 treatment (Qiagen, Valencia, CA).

treatment_protocol: Cells were transfected with 5nM of synthetic oligonucleotides: Sample R1=5nM M13 DNA oligonucleotide, sample R2=5nM anti-PCSK9 siRNA, and sample R3= 5nM UA31D4 Adaptor + 5nM UA31E Adaptor oligonucleotides. Lipofectamine-2000 (Invitrogen) was used as the transfection reagent as per manufacturer's instructions. 24 hours after transfection cells were collected and used to make total RNA.


title: cerebellum: CD 15 positive Conventional Patched medulloblastomas 3_e1_le1


title: R3=HeLa_anti-PCSK9_Adaptor_Aug5_2008


title: cerebellum: RNA extraction from conventional patched CD15 positive tumor cells_le1


title: R2=HeLa_anti-PCSK9_siRNA_Aug5_2008


title: hut78Sh4Bulk_1, biological rep 2

status: Public on Feb 07 2009

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

description: A human cell line derived from blood of a patient with Sezary syndrome

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: The data was normalized with Robust Multichip Analysis (RMA)

source_name: Hut 78 cells transduced with AHI-1/sh4 vector for suppression of AHI-1 expression, a bulk population

label_protocol: Affymetrix standard procedure

growth_protocol: Hut 78 cells (transduced and untransduced) were cultured in RPMI 1640 Medium with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 1 x 10-4 M β-mercaptoethanol.

extract_protocol: The Absolutely RNA® Miniprep Kit (Stratagene, La Jolla, CA) was used to isolate and purify total RNA using the procedure described for tissue culture cells grown in suspension.

tag: The transformed phenotypes can be normalized by suppression of AHI-1


title: hut78Rpg_1, biological rep 3

source_name: Hut 78 cells transduced with a control vector

tag: A transformed leukemic cell line


title: hut78_1,  biological rep 2

source_name: Parental Hut 78 cells


title: hut78Sh4Bulk_1, biological rep 3


title: hut78Rpg_1, biological rep 2


title: hut78Sh4Clone1_1,biological rep 1

source_name: Hut 78 cells transduced with AHI-1/sh4 vector for suppression of AHI-1 expression, a clonal population


title: hut78Sh4Clone1_1,biological rep 3


title: hut78Sh4Clone1_1,biological rep 2


title: hut78_1,  biological rep 1


title: hut78Sh4Bulk_1, biological rep 1


title: cerebellum: CD15 negative Conventional Patched medulloblastoma 6_le1

description: primary tumor cells isolat...


title: NORMAL MYELOBLASTS_CD117POS_GR1+_MAC1+_1

status: Public on Feb 06 2009

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: Normal myeloid lineage cell populations (C57BL/6 mice, aged 4-10 weeks, male or female) with three distinct immunophenotypes were prospectively isolated and characterized. In preparation for FACS sorting, bone marrow cells were separated into c-kit+ and c-kit- fractions using an AutoMACS device.  C-kit+ cells were further fractionated based on Gr1 and Mac1 expression, and absence of lineage antigen expression (B220, TER119, CD3, CD4, CD8 and IL7Rα), by cell sorting.  C-kit+ Gr1+ Mac1lo/- and c-kit+ Gr1+ Mac1+ displayed cytologic features of undifferentiated hematopoietic cells or myeloblasts, whereas c-kit- Gr1+ Mac1+ cells were mature neutrophils.

hyb_protocol: GeneChip Hybridization Control Kit (Affymetrix)

scan_protocol: Hybridized chips were scanned using the GeneChip Scanner 3000, with GeneChip operating software (v1.1.1) (Affymetrix)

data_processing: All normalizations and data set comparisons were performed using dChip 2007 (DNA-Chip Analyzer) software (Li and Wong, 2001; biosun1.harvard.edu/complab/dchip/manual.htm).  A perfect-match/mismatch (PM/MM) model was used for the calculation of expression values.

molecule: polyA RNA

source_name: Normal BM myeloblasts, c-kit+ Gr1+ Mac1+

label_protocol: GeneChip IVT Labeling Kit (Affymetrix)

extract_protocol: RNA was prepared using an RNeasy Mini kit (Qiagen). RNA quality was confirmed using an Agilent 2100 bioanalyzer (Agilent Technologies). RNA was amplified using a GeneChip Two-Cycle Target Labeling and Control Reagents kit (Affymetrix).

tag: Normal BM myeloblasts

tag: c-kit+ Gr1+ Mac1+

tag: Mouse 1


title: hut78Rpg_1, biological rep 1


title: NORMAL MYELOBLASTS_CD117POS_GR1+_MAC1-_3

source_name: Normal BM myeloblasts, c-kit+ Gr1+ Mac1-

tag: c-kit+ Gr1+ Mac1-

tag: Mouse 3


title: NORMAL MYELOBLASTS_CD117POS_GR1+_MAC1+_2

tag: Mouse 2


title: NORMAL MYELOBLASTS_CD117POS_GR1+_MAC1-_2


title: NORMAL MYELOBLASTS_CD117POS_GR1+_MAC1+_3


title: NORMAL BM NEUTROPHILS_1

source_name: Normal BM neutrophils, c-kit- Gr1+ Mac1+

tag: Normal BM neutrophils

tag: c-kit- Gr1+ Mac1+


title: MLL-AF10 LEUKEMIC SPLENOCYTES_CD117POS_953

description: MLL-AF10 leukemic splenocytes were FACS sorted for high or low level c-kit expression. AML was initiated by transplantation of retrovirally transduced immortalized c-kit+ BM stem and progenitor cells into sub-lethally irradiated syngeneic CD57BL/6 recipients.

source_name: MLL-AF10 leukemic splenocytes, CD117pos

tag: MLL-AF10 leukemic splenocytes

tag: Mouse 953


title: MLL-AF10 LEUKEMIC SPLENOCYTES_CD117NEG_953

source_name: MLL-AF10 leukemic splenocytes, CD117neg


title: NORMAL BM NEUTROPHILS_3


title: MLL-AF10 LEUKEMIC SPLENOCYTES_CD117NEG_951

tag: Mouse 951


title: NORMAL BM NEUTROPHILS_2


title: NORMAL MYELOBLASTS_CD117POS_GR1+_MAC1-_1


title: MLL-AF10 LEUKEMIC SPLENOCYTES_CD117POS_951


title: MLL-AF10 LEUKEMIC SPLENOCYTES_CD117POS_952

tag: Mouse 952


title: MLL-AF10 LEUKEMIC SPLENOCYTES_CD117NEG_952


title: MLL-AF10 LEUKEMIC SPLENOCYTES_CD117NEG_948

extract_protocol: RNA was prepared using an RNeasy Mini kit (Qiagen). RNA quality was confirmed using an Agilent 2100 bioanalyzer (Agilent Technologies). RNA was amplified using a GeneChip Two-Cycle Target Labeling and Control Reagents kit (Affymetrix)

tag: Mouse 948


title: BM_NORMAL4

description: BM from wild type C57BL/6 mouse (male or female)

hyb_protocol: GeneChip® Hybridization Control Kit (Affymetrix)

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software

data_processing: Normalisation of data and generation of values was performed using Microarray Analysis Software v5.0 (Affymetrix)

source_name: Normal BM for control

label_protocol: GeneChip® IVT Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted from cryopreserved BM cells using Trizol according to manufacturer's instructions.

tag: Normal BM for control 4


title: BM_MLL-ENL_702

description: Leukemia was initiated by transplanting c-kit+ BM progenitor cells infected with oncogene containing retroviruses in to lethally irradiated syngeneic C57BL/6 mice (male or female). Bone marrow was harvested from leukemic mice at euthanasia.

source_name: Leukemic BM, initiated by MLL-ENL

tag: Leukemic BM

tag: initiated by MLL-ENL

tag: Mouse #702


title: BM_MLL-ENL_741

tag: Mouse #741


title: BM_MLL-AF9_307

source_name: Leukemic BM, initiated by MLL-AF9

tag: initiated by MLL-AF9

tag: Mouse #307


title: BM_MLL-AF9_301

tag: Mouse #301


title: BM_MLL-ENL_701

tag: Mouse #701


title: BM_MLL-ENL_742

tag: Mouse #742


title: BM_MLL-ENL_774

tag: Mouse #774


title: BM_MLL-AF9-308

tag: Mouse #308


title: BM_MLL-AF9-310

tag: Mouse #310


title: BM_NORMAL3

tag: Normal BM for control 3


title: BM_MLL-GAS7_405

source_name: Leukemic BM, initiated by MLL-GAS7

tag: initiated by MLL-GAS7

tag: Mouse #405


title: BM_MLL-ENL_760

tag: Mouse #760


title: MLL-AF10 LEUKEMIC SPLENOCYTES_CD117POS_948

tag: MLL-AF10 leukemic splenocytes

tag: Mouse 948


title: BM_MLL-GAS7_410

tag: Leukemic BM

tag: Mouse #410


title: BM_MLL-GAS7_407

tag: Mouse #407


title: BM_NORMAL1

tag: Normal BM for control 1


title: BM_MLL-AF10_802A

source_name: Leukemic BM, initiated by MLL-AF10

tag: initiated by MLL-AF10

tag: Mouse #802A


title: BM_NORMAL2

tag: Normal BM for control 2


title: BM_MLL-ENL_703

tag: initiated by MLL-ENL

tag: Mouse #703


title: BM_MLL-AF10_799A

tag: Mouse #799A


title: cerebellum: cd15 positive math-1GFP tumor cells 1_le2

source_name: cerebellum


title: BM_MLL-AF10_780A

tag: Mouse #780A


title: BM_MLL-AF9-305

tag: initiated by MLL-AF9

tag: Mouse #305


title: BM_MLL-AF10_805A

tag: Mouse #805A


title: BM_MLL-AF10_783A

tag: Mouse #783A


title: BM_MLL-AF10_797A

tag: Mouse #797A


title: BM_MLL-GAS7_408

tag: initiated by MLL-GAS7

tag: Mouse #408


title: BM_MLL-AF10_798A

tag: Leukemic BM

tag: Mouse #798A


title: BM_MLL-GAS7_406

tag: Mouse #406


title: BM_MLL-AF1p_803

source_name: Leukemic BM, initiated by MLL-AF1p

tag: initiated by MLL-AF1p

tag: Mouse #803


title: BM_MLL-AF10_782A

tag: initiated by MLL-AF10

tag: Mouse #782A


title: BM_MLL-AF1p_804

tag: Mouse #804


title: BM_MLL-AF1p_810

tag: Mouse #810


title: BM_MLL-AF1p_805

tag: Mouse #805


title: BM_MLL-AF1p_806

tag: Mouse #806


title: BM_MLL-AF1p_808

tag: Mouse #808


title: BM_MLL-AF1p_811

tag: Mouse #811


title: BM_MLL-AF1p_801

tag: Mouse #801


title: Mbnl1_WT_3_Experiment 3

status: Public on Feb 05 2009

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: Hybridization, washes, and staining with phycoerythrin-streptavidin (including antibody enahncement step) were carried out exactly as recommended by Affymetrix for eukaryotic expression arrays, using hybridization oven and fluidics station purchased from Affymetrix.

scan_protocol: Scans were done with Affymetrix scanner exactly as recommended by Affymetrix.

data_processing: background subtraction and normalization were done with the GCRMA method.

source_name: quadriceps muscle

label_protocol: Biotinylated cRNA was prepared with kits from Enzo as recommended by supplier.

growth_protocol: Mice were reared under normal conditions. CUGexp mice were sacrificed at 6 months of age. Mbnl1-null and Clcn1-null mice were sacrificed at 3 months of age.

extract_protocol: Total RNA was extracted into Tri-Reagent as recommended by supplier.

treatment_protocol: No treatments other than constitutive genetic modifications

tag: Gender

value: male

tag: Age

value: 3 months old

tag: Genotype

value: FVB wild type


title: normal lymphocyte duplicate 2

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

country: Japan

institute: Tokyo Medical University

description: Normal control

hyb_protocol: GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Hybridization Oven 640 110V (Affymetrix 800138) Wash and staining: Fluidics Station 450 (Affymetrix 00-0079)

scan_protocol: GeneChip Scanner 3000 (Affymetrix 00-0074) GeneChip Operating Software ver.1.4 (Affymetrix 690036)

source_name: Control

label_protocol: One-cycle Target Labeling GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Section 2 Eukaryotic Sample and Array processing Chapter 1 Eukaryotic Target Prepartion

extract_protocol: RNeasy kit

tag: Normal lymphocyte


title: Mbnl1_WT_4_Experiment 3


title: Mbnl1_WT_1_Experiment 3


title: Mbnl1_Null_ 3_Experiment 3

description: Mbnl1_Null_ 3_Experiment3

value: Mbnl1 knockout with FVB background


title: Mbnl1_Null_ 2_Experiment 3

description: Mbnl1_Null_ 2_Experiment3


title: Mbnl1_Null_ 5_Experiment 3

description: Mbnl1_Null_ 5_Experiment3


title: Mbnl1_WT_2_Experiment 3


title: Mbnl1_Null_ 1_Experiment 3

description: Mbnl1_Null_ 1_Experiment3


title: Mbnl1_Null_ 4_Experiment 3

description: Mbnl1_Null_ 4_Experiment3


title: Mbnl1_WT_5_Experiment 3


title: eds16 whole leaf, 7d UI, biological rep 1

status: Public on Feb 04 2009

city: Berkeley

first: Mary

last: Wildermuth

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

description: Gene expression data from 7d uninfected mutant whole mature leaves

hyb_protocol: Microarray hybridizations to Affymetrix Arabidopsis ATH1 GeneChips were performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray® 2500 Scanner at the Harvard University Bauer Center for Genomics Research.

data_processing: Log2 (expression values) were extracted using robust multi-array analysis (RMA) implemented in the function rma() in the Bioconductor software package affy. Background correction was performed by correcting PM (perfect match) only, to reduce noise from signal intensity. Quantile normalization was performed to make the distributions of signal intensities uniform across chips. Quality assessment was done using the weights outputted from the linear model fitting function fitPLM() in the R package AffyExtensions.  One sample (Col whole leaf, 7d UI, biological rep 1; cel file MW 1.A.7) was not included in subsequent analyses as expression for this sample was not as highly correlated with its biological replicates.

source_name: eds16 whole leaf uninfected 7d

label_protocol: Target labeling was performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1.

growth_protocol: Arabidopsis seeds were stratified in 0.1% agarose for 3-5 days and planted in boxes containing Metromix 200 soil. Seeds were equally distributed in each box using a template, with 9 plants per box, alternating wild type and mutant.  The flats (6 boxes per flat) were covered with plastic trays for 1 week and then uncovered. Flats were watered from below and fertilized at 2-1/2 weeks. Plants were grown in Percival AR66L growth chambers at 22°C, 80% RH, 14 h photoperiod with photosynthetically active radiation=150 µE m-2 s-1.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Plant RNA Miniprep kit according to the manufacturer's instructions.  Samples were split in two before homogenization and repooled before loading on the RNA-binding column.  RNA quality was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

treatment_protocol: At four weeks, a subset of boxes was infected with a moderately heavy innoculum of G.orontii using a settling tower. Moderately heavy innoculum is 2-3 fully G.O.-infected leaves with conidia 10-14 dpi.  Infected plants were placed in a separate Percival growth chamber under the same conditions as the pathogen-free Percival. Infections, with the exception of the 6 hr timepoint, were performed at 2:30 pm to standardize experiments and minimize circadian effects. Samples were harvested at 0 h (just prior to infection), 6 hpi, 1 dpi, 3 dpi, 5 dpi, and 7 dpi. An uninfected 7 dpi sample was also collected.  For each sample, three fully expanded mature leaves were excised per plant, with leaves from two randomly selected plants used to prepare a single RNA sample.  Three independent experiments were performed with triplicate samples collected for each datapoint within each experiment.  Four biological replicates were processed.  One from each of the three separate experiments and an additional biological replicate from Experiment 2.

value: mutant

value: 4 weeks old at time 0 (innoculation)

tag: tissue

value: whole leaf


title: eds16 whole leaf, 5dpi, biological rep 2

description: Gene expression data from mutant whole mature leaves at 5d post Golovinomyces orontii infection

source_name: eds16 whole leaf infected with Golovinomyces orontii 5d


title: eds16 whole leaf, 7dpi, biological rep 4

description: Gene expression data from mutant whole mature leaves at 7d post Golovinomyces orontii infection

source_name: eds16 whole leaf infected with Golovinomyces orontii 7d


title: eds16 whole leaf, 7d UI, biological rep 4


title: eds16 whole leaf, 7dpi, biological rep 1


title: normal lymphocyte duplicate 1

description: Normal control

data_processing: GeneChip Operating Software ver.1.4 (Affymetrix 690036)


title: Jhdm2a null skeletal muscle expression

city: Barcelona

first: Eric

middle: M.

last: Kallin

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

institute: Center for Genomic Regulation

hyb_protocol: 10 ug of cRNA was used for hybridization.  Arrays were hybridized for 16 hours at 45oC in the GeneChip Hybridization Oven 640.  The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.

scan_protocol: the arrays were scanned with the Hewlett Packard GeneArray Scanner.  Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis.  Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.

data_processing: MAS5 algorithm was used for data generation.

source_name: Jhdm2a null skeletal muscle

label_protocol: 7 ug of total RNA was used to synthesize cDNA.  A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction.  Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit.  The cRNA was then fragmented in fragmentation buffer (5X fragmentation buffer: 200mM Tris-acetate, pH8.1, 500mM KOAc, 150mM MgOAc) at 94oC for 35 minutes before the chip hybridization.  15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD,  and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20).

extract_protocol: Qiagen RNeasy Kit by manufacturers protocol (RNeasy mini protocol for isolation of total RNA from heart, muscle, and skin tissue).

tag: Strain

value: 129 ES cell backcrossed onto C57BL/6 for 4 generations

value: Male

value: 3 months

tag: Tissue

value: Skeletal muscle


title: eds16 whole leaf, 3dpi, biological rep 3

description: Gene expression data from mutant whole mature leaves at 3d post Golovinomyces orontii infection

source_name: eds16 whole leaf infected with Golovinomyces orontii 3d


title: eds16 whole leaf, 7dpi, biological rep 2


title: eds16 whole leaf, 5dpi, biological rep 4


title: eds16 whole leaf, 7d UI, biological rep 3


title: eds16 whole leaf, 1dpi, biological rep 3

description: Gene expression data from mutant whole mature leaves at 1d post Golovinomyces orontii infection

source_name: eds16 whole leaf infected with Golovinomyces orontii 1d


title: eds16 whole leaf, 3dpi, biological rep 4


title: eds16 whole leaf, 7dpi, biological rep 3


title: eds16 whole leaf, 3dpi, biological rep 2


title: eds16 whole leaf, 3dpi, biological rep 1


title: eds16 whole leaf, 7d UI, biological rep 2


title: eds16 whole leaf, 5dpi, biological rep 3


title: eds16 whole leaf, 5dpi, biological rep 1


title: eds16 whole leaf, 1dpi, biological rep 4


title: eds16 whole leaf, 1dpi, biological rep 2


title: Jhdm2a wild-type skeletal muscle expression

source_name: wild-type skeletal muscle


title: eds16 whole leaf, 1dpi, biological rep 1


title: eds16 whole leaf, 6hpi, biological rep 4

description: Gene expression data from mutant whole mature leaves at 6h post Golovinomyces orontii infection

source_name: eds16 whole leaf infected with Golovinomyces orontii 6h


title: eds16 whole leaf, 6hpi, biological rep 3


title: eds16 whole leaf, 0h UI, biological rep 3

description: Gene expression data from 0h uninfected mutant whole mature leaves

source_name: eds16 whole leaf uninfected 0h


title: eds16 whole leaf, 0h UI, biological rep 4


title: eds16 whole leaf, 6hpi, biological rep 1


title: eds16 whole leaf, 0h UI, biological rep 2


title: eds16 whole leaf, 6hpi, biological rep 2


title: Col whole leaf, 7d UI, biological rep 2

description: Gene expression data from 7d uninfected wild type whole mature leaves

source_name: Col whole leaf uninfected 7d

value: wild type


title: eds16 whole leaf, 0h UI, biological rep 1


title: Col whole leaf, 7dpi, biological rep 1

description: Gene expression data from wild type whole mature leaves at 7d post Golovinomyces orontii infection

source_name: Col whole leaf infected with Golovinomyces orontii 7d


title: Col whole leaf, 7d UI, biological rep 3


title: Col whole leaf, 3dpi, biological rep 2

description: Gene expression data from wild type whole mature leaves at 3d post Golovinomyces orontii infection

source_name: Col whole leaf infected with Golovinomyces orontii 3d


title: Col whole leaf, 5dpi, biological rep 4

description: Gene expression data from wild type whole mature leaves at 5d post Golovinomyces orontii infection

source_name: Col whole leaf infected with Golovinomyces orontii 5d


title: Col whole leaf, 7dpi, biological rep 4


title: Col whole leaf, 7dpi, biological rep 2


title: Col whole leaf, 5dpi, biological rep 1


title: Col whole leaf, 3dpi, biological rep 4


title: Col whole leaf, 7dpi, biological rep 3


title: Col whole leaf, 1dpi, biological rep 3

description: Gene expression data from wild type whole mature leaves at 1d post Golovinomyces orontii infection

source_name: Col whole leaf infected with Golovinomyces orontii 1d


title: Col whole leaf, 5dpi, biological rep 2


title: Col whole leaf, 1dpi, biological rep 2


title: Col whole leaf, 3dpi, biological rep 3


title: Col whole leaf, 5dpi, biological rep 3


title: Col whole leaf, 7d UI, biological rep 1


title: Col whole leaf, 7d UI, biological rep 4


title: Col whole leaf, 1dpi, biological rep 1


title: Col whole leaf, 1dpi, biological rep 4


title: Col whole leaf, 3dpi, biological rep 1


title: Col whole leaf, 6hpi, biological rep 4

description: Gene expression data from wild type whole mature leaves at 6h post Golovinomyces orontii infection

source_name: Col whole leaf infected with Golovinomyces orontii 6h


title: Col whole leaf, 0h UI, biological rep 3

description: Gene expression data from 0h uninfected wild type whole mature leaves

source_name: Col whole leaf uninfected 0h


title: Col whole leaf, 0h UI, biological rep 2


title: Col whole leaf, 0h UI, biological rep 4


title: Col whole leaf, 6hpi, biological rep 2


title: Col whole leaf, 0h UI, biological rep 1


title: Col whole leaf, 6hpi, biological rep 3


title: Col whole leaf, 6hpi, biological rep 1


title: OPM2 transfected with lentiviral CS1 shRNA, rep4

city: Boston

first: Yu-Tzu

last: Tai

state: MA

address: 44 Binney Street

institute: Dana Farber Cancer Institute

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

source_name: CS1 null OPM2 cell total mRNA transcripts

label_protocol: Standard Affymetrix protocol.

growth_protocol: 1 million cells per ml of RPMI1640 and 10%FCS in 37 degree incubator containing 5%C02

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

treatment_protocol: regular cell culture with RPMI1640 medium and 10% FCS

tag: multiple myeloma cell line without CS1 expression


title: OPM2 transfected with lentiviral CS1 shRNA, rep2


title: U266 transfected with control vector, rep1

source_name: U266 control cell total mRNA transcripts

tag: multiple myeloma cell line with very low CS1 expression


title: OPM2 transfected with lentiviral CS1 shRNA, rep1


title: OPM2 transfected with lentiviral CS1 shRNA, rep3


title: U266 transfected with CS1 expression vector, rep1

source_name: CS1-overexpressing U266 cell total mRNA transcripts

tag: multiple myeloma cell line with CS1 overexpression


title: Ferucarbutran-labelled fMSC 3

status: Public on Feb 01 2009

city: Herston

first: Eddy Shoo-Ming

last: Lee

state: Queensland

address: Royal Brisbane and Women's Hospital

country: Australia

institute: University of Queensland

description:
1. CHP and CEL files from GCOS were imported into Genespring GX 7.3.1 along with other replicates. The sample groups were mock-labelled, M600-labelled, ferucarbotran-labelled. Each sample group consist of triplicate microarray data
2. Control strength was determined from the maximum of base/proportional of the 3 sample groups.
3. Only probes with raw signals above control strength in at least 1 out of the 3 sample groups were considered. The other probes were disregarded.
4. Probes that were flagged absent in triplicates from all sample groups were disregarded.
5. T-test was performed to identify M600-labelled probes or ferucarbotran-labelled probes that had significant difference in expression with respect to mock-labelled

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 degree Celsius on HG-U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned with GeneChip Scanner 3000 and GeneChip Operating Software 1.0 (GCOS, Affymetrix)

data_processing: The data were processed with MAS 5.0 of GCOS 1.0 with the normalization target set to 500

source_name: fetal mesenchymal stem cells (fMSC) total RNA

label_protocol: Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA

extract_protocol: Total RNA was extracted from fMSC in using the the RNeasy Mini-kit (Qiagen, Hilden, Germany) in accordance to the manufacturer’s protocol.

treatment_protocol: Underwent labelling procedure of a) 24 hours incubation with cell label (M600, ferucarbotran or mock), b) vigourous flashing with PBS, and  c) gradient centrifugation at 200g for 30min

tag: Adherent cell isolated from week 11 fetus

tag: Passage 6

tag: Incubated with cell label (M600, ferucarbotran or mock) and washed


title: U266 transfected with control vector, rep2


title: MGIO-labelled fMSC 2

treatment_protocol: Underwent labelling procedure of a) 24 hours incubation with cell label (MGIO, ferucarbotran or mock), b) vigourous flashing with PBS, and  c) gradient centrifugation at 200g for 30min


title: MGIO-labelled fMSC 3


title: Mock-labelled fMSC Control 3


title: Mock-labelled fMSC Control 1

data_processing: The data were condensed with MAS 5.0 using the Refiner software from Genedata, Basel, Switzerland using default settings. The normalization target was set to 500


title: OPM2 transfected with control vector, rep2

source_name: OPM2 control cell total mRNA transcripts

tag: multiple myeloma cell line with CS1 expression


title: MGIO-labelled fMSC 1


title: Expression data from RNAi SNCA treated human neuroblastoma cell line_transfected with siSNCA4_Replicate 2

city: Tuebingen

first: Karina

last: Haebig

address: Calwerstr. 7

department: Medical Genetics

country: Germany

institute: Institute of Human Genetics

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner G2500A.

data_processing: Probe level summary was performed with the MAS5 algorithm by the GeneChip Operating Software

source_name: SH-SY5Y cells, siRNA transfection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human SH-SH5Y cells were maintained in D-MEM medium (Invitrogen) supplemented with 15% fetal bovin serum and penicillin-streptomycin.

extract_protocol: Total RNA of transfected cells (48h after RNAi treatment) was isolated using the RNeasy® Mini Kit (Qiagen) including a DNase digest on the column with RNase-Free DNase Set (Qiagen).

treatment_protocol: RNAi of α-synuclein (SNCA) was performed with chemically synthesized siRNAs against SNCA (Qiagen). All transfection experiments were performed in independent triplicates, while 2x106 cells and 2 μg siRNA were used for electroporation with the Cell Line Nucleofection Kit V (Amaxa) applying program G-04.

tag: comparison of expression profil changes in cells with normal α-synuclein level (control siRNA treatment) and reduced α-synuclein level (siSNCA4 treatment), triplicatesof each condition


title: Ferucarbutran-labelled fMSC 2


title: OPM2 transfected with control vector, rep1


title: Expression data from RNAi SNCA treated human neuroblastoma cell line_transfected with siSNCA4_Replicate 1

treatment_protocol: "RNAi of α-synuclein (SNCA) was performed with chemically synthesized siRNAs against SNCA (Qiagen). All transfection experiments were performed in independent triplicates, while 2x106 cells and 2 μg siRNA were used for electroporation with the Cell Line Nucleofection Kit V (Amaxa) applying program G-04.


title: Expression data from RNAi SNCA treated human neuroblastoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  1 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: RNAi of α-synuclein (SNCA) was performed with two different chemically synthesized siRNAs against SNCA (Qiagen) and control siRNA (Qiagen) with a random sequence not present in the human genome. All transfection experiments were performed in independent triplicates, while 2x106 cells and 2 μg siRNA were used for electroporation with the Cell Line Nucleofection Kit V (Amaxa) applying program G-04.


title: Mock-labelled fMSC Control 2


title: Expression data from RNAi SNCA treated human neuroblastoma cell line_transfected with control siRNA_Replicate 3

treatment_protocol: RNAi was performed with control siRNA (Qiagen) with a random sequence not present in the human genome. All transfection experiments were performed in independent triplicates, while 2x106 cells and 2 μg siRNA were used for electroporation with the Cell Line Nucleofection Kit V (Amaxa) applying program G-04.


title: Expression data from RNAi SNCA treated human neuroblastoma cell line_transfected with siSNCA4_Replicate 3


title: Ferucarbutran-labelled fMSC 1


title: Expression data from RNAi SNCA treated human neuroblastoma cell line_si control_Repl2

tag: Comparison of expression profil changes in cells with normal α-synuclein level (control siRNA treatment) and reduced α-synuclein level (siSNCA4 treatment), triplicatesof each condition


title: 1 week 4 degrees rep 3

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from mice exposed to cold

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C

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

data_processing: GCRMA

source_name: White adipose tissue from mice kept 1 week at 4 degrees C

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

growth_protocol: Male mice, 6-8-wk old, of the C57/Bl6 strain, which had been maintained at 22˚C were divided into groups.

extract_protocol: Trizol

treatment_protocol: Mice were adapted at 18˚C for 1-3 weeks before being transferred to 4˚C for 1 or 5 weeks.

tag: age

value: 6-8 weeks

tag: gender

tag: strain


title: 5 weeks 4 degrees rep 2

source_name: White adipose tissue from mice kept 5 weeks at 4 degrees C


title: 1 week 4 degrees rep 1


title: 5 weeks 4 degrees rep 1


title: 5 weeks 4 degrees rep 3


title: 5 weeks 30 degrees rep 3

description: Gene expression data from control mice

source_name: White adipose tissue from mice kept 5 weeks at room temperature


title: 1 week 4 degrees rep 2


title: 1 week 30 degrees repl 3

description: Gene expression data from control mice

source_name: White adipose tissue from mice kept 1 week at room temperature


title: 5 weeks 30 degrees rep 2

description: Gene expression data from control mice


title: 5 weeks 30 degrees rep 1

description: Gene expression data from control mice


title: 1 week 30 degrees rep 2

description: Gene expression data from control mice


title: 1 week 30 degrees rep 1

description: Gene expression data from control mice


title: CTL no cyotkine, rep2

city: St. Louis

first: Andrey

last: Shaw

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: Followed the manufacturer's protocol for the Affymetrix GeneChip 3'IVT express labeling assay.

scan_protocol: GS3000 (Affymetrix); Fluidics Station 450 (Affymetrix)

data_processing: GCOS operating system (Affymetrix); Normalized using a scale factor of 1500.

source_name: OT-1 CTL no exogenous cytokine

growth_protocol: OT-1 splenocytes cultured with 1mM SIINFEKL peptide for 4 days in IMDM+10% FCS with b-mercaptoethanol and penn/strep.  Live cells were harvested with a ficoll gradient and put back in culture for 24 hours.

extract_protocol: Trizol (Invitrogen) followed by Qiagen RNeasy kit.

treatment_protocol: No exogenous cytokine added

tag: Cells from OT-1 transgenic mouse (C57BL/6)


title: CTL with IL-12, rep2

source_name: OT-1 CTL with IL-12

label_protocol: Followed the manufacturer's protocol for the Affymetrix GeneChip 3'IVT express labeling assay.

growth_protocol: OT-1 splenocytes cultured with 1mM SIINFEKL peptide for 4 days in IMDM+10% FCS with b-mercaptoethanol and penn/strep.  Live cells were harvested with a ficoll gradient and put back in culture for 24 hours with 20ng/ml rmIL-12 (Invitrogen).

treatment_protocol: 20ng/ml IL-12


title: CD8+ DCs unstim

city: New York

first: Hiroaki

last: Hemmi

address: 1230 York Avenue

department: Laboratory of Cellular Physiology and Immunology

institute: The Rockefeller University

description: In vivo expanded splenic DCs were purified from C57BL/6 mice carring Flt3L-producing B16 melanoma.

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

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

data_processing: Raw CEL intensity data were RMA normalized.

source_name: splenic CD8+ DCs, in vivo expanded

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

extract_protocol: Trizol, according to the manufacturer's instruction.


title: CTL with IL-12, rep1

data_processing: GCOS operating system (Affymetrix); Normalized using a scale factor of 1500

growth_protocol: OT-1 splenocytes were cultured with 1mM SIINFEKL peptide for 4 days in IMDM+10%FCS, b-mercaptoethanol, penn/strep.  Live cells were harvested using a ficoll gradient and the cells placed back in culture for 24 hours with 20ng/ml rmIL-12 (Invitrogen)

extract_protocol: Trizol (Invitrogen) followed by cleanup with Qiagen RNeasy kit.


title: Neural stem cell sample_3

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.

source_name: Neural stem cells (OG2/Rosa26)

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

growth_protocol: Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate.

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: Neural stem cells; Strain:OG2/Rosa26; Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.


title: One-factor (Oct4) iPS cell-derived NSCs sample_3

source_name: NSCs from 1F (Oct4) iPS cells

growth_protocol: Neural stem cells (NSCs) were derived from 1F (Oct4) iPS cells of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004). Cells were seeded at a density of 5x104 cells per 6-well plate.

treatment_protocol: Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vector encoding mouse cDNA of Oct4. Three days after infection cells were further subcultured in ESC medium containing LIF without any further selection to derived 1F (Oct4) iPS cells. These 1F iPS cells were differentiated into NSC according to Conti et al., (PLoS Biology, 2005) with modifications (Jeong Beom Kim, unpublished).

tag: Neural stem cells (NSCs) from one-factor (1F) iPS cells. Strain


title: One-factor (Oct4) iPS cell-derived NSCs sample_2

value: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.


title: One-factor (Oct4) iPS cell-derived NSCs sample_1


title: Neural stem cell sample_2

treatment_protocol: Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.


title: NSCs-derived iPS cells by one-factor (Oct4) sample_3

source_name: One-factor (1F) iPS cells

growth_protocol: Induced pluripotent stem (iPS) cell were grown on irradiated MEF and in ESC medium (DMEM supplemented with 15% FBS, nonessential amino acids, L-glutamine, penicillin/streptomycin, b-mercaptoethanol and 1,000 U/ml LIF).

treatment_protocol: Neural stem cells (NSC) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vector encoding mouse cDNA of Oct4. Three days after infection cells were further subcultured in ESC medium containing LIF without any further selection. Oct4-GFP–positive colonies were mechanically isolated, and individual cells were dissociated and subsequently replated onto MEF. Colonies were then selected for expansion.

tag: Induced pluripotent stem (iPS) cells from mouse neural stem cells (NSCs). Strain


title: CTL no cytokine, rep1

growth_protocol: OT-1 splenocytes were cultured with 1mM SIINFEKL peptide for 4 days in IMDM+10%FCS, b-mercaptoethanol, penn/strep.  Live cells were harvested using a ficoll gradient and the cells placed back in culture for 24 hours without the addition of exogenous cytokine.


title: NSCs-derived iPS cells by one-factor (Oct4) sample_2


title: Neural stem cell sample_4


title: NSCs-derived iPS cells by one-factor (Oct4) sample_1


title: CD8- DCs unstim

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

data_processing: Raw CEL intensity data were RMA normalized

source_name: splenic CD8- DCs, in vivo expanded

extract_protocol: Trizol, according to manufacturer's instraction.

tag: Strain


title: U266 transfected with CS1 expression vector, rep2


title: Neural stem cell sample_1


title: Expanded CD8 Tcells with Suppression function rep2

city: Augusta

first: Jin-Xiong

last: She

state: GA

address: 1120 15th Street, MCG, CA 4126

department: Center for Biotechnology and Genomic medicine

institute: Medical College of Georgia

description: Molecular profiles of CD8+ suppressor T cells

hyb_protocol: Hybridization according to Affymetrix protocol, 45 degrees celcius, 16 hours, 50 rpm

scan_protocol: Scanned on Affymetrix scanner 3000 with 7G upgrade

data_processing: The data were condensed with RMA transformation algorithm using the "R (Bioconductor)" - an open source and open development software project for the analysis and comprehension of genomic data.

source_name: CD8+ T cells

label_protocol: Labelled 2 microg Total RNA according to Eberwine protocol using Target Amp kit, Epicentre

extract_protocol: Total RNA was isolated from the cells of different samples using QIA shredder and RNeasy Mini Kit spin columns (Qiagen)

value: C57BL/6, Gender:Female, Age:8 - 12 weeks, Tissue:Spleen T cells


title: Fresh CD8 rep2


title: Stimulated CD8 rep1


title: Expanded CD4 Tcells with less suppression rep3

source_name: CD4+ T cells


title: Expanded CD4 Tcells with less suppression rep2


title: Expanded CD8 Tcells with Suppression function rep5


title: Stimulated CD8 rep2


title: Expanded CD8 Tcells with Suppression function rep1


title: CD4 T sells, Tumor Antigen, Rep 1

status: Public on Jan 31 2009

city: Baltimore

first: Charles

middle: G

last: Drake

state: MD

address: 1650 Orleans St CRB I #410

department: Department of Oncology

institute: Johns Hopkins Sidney Kimmel Comprehensive Cancer Center

description:
Gene Expression Profile of a T cell responding to Tumor
CDra-TTT-PT-1a-MOE430_2 [ProHAxTRAMP]

hyb_protocol: Samples were hybridized to separate Affymetrix Mouse 430 Plus2 expression array chips

scan_protocol: Expression array Chips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: Relative expression levels were calculated using the MAS5.0 normalization

source_name: Tumor-antigen model

label_protocol: Standard labeling following the manufacturers protocol was carried out after  cDNA was synthesized using the Nugen FL-Ovation cDNA Biotin Module V2 kit, (http://www.nugeninc.com/pdfs/flbv2_userguide.pdf).

growth_protocol: CFSE labeled TCR transgenic CD4 T cells specific for HA were harvested from donor mice, purified using Miltenyi’s magnetically labeled beads, and adoptively transferred into tumor-antigen recognition model (ProHA x TRAMP), Self-antigen recognition model (C3HA), viral-antigen recognition model (VaccHA) activation control, and naïve adoptive transfer control (Nontrangenic) mice

extract_protocol: Sorted cells were pelleted suspended in Trizol and stored at -80ºC prior to RNA extraction using the Trizol reagent according to the manufacturer's instructions. RNA integrity was analyzed using an Agilent 2100 Bioanalyzer, the RNA 6000 Pico, and Nano Kits (Agilent Technologies).

treatment_protocol: HA-specific CD4 T that had undergone antigen specific division in vivo (i.e. CFSE-diluted)cells were harvested from lymph nodes 3-7 days post adoptive transfer.  FACSVantage SE cell sorter (BD Biosciences) was used to sort T cells by  gating on CFSE-diluted and Thy1.1+ (donor origin) from enriched CD4 T cells

tag: B10.d2, Male,CFSE-diluted,Tumor-antigen activated CD4 T cell


title: Expanded CD8 Tcells with Suppression function rep4


title: Expanded CD4 Tcells with less suppression rep1


title: CD4 T sells, No Antigen, Rep 1a

description:
Gene Expression Profile of a Naive T cell
CDra-TTT-NT-1a-MOE430_2 [Nontransgenic 1a]

source_name: No Antigen Naïve Adoptive transfer control

tag: B10.d2, Male, CFSE-Undiluted,none-activated CD4 T cell


title: CD4 T sells, Viral Antigen, Rep 1

description:
Gene Expression Profile of a T cell responding to Virus
CDra-TTT-VaC-1a-MOE430_2 [VaccHA]

source_name: Viral antigen model

tag: B10.d2, Male, CFSE-diluted,Viral-antigen activated CD4 T cell


title: CD4 T sells, No Antigen, Rep 2a

description:
Gene Expression Profile of a Naive T cell
CDra-TTT-NT-2a-MOE430_2 [Nontransgenic 2a]

tag: B10.d2, Male, CFSE-Undiluted, none-activated CD4 T cell


title: CD4 T sells, Self Antigen, Rep 1

description:
Gene Expression Profile of a T cell responding to self
CDra-TTT-HA-1a-MOE430_2 [C3HA]

source_name: Self-antigen model (C3HA)

tag: B10.d2, Male,CFSE-diluted , Self-antigen activated CD4 T cell


title: Fresh CD8 rep1


title: Expanded CD8 Tcells with Suppression function rep3


title: Exp 2 SCL fl/fl +Cre a

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

description: Gene expression in mouse embryo megakaryocytes.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

source_name: Megakaryocytes, SCL fl/fl + Cre a

label_protocol: Affymetrix protocol

extract_protocol: Trizol (Gibco BRL) and RNEasy (Qiagen) kits

tag: Mouse embryos


title: Exp 2 SCL fl/fl

source_name: Megakaryocytes, SCL fl/fl


title: Exp 1 SCL fl/fl +Cre

source_name: Megakaryocytes, SCL fl/fl + Cre


title: Exp 2 SCL fl/fl +Cre +SCL

source_name: Megakaryocytes, SCL fl/fl + Cre + SCL


title: Exp 2 SCL fl/fl +Cre b

source_name: Megakaryocytes, SCL fl/fl + Cre b


title: Exp 1 SCL fl/fl


title: Exp 1 SCL fl/fl +Cre +SCL


title: Untreated at 72 h, biol. rep2 in Exp2

city: Geneva

first: Marc

last: Lamarine

state: Geneva

address: 9 Chemin des Mines

institute: Merck Serono S.A. · Geneva

description: Oli-neu after 72 h  Untreated in Experiment 2

hyb_protocol: In our study, 3 μg of total RNA isolated were first reverse tanscribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets were then cleaned up, an aliquot of 20 μg was fragmented, and finally 15 μg were hybridized to GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, P/N 900495, 900496, 900497). Chips were washed andlabeled in the fluidics station, using protocol EuKGE-WS2v_45 After scanning.

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G

data_processing: Intensity Profile pipeline from Rosetta© was used to create an intensity (expression) profile for each sample. Intensity Profile pipeline applies the actual error model to estimate error in the measurements for the reporters and derive the P-values for significance of expression. The estimated error of the hybridization intensity is the larger of the actual measurement error, computed as propagated from the errors of the probe cells, and the modeled error. Three terms are included in the error model: an additive term related to background noise, a term related to binding site randomness (a Poisson process), and multiplicative term related to fractional error of the intensity- Intensities are not log transformed.

source_name: Oli-neu after 72 h  Untreated

label_protocol: The One-Cycle Eukaryotic Target Labeling Assay (One-Cycle Target Labeling and Control Reagents,Affymetrix, P/N 900493) was used to produce fragmented biotinylated cRNA from total RNA as described in the standard Affymetrix protocol (P/N 701021 Rev. 5).

growth_protocol: Oli-Neu cell line were maintained in DMEMF12 (Invitrogen # 21331) supplemented with 50μg/ml apo-1 Transferrin (Sigma T-1147), 5ng/ml sodium selenite (Sigma S-9133), 5μg/ml Insulin (Sigma I-0516),100μM Putrescine (Sigma P-7505), 22nM Progesterone (Sigma P-7556), 0.5 nM T3 (Sigma T-6397), 1% HS (Invitrogen 26050), 1% nicillin/Streptomycin (Invitrogen 15070), 2mM glutamine Invitrogen 25030), 0.1% Sodium bicarbonate (Invitrogen 25080) and 15mM Hepes Invitrogen 15630)

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

treatment_protocol: Differentiation medium, DMEM,F12 supplemented with 50μg/ml apo-Transferrin, 5ng/ml sodium selenite, 100μM Putrescine, 130nM Progesterone, 200 nM T3, 1% HS, 1% Pennicilin/Streptomycin, 2mM glutamine, 0.1% Sodium bicarbonate and 15mM Hepes. Chemical treatments for micro-array analysis

tag: differentiation medium

value: DFEM supplemented with 50μg/ml apo-Transferrin, 5ng/ml sodium selenite,100μM Putrescine, 130nM Progesterone, 200 nM T3, 1% HS, 1% Pennicilin/Streptomycin, 2mM, glutamine, 0.1% Sodium bicarbonate and 15mM Hepes


title: Untreated at 72 h, biol. rep3 in Exp1

description: Oli-neu after 72 h  Untreated in Experiment 1


title: Untreated at 72 h, biol. rep2 in Exp1


title: Untreated at 72 h, biol. rep3 in Exp2


title: Untreated at 72 h, biol. rep1 in Exp1


title: Untreated at 24 h, biol. rep3 in Exp1

description: Oli-neu after 24 h  Untreated in Experiment 1

source_name: Oli-neu after 24 h  Untreated


title: Untreated at 72 h, biol. rep1 in Exp2


title: Untreated at 24 h, biol. rep2 in Exp1


title: Untreated at 24 h, biol. rep1 in Exp2

description: Oli-neu after 24 h  Untreated in Experiment 2


title: Untreated at 24 h, biol. rep1 in Exp1


title: Untreated at 10 h, biol. rep1 in Exp2

description: Oli-neu after 10 h  Untreated in Experiment 2

source_name: Oli-neu after 10 h  Untreated


title: RetinoicAcid at 72 h, biol. rep1 in Exp1

description: Oli-neu after 72 h treated with RetinoicAcid in Experiment 1

tag: 13-cis-Retinoic Acid (LKT Laboratories R1779) 1μM


title: RetinoicAcid at 24 h, biol. rep3 in Exp1

description: Oli-neu after 24 h treated with RetinoicAcid in Experiment 1


title: Untreated at 10 h, biol. rep1 in Exp1

description: Oli-neu after 10 h  Untreated in Experiment 1


title: RetinoicAcid at 24 h, biol. rep2 in Exp1

source_name: Oli-neu after 24 h treated with RetinoicAcid


title: RetinoicAcid at 10 h, biol. rep2 in Exp1

description: Oli-neu after 10 h treated with RetinoicAcid in Experiment 1


title: RetinoicAcid at 24 h, biol. rep1 in Exp1


title: RetinoicAcid at 72 h, biol. rep2 in Exp1

source_name: Oli-neu after 72 h treated with RetinoicAcid


title: PD174265 at 72 h, biol. rep2 in Exp1

description: Oli-neu after 72 h treated with PD174265 in Experiment 1


title: PD174265 at 72 h, biol. rep1 in Exp1

source_name: Oli-neu after 72 h treated with PD174265


title: RetinoicAcid at 72 h, biol. rep3 in Exp1


title: RetinoicAcid at 10 h, biol. rep3 in Exp1

source_name: Oli-neu after 10 h treated with RetinoicAcid


title: BM_MLL-AF1p_809

description: Leukemia was initiated by transplanting c-kit+ BM progenitor cells infected with oncogene containing retroviruses in to lethally irradiated syngeneic C57BL/6 mice (male or female). Bone marrow was harvested from leukemic mice at euthanasia.

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software

data_processing: Normalisation of data and generation of values was performed using Microarray Analysis Software v5.0 (Affymetrix)

source_name: Leukemic BM, initiated by MLL-AF1p

label_protocol: GeneChip® IVT Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted from cryopreserved BM cells using Trizol according to manufacturer's instructions.

tag: Leukemic BM

tag: initiated by MLL-AF1p

tag: Mouse #809


title: PD174265 at 24 h, biol. rep3 in Exp1

description: Oli-neu after 24 h treated with PD174265 in Experiment 1


title: PD174265 at 24 h, biol. rep1 in Exp1

source_name: Oli-neu after 24 h treated with PD174265


title: PD174265 at 10 h, biol. rep1 in Exp1

description: Oli-neu after 10 h treated with PD174265 in Experiment 1


title: PD174265 at 10 h, biol. rep3 in Exp1

source_name: Oli-neu after 10 h treated with PD174265


title: PD174265 at 72 h, biol. rep3 in Exp1


title: Untreated at 10 h, biol. rep2 in Exp1


title: PD174265 at 10 h, biol. rep2 in Exp1


title: PD174265 at 24 h, biol. rep2 in Exp1


title: Insulin at 72 h, biol. rep1 in Exp2

description: Oli-neu after 72 h treated with Insulin in Experiment 2

source_name: Oli-neu after 72 h treated with Insulin

tag: Insulin 10μg/ml,


title: Insulin at 24 h, biol. rep1 in Exp2

description: Oli-neu after 24 h treated with Insulin in Experiment 2

source_name: Oli-neu after 24 h treated with Insulin


title: Insulin at 72 h, biol. rep2 in Exp2


title: Insulin at 10 h, biol. rep1 in Exp2

description: Oli-neu after 10 h treated with Insulin in Experiment 2

source_name: Oli-neu after 10 h treated with Insulin


title: Forskolin at 72 h, biol. rep3 in Exp2

description: Oli-neu after 72 h treated with Forskolin in Experiment 2

tag: Forskolin (Sigma F6886) 10μM,


title: Forskolin at 24 h, biol. rep2 in Exp2

description: Oli-neu after 24 h treated with Forskolin in Experiment 2


title: Forskolin at 72 h, biol. rep2 in Exp2

source_name: Oli-neu after 72 h treated with Forskolin


title: Forskolin at 72 h, biol. rep1 in Exp2


title: RetinoicAcid at 10 h, biol. rep1 in Exp1


title: Dexamethasone at 72 h, biol. rep3 in Exp1

description: Oli-neu after 72 h treated with Dexamethasone in Experiment 1

tag: Dexamethasone (Sigma D4902) 1μM,


title: Forskolin at 10 h, biol. rep2 in Exp2

description: Oli-neu after 10 h treated with Forskolin in Experiment 2


title: Forskolin at 24 h, biol. rep1 in Exp2

source_name: Oli-neu after 24 h treated with Forskolin


title: Dexamethasone at 24 h, biol. rep3 in Exp1

description: Oli-neu after 24 h treated with Dexamethasone in Experiment 1


title: Dexamethasone at 72 h, biol. rep2 in Exp1

source_name: Oli-neu after 72 h treated with Dexamethasone


title: Dexamethasone at 24 h, biol. rep2 in Exp1

source_name: Oli-neu after 24 h treated with Dexamethasone


title: Dexamethasone at 72 h, biol. rep1 in Exp1


title: Dexamethasone at 24 h, biol. rep1 in Exp1


title: Dexamethasone at 10 h, biol. rep3 in Exp1

description: Oli-neu after 10 h treated with Dexamethasone in Experiment 1


title: Dexamethasone at 10 h, biol. rep1 in Exp1

source_name: Oli-neu after 10 h treated with Dexamethasone


title: Dexamethasone at 10 h, biol. rep2 in Exp1


title: DM806_Signal_8383

status: Public on Jan 29 2009

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

institute: Duke University Medical Center

description: cells grown in culture for less than 20 passages.

hyb_protocol: Labeled cRNA was hybridized to the HU133plus2 Affymetrix GeneChip for 16hrs followed by washing and staining with biotinylated antistreptavidin antibody according to standard Affymetrix protocols.

scan_protocol: Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000

data_processing: Expression values across 54675 probe sets or genes were calculated as a function of the difference between the perfect match and mismatch probe signal intensities.  Values were normalized with a scaling factor unique to each array such that average signal intensity for each array was equal to 500.

source_name: human melanoma, melphalan

label_protocol: one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA

growth_protocol: Cells were grown in a sterile incubator maintained at 37°C, 5%CO2.  Cells were split every 3 to 5 days at 1:5 to 1:10 (depending on growth rate) using 0.25% trypsin.

extract_protocol: Cells were harvested from a T150 flask at 80% confluence and RNA isolated using Qiagen RNeasy-plus kit which included a step to eliminate genomic DNA.  Cell pellets were lysed with Qiagen RLT lysis buffer containing 1% β-mercaptoethanol.

treatment_protocol: Cells were grown in standard media (Iscove) supplemented with 10% fetal bovine serum, 2mM L-glutaming and 1% penicillin/streptomycin.   No other drugs or treatments were added.

tag: treatment

value: melphalan

tag: metastatic melanoma

tag: BRAF Mutant

tag: NRAS WT


title: DM598_Signal_8385

source_name: human melanoma, temozolomide, melphalan

value: temozolomide, melphalan

tag: BRAF WT

tag: NRAS Mutant


title: DM711_Signal_8380

tag: not determined


title: DM792_Signal_8374


title: DM733_Signal_8373


title: DM459_Signal_11113


title: DM595_Signal_11110


title: DM787_Signal_11112


title: DM602_Signal_11115


title: DM745_Signal_8381


title: DM424_Signal_8371


title: CNMel_Signal_8375


title: DM779_Signal_11109


title: DM798_Signal_11108


title: DM497_Signal_8372


title: DM425_Signal_8382


title: DM578_Signal_8378


title: UW-1_Signal_8386


title: DM382_Signal_8377


title: DM401p_Signal_11114


title: SkMel31_Signal_8388


title: DM589_Signal_8379


title: DM422_Signal_8384


title: A375_Signal_11116


title: DM467_Signal_11111


title: 92.1_Signal_8387


title: DM414_Signal_8370


title: PRMel_Signal_8376


title: DM608_Signal_8369


title: DM555_Signal_11117


title: MkTBr_Signal_8367


title: OCM-1_Signal_8359


title: DM643_Signal_8360


title: DM738_Signal_8358


title: DM443_Signal_8368


title: DM646_Signal_8364


title: DM391_Signal_8357


title: CRMel_Signal_8356


title: DM175_Signal_8350


title: DM440_Signal_8355


title: DM868_Signal_8366


title: DM636_Signal_8352


title: DM451_Signal_8353


title: DM751_Signal_8349


title: DM366_Signal_8361


title: DM368_Signal_8354


title: DM6_Signal_8363


title: DM833_Signal_8351


title: vNormal11

city: Budapest

first: Norbert

last: Solymosi

state: Budapest

address: István u. 2.

country: Hungary

institute: ATE

description: Gene expression data from peripheral blood sample

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU133 Plus 2.0 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner

data_processing: The data were preprocessed by the function mas5 from the Bioconductor affy package

source_name: human peripheral blood sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Affymetrix Globin Reduction Protocol)

extract_protocol: PaxGene extraction of total RNA was performed according to the manufacturer instructions

tag: Blood

value: Normal


title: vNormal03


title: vNormal06


title: vCRCCD08

value: CRC stage Duke C, D


title: vNormal04


title: vCRCCD12


title: vNormal05


title: vNormal10


title: vNormal07


title: vNormal02


title: vCRCCD10


title: SkMel28_Signal_8365


title: vCRCCD06


title: vCRCCD03


title: vCRCCD05


title: vCRCAB07

value: CRC stage Duke A, B


title: vCRCAB04


title: vCRCAB05


title: vCRCCD09


title: vCRCCD07


title: vNormal01


title: vCRCCD02


title: vCRCCD01


title: vCRCCD04


title: vCRCAB09


title: vCRCCD11


title: vNormal08


title: vNormal09


title: vCRCAB06


title: vCRCAB01


title: vCRCAB02


title: UC02

description: Gene expression data from colonic biopsy sample

source_name: human colonic biopsy sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA

extract_protocol: Qiagen RNeasy Mini extraction of total RNA was performed according to the manufacturer instructions

tag: Biopsy

value: UC


title: UC01


title: A2058_Signal_8362


title: UC03


title: Hyperplast09

value: Hyperplastic polyp


title: Hyperplast11


title: Normal03


title: Hyperplast05


title: Hyperplast04


title: Hyperplast06


title: Hyperplast02


title: CRCCD01

value: CRC-CD


title: Normal02


title: Normal01


title: CRCCD02


title: Hyperplast10


title: CRCB01

value: CRC-B


title: CD04

value: CD


title: Hyperplast03


title: CRCB03


title: CD03


title: CRCB02


title: CRCCD03


title: CD01


title: CD02


title: Hyperplast01


title: ADLGD03

value: Adenoma with low-grade dysplasia


title: CRCCD04


title: ADLGD01


title: ADLGD02


title: ADHGD02

value: Adenoma with high-grade dysplasia


title: Dendritic cells after Poly(I:C) treatment, time point 4 hours

city: Berlin

first: Elke

last: Krueger

address: Monbijoustr. 2

department: Institute of Biochemistry

institute: Charité Universitaetsmedizin Berlin

description: Gene expression data from monocyte-derived dendritic cells 4 hours after stimulation with Poly(I:C)

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133  Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS_v5_450 protocol

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4.0.036 (MAS 5.0) using Affymetrix default analysis settings. Normalization was performed by GCRMA.

label_protocol: Total RNA was amplified and labelled using Message AmpII-Biotin enhanced Kit, Ambion

growth_protocol: Immature DC were generated from Buffy coats of healthy donors obtained from the German Red Cross after informed consent. Peripheral blood mononuclear cells (PBMC) were separated by Ficoll-Paque gradient centrifugation and DC were generated from purified CD14+ cells by using antibody-coated microbeads and magnetic separation . Selected CD14+ cells were cultured for 5 days at a concentration of 2×106/ml in the presence of GM-CSF (500 U/ml) and IL-4 (100 U/ml) (both purchased from Strahtmann Biotec, Hamburg, Germany).

extract_protocol: Total RNA was extracted from frozen cell pellets using the High Pure RNA Isolation kit according to the manufacturer’s (Roche) protocol.

treatment_protocol: Day 5-immature DC were seeded on 24-well plates at 1×106 cells/ml with GM-CSF and IL-4. DC maturation was induced by addition of either a cocktail of pro-inflammatory cytokines and prostaglandins including TNF-alpha (10 ng/ml), IL-1-beta (10 ng/ml), IL-6 (1000 U/ml) and PGE2 (1 µg/ml), LPS (1 µg/ml),  Poly(I:C) (50 µg/ml) or flagged CD40L (500 ng/ml) + anti-Flag mAb (1 µg/ml) for 4, 8 and 16 hours.

tag: healthy donor


title: Dendritic cells after LPS treatment, time point 16 hours

description: Gene expression data from monocyte-derived dendritic cells 16 hours after stimulation with LPS


title: Dendritic cells after LPS treatment, time point 8 hours

description: Gene expression data from monocyte-derived dendritic cells 8 hours after stimulation with LPS


title: Dendritic cells after Schuler treatment, time point 16 hours

description: Gene expression data from monocyte-derived dendritic cells 16 hours after combined treatment with IL-1-b, IL-6, TNF-a and PGE2


title: Dendritic cells after Poly(I:C) treatment, time point 8 hours

description: Gene expression data from monocyte-derived dendritic cells 8 hours after stimulation with Poly(I:C)


title: NKDIL15tg BM NK cells, biologic replicate 3

city: Saint Louis

first: John

last: Sunwoo

state: MO

address: 660 S. Euclid Avenue, Campus Box 8115

institute: Washington University School of Medicine

description: NK cells sorted from NKDxIL15tg mouse bone marrow

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (FS450).

scan_protocol: GeneChips were scanned using the Affymetrix GS3000 scanner.

data_processing: The data was analyzed using the dChip Software from the Harvard School of Public Health (http://biosun1.harvard.edu/complab/dchip/).  dChip uses invariant set normalization method and model-based expression indexes (MBEI).  Normalization was performed with the baseline array having the median brightness.  Model-based expression was performed with a PM-only model.

source_name: NKDxIL15tg mouse BM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA using the Affymetrix GeneChip Expression 3' Amplification 2 Cycle Target Labeling Kit.

tag: bone marrow


title: NKDIL15tg BM NK cells, biologic replicate 1


title: ADHGD01


title: Dendritic cells after LPS treatment, time point 4hours

description: Gene expression data from monocyte-derived dendritic cells 4 hours after stimulation with LPS


title: Dendritic cells after CD40L treatment, time point 4 hours

description: Gene expression data from monocyte-derived dendritic cells 4 hours after stimulation with CD40L


title: NKDIL15tg BM NK cells, biologic replicate 2


title: Immature dendritic cells unstimulated

description: Gene expression data from unstimulated monocyte-derived dendritic cells


title: NKDIL15tg Spleen NK cells, biologic replicate 1

description: NK cells sorted from NKDxIL15tg mouse spleens

source_name: NKDxIL15tg mouse spleen

tag: spleen


title: Dendritic cells after Schuler treatment, time point 8 hours

description: Gene expression data from monocyte-derived dendritic cells 8 hours after combined treatment with IL-1-b, IL-6, TNF-a and PGE2


title: Dendritic cells after CD40L treatment, time point 8 hours

description: Gene expression data from monocyte-derived dendritic cells 8 hours after stimulation with CD40L


title: Dendritic cells after Schuler treatment, time point 4 hours

description: Gene expression data from monocyte-derived dendritic cells 4 hours after combined treatment with IL-1-b, IL-6, TNF-a and PGE2


title: IL15tg Spleen NK cells, biological replicate 3

description: NK cells sorted from IL15tg mouse spleens

source_name: IL15tg mouse spleen


title: Dendritic cells after CD40L treatment, time point 16 hours

description: Gene expression data from monocyte-derived dendritic cells 16 hours after stimulation with CD40L


title: NKDIL15tg Spleen NK cells, biologic replicate 3


title: NKDIL15tg Spleen NK cells, biologic replicate 2


title: Dendritic cells after Poly(I:C) treatment, time point 16 hours

description: Gene expression data from monocyte-derived dendritic cells 16 hours after stimulation with Poly(I:C)


title: IL15tg Spleen NK cells, biological replicate 1


title: IL15tg Spleen NK cells, biological replicate 2


title: MEFs (female) #2

status: Public on Jan 28 2009

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

hyb_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)

data_processing: all data were quantile normalized

source_name: Cell culture

extract_protocol: Trizol and RNEasy purification

tag: MEFs


title: MEFs (male) #1

scan_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)


title: 1A2 partial iPS clone #1

label_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)

tag: partial iPS clone 1A2


title: MEFs (male) #2


title: E14 ES cells #1 - control

tag: ES Cell Control


title: 1A2 partial iPS clone #2


title: MEFs (female) #1


title: 1D4 iPS clone #1

tag: iPS Clone


title: v6.5 ES cells #2 - control

tag: ES Cell control


title: 1B3 partial iPS clone #1

tag: partial iPS clone 1B3


title: 1D4 iPS clone #2


title: 2D4 iPS clone #2


title: Hyperplast07

description: Gene expression data from colonic biopsy sample


title: E14 ES cells #2 - control


title: Sorted GFP+ cells from 1A2 partial iPS clone

tag: Sorted GFP+ cells from 1A2 partially reprogrammed clone


title: 2D4 iPS clone #1


title: mpkCCD_clone_9_dDAVP

status: Public on Jan 26 2009

city: Taipei

first: Ming-Jiun

last: Yu

address: Rm 816, No. 1 Ren-Ai Road Section 1

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Taiwan University College of Medicine

description: Profiling of gene expression in mpkCCD clone 9 cells that express aquaporin 2 in the presence of vasopressin analog dDAVP (0.1 nM) for 5 days.

hyb_protocol: Labeled cRNA were hybridized to Mouse Genome 430 2.0 Arrays in Affymetrix Hybridization Oven 640 and washed in GeneChip® Fluidics Station 450 according to the manufacturer's recomended protocols.

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

data_processing: Transscript intensity values were obtained with Affymetrix GeneChip Operating System software version 1.4 and normalized based on MAS5 algorism using Affymetrix Expression Console software version 1.1.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocols.

extract_protocol: Total RNA of mpkCCD cells was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. The total RNA was treated with DNAse and heat inactivation followed by isopropanol precipitation. The concentration of total RNA was measured using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). The quality of the total RNA was analyzed by an Agilent 2100 Bioanalyzer to visualized ribosomal RNA (Agilent Technology Inc, Santa Clara, CA).

tag: The microarray data contain transcript intensity for mouse cortical collecting duct (mpkCCDc14) clone 9 cells exposed to vasopressin analog dDAVP in the basolateral medium for 5 days.  Clone 9 expresses detectable aquaporin 2 mRNA or protein in the presence of dDAVP.


title: Spleen-Th1-rep1

status: Public on Jan 27 2009

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

hyb_protocol: Default hybridization protocol of the UAB Gene Expression Shared Facility.

scan_protocol: Default scan protocol of the UAB Gene Expression Shared Facility.

data_processing: The raw data were obtained through GCOS, background subtracted and normalized through GC-RMA methods.

source_name: spleen, lymph nodes

label_protocol: Default label protocol of the UAB Gene Expression Shared Facility.

growth_protocol: tissue culture

extract_protocol: Default extract protocol of the UAB Gene Expression Shared Facility.

treatment_protocol: Th1 cytokine treated, spleen cells of transgenic mouse

tag: B6 strain


title: mpkCCD_clone_10_dDAVP

description: Profiling of gene expression in mpkCCD clone 10 cells that express aquaporin 2 in the presence of vasopressin analog dDAVP (0.1 nM) for 5 days.

tag: The microarray data contain transcript intensity for mouse cortical collecting duct (mpkCCDc14) clone 10 cells exposed to vasopressin analog dDAVP in the basolateral medium for 5 days.  Clone 10 expresses detectable aquaporin 2 mRNA or protein in the presence of dDAVP.


title: mpkCCD_original_clone_dDAVP

description: Profiling of gene expression in the original mpkCCD cells that express aquaporin 2 in the presence of vasopressin analog dDAVP (0.1 nM) for 5 days.

tag: The microarray data contain transcript intensity for mouse cortical collecting duct (mpkCCDc14) original clone cells exposed to vasopressin analog dDAVP in the basolateral medium for 5 days.  The original mpkCCD clone expresses detectable aquaporin 2 mRNA or protein in the presence of dDAVP.


title: Spleen-Th17-rep1

data_processing: The raw data were obtained through GCOS, background subtracted, and normalized through GC-RMA methods.

treatment_protocol: Th17 cytokine treated, spleen cells of transgenic mice.


title: Spleen-Th17-rep2


title: Spleen-Th1-rep2

hyb_protocol: Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

label_protocol: The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA).  Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.


title: Hyperplast08


title: mpkCCD_clone_11_dDAVP

description: Profiling of gene expression in mpkCCD clone 11 cells that express aquaporin 2 in the presence of vasopressin analog dDAVP (0.1 nM) for 5 days.

tag: The microarray data contain transcript intensity for mouse cortical collecting duct (mpkCCDc14) clone 11 cells exposed to vasopressin analog dDAVP in the basolateral medium for 5 days.  Clone 11 expresses detectable aquaporin 2 mRNA or protein in the presence of dDAVP.


title: mpkCCD_clone_3_dDAVP

description: Profiling of gene expression in mpkCCD clone 3 cells that express aquaporin 2 in the presence of vasopressin analog dDAVP (0.1 nM) for 5 days.

tag: The microarray data contain transcript intensity for mouse cortical collecting duct (mpkCCDc14) clone 3 cells exposed to vasopressin analog dDAVP in the basolateral medium for 5 days.  Clone 3 expresses detectable aquaporin 2 mRNA or protein in the presence of dDAVP.


title: mpkCCD_clone_2_dDAVP

description: Profiling of gene expression in mpkCCD clone 2 cells that do not express aquaporin 2 in the presence of vasopressin analog dDAVP (0.1 nM) for 5 days.

tag: The microarray data contain transcript intensity for mouse cortical collecting duct (mpkCCD) clone 2 cells exposed to vasopressin analog dDAVP in the basolateral medium for 5 days.  Clone 2 does not express detectable aquaporin 2 mRNA or protein in the presence of dDAVP.


title: v6.5 ES cells #1 - control


title: Mammary Gland_Cav-3KO_rep1

city: Philadelphia

first: Mathew

last: Casimiro

state: PA

address: 1035 BLSB, 233 South 10th street

department: Cancer Biology

institute: Thomas Jefferson University

description: Gene expression data from WT mouse mammary gland compared to mice deficient for Caveolin-3

hyb_protocol: The hybridization protocol was followed for single probe array 49 format (standard)/64 format array outlined in genechip expression analysis technical manual provided by Affymetrix. This was also true for washing, staining and scanning procedures.

scan_protocol: Mouse 430 2.0 chips scanned using Gene chip scanner 3000 with autoloader following Affymetrix guidelines. Image aquired using Gene Chip Operating Sofware version 1.4.

data_processing: The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm.

source_name: Mammary Gland

label_protocol: Total RNA (5µg of RNeasy purified) was reverse transcribed using Superscript III First-Strand Synthesis System (Invitrogen) using a HPLC purified T7-dT24 primer (Sigma Genosys) which contains the T7 polymerase promoter sequence. The single stranded cDNA was converted to double stranded cDNA using DNA polymerase I (promega) and purified by cDNA spin column purification using GeneChip Sample Cleanup Module (Affymetrix). The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix). 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module.

growth_protocol: No specific growth protocol

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: No treatment

tag: FVB/N genetic background. 4-month old

tag: virgin female mice were used, mice were kept on a 12-hour

tag: light/dark cycle with ad libitum access to chow and water


title: Mammary Gland_Cav-3KO_rep3


title: U2OS_empty pSG213 vector_48 hours of doxycycline induction - Replica 1

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: U2OS cells transfected with an empty pSG213 vector after 48 hours of doxycycline induction - Replica 1

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.

data_processing: The data were analyzed with GeneChip operating system (GCOS) 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: U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 48h induction

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.  The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.

growth_protocol: U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.

treatment_protocol: Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.

tag: U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 48h with 2ug/ml doxycycline.


title: U2OS_empty pSG213 vector_8 hours of doxycycline induction - Replica 1

description: U2OS cells transfected with an empty pSG213 vector after 8 hours of doxycycline induction - Replica 1

source_name: U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 8h induction

tag: U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 8h with 2ug/ml doxycycline.


title: U2OS_HA-tagged PRDM5_48 hours of doxycycline induction - Replica 1

description: U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 48 hours of doxycycline induction - Replica 1

source_name: U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 48h induction

tag: U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 48h with 2ug/ml doxycycline to induce transgene expression.


title: U2OS_empty pSG213 vector_48 hours of doxycycline induction - Replica 2

description: U2OS cells transfected with an empty pSG213 vector after 48 hours of doxycycline induction - Replica 2