title: Cells isolated from OA Meniscal tissue 4

city: Charlotte

first: Helen

last: Gruber

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

description: Passage 2 cells

hyb_protocol: Fragmented cRNA was hybridized to the  X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned once via the Affymetrix 3000G scanner.

data_processing: The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).

source_name: Meniscal Tissue

label_protocol: cRNA was synthesized and biotin labeled using BioArray high yield RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY)

growth_protocol: Cells were seeded in 100 mm plates at 75% confluence and incubated at 37oC in Dulbecco’s modified eagle medium containing 0.5% antibiotic/antimycotic solution and 10% fetal bovin serum for 24 hours. Cells were incubated an additional 48 hours with the medium (containing only 1% serum) being changed every 24 hrs.

extract_protocol: Total RNA was extracted using Trizol reagent

value: OA


title: Quint_2-67_Col-0-1h_Rep1_ATH1

status: Public on Nov 18 2009

type: RNA

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description:
After sterilization, seeds were incubated in sterile water in the dark for 5 days at 4Â°C prior to cultivation  Seed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification  Sterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 Â°C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.  Reference for ATS medium:
Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080  autoclaved  22 Â°C average, 22 Â°C day, 22 Â°C night 70 % average, 70 % day, 70 % night Own medium: ATS medium according to Lincoln et al. (1990)  Constant light

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Col-0 (Columbia)

label_protocol: Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"

extract_protocol: Qiagen RNeasy kit protocol

tag: strain/ecotype

value: Col-0 (Columbia)

tag: developmental stage

tag: tissue

value: whole plant

tag: stock code


title: Cells isolated from OA Meniscal tissue 2

country: USA

description: Passage 2 cells

organism: Homo sapiens


title: Cells isolated from OA Meniscal tissue 5

description: Passage 2 cells


title: Quint_2-66_Col-0-30min_Rep3_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: Quint_2-70_Col-0-3h_Rep1_ATH1


title: Quint_2-69_Col-0-1h_Rep3_ATH1


title: Cells isolated from OA Meniscal tissue 3

description: Passage 2 cells


title: tcr-cHL_4

status: Public on Nov 16 2009

city: Essen

first: Ralf

last: Küppers

address: Virchowstr. 173

department: Institute for Cell Biology (Tumor Research)

country: Germany

institute: University of Duisburg-Essen, Medical School

description: Analysis of differential gene expression in primary human lymphoma cells of ALK-positive, ALK-negative and cutaneous anaplastic large cell lymphoma (ALCL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and subsets of non-neoplastic T and NK lymphocytes isolated from tonsils or blood.

hyb_protocol: Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol.

data_processing: Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)

label: SAPE (streptavidin-phycoerythrin)

source_name: tcr-cHL donor 4

label_protocol: The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 g T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).

extract_protocol: The Purescript RNA Isolation Kit (Gentra) was applied using 80 g glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.

treatment_protocol: Five m-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells or groups of two to ten cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.

value: primary lymphoma cells laser-microdissected from a patient diagnosed with tumor cell rich classical Hodgkin Lymphoma (tcr-cHL)


title: Cells isolated from Normal  Meniscal tissue 3

description: Passage 2 cells

value: Normal


title: tcr-cHL_1

source_name: tcr-cHL donor 1


title: tcr-cHL_3

source_name: tcr-cHL donor 3


title: Cells isolated from Normal  Meniscal tissue 1

description: Passage 2 cells


title: Cells isolated from OA Meniscal tissue 1

description: Passage 2 cells


title: tcr-cHL_2

source_name: tcr-cHL donor 2


title: NKT_B2

source_name: NKT cells donor 2

treatment_protocol: NKT cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. NKT cells from freshly isolated, heparinised blood were also isolated by MACS enrichment. Cells were stained with anti-V24JQ (clone 6B11)-PE and subsequently enriched with PE-Mircobeads (PE MicroBeads, Miltenyi Biotech, Bergisch Gladbach, Germany) followed by FACS of CD3+ V24JQ+ V11+ cells.

tag: cells

value: NKT cells, isolated from peripheral blood by fluorescence-activated cell sorting


title: CD8R_T15

source_name: resting cytotoxic T-cells donor 15

treatment_protocol: Tonsils for the isolation of resting cytotoxic T-cells (CD8R) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. CD8+ T-cells were isolated by MACS depletion of CD4+, CD14+, CD16+, CD19+, CD36+, CD56+, CD123+, TCR γ/δ, and CD235a+ (CD4+ T cells, γ/δ T cells, B cells, NK cells, dendritic cells, monocytes, granulocytes, and erythroid cells)(CD8+ T cell isolation kit II, Miltenyi Biotech, Bergisch Gladbach, Germany) followed by FACS-sorting of 2000 CD3+ CD8+ HLA-DR- cells cells.

value: resting cytotoxic T-cells, isolated from tonsils by fluorescence-activated cell sorting


title: NK_T17

source_name: NK cells donor 17

treatment_protocol: Tonsils for the isolation of natural killer cells (NK) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. NK cells were isolated by MACS technology depleting non-NK cells, i.e.,T  cells, B cells, stem cells, dendritic cells, monocytes, granulocytes, and erythroid cells (NK cell isolation kit, Miltenyi Biotech, Bergisch Gladbach, Germany) followed by FACS-sorting of 2000 CD3- CD56+  cells.

value: NK cells, isolated from tonsils by fluorescence-activated cell sorting


title: CD8R_T12

source_name: resting cytotoxic T-cells donor 12


title: NKT_B4

source_name: NKT cells donor 4

treatment_protocol: NKT cells were isolated from peripheral blood of five healthy adult donors. Blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. NKT cells from freshly isolated, heparinised blood were also isolated by MACS enrichment. Cells were stained with anti-V24JQ (clone 6B11)-PE and subsequently enriched with PE-Mircobeads (PE MicroBeads, Miltenyi Biotech, Bergisch Gladbach, Germany) followed by FACS of CD3+ V24JQ+ V11+ cells.


title: CD8A_T17

source_name: activated cytotoxic T-cells donor 17

treatment_protocol: Tonsils for the isolation of activated cytotoxic T-cells (CD8A) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. CD8+ T-cells were isolated by MACS depletion of CD4+, CD14+, CD16+, CD19+, CD36+, CD56+, CD123+, TCR γ/δ, and CD235a+ (CD4+ T cells, γ/δ T cells, B cells, NK cells, dendritic cells, monocytes, granulocytes, and erythroid cells)(CD8+ T cell isolation kit II, Miltenyi Biotech, Bergisch Gladbach, Germany) followed by FACS-sorting of 2000 CD3+ CD8+ HLA-DR+ cells (CD8A).

value: activated cytotoxic T-cells, isolated from tonsils by fluorescence-activated cell sorting


title: NKT_B3

source_name: NKT cells donor 3


title: CD30_T14

source_name: CD30+ T-cells donor 14

treatment_protocol: Tonsils for the isolation of CD30+ T-cells (CD30) were were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. CD30+ T cells were isolated applying CD30 MicroBeads to the cell suspension (CD30 MicroBeads, Miltenyi Biotech, Bergisch Gladbach, Germany) and enrichment with MACS technology followed by FACS of CD3+ CD30+ cells.

value: CD30+ T-cells, isolated from tonsils by fluorescence-activated cell sorting


title: CD8R_T14

source_name: resting cytotoxic T-cells donor 14


title: CD8A_T11

source_name: activated cytotoxic T-cells donor 11


title: CD30_T12

source_name: CD30+ T-cells donor 12


title: CD8A_T14

source_name: activated cytotoxic T-cells donor 14


title: NK_T12

source_name: NK cells donor 12


title: CD8R_T11

source_name: resting cytotoxic T-cells donor 11


title: NKT_B5

source_name: NKT cells donor 5


title: NK_T15

source_name: NK cells donor 15


title: CD8A_T8

source_name: activated cytotoxic T-cells donor 8


title: CD8R_T8

source_name: resting cytotoxic T-cells donor 8


title: CD8A_T15

source_name: activated cytotoxic T-cells donor 15


title: Cells isolated from Normal  Meniscal tissue 2

description: Passage 2 cells

source_name: Meniscal Tissue


title: NK_T8

source_name: NK cells donor 8


title: NKT_B1

source_name: NKT cells donor 1


title: NK_T11

source_name: NK cells donor 11


title: CD8A_T16

source_name: activated cytotoxic T-cells donor 17


title: CD30_T10

source_name: CD30+ T-cells donor 10


title: CD4A_T5

source_name: activated T-helper cells donor 5

treatment_protocol: Tonsils for the isolation of activated T-helper cells (CD4A) were were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. CD4+ T-cells were isolated by MACS depletion of CD8+, CD14+, CD16+, CD19+, CD36+, CD56+, CD123+, TCR γ/δ, and CD235a+cells (CD8+ T cells, γ/δ T cells, B cells, NK cells, dendritic cells, monocytes, granulocytes, and erythroid cells) followed by FACS-sorting of 2000 CD3+ CD4+ CD25+ cells (CD4A).

value: activated T-helper cells, isolated from tonsils by fluorescence-activated cell sorting


title: CD4R_T5

source_name: resting T-helper cells donor 5

treatment_protocol: Tonsils for the isolation of resting T-helper cells (CD4R) were were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. CD4+ T-cells were isolated by MACS depletion of CD8+, CD14+, CD16+, CD19+, CD36+, CD56+, CD123+, TCR γ/δ, and CD235a+cells (CD8+ T cells, γ/δ T cells, B cells, NK cells, dendritic cells, monocytes, granulocytes, and erythroid cells) followed by FACS-sorting of 2000 CD3+ CD4+ CD25- cells (CD4R).

value: resting T-helper cells, isolated from tonsils by fluorescence-activated cell sorting


title: CD30_T5

source_name: CD30+ T-cells donor 5


title: CD4R_T2

source_name: resting T-helper cells donor 2


title: CD4R_T6

source_name: resting T-helper cells donor 6


title: CD4R_T3

source_name: resting T-helper cells donor 3


title: CD4R_T1

source_name: resting T-helper cells donor 1


title: CD30_T15

source_name: CD30+ T-cells donor 15


title: Treg_T6

source_name: regulatory T cells donor 6

treatment_protocol: Tonsils for the isolation of regulatory T-cells (Treg) were were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. CD4+ T-cells were isolated by MACS depletion of CD8+, CD14+, CD16+, CD19+, CD36+, CD56+, CD123+, TCR γ/δ, and CD235a+cells (CD8+ T cells, γ/δ T cells, B cells, NK cells, dendritic cells, monocytes, granulocytes, and erythroid cells) followed by FACS-sorting of 2000 CD3+ CD4+ CD25high cells (T-reg), respectively.

value: regulatory T-cells, isolated from tonsils by fluorescence-activated cell sorting


title: Treg_T15

source_name: regulatory T cells donor 15


title: Treg_T5

source_name: regulatory T cells donor 5


title: Karpas299

source_name: ALK+ ALCL cell line Karpas 299

treatment_protocol: 2000 cells of ALK+ ALCL cell line Kapras 299 cells were cooled at 0-4°C and immediately isolated by fluorescence-activated cell sorting at this low temperature to avoid changes in gene expression due to RNA turnover

value: ALK+ ALCL cell line Karpas 299 cells, isolated by fluorescence-activated cell sorting


title: SUDHL1

source_name: ALK+ ALCL cell line SUDHL1

treatment_protocol: 2000 cells of ALK+ ALCL cell line SR786 cells were cooled at 0-4°C and immediately isolated by fluorescence-activated cell sorting at this low temperature to avoid changes in gene expression due to RNA turnover

value: ALK+ ALCL cell line SUDHL1 cells, isolated by fluorescence-activated cell sorting


title: CD4A_T1

source_name: activated T-helper cells donor 1

treatment_protocol: Tonsils for the isolation of activated T-helper cells (CD4A) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. CD4+ T-cells were isolated by MACS depletion of CD8+, CD14+, CD16+, CD19+, CD36+, CD56+, CD123+, TCR γ/δ, and CD235a+cells (CD8+ T cells, γ/δ T cells, B cells, NK cells, dendritic cells, monocytes, granulocytes, and erythroid cells) followed by FACS-sorting of 2000 CD3+ CD4+ CD25+ cells (CD4A).


title: SR786

source_name: ALK+ ALCL cell line SR786

value: ALK+ ALCL cell line SR786 cells, isolated by fluorescence-activated cell sorting


title: CD4A_T2

source_name: activated T-helper cells donor 2


title: Treg_T2

source_name: regulatory T cells donor 2


title: Treg_T7

source_name: regulatory T cells donor 7


title: CD4A_T3

source_name: activated T-helper cells donor 3


title: cALCL 5

source_name: cALCL case 5

value: primary lymphoma cells laser-microdissected from a patient diagnosed with primary cutaneous anaplastic large cell lymphoma (cALCL)


title: cALCL 1

source_name: cALCL case 1


title: cALCL 6

source_name: cALCL case 6


title: cALCL 4

source_name: cALCL case 4


title: cALCL 3

source_name: cALCL case 3


title: ALK+ ALCL 2

source_name: ALK+ ALCL case 2

value: primary lymphoma cells laser-microdissected from a patient diagnosed with ALK-positive anaplastic large cell lymphoma (ALK+ ALCL)


title: cALCL 2

source_name: cALCL case 2


title: ALK+ ALCL 4

source_name: ALK+ ALCL case 4


title: ALK+ ALCL 5

source_name: ALK+ ALCL case 5


title: ALK+ ALCL 3

source_name: ALK+ ALCL case 3


title: ALK- ALCL 4

source_name: ALK- ALCL case 4

value: primary lymphoma cells laser-microdissected from a patient diagnosed with ALK-negative anaplastic large cell lymphoma (ALK- ALCL)


title: cALCL 7

source_name: cALCL case 7


title: ALK+ ALCL 1

source_name: ALK+ ALCL case 1


title: ALK- ALCL 2

source_name: ALK- ALCL case 2


title: ALK- ALCL 3

source_name: ALK- ALCL case 3


title: VMC Patient 53

status: Public on Nov 14 2009

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

description: Gene expression

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy HGU133 2.0 plus array were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: Bioconductor's affy package was used for RMA normalization and raw data processing using default settings for background correction and normalization. Cox regression hazards model was applied to the processed data using the survival package. All analyses were performed using R software.

source_name: Vanderbilt University Medical Center

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

tag: age

tag: gender

value: female

tag: ethnicity

value: caucasian

tag: grade

value: 2 - Moderately differentiated(MD)

tag: overall_event (death from any cause)

value: death

tag: dfs_event (disease free survival; cancer recurrence)

value: recurrence

tag: overall survival follow-up time


title: VMC Patient 49

description: Gene expression

value: male

value: 2 - Moderately differentiated(MD).1 - Well differentiated (WD) - Moderate to poorly differentiated (MPD)


title: VMC Patient 54

description: Gene expression

value: no recurrence


title: VMC Patient 52

description: Gene expression


title: VMC Patient 50

description: Gene expression


title: VMC Patient 55

description: Gene expression

value: no death


title: Farage DLBCL tumor xenograft_6h PU-H71_replicate 2

status: Public on Nov 15 2009

city: Bethesda

first: Ana

middle: I

last: Robles

state: MD

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

description: The purine scaffold HSP90 inhibitor PU-H71 induces specific changes in gene expression in DLBCL xenografts.

hyb_protocol: RNA (6 µg) was hybridized to GeneChip Human Genome U133 Plus 2.0 Expression arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations. After hybridization, the chips were processed using fluidics station 450.

scan_protocol: GeneChips were scanned using a high-resolution microarray scanner 3000, and GeneChip Operating Software workstation version 1.3.

data_processing: The .CEL files were imported into BRB-ArrayTools software (Biometric Research Branch-NCI, MD) by setting up robust multiarray analysis (RMA) background correction.

source_name: Farage DLBCL tumor xenograft, 6h post PU-H71

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

extract_protocol: Total RNA was isolated using miRNeasy mini kit (Qiagen, Valencia, CA). RNA integrity was determined using the RNA 6000 Nano LabChip Kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice bearing Farage tumors were administered 75mg/kg PU-H71 purine scaffold HSP90 inhibitor by intra-peritoneal injection.

tag: Xenograft of Farage DLBCL human cell line subcutaneously injected in SCID mice.


title: Farage DLBCL tumor xenograft_Control_replicate 1

source_name: Farage DLBCL tumor xenograft, no treatment control

treatment_protocol: No treatment.


title: Farage DLBCL tumor xenograft_Control_replicate 2


title: Farage DLBCL tumor xenograft_12h PU-H71_replicate 2

source_name: Farage DLBCL tumor xenograft, 12h post PU-H71


title: ALK- ALCL 1

description: Analysis of differential gene expression in primary human lymphoma cells of ALK-positive, ALK-negative and cutaneous anaplastic large cell lymphoma (ALCL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and subsets of non-neoplastic T and NK lymphocytes isolated from tonsils or blood

source_name: ALK- ALCL case 1


title: VMC Patient 42

description: Gene expression


title: Farage DLBCL tumor xenograft_6h PU-H71_replicate 1


title: VMC Patient 47

description: Gene expression


title: VMC Patient 40

description: Gene expression

value: 3 - Poorly differentiated (PD)


title: VMC Patient 48

description: Gene expression


title: VMC Patient 35

description: Gene expression


title: VMC Patient 44

description: Gene expression


title: VMC Patient 34

description: Gene expression

value: black


title: VMC Patient 51

description: Gene expression


title: VMC Patient 38

description: Gene expression


title: VMC Patient 43

description: Gene expression


title: VMC Patient 37

description: Gene expression


title: VMC Patient 39

description: Gene expression


title: Farage DLBCL tumor xenograft_12h PU-H71_replicate 1


title: CD4A_T6

source_name: activated T-helper cells donor 6

value: activated T-helper cells, isolated from tonsils by fluorescence-activated cell sorting


title: VMC Patient 41

description: Gene expression

value: hispanic


title: VMC Patient 46

description: Gene expression


title: VMC Patient 45

description: Gene expression


title: VMC Patient 36

description: Gene expression


title: VMC Patient 31

description: Gene expression


title: VMC Patient 28

description: Gene expression


title: VMC Patient 30

description: Gene expression


title: VMC Patient 24

description: Gene expression


title: VMC Patient 29

description: Gene expression


title: VMC Patient 23

description: Gene expression


title: VMC Patient 32

description: Gene expression


title: VMC Patient 25

description: Gene expression


title: VMC Patient 26

description: Gene expression


title: VMC Patient 33

description: Gene expression


title: VMC Patient 16

description: Gene expression


title: VMC Patient 21

description: Gene expression


title: VMC Patient 11

description: Gene expression


title: VMC Patient 19

description: Gene expression


title: VMC Patient 14

description: Gene expression


title: VMC Patient 22

description: Gene expression


title: VMC Patient 4

description: Gene expression

value: 1 - Well differentiated (WD)


title: VMC Patient 12

description: Gene expression


title: VMC Patient 9

description: Gene expression


title: VMC Patient 17

description: Gene expression


title: VMC Patient 27

description: Gene expression


title: VMC Patient 13

description: Gene expression


title: VMC Patient 18

description: Gene expression


title: VMC Patient 20

description: Gene expression


title: VMC Patient 15

description: Gene expression


title: VMC Patient 10

description: Gene expression


title: VMC Patient 7

description: Gene expression


title: VMC Patient 5

description: Gene expression


title: VMC Patient 8

description: Gene expression


title: VMC Patient 6

description: Gene expression


title: VMC Patient 2

description: Gene expression


title: VMC Patient 3

description: Gene expression


title: MCC Patient 61

description: Gene expression

source_name: Moffitt Cancer Center

value: other (not caucasian, black, or hispanic)

value: 2 - Moderately differentiated (MD)

tag: dss_event (disease specific survival; death from cancer)


title: MCC Patient 53

description: Gene expression


title: MCC Patient 86

description: Gene expression


title: VMC Patient 1

description: Gene expression


title: MCC Patient 89

description: Gene expression


title: Sc3_1

status: Public on Nov 13 2009

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

institute: University Hospital Hamburg-Eppendorf

description: Human testis Score 3 Replicate 1

hyb_protocol: Hybridization cocktails containing fragmented cRNA at a concentration of 0.05 µg/µl were transferred to Human Genome U133 Plus 2.0 Array Gene Chips (Affymetrix) and incubated for 16h 60 rpm at 45°C on a rotator (Affymetrix). Arrays were washed and stained using a steptavidine-phycoerythrin conjugate. To increase signal strength, the antibody amplification protocol was used (EukGE-WS2v4)

scan_protocol: Arrays were scanned with a HP GeneArray Scanner (Affymetrix) by using default settings.

data_processing: DAT image files of the microarrays were generated using Microarray Analysis Suite 5.0 (Affymetrix). DAT image files of the microarrays were generated using Microarray Analysis Suite 5.0 (Affymetrix). RMA values from the affy package of www.bioconductor.org.

source_name: Spermatogonial presence in tubuli

label_protocol: Biotin-labeled cRNA was synthesized following the Eukaryotic Sample and Array Processing Protocol (Affymetrix).

extract_protocol: RNA was extracted with RNAclean/RNApure (Biozym/Peqlab) by aid of an UltraTurrax and subsequently re-purified over RNeasy columns (Qiagen). RNA integrity was checked on a Bioanalyzer (Agilent).

treatment_protocol: Testicular biopsies were obtained with the 'open biopsy' method and immediately submerged in RNAlater (Ambion).

tag: tissue type

value: testicular biopsy

tag: spermatogenic stage (johnsen score)

value: Score 3


title: MCC Patient 73

description: Gene expression

value: female

value: caucasian


title: MCC Patient 19

description: Gene expression


title: Sc2_2

description: Human testis Score 2 Replicate 2

source_name: Sertoli cell only syndrome

value: Score 2


title: MCC Patient 35

description: Gene expression

value: death

value: recurrence


title: Sc3_3

description: Human testis Score 3 Replicate 3


title: Sc2_3

description: Human testis Score 2 Replicate 3


title: Sc2_1

description: Human testis Score 2 Replicate 1


title: Sc3_2

description: Human testis Score 3 Replicate 2


title: DNMT1i_replicate_1_RMA_normalized

status: Public on Nov 12 2009

city: Stanford

first: Paul

middle: A

last: Khavari

state: CA

address: 259 Campus Dr

department: Dermatology

institute: Stanford University

description: Human primary keratinocytes isolated from multiple foreskin samples. Short-hairpin knock down of DNMT1.

hyb_protocol: Hybrization was performed by the Stanford P.A.N. facility.

scan_protocol: Scanning was performed by the Stanford P.A.N. facility.

data_processing: Raw Cel files was loaded into GeneSpring GX software and RMA normalized.

source_name: RNA; human keratinocytes; DNMT1 knock down

label_protocol: Labeling was performed by the Stanford P.A.N. facility.

growth_protocol: Cells were infected with retrovirus (pSuper-retro) designed to knock down DNMT1 mRNA. Post-infection the cells were selected in puromycin (2ug/ml) for 9 days prior to isolating RNA. Cells were not exposed to Ca2+ or confluence.

extract_protocol: Qiagen RNeasy kits were used to isolate total RNA.

treatment_protocol: Primary human foreskin keratinoctyes; Male; Short-hairpin knockdown of DNMTi; Puroselected

tag: cell type

value: primary keratinocytes

value: male

value: foreskin

tag: status

value: DNMT1 knockdown


title: Sc2_4

description: Human testis Score 2 Replicate 4


title: MCC Patient 7

description: Gene expression

value: no death

value: no recurrence


title: +Ca_replicate_2_RMA_normalized

description: Human primary keratinocytes isolated from multiple foreskin samples; passage is less than 4.

source_name: RNA isolated from primary human keratinocytes in differentiation conditions

growth_protocol: Keratinocytes were grown in Gibco SFM medium till 100% confluent with addition of 1.2 mM Ca2+ for 3 Days to induce differentiation.

value: differentiated


title: DNMT1i_replicate_2_RMA_normalized

growth_protocol: Cells were infected with retrovirus (pSuper-retro) designed to knock down DNMT1 protein. Post-infection the cells were selected in puromycin (2ug/ml) for 9 days prior to isolating RNA. Cells were not exposed to Ca2+ or confluence.


title: -Ca_replicate_2_RMA_normalized

source_name: RNA isolated from primary human keratinocytes in subconfluent growth conditions

growth_protocol: Keratinocytes were grown in Gibco SFM medium.

value: undifferentiated


title: MCC Patient 31

description: Gene expression


title: Naive Huh7 -2

city: Manhattan

first: Kyeong-Ok

last: Chang

address: 1800 Denison Ave

institute: Kansas State Univerisity

description: Naive Huh7

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using GCS3000 scanner

label: Biotin

source_name: Naive Huh7

label_protocol: 5 ug total RNA was used in a standard Affymetrix single amplification protocol.

extract_protocol: Total RNA was isolated from cells using the RNeasy kit (Qiagen, Valencia, CA, USA).


title: Norwalk virus replicon-harboring cells, HG23 -3


title: Sc2_5

description: Human testis Score 2 Replicate 5


title: Norwalk virus replicon-harboring cells, HG23 -2


title: -Ca_replicate_1_RMA_normalized


title: Naive Huh7 -1

description: Naive Huh7


title: Norwalk virus replicon-harboring cells, HG23 -1


title: Naive Huh7 -3

description: Naive Huh7


title: +Ca_replicate_1_RMA_normalized


title: normal fetal kidney, biological rep1

status: Public on Nov 11 2009

city: Vancouver

first: Douglas

last: Matsell

state: BC

address: 4480 Oak Street, Rm K4-150

country: Canada

institute: BC Children's Hospital

description: no additional information

hyb_protocol: A Hybridization cocktail mixture was made for each labeled RNA sample. The cocktail icluded  spikes of  GeneChip® hybridization  controls. Each sample was hybridized to an Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array. Sixteen hour hybridizations were performed in a GeneChip® Hybridization Oven 640. This was followed by automated washes and staining in a GeneChip® Fluidics Station 450 contolled by GeneChip® Operating Software (GCOS).

scan_protocol: The scanning and raw image capture was performed with a solidstate green laser GeneChip® Scanner 3000 7G.

data_processing: Statistical analysis for the gene microarray data was conducted using the LMGene software for data transformation and identification of differentially expressed genes in gene expression arrays, and data was normalized using Affy/RMA. The new version 2.6.0 of R was used for the analysis. To identify differentially expressed genes, posterior-FDR p value was computed for each probe set.

source_name: 18 weeks normal

label_protocol: Labeling of cRNA was performed according to the standard Affimemetrix protocol  (Expression Analysis Technical Manual, 2001, Affymetrix. www.affymetrix.com )

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions of RNesay Mini Kit (Qiagen).

treatment_protocol: RNA was extracted from 5 frozen human fetal  kidney samples

value: 18 weeks gestation

value: kidney

tag: kidney status

value: normal


title: obstructed fetal kidney, biological rep2

description: no additional information

source_name: 18 weeks obstructed

tag: tissue

value: obstructed


title: normal fetal kidney, biological rep3

description: no additional information

source_name: 8 weeks normal

value: 8 weeks gestation


title: normal fetal kidney, biological rep2

description: no additional information


title: KOPT-K1_DMSO_02

city: Cambridge

first: Raymond

last: Moellering

state: MA

address: 12 Oxford Street

department: Chemistry and Chemical Biology

institute: Harvard University

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner.

data_processing: Data was processed using GenePattern software available at the Broad Insititute. RMA processing was used with quantile normalization.

source_name: KOPT-K1 cells treated with DMSO

label_protocol: Biotinylated cRNA was generated using standard Affymetrix protocols.

growth_protocol: T-ALL cells were grown in1640 RPMI with 10% FBS and 1% pen/strep.

extract_protocol: Treated cells were centrifuged at 1000 rpm, washed with cold PBS and total RNA was extracted using a Qiagen Rneasy Kit according to manufacturers instructions.

treatment_protocol: Cells were cultured in 24-well plates and indicated with SAHM1 or the equivalent amount of DMSO for 24 hours.

value: T-cell

tag: cell line


title: KOPT-K1_SAHM1_03

source_name: KOPT-K1 cells treated with SAHM1


title: KOPT-K1_SAHM1_01


title: Day-210 RA-specificed astrocytes

city: Madison

first: Robert

last: Krencik

state: WI

address: 1500 Highland Ave #641B

department: Waisman Center

institute: University of Wisconsin-Madison

description: Day-210 RA-specificed astrocytes

hyb_protocol: According to Affymetrix protocol, performed at the NIH Neuroscience Microarray Consortium (http://arrayconsortium.tgen.org/np2/home.do)

data_processing: Algorithm: ExpressionStat 5.0

source_name: Day-210 RA-specified astrocytes

growth_protocol: Differentiation of hESCs began at day 0 by removal from mouse embryonic fibroblasts and forming of embryoid bodies.

extract_protocol: RNA was extracted with Trizol (Invitrogen) and RNase easy cleanup (Qiagen).

treatment_protocol: Astrocytes subtypes were generated by application of retinoic acid or FGF8 from days 10-21.  Neuroepithelial cells and neurons were not specified with morphogens.

value: Day-210 RA-specified astrocytes

tag: genotype

value: Line H9


title: KOPT-K1_DMSO_03


title: KOPT-K1_DMSO_01


title: Day-17 neuroepithelial cells

description: Day-17 neuroepithelial cells

scan_protocol: According to Affymetrix protocol, performed at the NIH Neuroscience Microarray Consortium (http://arrayconsortium.tgen.org/np2/home.do)

source_name: Day-17 neuroepithelia from hESC

value: Day-17 neuroepithelia from hESC


title: KOPT-K1_SAHM1_02


title: obstructed fetal kidney, biological rep1

description: no additional information

tag: age


title: DLPFC age in years 21.93

first: Laura

middle: Wiseman

last: Harris

address: Tennis Court Road

department: Insitute of Chemical Engineering and Biotechnology

institute: University of Cambridge

hyb_protocol: Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer.

scan_protocol: The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software

data_processing: Raw data were processed and analysed using the R statistical program and Bioconductor packages. QC procedures included an assessment of chip quality using the AffyPLM package to fit a probe level model to the data, calculation of pairwise correlation coefficients between chips and boxplots of RMA normalised expression values for each chip to identify outlier chips. Normalised expression values (log base 2) for each probe-set on the 44 chips passing our stringent quality standards were computed using the robust multi-chip average (RMA) method.

source_name: DLPFC age in years 21.93

label_protocol: Isolated total RNA was biotin labelled following the Affymetrix preparation protocol

extract_protocol: Total RNA was extracted from fresh-frozen prefrontal cortex grey matter samples using Tri-reagent (Sigma)

tag: Age (yrs),21.93,PMI (hrs),13,gender,m


title: Day-210 FGF8-specified astrocytes

description: Day-210 FGF8-specified astrocytes

source_name: Day-210 FGF8-specified astrocytes

label_protocol: According to Affymetrix protocol, performed at the NIH Neuroscience Microarray Consortium (http://arrayconsortium.tgen.org/np2/home.do)

value: Day-210 FGF8-specified astrocytes


title: DLPFC age in years 22.92

source_name: DLPFC age in years 22.92

tag: Age (yrs),22.92,PMI (hrs),4,gender,m


title: DLPFC age in years 49.22

source_name: DLPFC age in years 49.22

tag: Age (yrs),49.22,PMI (hrs),7,gender,f


title: DLPFC age in years 38.42

source_name: DLPFC age in years 38.42

tag: Age (yrs),38.42,PMI (hrs),19,gender,f


title: DLPFC age in years 42.94

source_name: DLPFC age in years 42.94

tag: Age (yrs),42.94,PMI (hrs),18,gender,m


title: DLPFC age in years 24.93

source_name: DLPFC age in years 24.93

tag: Age (yrs),24.93,PMI (hrs),7,gender,m


title: DLPFC age in years 35.99

source_name: DLPFC age in years 35.99

tag: Age (yrs),35.99,PMI (hrs),13,gender,m


title: DLPFC age in years 25.38

source_name: DLPFC age in years 25.38

tag: Age (yrs),25.38,PMI (hrs),16,gender,f


title: DLPFC age in years 20.14

source_name: DLPFC age in years 20.14

tag: Age (yrs),20.14,PMI (hrs),18,gender,m


title: DLPFC age in years 38.63

source_name: DLPFC age in years 38.63

tag: Age (yrs),38.63,PMI (hrs),8,gender,m


title: DLPFC age in years 46.18

source_name: DLPFC age in years 46.18

tag: Age (yrs),46.18,PMI (hrs),18,gender,m


title: DLPFC age in years 17.82

source_name: DLPFC age in years 17.82

tag: Age (yrs),17.82,PMI (hrs),12,gender,m


title: DLPFC age in years 23.62

source_name: DLPFC age in years 23.62

tag: Age (yrs),23.62,PMI (hrs),14,gender,f


title: DLPFC age in years 15

source_name: DLPFC age in years 15

tag: Age (yrs),15,PMI (hrs),13,gender,m


title: DLPFC age in years 16.68

source_name: DLPFC age in years 16.68

tag: Age (yrs),16.68,PMI (hrs),16,gender,f


title: DLPFC age in years 17.69

source_name: DLPFC age in years 17.69

tag: Age (yrs),17.69,PMI (hrs),16,gender,m


title: DLPFC age in years 17.05

source_name: DLPFC age in years 17.05

tag: Age (yrs),17.05,PMI (hrs),25,gender,m


title: DLPFC age in years 22.51

source_name: DLPFC age in years 22.51

tag: Age (yrs),22.51,PMI (hrs),12,gender,m


title: MCC Patient 70

description: Gene expression

source_name: Moffitt Cancer Center

tag: age

tag: gender

value: male

tag: ethnicity

value: caucasian

tag: grade

value: 2 - Moderately differentiated (MD)

tag: overall_event (death from any cause)

tag: dss_event (disease specific survival; death from cancer)

tag: dfs_event (disease free survival; cancer recurrence)

tag: overall survival follow-up time


title: DLPFC age in years 8 2

source_name: DLPFC age in years 8 2

tag: Age (yrs),8,PMI (hrs),5,gender,f


title: DLPFC age in years 5.39

source_name: DLPFC age in years 5.39

tag: Age (yrs),5.39,PMI (hrs),17,gender,m


title: DLPFC age in years 4.64

source_name: DLPFC age in years 4.64

tag: Age (yrs),4.64,PMI (hrs),18,gender,m


title: DLPFC age in years 11.54

source_name: DLPFC age in years 11.54

tag: Age (yrs),11.54,PMI (hrs),12,gender,f


title: DLPFC age in years 8 1

source_name: DLPFC age in years 8 1

tag: Age (yrs),8,PMI (hrs),20,gender,f


title: DLPFC age in years 2.45

source_name: DLPFC age in years 2.45

tag: Age (yrs),2.45,PMI (hrs),22,gender,f


title: DLPFC age in years 12.42

source_name: DLPFC age in years 12.42

tag: Age (yrs),12.42,PMI (hrs),16,gender,m


title: DLPFC age in years 4.86

source_name: DLPFC age in years 4.86

tag: Age (yrs),4.86,PMI (hrs),19,gender,m


title: DLPFC age in years 12.97

source_name: DLPFC age in years 12.97

tag: Age (yrs),12.97,PMI (hrs),18,gender,f


title: DLPFC age in years 0.91

source_name: DLPFC age in years 0.91

tag: Age (yrs),0.91,PMI (hrs),18,gender,m


title: DLPFC age in years 1.58

source_name: DLPFC age in years 1.58

tag: Age (yrs),1.58,PMI (hrs),24,gender,f


title: DLPFC age in years 0.54

source_name: DLPFC age in years 0.54

tag: Age (yrs),0.54,PMI (hrs),24,gender,m


title: DLPFC age in years 2.21

source_name: DLPFC age in years 2.21

tag: Age (yrs),2.21,PMI (hrs),11,gender,f


title: DLPFC age in years 2.71

source_name: DLPFC age in years 2.71

tag: Age (yrs),2.71,PMI (hrs),44,gender,f


title: DLPFC age in years 0.38

source_name: DLPFC age in years 0.38

tag: Age (yrs),0.38,PMI (hrs),9,gender,m


title: DLPFC age in years 2.19

source_name: DLPFC age in years 2.19

tag: Age (yrs),2.19,PMI (hrs),27,gender,m


title: Kc167_sample_2

status: Public on Nov 10 2009

city: Durham

first: David

middle: M

last: MacAlpine

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

description: Gene expression from Kc167 cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

organism: Drosophila melanogaster

source_name: Kc167 cells

label_protocol: standard Affymetrix protocol

growth_protocol: Kc167 cells were cultured in Schneider's medium at 25C at 1x10^6 cells per ml

extract_protocol: RNA was recovered by Trizol

treatment_protocol: No treatment

tag: cell line


title: DLPFC age in years 0.52

source_name: DLPFC age in years 0.52

tag: Age (yrs),0.52,PMI (hrs),22,gender,f


title: Kc167_sample_1

description: Gene expression from Kc167 cells


title: low metastatic potential cell subline of Saos-2

city: Xi'an

first: xiang

last: chen

address: Xinsi Rd

country: China

institute: Tangdu Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human osteosarcoma cell subline with low pulmonary metastasis potential

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: All the cell lines were maintained in complete RPMI 1640 medium (HyClone) supplemented with 10% fetal calf serum (FCS) (Sijiqing Co.) at 37°C under 5% CO2 atmosphere.

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


title: DLPFC age in years 0.25

source_name: DLPFC age in years 0.25

tag: Age (yrs),0.25,PMI (hrs),14,gender,f


title: DLPFC age in years 0.15 2

source_name: DLPFC age in years 0.15 2

tag: Age (yrs),0.15,PMI (hrs),11,gender,m


title: DLPFC age in years 0.35

source_name: DLPFC age in years 0.35

tag: Age (yrs),0.35,PMI (hrs),27,gender,m


title: DLPFC age in years 0.11

source_name: DLPFC age in years 0.11

tag: Age (yrs),0.11,PMI (hrs),27,gender,m


title: high metastatic potential cell subline of Saos-2

source_name: Human osteosarcoma cell subline with high pulmonary metastasis potential


title: high metastatic potential cell subline of Sosp-9607, biological rep1


title: DLPFC age in years 0.24

source_name: DLPFC age in years 0.24

tag: Age (yrs),0.24,PMI (hrs),24,gender,f


title: DLPFC age in years 0.39

source_name: DLPFC age in years 0.39

tag: Age (yrs),0.39,PMI (hrs),5,gender,m


title: low metastatic potential cell subline of Sosp-9607, biological rep2


title: DLPFC age in years 0.33

source_name: DLPFC age in years 0.33

tag: Age (yrs),0.33,PMI (hrs),22,gender,m


title: DLPFC age in years 0.15 1

source_name: DLPFC age in years 0.15 1

tag: Age (yrs),0.15,PMI (hrs),17,gender,m


title: DLPFC age in years 0.19

source_name: DLPFC age in years 0.19

tag: Age (yrs),0.19,PMI (hrs),25,gender,m


title: high metastatic potential cell subline of Sosp-9607, biological rep2


title: low metastatic potential cell subline of Sosp-9607, biological rep1


title: MCF-7R4, replicate 2

status: Public on Nov 06 2009

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

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 using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) for Absent/Marginal/Present calls. CEL files reading, normalization, and gene expression calculation were performed using dChip PM-only model and invariant set normalization.

source_name: total RNA from MCF-7R4 cells

growth_protocol: MCF-7 cells were cultured as recommended by ATCC. MCF-7R4 cells were generated by step-wise growth in increasing concentrations of BMS-554417.  At a concentration of 10 µM, ~40-fold greater than reported IC50, individual clones were selected.  MCF-7R4 represented a clone isolated that proliferated under continued selection with BMS-554417 at 10 µM and is cross-resistant to BMS-536924.

extract_protocol: RNeasy Midi kit (Qiagen, Valencia, CA)

tag: tissue

value: Breast


title: MCF-7R4, replicate 5


title: MCF-7R4, replicate 4


title: MCF-7R4, replicate 3


title: MCF-7, replicate 1

source_name: total RNA from MCF-7 cells


title: Spike groups J=0.75, K=1.5, L=3, M=0 Rep 3

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

institute: Ohio State University

description: Detection call p-values

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

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 by Affymetrix.

data_processing: The Detection call algorithm was applied using the R affy package and mas5calls function to obtain probe set detection p-values.

source_name: human cell line HeLa

growth_protocol: Common background sample derived from the human cell line HeLa (ATCC CCL-2)

extract_protocol: According to the manufacturer's instructions.

treatment_protocol: Four different groups containing 6-7 transcripts each were spiked in at known concentrations (0, 0.75, 1.5, and 3 pM)

value: HeLa

tag: experimental group


title: Spike groups J=1.5, K=3, L=0, M=0.75 Rep 3

description: Detection call p-values


title: Spike groups J=3, K=0, L=0.75, M=1.5 Rep 1

description: Detection call p-values


title: Spike groups J=3, K=0, L=0.75, M=1.5 Rep 3

description: Detection call p-values


title: Spike groups J=1.5, K=3, L=0, M=0.75 Rep 1

description: Detection call p-values


title: Spike groups J=3, K=0, L=0.75, M=1.5 Rep 2

description: Detection call p-values


title: Mammary epithelial cells, FACS sorted, PKH-Negative, Pool 1

status: Public on Nov 07 2009

city: Milano

first: Stefano

last: Confalonieri

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute for Molecular Oncology Foundation

description: Gene expression data from FACS sorted PKH-Negative cells derived from dissociated mammospheres

hyb_protocol: Total RNA (50-100 ng) was amplified using the Affymetrix T7 Polymerase-based double linear amplification protocol. cRNA probes (10 ug) were hybridized onto the Affymetrix HG-U133_Plus_2 ChipSet (Santa Clara, CA, USA), according to Affymetrix technical protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 30007G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Epithelial cells, from dissociated mammospheres obtained from reductive mammoplasties

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

growth_protocol: Epithelial cells, from reductive mammoplasties , were allowed to adhere for 24 h in complete SC medium. Cells were trypsinized, filtered through a 100um and a 40um cell strainer, resuspendend in PBS (500,000/ml), and labeled with PKH26 (Sigma, 10-7 M, 5 min). Labeled cells were plated (30,000 cells/ml) in suspension. After 7-10 days, mammospheres were harvested, dissociated enzymatically (0.05% trypsin/0.5 mM EDTA for 10 min, plus filtering though a 40um cell strainer), and subjected to FACS analysis using a FACS Vantage SE flow cytometer (Becton&Dickinson) to yield PKH-POS and PKH-NEG cells.

extract_protocol: Total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Arcturus Engineering, CA, USA) according to the manufacturer’s instructions, and analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell type

value: Mammary Epithelial Cells


title: Spike groups J=0, K=0.75, L=1.5, M=3 Rep 3

description: Detection call p-values


title: Spike groups J=0.75, K=1.5, L=3, M=0 Rep 2

description: Detection call p-values


title: MCF-7, replicate 4


title: Spike groups J=0.75, K=1.5, L=3, M=0 Rep 1

description: Detection call p-values


title: Mammary epithelial cells, FACS sorted, PKH-Negative, Pool 2


title: MCF-7, replicate 5


title: Mammary epithelial cells, FACS sorted, PKH-Positive, Pool 3

description: Gene expression data from FACS sorted PKH-Positive cells derived from dissociated mammospheres


title: Spike groups J=1.5, K=3, L=0, M=0.75 Rep 2

description: Detection call p-values


title: Mammary epithelial cells, FACS sorted, PKH-Positive, Pool 1


title: MCF-7, replicate 2


title: MCF-7R4, replicate 1


title: MCF-7, replicate 3


title: Spike groups J=0, K=0.75, L=1.5, M=3 Rep 1

description: Detection call p-values


title: Spike groups J=0, K=0.75, L=1.5, M=3 Rep 2

description: Detection call p-values


title: Mammary epithelial cells, FACS sorted, PKH-Positive, Pool 2


title: Mammary epithelial cells, FACS sorted, PKH-Negative, Pool 3


title: Human XaXaXi triploid, clone 3

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

hyb_protocol: Hybridization and washing were performed according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned and processed by the University of Washington Microarray Center.

data_processing: The data were analyzed with the Affymetrix GCOS1.4.0 software.

source_name: Fibroblast from aborted human triploid fetus

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

growth_protocol: Standard cell culture conditions.

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy kit with on-column DNaseI digestion.

value: fibroblast

tag: cell culture

value: cloned fibroblast cell line

tag: genotype

value: XXX;AAA

tag: gender

value: female


title: MCF-7-14

city: Nagareyama-shi

first: Masahiro

last: Uchino

state: Chiba

address: 105 Higashifukai

country: Japan

institute: Bio Matrix Research, Inc

description: Gene expression data from cultured MCF-7-14 cell line

hyb_protocol: 15 μg of the labeled cRNA was hybridized to a Human Genome U133 Plus 2.0 Array (Affymetrix, CA, USA).

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Invasive MCF-7-14 breast cancer cell line established from non-aggressive MCF7

label_protocol: In vitro transcription reactions were performed using a GeneChip IVT Labeling Kit, which includes T7 RNA polymerase and Biotin-labeled ribonucleotides.

growth_protocol: Cell lines were maintained in RPMI 1640 (Sigma) containing 10% fetal bovine serum (FBS) and antibiotic-antimycotic.

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

treatment_protocol: MCF-7,  MCF-7-14  and  MDA-MB-231  cells  were  synchronized  in  S-phase  with  the thymidine-hydroxyurea  block  method.

tag: tissue type

value: breast cancer

tag: cell line


title: Human XaXiXi triploid, clone 3


title: Human XYY triploid, culture 2

source_name: Fibroblast from human triploid fetus

value: fibroblast culture

value: XYY;AAA


title: Human male diploid, culture 1

source_name: Fibroblast from human fetus

value: diploid fibroblast culture

value: XY;AA


title: Human female diploid, culture 2; biological replicate 1

source_name: Fibroblast

value: XX;AA


title: Human XaXaXi triploid, clone 1


title: Human XaXiXi triploid, clone 2


title: Human XYY triploid, culture 3


title: MCF-7

description: Gene expression data from cultured MCF-7 cell line

source_name: MCF-7 breast cancer cell line


title: GBS6 cells transfected with POU5F1 siRNA-2 (3rd)

status: Public on Nov 05 2009

city: Koto ward

first: Takashi

last: Fujino

state: Tokyo

address: 3-10-6 Ariake

department: Carcinogenesis

institute: The Cancer Institute of Japanese Foundation of Cancer Research

description: Gene expression analysis of t(6;22) undifferentiated sarcoma cell line GBS6 transfected with POU5F1 specific siRNA-2.

hyb_protocol: According to Affymetrix's instructions.

scan_protocol: According to Affymetrix's instructions.

data_processing: Affymetrix MAS5.0

source_name: GBS6 cells established from a t(6;22) undifferentiated bone sarcoma

label_protocol: Biotin-labelled.

growth_protocol: Cells were grown in RPMI1640 medium.

extract_protocol: Total RNA was extracted using the RNA-Bee (Tel-Test) according to manufacturer’s protocol.

tag: transfection

value: POU5F1 siRNA-2

tag: protocol

value: EWS-POU5F1 knockdown


title: GBS6 cells transfected with POU5F1 siRNA-1 (3rd)

description: Gene expression analysis of t(6;22) undifferentiated sarcoma cell line GBS6 transfected with POU5F1 specific siRNA-1.

value: POU5F1 siRNA-1


title: Human female diploid, culture 2; biological replicate 3


title: Human male diploid, culture 2

value: male


title: Human female diploid, culture 2; biological replicate 2


title: Human female diploid, culture 1


title: GBS6 cells transfected with POU5F1 siRNA-2 (2nd)


title: Human XaXaXi triploid, clone 2


title: Human XYY triploid, culture 1


title: MDA-MB-231

description: Gene expression data from cultured MDA-MB-231 cell line

source_name: MDA-MB-231 breast cancer cell line


title: Human XaXiXi triploid, clone 1


title: GBS6 cells transfected with negative control siRNA (3rd)

description: Gene expression analysis of t(6;22) undifferentiated sarcoma cell line GBS6 transfected with negative control siRNA.

value: control siRNA

value: control


title: GBS6 cells transfected with POU5F1 siRNA-1 (2nd)


title: GBS6 cells transfected with negative control siRNA (2nd)


title: Lean_1 day_subject17

first: SUJOY

last: GHOSH

address: 700 George Street

institute: North Carolina Central University

description: Lean_1 day_subject17

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

data_processing: Data was processed using GC-RMA

source_name: Whole blood

label_protocol: Biotinylated cRNA were prepared from 100 ng  total RNA according to instructions provided by Affymetrix

extract_protocol: RNA was isolated from PAXGENE tubes according to the manufacturer's instructions

tag: diet

value: Lean

tag: time point

value: 1 day

tag: subject

value: Male


title: Lean_1 day_subject12

description: Lean_1 day_subject12

value: Female


title: Lean_1 day_subject19

description: Lean_1 day_subject19


title: Lean_1 day_subject15

description: Lean_1 day_subject15


title: Lean_1 day_subject20

description: Lean_1 day_subject20


title: Lean_1 day_subject18

description: Lean_1 day_subject18


title: Lean_1 day_subject14

description: Lean_1 day_subject14


title: Lean_1 day_subject6

description: Lean_1 day_subject6


title: Lean_1 day_subject9

description: Lean_1 day_subject9


title: Lean_1 day_subject10

description: Lean_1 day_subject10


title: Lean_1 day_subject16

description: Lean_1 day_subject16


title: DietResistant _6 weeks_subject10

description: DietResistant _6 weeks_subject10

value: Resistant

value: 6 weeks


title: Lean_1 day_subject2

description: Lean_1 day_subject2


title: Lean_1 day_subject7

description: Lean_1 day_subject7


title: Lean_1 day_subject11

description: Lean_1 day_subject11


title: DietResistant _6 weeks_subject3

description: DietResistant _6 weeks_subject3


title: Lean_1 day_subject8

description: Lean_1 day_subject8


title: DietResistant _6 weeks_subject5

description: DietResistant _6 weeks_subject5


title: DietResistant _6 weeks_subject6

description: DietResistant _6 weeks_subject6


title: Lean_1 day_subject5

description: Lean_1 day_subject5


title: DietResistant _6 weeks_subject2

description: DietResistant _6 weeks_subject2


title: Lean_1 day_subject4

description: Lean_1 day_subject4


title: DietResistant _3 weeks_subject8

description: DietResistant _3 weeks_subject8

value: 3 weeks


title: DietResistant _3 weeks_subject7

description: DietResistant _3 weeks_subject7


title: DietResistant _6 weeks_subject9

description: DietResistant _6 weeks_subject9


title: DietResistant _6 weeks_subject7

description: DietResistant _6 weeks_subject7


title: DietResistant _6 weeks_subject8

description: DietResistant _6 weeks_subject8


title: Lean_1 day_subject1

description: Lean_1 day_subject1


title: DietResistant _6 weeks_subject4

description: DietResistant _6 weeks_subject4


title: DietResistant _3 weeks_subject10

description: DietResistant _3 weeks_subject10


title: Lean_1 day_subject13

description: Lean_1 day_subject13


title: Lean_1 day_subject3

description: Lean_1 day_subject3


title: DietResistant _3 weeks_subject4

description: DietResistant _3 weeks_subject4


title: DietResistant _3 weeks_subject2

description: DietResistant _3 weeks_subject2


title: DietResistant _6 weeks_subject1

description: DietResistant _6 weeks_subject1


title: DietResistant _3 weeks_subject9

description: DietResistant _3 weeks_subject9


title: DietResistant _3 weeks_subject1

description: DietResistant _3 weeks_subject1


title: DietResistant _1 day_subject5

description: DietResistant _1 day_subject5


title: DietResistant _1 day_subject10

description: DietResistant _1 day_subject10


title: DietResistant _1 day_subject8

description: DietResistant _1 day_subject8


title: DietResistant _3 weeks_subject5

description: DietResistant _3 weeks_subject5


title: DietResistant _3 weeks_subject6

description: DietResistant _3 weeks_subject6


title: DietResistant _1 day_subject7

description: DietResistant _1 day_subject7


title: DietResistant _1 day_subject4

description: DietResistant _1 day_subject4


title: DietSensitive _3 weeks_subject7

description: DietSensitive _3 weeks_subject7

value: Sensitive


title: DietResistant _3 weeks_subject3

description: DietResistant _3 weeks_subject3


title: DietSensitive _3 weeks_subject9

description: DietSensitive _3 weeks_subject9


title: DietSensitive _6 weeks_subject4

description: DietSensitive _6 weeks_subject4


title: DietSensitive _6 weeks_subject8

description: DietSensitive _6 weeks_subject8


title: DietResistant _1 day_subject9

description: DietResistant _1 day_subject9


title: DietSensitive _6 weeks_subject7

description: DietSensitive _6 weeks_subject7


title: DietSensitive _6 weeks_subject5

description: DietSensitive _6 weeks_subject5


title: DietSensitive _6 weeks_subject6

description: DietSensitive _6 weeks_subject6


title: DietResistant _1 day_subject3

description: DietResistant _1 day_subject3


title: DietSensitive _6 weeks_subject9

description: DietSensitive _6 weeks_subject9


title: DietResistant _1 day_subject6

description: DietResistant _1 day_subject6


title: DietSensitive _6 weeks_subject3

description: DietSensitive _6 weeks_subject3


title: DietSensitive _3 weeks_subject3

description: DietSensitive _3 weeks_subject3


title: DietResistant _1 day_subject1

description: DietResistant _1 day_subject1


title: DietResistant _1 day_subject2

description: DietResistant _1 day_subject2


title: DietSensitive _6 weeks_subject1

description: DietSensitive _6 weeks_subject1


title: DietSensitive _3 weeks_subject10

description: DietSensitive _3 weeks_subject10


title: DietSensitive _6 weeks_subject10

description: DietSensitive _6 weeks_subject10


title: DietSensitive _3 weeks_subject8

description: DietSensitive _3 weeks_subject8


title: DietSensitive _6 weeks_subject2

description: DietSensitive _6 weeks_subject2


title: DietSensitive _3 weeks_subject5

description: DietSensitive _3 weeks_subject5


title: DietSensitive _3 weeks_subject4

description: DietSensitive _3 weeks_subject4


title: DietSensitive _1 day_subject9

description: DietSensitive _1 day_subject9


title: DietSensitive _3 weeks_subject2

description: DietSensitive _3 weeks_subject2


title: DietSensitive _1 day_subject7

description: DietSensitive _1 day_subject7


title: DietSensitive _3 weeks_subject1

description: DietSensitive _3 weeks_subject1


title: DietSensitive _1 day_subject10

description: DietSensitive _1 day_subject10


title: DietSensitive _1 day_subject5

description: DietSensitive _1 day_subject5


title: DietSensitive _1 day_subject8

description: DietSensitive _1 day_subject8


title: DietSensitive _1 day_subject4

description: DietSensitive _1 day_subject4


title: DietSensitive _1 day_subject6

description: DietSensitive _1 day_subject6


title: DietSensitive _1 day_subject2

description: DietSensitive _1 day_subject2


title: DietSensitive _1 day_subject1

description: DietSensitive _1 day_subject1


title: DietSensitive _3 weeks_subject6

description: DietSensitive _3 weeks_subject6


title: hES-rep1

status: Public on Nov 04 2009

city: The Bronx

first: Eric

last: Bouhassira

address: 1300 Morris Park avenue

institute: Albert Einstein College of Medicine

description: Gene expression data from Human embryonic stem cells

hyb_protocol: AffyU133plus 2 were hybridized with labeled probes using standard conditions recommended by the manufacturer.

scan_protocol: Standard Affymetrix protocol was followed.

data_processing: The results of three hybridizations from erythroblasts (2 for the undifferentiated hES cells) were averaged after normalization by RMA using the RMAexpress software (Bolstad, et al, 2003)(Version: 1.0.3 Release, http://rmaexpress.bmbolstad.com), the results are given as log results. Some of the probe-set were eliminated because they have been flagged as repetitive in a study by Dr Jean and Danielle Thierry-Mieg (Thierry-Mieg, D. and Thierry-Mieg, J. 2006. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 7 Suppl 1: S12.1-14).

source_name: Human embryonic stem cells

label_protocol: Total RNA was labeled with a fluorophore using standard Affymetrix procedure (primer extension usig a polydT primer).

growth_protocol: ES cells were grown on matrigel using standard protocols. Erythroblasts were produced in vitro from CD34 positive cells as decribed in Qiu et al (see text of the paper). mRNA was extracted after 14 days of liquid culture.

extract_protocol: Total RNA were extracted using the RNAeasy kit (Qiagen).

value: embryonic stem cells


title: ERY-rep3

description: Gene expression data from Human erythroblasts

source_name: Human erythroblast

value: erythroid cells


title: hES-rep2


title: ERY-rep2


title: ERY-rep1


title: Reference tumor 122

city: Lyngby

first: Aron

middle: C

last: Eklund

address: Kemitorvet, Building 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

description: Gene expression data from reference primary breast tumor

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Human U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Expression values were calculated with the RMA algorithm.

source_name: Reference primary tumor sample

label_protocol: First round linear amplification was performed using RiboAmp HS kit (Arcturus). Biotinylated cRNA was prepared by in vitro transcription using the Affymetrix IVT kit.

extract_protocol: RNA was extracted using the Absolutely RNA Nanoprep kit (Stratagene).

treatment_protocol: Two 5μ frozen sections were stained with hematoxylin and eosin, manually scraped to remove normal stroma and enrich for tumor cells.

tag: age

tag: miller-payne response

tag: p53 status

value: n/d

tag: er/pr/her2 status

value: neg/neg/pos

tag: grade

value: II

tag: brca genotype

value: Unknown


title: Reference tumor 123

value: neg/neg/neg

value: III


title: Reference tumor 141


title: Reference tumor 145


title: Reference tumor 120

value: neg/neg/unk


title: Reference tumor 147

value: BRCA1 germline mutation


title: Reference tumor 134


title: Reference tumor 140


title: DietSensitive _1 day_subject3

description: DietSensitive _1 day_subject3

value: 1 day


title: Reference tumor 136


title: Reference tumor 124


title: Reference tumor 187

value: pos/pos/neg


title: Reference tumor 118


title: Reference tumor 116


title: Reference tumor 85


title: Reference tumor 80 replicate

description: Gene expression data from reference primary breast tumor (replicate)


title: Reference tumor 115


title: Reference tumor 125


title: Reference tumor 113


title: Reference tumor 80


title: Reference tumor 98


title: Reference tumor 116 replicate


title: Reference tumor 90

value: I


title: Reference tumor 72


title: Reference tumor 117


title: Reference tumor 96


title: Reference tumor 70

value: pos/pos/pos


title: Reference tumor 91


title: Reference tumor 66


title: Reference tumor 71


title: Reference tumor 55 replicate


title: Reference tumor 63 replicate


title: Reference tumor 63


title: Reference tumor 55


title: Reference tumor 43


title: Reference tumor 54


title: Reference tumor 40


title: Reference tumor 47


title: Reference tumor 44


title: Reference tumor 38 replicate


title: Reference tumor 30


title: Reference tumor 35


title: Reference tumor 28


title: Reference tumor 25 replicate


title: Reference tumor 25


title: Reference tumor 29


title: Reference tumor 17


title: Reference tumor 11


title: Reference tumor 21 replicate


title: Reference tumor 12 replicate


title: Reference tumor 20


title: Reference tumor 22


title: Reference tumor 1 replicate


title: Reference tumor 2


title: Patient 29

description: Gene expression data from pretreatment tumor sample of patient 29

source_name: Cisplatin trial pretreatment tumor biopsy

value: NSM

value: WT


title: Reference tumor 1


title: Reference tumor 5


title: Reference tumor 21


title: Reference tumor 12


title: Patient 26

description: Gene expression data from pretreatment tumor sample of patient 26

value: unknown


title: Reference tumor 7


title: Patient 28

description: Gene expression data from pretreatment tumor sample of patient 28


title: Patient 27

description: Gene expression data from pretreatment tumor sample of patient 27


title: Reference tumor 10


title: Patient 24

description: Gene expression data from pretreatment tumor sample of patient 24

value: MSM


title: Patient 17

description: Gene expression data from pretreatment tumor sample of patient 17


title: Patient 22

description: Gene expression data from pretreatment tumor sample of patient 22


title: Patient 23

description: Gene expression data from pretreatment tumor sample of patient 23


title: Patient 21

description: Gene expression data from pretreatment tumor sample of patient 21


title: Patient 16

description: Gene expression data from pretreatment tumor sample of patient 16


title: Patient 25

description: Gene expression data from pretreatment tumor sample of patient 25


title: Patient 15

description: Gene expression data from pretreatment tumor sample of patient 15


title: Patient 11

description: Gene expression data from pretreatment tumor sample of patient 11


title: Patient 12

description: Gene expression data from pretreatment tumor sample of patient 12


title: Patient 8

description: Gene expression data from pretreatment tumor sample of patient 8


title: Patient 10

description: Gene expression data from pretreatment tumor sample of patient 10


title: Patient 5

description: Gene expression data from pretreatment tumor sample of patient 5


title: Patient 14

description: Gene expression data from pretreatment tumor sample of patient 14


title: Patient 6

description: Gene expression data from pretreatment tumor sample of patient 6


title: Patient 3

description: Gene expression data from pretreatment tumor sample of patient 3


title: Patient 2

description: Gene expression data from pretreatment tumor sample of patient 2


title: Patient 4

description: Gene expression data from pretreatment tumor sample of patient 4


title: Patient 1

description: Gene expression data from pretreatment tumor sample of patient 1


title: Patient 7

description: Gene expression data from pretreatment tumor sample of patient 7


title: Blood - Sarcoidosis - 049A

city: Portland

first: James

last: Rosenbaum

state: OR

address: 3181 SW Sam Jackson Park Road

department: Casey Eye Institute

institute: Oregon Health & Science University

hyb_protocol: Labeled cRNA targets were chemically fragmented at 95C for 35 min as per Affymetrix’s recommendations. The fragmented material was combined with Affymetrix hybridization controls: biotinylated control oligomer (B2) and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer. Following the manufacturer’s recommendations, 6.5 µg of target were hybridized with the Human Genome U133 Plus 2.0 GeneChip array (Affymetrix) for 16 hours at 45C. Post-hybridization array processing was performed on the Fluidics Station 450 (Affymetrix); array staining and signal amplification were performed according to manufacturer’s recommendations.

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade. Image inspection was performed manually immediately following each scan. The array image scan was processed with Affymetrix Microarray Suite, version 5.0, (MAS 5.0) software.

data_processing: R2.4.0 64bit locally compiled by Sun compilers on Solaris 64/Bioconductor, gcrma background correction + invariant normalization + median polishing using PM only. Significance Analysis of Microarray (SAM) was utilized for statistical testing using samr package within R2.4.0 on Solaris 64.  Sets 1 and 2 were normalized independently, and each normalization set included additional array data from subjects with other inflammatory disease diagnoses.

source_name: peripheral blood

label_protocol: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with PNA treatment of total RNA: The standard Affymetrix amplification and labeling was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx (3 µg of total RNA as input), with the following modification: four peptide nucleic acid (PNA) oligonucleotides (Applied Biosystems, Foster City, CA, USA) designed to anneal to human α- and β-globin mRNA were added to the total RNA preparations immediately prior to initiation of the target synthesis step in order to bind globin mRNA and block cDNA synthesis. The PNA oligonucleotide stocks were prepared on day of use at concentrations recommended by Affymetrix (www.affymetrix.com/support/technical/byproduct.affx?product=bloodrna). Globin reduction PNA master mix was prepared by adding equal amounts of the globin PNA stocks. 5 µg of total RNA were incubated with oligo-dT primer and 1 µl PNA master mix for 10 minutes at 70C prior to first strand cDNA synthesis.  Samples characterized as Set 1 were labeled and hybridized as one group and samples characterized as set 2 were processed as a second group a year later.

extract_protocol: Total RNA isolation was performed using the PAXgene Blood RNA Isolation System (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) following the manufacturer's recommendations.  Following RNA isolation, DNase-treatment was performed as per PAXGene manufacturer’s recommendation.  RNA recovery and quality was then assessed by examining UV 260/280 absorbance ratios and RNA size distribution on RNA Nano LabChips (Agilent Technologies, Santa Clara, CA, USA) processed on the Agilent 2100 Bioanalyzer.  RNA from 4 PAXGene tubes was pooled for each subject.

treatment_protocol: Whole blood was collected and incubated in 4 PAXGene tubes/subject (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and stored frozen at -80C until the RNA was isolated.

tag: uveitis status

value: No uveitis

value: Female

tag: set

tag: tissue

value: Blood

tag: disease state

value: Sarcoidosis


title: Blood - Sarcoidosis - 086A

tag: gender


title: Blood - Sarcoidosis - 050A

value: Uveitis

value: Male


title: Blood - Sarcoidosis - 003A


title: Blood - Sarcoidosis - 059A


title: Blood - Sarcoidosis - 001A


title: Blood - Sarcoidosis - 034A


title: Blood - Sarcoidosis - 005A


title: Reference tumor 38

description: Gene expression data from reference primary breast tumor

value: n/d

value: neg/neg/neg

value: III

value: Unknown


title: Blood - Sarcoidosis - 064A


title: Blood - Control - 153A

value: Control


title: Blood - Sarcoidosis - 031A


title: Blood - Sarcoidosis - 077A


title: Blood - Control - 141A


title: Blood - Control - 156A


title: Blood - Sarcoidosis - 013A


title: Blood - Control - 155A


title: Blood - Control - 157A


title: Blood - Control - 154A


title: Blood - Control - 138A


title: Blood - Control - 111A


title: Blood - Control - 140A


title: Blood - Control - 092A


title: Blood - Control - 088A


title: Blood - Control - 067A


title: Blood - Control - 090A


title: Blood - Control - 112A


title: Blood - Control - 055A


title: Blood - Control - 022A


title: Blood - Control - 052A


title: Blood - Control - 032A


title: Blood - Control - 051A


title: Blood - Control - 023A


title: Blood - Control - 065A


title: Blood - Control - 017A


title: Blood - Axial Spondyloarthropathy - 152A

value: Axial Spondyloarthropathy


title: Blood - Axial Spondyloarthropathy - 058A


title: Blood - Control - 020A


title: Blood - Axial Spondyloarthropathy - 083A


title: Blood - Control - 021A


title: Blood - Axial Spondyloarthropathy - 159A


title: Blood - Axial Spondyloarthropathy - 033A


title: Blood - Axial Spondyloarthropathy - 069A


title: Blood - Axial Spondyloarthropathy - 083B


title: Blood - Axial Spondyloarthropathy - 096A


title: Blood - Axial Spondyloarthropathy - 015A


title: Blood - Axial Spondyloarthropathy - 066A


title: Blood - Axial Spondyloarthropathy - 074A


title: Blood - Axial Spondyloarthropathy - 062A


title: Blood - Axial Spondyloarthropathy - 162A


title: Blood - Axial Spondyloarthropathy - 089A


title: Blood - Axial Spondyloarthropathy - 019A


title: Blood - Axial Spondyloarthropathy - 097A


title: Blood - Axial Spondyloarthropathy - 029A


title: Blood - Axial Spondyloarthropathy - 030A


title: Blood - Control - 056A


title: CDiNR8_afterT

status: Public on Nov 03 2009

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Ileal mucosal gene expression data from CDi non-responder after first infliximab treatment

hyb_protocol: Fragmented cRNA (15 µg) was hybridized overnight to the Human Genome U133 Plus 2.0 Array (Affymetrix).

scan_protocol: The arrays were washed and stained with streptavidin-phycoerytrin on an automated Fluidics Station (Affymetrix) and scanned on the Affymetrix 3000 GeneScanner.

data_processing: The resulting image files (.dat files) were analyzed using Affymetrix GCOS software, and intensity values for each probe cell (.cel file) were calculated. Intensity values were scaled to an average of 150 per array according to the method of global scaling provided in the GCOS.

source_name: Ileal mucosal biopsy from CDi non-responder after first infliximab treatment

label_protocol: Total RNA (2 µg) was reverse-transcribed into cDNA using the SuperScript Choice System (Invitrogen, Carlsbad, CA, USA) with oligo-dT primers containing a T7 RNA polymerase promoter site. cDNA was in vitro transcribed to cRNA and biotin labeled using the IVT labeling kit (Affymetrix, Santa Clara, CA, USA), according to Affymetrix expression analysis technical manual 701021Rev.5. Biotinylated cRNA was purified and fragmented. The quality of labeled and fragmented cRNA, respectively, was assessed with the Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions. The total RNA integrity and quantity were assessed with the Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and Nanodrop ND-1000 spectrophotometer (Nanodrop technologies), respectively.

value: Ileum

tag: disease

value: CD

tag: response to infliximab

value: No

tag: before or after first infliximab treatment

value: After first infliximab treatment


title: CDiNR5_beforeT

description: Ileal mucosal gene expression data from CDi non-responder before first infliximab treatment

source_name: Ileal mucosal biopsy from CDi non-responder before first infliximab treatment

value: Before first infliximab treatment


title: CDiNR2_beforeT


title: CDiNR10_beforeT


title: RNAi KIAA1718 shRNA1-3

city: shanghai

first: Huang

last: Chengyang

address: Yue Yang Road 320

institute: Institute of biochemistry and cell biology

description: RNAi KIAA1718 shRNA1-3

hyb_protocol: Standard manufacturer protocol (www.affymetrix.com)

data_processing: Data was normalized and analyzed by GCOS software (affymetrix).

organism: Mus musculus

source_name: RNAi KIAA1718 shRNA1

extract_protocol: Cell total RNA was extracted by using trizol reagent. The total RNA was then purified by using Qiagen Rnaesy mini Kit

tag: cell type

value: embryonic stem (ES)

tag: cell line


title: RNAi KIAA1718 shRNA1-1

description: RNAi KIAA1718 shRNA1-1

scan_protocol: Standard manufacturer protocol (www.affymetrix.com)


title: CDiNR3_afterT


title: CDiNR7_beforeT


title: CDiNR5_afterT


title: CDiR7_beforeT

description: Ileal mucosal gene expression data from CDi responder before first infliximab treatment

source_name: Ileal mucosal biopsy from CDi responder before first infliximab treatment

value: Yes


title: CDiNR10_afterT


title: CDiNR2_afterT


title: CDiR7_afterT

description: Ileal mucosal gene expression data from CDi responder after first infliximab treatment

source_name: Ileal mucosal biopsy from CDi responder after first infliximab treatment


title: CDiNR4_afterT


title: CDiNR8_beforeT


title: CDiNR9_afterT


title: CDiNR7_afterT


title: CDiNR3_beforeT


title: CDiNR1_afterT


title: RNAi Luc-2

description: RNAi Luc-2

source_name: RNAi Luc

label_protocol: Standard manufacturer protocol (www.affymetrix.com)


title: CDiNR6_afterT


title: RNAi Luc-1

description: RNAi Luc-1


title: RNAi KIAA1718 shRNA1-2

description: RNAi KIAA1718 shRNA1-2


title: CDiR8_afterT


title: CDiNR6_beforeT


title: CDiNR1_beforeT


title: CDiNR4_beforeT


title: CDiR8_beforeT


title: RNAi Luc-3

description: RNAi Luc-3


title: CDiR6_afterT


title: CDiR6_beforeT


title: IL6

description: Ileal mucosal gene expression data from control individual

source_name: Ileal mucosal biopsy from control individual

value: Not applicable


title: CDiR2_afterT


title: CDiR5_afterT


title: CDiR2_beforeT


title: IL3


title: CDiR5_beforeT


title: CDiR3_afterT


title: CDiR1_afterT


title: CDcNR5_afterT

description: Colonic mucosal gene expression data from CDc non-responder after first infliximab treatment

source_name: Colonic mucosal biopsy from CDc non-responder after first infliximab treatment

value: Colon


title: CDcNR7_beforeT

description: Colonic mucosal gene expression data from CDc non-responder before first infliximab treatment

source_name: Colonic mucosal biopsy from CDc non-responder before first infliximab treatment


title: CDcNR4_beforeT


title: CDcNR6_beforeT


title: CDiR3_beforeT


title: IL4


title: CDcNR3_afterT


title: IL5


title: CDiR4_afterT


title: CDcNR6_afterT


title: CDcNR7_afterT


title: CDiR1_beforeT


title: IL2


title: IL1


title: CDcNR5_beforeT


title: CDcNR3_beforeT


title: CDiR4_beforeT


title: CDcNR4_afterT


title: CDcNR2_afterT


title: CDcNR1_beforeT


title: CDcR12_beforeT

description: Colonic mucosal gene expression data from CDc responder before first infliximab treatment

source_name: Colonic mucosal biopsy from CDc responder before first infliximab treatment


title: CDcR11_beforeT


title: CDcR12_afterT

description: Colonic mucosal gene expression data from CDc responder after first infliximab treatment

source_name: Colonic mucosal biopsy from CDc responder after first infliximab treatment


title: CDcNR1_afterT


title: CDcR9_afterT


title: CDcR10_afterT


title: CDcR9_beforeT


title: CDcR8_beforeT


title: CDcNR2_beforeT


title: CDcR8_afterT


title: CDcR3_beforeT


title: CDcR4_beforeT


title: CDcR1_beforeT


title: CDcR5_beforeT


title: CDcR6_beforeT


title: CDcR5_afterT


title: CDcR7_afterT


title: CDcR2_beforeT


title: CDcR3_afterT


title: CDcR1_afterT


title: CDcR6_afterT


title: CDcR7_beforeT


title: CDcR4_afterT


title: UCNR15_afterT

description: Colonic mucosal gene expression data from UC non-responder after first infliximab treatment

source_name: Colonic mucosal biopsy from UC non-responder after first infliximab treatment

value: UC


title: UCNR14_afterT


title: UCNR11_afterT


title: UCNR8_afterT


title: UCNR10_afterT


title: CDcR10_beforeT


title: UCNR16_afterT


title: UCNR12_afterT


title: UCNR9_afterT


title: UCNR13_afterT


title: UCNR7_afterT


title: UCNR6_afterT


title: UCNR5_afterT


title: UCNR4_afterT


title: CDiNR9_beforeT


title: UCNR3_afterT


title: UCR7_afterT

description: Colonic mucosal gene expression data from UC responder after first infliximab treatment

source_name: Colonic mucosal biopsy from UC responder after first infliximab treatment


title: UCR6_afterT


title: UCNR2_afterT


title: UCR4_afterT


title: UCR5_afterT


title: UCNR1_afterT


title: Fus KSL1

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

institute: Graduate School of Medicine, Chiba University

description: Gene expression data from Fus-/- KSL hematopoietic stem/progenitor cells from recipient mouse bone marrow post-transplantation

hyb_protocol: Standard Affymetrix Protocol

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

source_name: Fus-/- KSL

label_protocol: Biotinylated cRNA were prepared  from the purified total RNA equivalent to 10,000 cells according to the standard Affymetrix protocol.

value: Hematopoietic stem/progenitor cells

tag: genotype

value: Fus-null

tag: developmental stage

value: post-tranplantation BM


title: UCR8_afterT


title: Fus KSL2


title: WT KSL2

description: Gene expression data from wild-type KSL hematopoietic stem/progenitor cells from recipient mouse bone marrow post-transplantation

source_name: Wild-type KSL

value: Wild type


title: UCNR9_beforeT

description: Colonic mucosal gene expression data from UC non-responder before first infliximab treatment

source_name: Colonic mucosal biopsy from UC non-responder before first infliximab treatment


title: UCNR6_beforeT


title: UCNR4_beforeT


title: UCNR5_beforeT


title: UCR1_afterT


title: UCR3_afterT


title: UCNR10_beforeT


title: WT KSL1


title: UCR2_afterT


title: UCNR12_beforeT


title: UCNR14_beforeT


title: UCNR13_beforeT


title: UCNR16_beforeT


title: UCNR15_beforeT


title: UCNR11_beforeT


title: UCNR7_beforeT


title: UCNR8_beforeT


title: UCNR2_beforeT


title: UCNR3_beforeT


title: UCR8_beforeT

description: Colonic mucosal gene expression data from UC responder before first infliximab treatment

source_name: Colonic mucosal biopsy from UC responder before first infliximab treatment


title: UCR5_beforeT


title: UCR6_beforeT


title: UCR4_beforeT


title: UCR7_beforeT


title: UCNR1_beforeT


title: UCR2_beforeT


title: UCR3_beforeT


title: CO3

description: Colonic mucosal gene expression data from control individual

source_name: Colonic mucosal biopsy from control individual


title: CO4


title: UCR1_beforeT


title: CDcR11_afterT


title: CO1


title: Placenta, Term cesarean delivery, Biological Replicate #1

status: Public on Nov 02 2009

city: Shatin

first: Stephen

middle: S

last: Chim

address: Dept of Obstetrics & Gynaecology, The Chinese University of Hong Kong

department: Obstetrics & Gynaecology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: ethinicity of pregnant mother: Chinese; delivery location: Prince of Wales Hospital, Hong Kong

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

data_processing: The data were analyzed with GeneSpring GX10 using the quantile normalization by the RMA method.

source_name: term cesarean delivery (38-39 weeks)

growth_protocol: Not applicable. The placental biopsy was collected and extracted for RNA without culturing.

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

treatment_protocol: Each placental biopsy was collected, rinsed in phosphate buffered saline, and submerged into RNA later (Ambion) as soon as possible after delivery.

value: placenta

tag: ethinicity of pregnant mother

value: Chinese

tag: delivery location

value: Prince of Wales Hospital, Hong Kong


title: Placenta, Term labour spontaneous delivery, Biological Replicate #1

source_name: term spontaneous delivery (38-39 weeks)


title: CO6

value: Control


title: Placenta, Term labour spontaneous delivery, Biological Replicate #5


title: Placenta, Term labour spontaneous delivery, Biological Replicate #3


title: Placenta, Term cesarean delivery, Biological Replicate #3


title: Placenta, Term cesarean delivery, Biological Replicate #5


title: Placenta, Term cesarean delivery, Biological Replicate #2


title: Placenta, Term labour spontaneous delivery, Biological Replicate #4


title: Placenta, Term cesarean delivery, Biological Replicate #4


title: petiole in FRD, rep3

status: Public on Nov 01 2009

city: Kitashirakawa, Sakyoku

first: Toshiaki

last: Kozuka

state: Kyoto

address: Oiwakecho

department: Depertment of Botany

institute: Kyoto University

description: The 3rd and 4th rosette leaves were used.

hyb_protocol: Followed Affymetrix experimental procedure. 200 micro liter of hybrization solution was used for 16 hrs at 45°C.

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

data_processing: Array data were processed and analyzed with Microarray Suites 5.0 software (Affymetrix) and GeneSpring 7.3 (Agilent). Data values were normalized per chip to the 50th percentile and per gene to the median of that gene measurement in WL2.

source_name: petiole in FRD

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

growth_protocol: Seedlings were grown at 22 degrees on rocklwools under continuous white light for 19 days.

extract_protocol: Total RNA was separately prepared from leaf blades and petioles using Sepazol RNA I super kit (Nacalai Tesque), and  purified with  RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Seedlings were either treated with white light for 2 h (WL), incubated in the dark condition for 2 h (D), or pulse irradiation of FR light before incubated in the dark condition for 2 h (FRD).

value: petioles


title: Placenta, Term labour spontaneous delivery, Biological Replicate #2


title: petiole in D, rep3

source_name: petiole in D


title: petiole in D, rep1


title: petiole in FRD, rep2


title: petiole in D, rep2


title: petiole in WL, rep2

source_name: petiole in WL


title: leaf blade in FRD, rep2

source_name: leaf blade in FRD

value: leaf blades


title: leaf blade in FRD, rep3


title: petiole in WL, rep3


title: petiole in WL, rep1


title: petiole in FRD, rep1


title: leaf blade in FRD, rep1


title: leaf blade in D, rep3

source_name: leaf blade in D


title: leaf blade in WL, rep1

source_name: leaf blade in WL


title: leaf blade in D, rep2


title: leaf blade in WL, rep3


title: leaf blade in WL, rep2


title: Fibroblast 5

city: Baltimore

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

description: Gene expression data obtained from fibroblasts

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA

source_name: fibroblast

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine. iPS cells were cultured in hES medium (80% DMEM/F12, 20% KO Serum Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 uM nonessential amino acids, 100 uM 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications


title: Fibroblast 4

value: Parental cells for PD-iPS5


title: iPS 1

description: Gene expression data obtained from iPS cells

source_name: iPS

value: iPS cells derived from DMD


title: leaf blade in D, rep1


title: iPS 6

value: iPS cells derived from MRC5


title: iPS 3

value: iPS cells derived from 551


title: Fibroblast 2

value: GM00852A from Coriell


title: iPS 5

value: iPS cells derived from SBDS


title: Fibroblast 3

value: Detroit 551 fetal skin fibroblast from ATCC


title: CO2

value: Colon

value: Not applicable


title: Fibroblast 6

value: 14 week old fetal lung fibroblast from ATCC


title: miR393 0h 3rd rep

city: Norwich

first: Daniel

last: MacLean

address: Colney Lane

department: Bioinformatics

institute: The Sainsbury Laboratory

description: Genes expression on leaf tissue on 35S:miR393 plant

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis Genome ATH1 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: background corrected using RMA, quantile normalized, values summarised by median-polish

source_name: 5weeks old arabidopsis leaves

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

growth_protocol: Plants were grown in short day environment (8hrs light/16 hrs dark) for 5 weeks at 20C.

extract_protocol: Trizol extraction according to the manufacturer instruction. The total RNA was then DNAse treated using the Qiagen DNAse. Purification was performed using the RNAeasy columns following the manufacturer instruction

treatment_protocol: Leaves were inoculated with PstDc3000 at 10^6cfu/ml or with water. Tissues were harvested at 24hrs post inoculation

value: Leaf tissue


title: Wild type flg22 1h   3rd rep

description: Genes expression on leaf tissue after flg22 (100nM) treatment


title: AFB1 flg22 2h 3rd rep

description: Genes expression on leaf tissue in 35S:AFB1 plant after flg22 (100nM) treatment


title: Wild type NAA/flg 1h 3rd rep

description: Genes expression on leaf tissue after auxin (NAA, 10µM) and flg22 (100nM) treatment


title: miR393 flg22 1h 3rd rep

description: Genes expression on leaf tissue in 35S:miR393 plant after flg22 (100nM) treatment


title: Wild type 0h    3rd rep

description: Genes expression on leaf tissue


title: miR393 flg22 2h 2nd rep


title: Fibroblast 1

value: GM04981 from Coriell


title: Wild type NAA 2h 3rd rep

description: Genes expression on leaf tissue after auxin (NAA, 10µM) treatment


title: iPS 4

value: iPS cells derived from PD


title: AFB1 flg22 1h 3rd rep


title: Wild type NAA/flg 2h 2nd rep


title: AFB1 0h 2nd rep

description: Genes expression on leaf tissue in 35S:AFB1 plant


title: Wild type Atum 2h 3rd rep

description: Genes expression on leaf tissue after treatment with inactive flg22(100nM) from Agrobacterium tumefasciens


title: iPS 2

value: iPS cells derived from GD


title: AFB1 flg22 1h 2nd rep


title: miR393 flg22 1h 2nd rep


title: Wild type flg22 2h  3rd rep


title: Wilt type flg22 1h 2nd rep


title: miR393 0h 1st rep


title: Wild type NAA 2h 2nd rep


title: Wild type Atum 2h 2nd rep


title: miR393 flg22 1h 1st rep


title: Wild type flg22 1h   1st rep


title: Wild type Atum 1h 1st rep

description: Genes expression on leaf tissue after treatment with inactive flg22 (100nM) from Agrobacterium tumefasciens


title: Wild type 0h     1st rep

description: Genes expression on leaf tissue


title: Wild type NAA/flg 1h 1st rep


title: Wild type NAA/flg 2h 1st rep


title: Wild type flg22 2h  1st rep


title: AFB1 flg22 1h 1st rep


title: Wild type Atum 2h 1st rep


title: AFB1 flg22 2h 1st rep


title: Wild type NAA 1h 1st rep


title: 2d red light grown WT(Col-0) seedlings/replicate 2

city: Albany

first: james

middle: m

last: tepperman

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center/UC Berkeley

description: 2d Red light (6.7 μmol/m2/s)/replicate 2

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: BioConductor software (RMA) to normalize and correct background on all the data

source_name: whole seedling (root, hypocotyl,cotyledon)

label_protocol: standard Affymetrix procedures

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s).Seeds were then placed in constant red light (Rc) (6.7 μmol/m2/s) at 21°C for 45h

extract_protocol: Total RNA was extracted from ~400 mg (fw) tissue using the method of Chang et al. (Chang, S., Puryear, J. & Cairney, J. (1993) Plant Mol. Biol. Rep. 11, 113-116) followed by further purification using Qiagen RNeasy columns.

treatment_protocol: 2d Red light (6.7 μmol/m2/s)

value: WT (Col-0)