title: Sample 1 from patient 72, Affected site

source_name: Patient 72 gingival tissue sample collected as Affected


title: Sample 2 from patient 76, Affected site

status: Public on Dec 22 2009

type: RNA

city: New York

first: Ryan

middle: T

last: Demmer

state: NY

department: Epidemiology

country: USA

institute: Columbia University

description: A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4) from a maxillary posterior. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each papilla. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total)

hyb_protocol: According to the manufacturer's instructions.

data_processing: All CEL files in the series were processed using RMA in R using justRMA with default parameters.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patient 76 gingival tissue sample collected as Affected

label_protocol: Synthesis of Biotin-Labeled cRNA was performed using the GeneChip Expression 3'-Amplification Reagents for IVT labeling kit (Affymetrix). The cRNA yield was determined spectrophotometrically at 260 nm. Finally, the cRNA was fragmented by incubation in fragmentation buffer  at 94 0C for 35 min and stored at ?80 0C until hybridizations.

extract_protocol: Gingival tissue specimens were homogenized in Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA collected in the upper aqueous phase was precipitated by mixing with isopropyl alcohol and additional centrifugation and washed in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. The purified RNA was quantitated spectrophotometrically, and 7.5 micrograms of total RNA was reverse transcribed using GeneChip Expression 3' amplification one-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions.

treatment_protocol: After collection gingival tissue specimens were thoroughly rinsed with sterile normal saline solution and transferred into Eppendorf tubes containing 5 volumes of a RNA stabilization reagent (RNAlater, Ambion, Austin, TX, USA).  Specimens were stored in RNAlater overnight at 4.0 C and thereafter snap-frozen and stored in liquid nitrogen. All further processing occurred simultaneously for gingival biopsies originating from the same donor.

tag: gingival tissue phenotype

value: Diseased (BoP + interproximal PPD of>3 mm + concomitant CAL of>2 mm)

tag: tissue

value: Gingival


title: Sample 1 from patient 75, Affected site

scan_protocol: According to the manufacturer's instructions.

source_name: Patient 75 gingival tissue sample collected as Affected


title: Sample 1 from patient 74, Affected site

source_name: Patient 74 gingival tissue sample collected as Affected


title: Sample 1 from patient 73, Affected site

source_name: Patient 73 gingival tissue sample collected as Affected


title: Sample 2 from patient 84, Affected site

source_name: Patient 84 gingival tissue sample collected as Affected


title: Sample 2 from patient 74, Affected site


title: Sample 3 from patient 74, Unaffected site

source_name: Patient 74 gingival tissue sample collected as Unaffected

value: Healthy (no BoP + PPD of<5 mm + CAL of<3 2 mm


title: Sample 3 from patient 72, Unaffected site

source_name: Patient 72 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 70, Affected site

source_name: Patient 70 gingival tissue sample collected as Affected


title: Sample 2 from patient 70, Affected site


title: Sample 2 from patient 69, Affected site

source_name: Patient 69 gingival tissue sample collected as Affected


title: Sample 2 from patient 73, Affected site


title: Sample 2 from patient 72, Affected site


title: Sample 2 from patient 82, Affected site

source_name: Patient 82 gingival tissue sample collected as Affected


title: Sample 1 from patient 71, Affected site

source_name: Patient 71 gingival tissue sample collected as Affected


title: Sample 3 from patient 69, Unaffected site

source_name: Patient 69 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 66, Affected site

source_name: Patient 66 gingival tissue sample collected as Affected


title: Sample 2 from patient 67, Affected site

source_name: Patient 67 gingival tissue sample collected as Affected


title: Sample 3 from patient 68, Unaffected site

source_name: Patient 68 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 69, Affected site


title: Sample 1 from patient 68, Affected site

source_name: Patient 68 gingival tissue sample collected as Affected


title: Sample 2 from patient 65, Affected site

source_name: Patient 65 gingival tissue sample collected as Affected


title: Sample 1 from patient 65, Affected site


title: Sample 2 from patient 68, Affected site


title: Sample 2 from patient 64, Affected site

source_name: Patient 64 gingival tissue sample collected as Affected


title: Sample 1 from patient 66, Affected site


title: Sample 1 from patient 67, Affected site


title: Sample 3 from patient 66, Unaffected site

source_name: Patient 66 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 63, Affected site

source_name: Patient 63 gingival tissue sample collected as Affected


title: Sample 4 from patient 65, Unaffected site

source_name: Patient 65 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 63, Unaffected site

source_name: Patient 63 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 62, Affected site

source_name: Patient 62 gingival tissue sample collected as Affected


title: Sample 2 from patient 61, Affected site

source_name: Patient 61 gingival tissue sample collected as Affected


title: Sample 1 from patient 61, Affected site


title: Sample 1 from patient 64, Affected site


title: Sample 3 from patient 64, Unaffected site

source_name: Patient 64 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 59, Affected site

source_name: Patient 59 gingival tissue sample collected as Affected


title: Sample 1 from patient 60, Affected site

source_name: Patient 60 gingival tissue sample collected as Affected


title: Sample 4 from patient 61, Unaffected site

source_name: Patient 61 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 60, Affected site


title: Sample 1 from patient 59, Affected site


title: Sample 4 from patient 59, Unaffected site

source_name: Patient 59 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 58, Unaffected site

source_name: Patient 58 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 62, Affected site


title: Sample 3 from patient 62, Unaffected site

source_name: Patient 62 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 56, Affected site

source_name: Patient 56 gingival tissue sample collected as Affected


title: Sample 2 from patient 58, Affected site

source_name: Patient 58 gingival tissue sample collected as Affected


title: Sample 1 from patient 58, Affected site


title: Sample 2 from patient 56, Affected site


title: Sample 1 from patient 55, Affected site

source_name: Patient 55 gingival tissue sample collected as Affected


title: Sample 2 from patient 55, Affected site


title: Sample 4 from patient 56, Unaffected site

source_name: Patient 56 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 55, Unaffected site

source_name: Patient 55 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 53, Affected site

source_name: Patient 53 gingival tissue sample collected as Affected


title: Sample 1 from patient 52, Affected site

source_name: Patient 52 gingival tissue sample collected as Affected


title: Sample 3 from patient 54, Unaffected site

source_name: Patient 54 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 49, Affected site

source_name: Patient 49 gingival tissue sample collected as Affected


title: Sample 1 from patient 54, Affected site

source_name: Patient 54 gingival tissue sample collected as Affected


title: Sample 2 from patient 53, Affected site


title: Sample 3 from patient 49, Unaffected site

source_name: Patient 49 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 47, Affected site

source_name: Patient 47 gingival tissue sample collected as Affected


title: Sample 3 from patient 48, Unaffected site

source_name: Patient 48 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 46, Affected site

source_name: Patient 46 gingival tissue sample collected as Affected


title: Sample 1 from patient 50, Affected site

source_name: Patient 50 gingival tissue sample collected as Affected


title: Sample 2 from patient 54, Affected site


title: Sample 1 from patient 48, Affected site

source_name: Patient 48 gingival tissue sample collected as Affected


title: Sample 2 from patient 52, Affected site


title: Sample 2 from patient 48, Affected site


title: Sample 1 from patient 47, Affected site


title: Sample 2 from patient 50, Affected site


title: Sample 3 from patient 47, Unaffected site

source_name: Patient 47 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 46, Unaffected site

source_name: Patient 46 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 46, Affected site


title: Sample 1 from patient 49, Affected site


title: Sample 3 from patient 45, Unaffected site

source_name: Patient 45 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 45, Affected site

source_name: Patient 45 gingival tissue sample collected as Affected


title: Sample 1 from patient 45, Affected site


title: Sample 2 from patient 44, Affected site

source_name: Patient 44 gingival tissue sample collected as Affected


title: Sample 4 from patient 43, Unaffected site

source_name: Patient 43 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 43, Affected site

source_name: Patient 43 gingival tissue sample collected as Affected


title: Sample 2 from patient 42, Affected site

source_name: Patient 42 gingival tissue sample collected as Affected


title: Sample 1 from patient 41, Affected site

source_name: Patient 41 gingival tissue sample collected as Affected


title: Sample 3 from patient 39, Unaffected site

source_name: Patient 39 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 38, Unaffected site

source_name: Patient 38 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 44, Affected site


title: Sample 2 from patient 38, Affected site

source_name: Patient 38 gingival tissue sample collected as Affected


title: Sample 3 from patient 36, Unaffected site

source_name: Patient 36 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 40, Affected site

source_name: Patient 40 gingival tissue sample collected as Affected


title: Sample 1 from patient 42, Affected site


title: Sample 3 from patient 42, Unaffected site

source_name: Patient 42 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 39, Affected site

source_name: Patient 39 gingival tissue sample collected as Affected


title: Sample 3 from patient 37, Unaffected site

source_name: Patient 37 gingival tissue sample collected as Unaffected


title: Sample 4 from patient 35, Unaffected site

source_name: Patient 35 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 37, Affected site

source_name: Patient 37 gingival tissue sample collected as Affected


title: Sample 2 from patient 35, Affected site

source_name: Patient 35 gingival tissue sample collected as Affected


title: Sample 1 from patient 37, Affected site


title: Sample 2 from patient 63, Affected site

source_name: Patient 63 gingival tissue sample collected as Affected


title: Sample 1 from patient 38, Affected site


title: Sample 2 from patient 36, Affected site

source_name: Patient 36 gingival tissue sample collected as Affected


title: Sample 2 from patient 41, Affected site


title: Sample 1 from patient 35, Affected site


title: Sample 1 from patient 40, Affected site


title: Sample 1 from patient 36, Affected site


title: Sample 1 from patient 39, Affected site


title: Sample 2 from patient 34, Affected site

source_name: Patient 34 gingival tissue sample collected as Affected


title: Sample 1 from patient 34, Affected site


title: Sample 3 from patient 34, Unaffected site

source_name: Patient 34 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 33, Affected site

source_name: Patient 33 gingival tissue sample collected as Affected


title: Sample 1 from patient 33, Affected site


title: Sample 2 from patient 31, Affected site

source_name: Patient 31 gingival tissue sample collected as Affected


title: Sample 3 from patient 27, Unaffected site

source_name: Patient 27 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 31, Unaffected site

source_name: Patient 31 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 29, Unaffected site

source_name: Patient 29 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 32, Affected site

source_name: Patient 32 gingival tissue sample collected as Affected


title: Sample 2 from patient 32, Affected site


title: Sample 4 from patient 32, Unaffected site

source_name: Patient 32 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 30, Affected site

source_name: Patient 30 gingival tissue sample collected as Affected


title: Sample 1 from patient 30, Affected site


title: Sample 2 from patient 29, Affected site

source_name: Patient 29 gingival tissue sample collected as Affected


title: Sample 2 from patient 26, Affected site

source_name: Patient 26 gingival tissue sample collected as Affected


title: Sample 2 from patient 28, Affected site

source_name: Patient 28 gingival tissue sample collected as Affected


title: Sample 1 from patient 28, Unaffected site

source_name: Patient 28 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 29, Affected site


title: Sample 1 from patient 31, Affected site


title: Sample 2 from patient 27, Affected site

source_name: Patient 27 gingival tissue sample collected as Affected


title: Sample 3 from patient 28, Affected site


title: Sample 1 from patient 27, Affected site


title: Sample 1 from patient 26, Affected site


title: Sample 2 from patient 25, Affected site

source_name: Patient 25 gingival tissue sample collected as Affected


title: Sample 1 from patient 25, Affected site


title: Sample 4 from patient 23, Unaffected site

source_name: Patient 23 gingival tissue sample collected as Unaffected


title: Sample 4 from patient 26, Unaffected site

source_name: Patient 26 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 22, Affected site

source_name: Patient 22 gingival tissue sample collected as Affected


title: Sample 1 from patient 23, Affected site

source_name: Patient 23 gingival tissue sample collected as Affected


title: Sample 1 from patient 24, Affected site

source_name: Patient 24 gingival tissue sample collected as Affected


title: Sample 2 from patient 23, Affected site


title: Sample 2 from patient 24, Affected site


title: Sample 1 from patient 22, Affected site


title: Sample 3 from patient 21, Unaffected site

source_name: Patient 21 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 20, Affected site

source_name: Patient 20 gingival tissue sample collected as Affected


title: Sample 2 from patient 21, Affected site

source_name: Patient 21 gingival tissue sample collected as Affected


title: Sample 1 from patient 21, Affected site


title: Sample 3 from patient 20, Affected site


title: Sample 4 from patient 18, Unaffected site

source_name: Patient 18 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 17, Affected site

source_name: Patient 17 gingival tissue sample collected as Affected


title: Sample 2 from patient 18, Affected site

source_name: Patient 18 gingival tissue sample collected as Affected


title: Sample 4 from patient 17, Unaffected site

source_name: Patient 17 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 20, Unaffected site

source_name: Patient 20 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 14, Affected site

source_name: Patient 14 gingival tissue sample collected as Affected


title: Sample 2 from patient 15, Affected site

source_name: Patient 15 gingival tissue sample collected as Affected


title: Sample 1 from patient 15, Affected site


title: Sample 3 from patient 13, Unaffected site

source_name: Patient 13 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 14, Affected site


title: Sample 3 from patient 14, Unaffected site

source_name: Patient 14 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 18, Affected site


title: Sample 2 from patient 16, Affected site

source_name: Patient 16 gingival tissue sample collected as Affected


title: Sample 2 from patient 13, Affected site

source_name: Patient 13 gingival tissue sample collected as Affected


title: Sample 1 from patient 17, Affected site


title: Sample 1 from patient 16, Affected site


title: Sample 1 from patient 18, Affected site


title: Sample 1 from patient 13, Affected site


title: Sample 4 from patient 10, Unaffected site

source_name: Patient 10 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 11, Affected site

source_name: Patient 11 gingival tissue sample collected as Affected


title: Sample 1 from patient 9, Affected site

source_name: Patient 9 gingival tissue sample collected as Affected


title: Sample 3 from patient 9, Unaffected site

source_name: Patient 9 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 12, Affected site

source_name: Patient 12 gingival tissue sample collected as Affected


title: Sample 2 from patient 12, Affected site


title: Sample 1 from patient 10, Affected site

source_name: Patient 10 gingival tissue sample collected as Affected


title: Sample 4 from patient 12, Unaffected site

source_name: Patient 12 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 10, Affected site


title: Sample 3 from patient 8, Unaffected site

source_name: Patient 8 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 8, Affected site

source_name: Patient 8 gingival tissue sample collected as Affected


title: Sample 3 from patient 7, Affected site

source_name: Patient 7 gingival tissue sample collected as Affected


title: Sample 2 from patient 11, Affected site


title: Sample 2 from patient 9, Affected site


title: Sample 2 from patient 8, Affected site


title: Sample 2 from patient 7, Affected site


title: Sample 2 from patient 5, Affected site

source_name: Patient 5 gingival tissue sample collected as Affected


title: Sample 1 from patient 5, Unaffected site

source_name: Patient 5 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 3, Affected site

source_name: Patient 3 gingival tissue sample collected as Affected


title: Sample 3 from patient 3, Unaffected site

source_name: Patient 3 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 4, Affected site

source_name: Patient 4 gingival tissue sample collected as Affected


title: Sample 1 from patient 7, Affected site


title: Sample 3 from patient 5, Affected site


title: Sample 1 from patient 4, Affected site


title: Sample 3 from patient 4, Unaffected site

source_name: Patient 4 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 3, Affected site


title: Sample 1 from patient 2, Affected site

source_name: Patient 2 gingival tissue sample collected as Affected


title: Sample 4 from patient 1, Unaffected site

source_name: Patient 1 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 1, Affected site

source_name: Patient 1 gingival tissue sample collected as Affected


title: Sample 4 from patient 2, Unaffected site

source_name: Patient 2 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 1, Affected site


title: Sample 2 from patient 2, Affected site


title: control-2, cells cultured in regular DMEM

status: Public on Dec 20 2009

city: Gainesville

first: jixiu

last: shan

state: FL

address: 1600 SW Archer Road

department: Biochemistry and Molecular Biology

institute: University of Florida

description:
none
none

hyb_protocol: Biotin-labeled cRNA was fragmented for 35 min at 94°C. This fragmented cRNA (0.05 μg/μl) was then mixed with the control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls (BioB at 1.5 pM, BioC at 5 pM, BioDn at 25 pM, and CreX at 100 pM, Affymetrix 900454), herring sperm DNA (0.1 mg/ml, Promega), acetylated BSA (50 mg/ml, GIBCO-BRL), and 2X hybridization buffer. The reaction was heated to 99°C for 5 min, then transferred to 45°C for 5 min, and finally centrifuged at 15,000 x g in a microcentrifuge for 5 min. A 200μl aliquot was injected into a Human Genome U133 Plus 2.0 Array (Affymetrix) representing over 47,000 mRNA species and 38,500 known human genes. Hybridization was completed in a 45°C oven for 16 h. The solution was removed and the array was washed and stained using the Euk-WS2 fluidics protocol and the streptavidin-phycoerythrin reagent (Affymetrix).

scan_protocol: The Genechips were scanned with an Affymetrix G7 scanner

data_processing: Microarray data were normalized and a model-based expression matrix was derived using the perfect-match-only algorithms of dChip (Li and Wong 31-36). For unsupervised analysis, probe sets for which the hybridization signal intensity varied across the data set with a coefficient of variation of >0.5 were identified and visualized by average linkage hierarchal clustering using the clustering algorithms implemented in dChip.

source_name: Human Hepatoma Cells

label_protocol: A 200 ng aliquot of total RNA from four independent incubations for each condition was labeled using the Affymetrix GeneChip® 3' IVT Express Kit.

growth_protocol: Human Heptoma cells were cultured in DMEM plus 10 % FBS

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen), including DNase I treatment before the final elution to eliminate any DNA contamination

treatment_protocol: 12 hours prior to treatement, cells were replenished with fresh medium.

tag: cell type

value: Human Hepatoma Cells


title: control-1, cells cultured in regular DMEM


title: control-4, cells cultured in regular DMEM

description:
none
none


title: Treatment-4, cells cultured in DMEM plus 5 mM HisOH

description:
none
none

treatment_protocol: 12 hours prior to treatement, cells were replenished with fresh medium. For treatment, cells were cultured in DMEM medium containing 5 mM HisOH for 4 hours.


title: Treatment-3, cells cultured in DMEM plus 5 mM HisOH

description:
none
none


title: Treatment-2, cells cultured in DMEM plus 5 mM HisOH

description:
none
none


title: RWPE1 cells, vehicle, 48h, biological rep2

status: Public on Dec 18 2009

city: West Lafayette

first: Pavlo

last: Kovalenko

state: IN

address: 700 W State st

department: Foods and Nutrition

institute: Purdue University

description: Gene expression of vehicle treated RWPE1 at 48h.

hyb_protocol: Chip hybridization was carried by using standard Affymetrix protocols (Affymetrix, Santa Clara, CA) at the Ohio State University Comprehensive Cancer Center (Columbus, OH).

scan_protocol: Chip scanning was carried out by using standard Affymetrix protocols (Affymetrix, Santa Clara, CA) at the Ohio State University Comprehensive Cancer Center  (Columbus, OH).

data_processing: Microarray data from CEL files for all 24 chips was normalized simultaneously and expression levels were generated using the gcRMA package in Bioconductor.

source_name: RWPE1 cells treated for 48 hours with vehicle (0.1% ethanol)

label_protocol: The transcripts levels in each sample were measured by using the Affymetrix HU133 plus 2.0 GeneChip (Affymetrix, Santa Clara, CA;  54,210 probe sets covering over 47,000 transcripts and splice variants).  RNA labeling was carried out by using standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

growth_protocol: RWPE1 cells were plated in T75 flasks (1x10^6 cells per flask) and grown until cells reached 60% confluence. For the 48 hours time point media was replaced at 24 hours.

extract_protocol: Total RNA was isolated from the cells using TriReagent (Molecular Research Center, Inc., Cincinnati, OH) in accordance with the manufacturer’s instructions. Isolated total RNA was further purified using the RNeasy kit (Qiagen, Valencia, CA). The quality of the isolated RNA was confirmed using agarose gel electrophoresis.

treatment_protocol: RWPE1 cells were treated with medium containing 100 nM of 1,25(OH)2D or vehicle (0.1% ethanol) for 6, 24 or 48 hours (n=4 per treatment, 24 total samples).

tag: cell line

value: Immortalized normal prostate epithelial cells.

tag: treatment

value: Vehicle (0.1% ethanol)

tag: time point

value: 48 hours


title: RWPE1 cells, vehicle, 48h, biological rep1


title: Treatment-1, cells cultured in DMEM plus 5 mM HisOH

description:
none
none


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 24h, biological rep3

description: Gene expression of 1,25(OH)2D treated RWPE1 at 24h.

source_name: RWPE1 cells treated for 24 hours with 100 nM 1,25(OH)2D

value: 24 hours


title: RWPE1 cells, vehicle, 48h, biological rep3


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 24h, biological rep4


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 24h, biological rep2


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 48h, biological rep3

description: Gene expression of 1,25(OH)2D treated RWPE1 at 48h.

source_name: RWPE1 cells treated for 48 hours with 100 nM 1,25(OH)2D


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 48h, biological rep4


title: RWPE1 cells, vehicle, 24h, biological rep3

description: Gene expression of vehicle treated RWPE1 at 24h.

source_name: RWPE1 cells treated for 24 hours with vehicle (0.1% ethanol)


title: RWPE1 cells, vehicle, 24h, biological rep2


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 6h, biological rep4

description: Gene expression of 1,25(OH)2D treated RWPE1 at 6h.

source_name: RWPE1 cells treated for 6 hours with 100 nM 1,25(OH)2D

value: 6 hours


title: control-3, cells cultured in regular DMEM

description:
none
none


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 48h, biological rep1


title: RWPE1 cells, vehicle, 48h, biological rep4


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 48h, biological rep2


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 24h, biological rep1


title: RWPE1 cells, vehicle, 24h, biological rep4


title: RWPE1 cells, vehicle, 24h, biological rep1


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 6h, biological rep2


title: RWPE1 cells, vehicle, 6h, biological rep4

description: Gene expression of vehicle treated RWPE1 at 6h.

source_name: RWPE1 cells treated for 6 hours with vehicle (0.1% ethanol)


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 6h, biological rep1


title: RWPE1 cells, 100 nM of 1,25(OH)2D, 6h, biological rep3


title: RWPE1 cells, vehicle, 6h, biological rep3


title: RWPE1 cells, vehicle, 6h, biological rep2


title: Infant ALL germline MLL sample 14

status: Public on Dec 16 2009

city: Rotterdam

first: Ronald

last: Stam

address: Dr. Molewaterplein 60

country: Netherlands

institute: Erasmus MC - Sophia Children's Hospital

description: Gene expression profiling data (HU133plus2.0) primary infant ALL cells

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix HU133plus 2.0 microarrays. 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 CEL files represent the raw (unscaled; scaling factor = 1) gene expression data. Raw (unscaled) array data was collectively normalized using variance-stabilizing normalization (VSN), performed in the statistical environment R (version 2.10.1) using Bioconductor packages.

source_name: Primary infant (<1 year of age) ALL cells at diagnosis (untreated) (>90% blasts)

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

extract_protocol: Total RNA was extracted from leukemic cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Primary ALL samples were obtained at diagnosis (before treatment) and processed within 24 hours after sampling. All samples contained >90% leukemic blasts.

value: Acute Lymphoblastic Leukemia cells (>90% blasts)

tag: genome/variation

tag: sex

value: female

tag: age (months)

value: Precursor B-cell acute lymphoblastic leukemia (ALL)


title: RWPE1 cells, vehicle, 6h, biological rep1


title: Infant ALL germline MLL sample 11

value: male


title: Infant ALL germline MLL sample 12


title: Infant ALL germline MLL sample 8


title: Infant ALL germline MLL sample 3


title: HGC-27 parental

status: Public on Dec 17 2009

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

hyb_protocol: Following fragmentation, 10 ug cRNA were hybridized for 16 hr at 45C on GeneChip Human HGU133_Plus_2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: dChip was used to normalize and model all chips in this series. Chips were analyzed by dChip to identify genes expressed in both MIST1-transfected cell populations relative to their respective controls in multiple Boolean 'AND' comparisons.

source_name: Untransfected, parental gastric cell line

label_protocol: 5 ug total RNA was used to prepare labeled target using Affymetrix GeneChip One-Cycle Target Labeling reagents.

growth_protocol: AGS and HGC cells were cultured at 37C and 5% CO2 in DMEM or RPMI + 10% serum, passaged every 3 days; cells were sorted 24h post transfection and grown 24 hrs more before harvesting RNA for GeneChips.

extract_protocol: Total RNA was extracted by Qiagen RNeasy kit.

treatment_protocol: Transfection was by Nucleofection in 10^6 cells, program B-023, transfection solution V with 3 ug MIST1 (or empty vector) and 1.5 ug pmaxGFP.

value: cultured gastric cell lines

tag: genetic modification


title: Infant ALL MLL-AF9 positive sample 6


title: Infant ALL germline MLL sample 6


title: Infant ALL germline MLL sample 2


title: AGS cells +MIST1

description: AGS + MIST1.CEL

source_name: GFP and MIST1 transfected, GFP sorted

value: AGS

value: GFP and MIST1


title: HGC+GFP control

description: HGC + GFP.CEL

source_name: GFP and empty vector-transfected, GFP sorted control

value: GFP and empty vector


title: HGC+MIST1

description: HGC + MIST1.CEL


title: Infant ALL germline MLL sample 4


title: AGS cells parental

description: AGS.CEL


title: AGS cells GFP control

description: AGS + GFP.CEL


title: Infant ALL germline MLL sample 10


title: Infant ALL germline MLL sample 1


title: Infant ALL germline MLL sample 5


title: Infant ALL germline MLL sample 7


title: Infant ALL MLL-AF9 positive sample 4


title: Infant ALL MLL-AF9 positive sample 7


title: Infant ALL germline MLL sample 13


title: Infant ALL MLL-AF9 positive sample 3


title: Infant ALL germline MLL sample 9


title: Infant ALL MLL-AF9 positive sample 2


title: Infant ALL MLL-ENL positive sample 22


title: Infant ALL MLL-ENL positive sample 21


title: Infant ALL MLL-AF9 positive sample 1


title: Infant ALL MLL-ENL positive sample 19


title: Infant ALL MLL-ENL positive sample 17


title: Infant ALL MLL-ENL positive sample 12


title: Infant ALL MLL-ENL positive sample 6


title: Infant ALL MLL-ENL positive sample 7


title: Infant ALL MLL-ENL positive sample 2


title: Infant ALL MLL-AF4 positive sample 27


title: Infant ALL MLL-ENL positive sample 14


title: Infant ALL MLL-ENL positive sample 11


title: Infant ALL MLL-ENL positive sample 8


title: Infant ALL MLL-ENL positive sample 9


title: Infant ALL MLL-ENL positive sample 16


title: Infant ALL MLL-ENL positive sample 1


title: Infant ALL MLL-ENL positive sample 4


title: Infant ALL MLL-ENL positive sample 5


title: Infant ALL MLL-ENL positive sample 13


title: Infant ALL MLL-ENL positive sample 15


title: Infant ALL MLL-ENL positive sample 3


title: Infant ALL MLL-ENL positive sample 18


title: Infant ALL MLL-ENL positive sample 10


title: Infant ALL MLL-AF4 positive sample 26


title: Infant ALL MLL-ENL positive sample 20


title: Infant ALL MLL-AF4 positive sample 29


title: Infant ALL MLL-AF4 positive sample 24


title: Infant ALL MLL-AF4 positive sample 21


title: Infant ALL MLL-AF4 positive sample 25


title: Infant ALL MLL-AF4 positive sample 19


title: Infant ALL MLL-AF4 positive sample 22


title: Infant ALL MLL-AF4 positive sample 16


title: Infant ALL MLL-AF4 positive sample 4


title: Infant ALL MLL-AF4 positive sample 9


title: Infant ALL MLL-AF4 positive sample 11


title: Infant ALL MLL-AF4 positive sample 20


title: Infant ALL MLL-AF4 positive sample 14


title: Infant ALL MLL-AF4 positive sample 23


title: Infant ALL MLL-AF4 positive sample 15


title: Infant ALL MLL-AF4 positive sample 1


title: Infant ALL MLL-AF4 positive sample 3


title: Infant ALL MLL-AF4 positive sample 17


title: Infant ALL MLL-AF4 positive sample 7


title: Infant ALL MLL-AF4 positive sample 13


title: Infant ALL MLL-AF4 positive sample 5


title: Infant ALL MLL-AF4 positive sample 10


title: Infant ALL MLL-AF4 positive sample 18


title: Infant ALL MLL-AF4 positive sample 8

value: unknown


title: Infant ALL MLL-AF4 positive sample 6


title: Infant ALL MLL-AF4 positive sample 12


title: Infant ALL MLL-AF4 positive sample 2


title: YAP-WT

city: Ja Jolla

first: Bin

last: Zhao

state: CA

address: 3855 Health Sciences Dr.

institute: University of California, San Diego

description: MCF10A human mammary epithelial cell line with expression of YAP wild-type protein

hyb_protocol: Following fragmentation, 12ug of cRNA were hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the Affymetrix standard protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: After scanning the chips, the data were analyzed using GCOS software. Scaling was performed with a target intensity of 500 to facilitate the comparison of multiple arrays. A cut-off value of 0.05 was applied to the detection p value to assign a present (P), marginal (M), or absent (A) call to each probe set. A signal value was calculated using the One-Step Tukey’s Biweight Estimate to represent the relative abundance of a transcript.

source_name: MCF10A human mammary epithelial cell line with pQCXIH-YAP-WT

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

growth_protocol: MCF10A cells were cultured in DMEM/F12 (Invitrogen) supplemented with 5% horse serum (Invitrogen), 20ng/ml EGF, 0.5μg/ml hydrocortisone, 10μg/ml insulin, 100ng/ml cholera toxin, and 50μg/ml P/S.

extract_protocol: Trizol

treatment_protocol: Infection with retrovirus generated from pQCXIH-YAP-WT.


title: MCF10A human mammary epithelial cell line with pQCXIH-YAP-W1W2

description: MCF10A human mammary epithelial cell line with expression of YAP W1W2 mutant protein

treatment_protocol: Infection with retrovirus generated from pQCXIH-YAP-W1W2.


title: Infant ALL MLL-AF9 positive sample 5


title: Infant ALL MLL-AF9 positive sample 8


title: MCF10A human mammary epithelial cell line with pQCXIH-YAP-S94A

description: MCF10A human mammary epithelial cell line with expression of YAP S94A protein

treatment_protocol: Infection with retrovirus generated from pQCXIH-YAP-S94A.


title: miR mutant, biological rep1 (higher order mutant)

status: Public on Dec 15 2009

city: Albany

first: Atsunari

last: Tsuchisaka

address: 800 Buchanan St.

department: Plant Gene Expression Center

institute: University of California, Berkeley / USDA

hyb_protocol: 10 microgram of cRNA were hybridized to the  GeneChip® Arabidopsis ATH1 Genome Array chip according to the protocols provided by the manufacturer.  GeneChips were scanned with the default settings using the  > GeneChip® Scanner 3000 7G.

scan_protocol: GeneChips were scanned with the default settings using the GeneChip® Scanner 3000 7G.

data_processing: RMA

organism: Arabidopsis thaliana

source_name: 10-day old, light grown seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Seeds were surface sterilized for 8min in 5% sodium hypochlorite, 0.15% Tween 20, excessively rinsed in distilled water, and germinated on MS medium (0.8% Select Agar (Life Technologies, Inc., Rockville, MD), 0.5X Murashige-Skoog (MS) salts (Life Technologies, Inc.), 0.5mM MES, pH5.7, 1% sucrose, 1X B5 vitamins. After cold treatment at 4 C for 2 days, the plates were incubated at 25 C under 16h light / 8h for 10 days.

extract_protocol: Total RNA was prepared using RNAqueous RNA isolation kit with Plant RNA isolation aid (Ambion, Austin, TX). After LiCl precipitation, RNA was purified using RNeasy columns (Qiagen, Valencia, CA) and re-precipitated with LiCl. RNA pellets were washed with 70% EtOH (three times), and resuspended in DEPC-treated water.

tag: T-DNA insertion in ACS2,4,5,6,7,9 and miRNA for ACS8 and 11


title: mutant acs6E, biological rep1 (single mutant)

tag: T-DNA insertion in ACS6


title: col control, biological rep2 (higher order mutant)


title: hepta mutant, biological rep3 (higher order mutant)

tag: T-DNA insertion in ACS1,2,4,5,6,7 and 9


title: Vector

description: MCF10A human mammary epithelial cell line with pQCXIH vector as a control.

treatment_protocol: Infection with retrovirus generated from pQCXIH vector.


title: mutant acs9B, biological rep1 (single mutant)

tag: T-DNA insertion in ACS9


title: hexa mutant, biological rep1 (higher order mutant)

tag: T-DNA insertion in ACS2,4,5,6,7 and 9


title: miR mutant, biological rep3 (higher order mutant)


title: hepta mutant, biological rep1 (higher order mutant)


title: penta mutant, biological rep2 (higher order mutant)

tag: T-DNA insertion in ACS2,4,5,6 and9


title: mutant acs6E, biological rep2 (single mutant)


title: mutant acs9B, biological rep3 (single mutant)


title: miR mutant, biological rep2 (higher order mutant)


title: hexa mutant, biological rep3 (higher order mutant)


title: mutant acs9B, biological rep2 (single mutant)


title: mutant acs6E, biological rep3 (single mutant)


title: penta mutant, biological rep3 (higher order mutant)


title: col control, biological rep1 (higher order mutant)


title: col control, biological rep3 (higher order mutant)


title: hepta mutant, biological rep2 (higher order mutant)


title: hexa mutant, biological rep2 (higher order mutant)


title: mutant acs5D, biological rep3 (single mutant)

tag: T-DNA insertion in ACS5


title: mutant acs5D, biological rep2 (single mutant)


title: mutant acs5D, biological rep1 (single mutant)


title: mutant acs5C, biological rep1 (single mutant)


title: mutant acs4A, biological rep3 (single mutant)

tag: T-DNA insertion in ACS4


title: mutant acs5C, biological rep3 (single mutant)


title: mutant acs5C, biological rep2 (single mutant)


title: mutant acs2C, biological rep3 (single mutant)

tag: T-DNA insertion in ACS2


title: mutant acs4A, biological rep2 (single mutant)


title: mutant acs2C, biological rep2 (single mutant)


title: mutant acs2B, biological rep3 (single mutant)


title: mutant acs4A, biological rep1 (single mutant)


title: mutant acs2B, biological rep2 (single mutant)


title: mutant acs2C, biological rep1 (single mutant)


title: mutant acs1A, biological rep3 (single mutant)

tag: T-DNA insertion in ACS1


title: mutant acs1A, biological rep2 (single mutant)


title: mutant acs1A, biological rep1 (single mutant)


title: col control, biological rep2 (single mutant)


title: mutant acs2B, biological rep1 (single mutant)


title: col control, biological rep1 (single mutant)


title: col control, biological rep3 (single mutant)


title: Ethanol 120

city: Emeryville

first: Fred

last: Wolf

address: 5858 Horton St Suite 200

institute: Ernest Gallo Clinic and Research Center

description: Head RNA extracted 90' after Drosophila exposed for 30' to ethanol.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: R/Bioconductor GCRMA

organism: Drosophila melanogaster

source_name: Ethanol 120

label_protocol: single labeling protocol

growth_protocol: 200 2-4 day old male flies from synchronized cultures were used for all conditions

extract_protocol: RNA was extracted using the Trizol reagent

treatment_protocol: Flies were either untreated (2 replicates), or treated with 30 min ethanol vapor or humidified air. RNA was extracted 0, 30, 60, 90, 120, 180, or 210 min following exposure termination, and were snap frozen in liquid nitrogen.

tag: tissue

value: head

tag: exposure type

value: Ethanol

tag: minutes after exposure

tag: gender


title: Ethanol 60

description: Head RNA extracted 30' after Drosophila exposed for 30' to ethanol.

source_name: Ethanol 60


title: Unexposed B

description: Head RNA extracted from Drosophila.

source_name: Unexposed B


title: Ethanol 30

description: Head RNA extracted 0' after Drosophila exposed for 30' to ethanol.

source_name: Ethanol 30


title: Unexposed A

description: Head RNA extracted from Drosophila.

source_name: Unexposed A


title: Ethanol 210

description: Head RNA extracted 180' after Drosophila exposed for 30' to ethanol.

source_name: Ethanol 210


title: Air 210

description: Head RNA extracted 180' after Drosophila exposed for 30' to humidified air.

source_name: Air 210

value: Humidified air


title: Air 150

description: Head RNA extracted 120' after Drosophila exposed for 30' to humidified air.

source_name: Air 150


title: Ethanol 150

description: Head RNA extracted 120' after Drosophila exposed for 30' to ethanol.

source_name: Ethanol 150


title: Air 90

description: Head RNA extracted 60' after Drosophila exposed for 30' to humidified air.

source_name: Air 90


title: Air 60

description: Head RNA extracted 30' after Drosophila exposed for 30' to humidified air.

source_name: Air 60


title: Air 120

description: Head RNA extracted 90' after Drosophila exposed for 30' to humidified air.

source_name: Air 120


title: Air 240

description: Head RNA extracted 210' after Drosophila exposed for 30' to humidified air.

source_name: Air 240


title: Ethanol 240

description: Head RNA extracted 210' after Drosophila exposed for 30' to ethanol.

source_name: Ethanol 240


title: Air 30

description: Head RNA extracted 0' after Drosophila exposed for 30' to humidified air.

source_name: Air 30


title: Transfection Reagent Only Technical Replicate 3

status: Public on Dec 14 2009

city: London

first: Helen

last: Hurst

address: Charterhouse Square

department: Centre for Tumour Biology

country: United Kingdom

institute: Institute of Cancer

description: transfection reagent only

hyb_protocol: 15 ug of cRNA was hybridized for 16 hr at 45C to Human Genome U133 Plus 2.0 oligonucleotide arrays (as described at http://www.affymetrix.com/products/arrays/specific/hgu133plus.affx).  Arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneArray 3000 scanner.  Array images were assessed by eye to confirm scanner alignment, the absence of significant bubbles or scratches, and a low background.

data_processing: The data were pre-processed using the “affy” package in BioConductor: “mas5” background correction, “quantiles” normalisation (Bolstad et al. 2003), “pmonly” correction and “medianpolish” summarisation. The resulting log2 scale transformed data were imported into the Genespring package (Genespring GX 7.3, Agilent Technologies) and filtered to retain the 2500 probe sets with the highest variance across all the arrays. Welch’s t-test was then applied in conjunction with a False Discovery Rate (FDR) multiple test correction to identify the most significantly regulated genes (p<0.01).

source_name: siRNA treated MCF-7 breast carcinoma cell line

label_protocol: Total RNA (8ug) from each sample was used to prepare biotinylated target RNA, using the One Cycle Target Labelling kit (Invitrogen) according to the manufacturer’s recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

growth_protocol: MCF-7 cells were cultured in DMEM, 10% FCS; plus insulin (10ug/ml).

extract_protocol: Total RNA was extracted using Trizol (Sigma) following the standard protocol but including a Qiagen RNAeasy Mini column (with RNAse free DNAse step) for clean up and elution.

treatment_protocol: Cells were transfected (using Oligofectamine; Invitrogen) with 25nM siRNA targetting AP-2gamma or non-silencing control siRNA or no siRNA (transfection reagent only).

tag: protocol

value: Transfection Reagent

tag: cell line


title: Non-silencing control siRNA: AAUUCUCCGAACGUGUCACGU Technical Replicate 1

description: non silencing control

value: Non-silencing control siRNA


title: AP-2 gamma targetting siRNA 2: GCGGCCCAGCAACUGUGUAAA Technical Replicate 2

description: AP-2 gamma silenced

value: AP-2 gamma targetting siRNA 2


title: Non-silencing control siRNA: AAUUCUCCGAACGUGUCACGU Technical Replicate 2

description: non silencing control


title: AP-2 gamma targetting siRNA 3: CCACACUGGAGUCGCCGAAUA Technical Replicate 3

description: AP-2 gamma silenced

value: AP-2 gamma targetting siRNA 3


title: AP-2 gamma targetting siRNA 2: GCGGCCCAGCAACUGUGUAAA Technical Replicate 1

description: AP-2 gamma silenced


title: AP-2 gamma targetting siRNA 3: CCACACUGGAGUCGCCGAAUA Technical Replicate 2

description: AP-2 gamma silenced


title: AP-2 gamma targetting siRNA 1: AAUGAGAUGGCAGCUAGGAAG Technical Replicate 2

description: AP-2 gamma silenced

value: AP-2 gamma targetting siRNA 1


title: AP-2 gamma targetting siRNA 3: CCACACUGGAGUCGCCGAAUA Technical Replicate 1

description: AP-2 gamma silenced


title: AP-2 gamma targetting siRNA 1: AAUGAGAUGGCAGCUAGGAAG Technical Replicate 3

description: AP-2 gamma silenced


title: Non-silencing control siRNA: AAUUCUCCGAACGUGUCACGU Technical Replicate 3

description: non silencing control


title: IV-9

status: Public on Dec 11 2009

first: J.

last: Verkerk

address: Molewaterplein 50

department: Bioinformatics

institute: Erasmus Medical Center

description: no further description

hyb_protocol: The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).

scan_protocol: Fluorescence intensities were captured with an argonion laser confocal scanner.

data_processing:
Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.

label: Biotin

source_name: skin fibroblasts

label_protocol: Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.

extract_protocol: Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.

value: skin

tag: cell type

value: fibroblasts


title: AP-2 gamma targetting siRNA 2: GCGGCCCAGCAACUGUGUAAA Technical Replicate 3

description: AP-2 gamma silenced


title: Transfection Reagent Only Technical Replicate 2

description: transfection reagent only


title: AP-2 gamma targetting siRNA 1: AAUGAGAUGGCAGCUAGGAAG Technical Replicate 1

description: AP-2 gamma silenced


title: IV_5

description: no further description


title: IV_2

description: no further description

value: female


title: Transfection Reagent Only Technical Replicate 1

description: transfection reagent only


title: IV_6

description: no further description

value: male


title: penta mutant, biological rep1 (higher order mutant)

source_name: 10-day old, light grown seedlings


title: Female Control

description: no further description


title: IV_1

description: no further description

data_processing:
Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software

label_protocol: Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides


title: Male Control

description: no further description


title: IV_3

description: no further description


title: IV_4

description: no further description


title: Marco_3-4_Pip3-3HA-9_Rep1_ATH1_2

status: Public on Dec 10 2009

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

description: 20 min with a 12% sodium hypochlorite solution, washed several times with sterile water.  Seeds were sown on MS medium (Murashige and Skoog 1962). Plantlets grown for 8 days at 20C in a growth chamber.  8% agarose. Autoclave 125C 30 min. 1.5/cm2. 20 C average, 20 C day, 20 C night. 100 % average, 100 % day, 100 % night. Murashige & Skoog basal salt mixture.

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_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

extract_protocol: Qiagen RNAeasy kit protocol

tag: developmental stage

value: whole plant

tag: genetic background

tag: genetic variation

value: T-DNA knock out mutation in At2g19270


title: Marco_3-2_Nd-1_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

tag: ecotype

tag: genotype

value: wild type


title: Marco_3-1_Col-0_Rep1_ATH1


title: Marco_3-6_Pip3-3HA6H-5_Rep1_ATH1


title: Marco_3-5_Pip3-3HA6H-1_Rep1_ATH1


title: Marco_3-10_Col-0-2_Rep2_ATH1


title: Marco_3-3_Pip3-3HA-1_Rep1_ATH1


title: Marco_3-8_pGli-69-24_Rep1_ATH1

value: RNAi knock out mutation in At2g19270


title: Marco_3-9_KO-Pip3_Rep1_ATH1

tag: stock code


title: Marco_3-13_Pip3-3HA-9-2_Rep2_ATH1


title: Marco_3-16_pGli-69-31-2_Rep2_ATH1


title: Marco_3-11_Nd-1-2_Rep2_ATH1


title: Marco_3-12_Pip3-3HA-1-2_Rep2_ATH1


title: Marco_3-19_Col-0-3_Rep3_ATH1


title: Marco_3-15_Pip3-3HA6H-5-2_Rep2_ATH1


title: Marco_3-14_Pip3-3HA6H-1-2_Rep2_ATH1


title: Marco_3-24_Pip3-3HA6H-5-3_Rep3_ATH1


title: Marco_3-21_Pip3-3HA-1-3_Rep3_ATH1


title: Marco_3-25_pGli-69-31-3_Rep3_ATH1


title: Marco_3-22_Pip3-3HA-9-3_Rep3_ATH1


title: Marco_3-17_pGli-69-24-2_Rep2_ATH1


title: Marco_3-23_Pip3-3HA6H-1-3_Rep3_ATH1


title: Marco_3-20_Nd-1-3_Rep3_ATH1


title: Marco_3-18_KO-Pip3-2_Rep2_ATH1


title: Robertson_1-67_toc1-1-73hr_Rep2_ATH1

description: The seeds were stratified at 4C for 48 hours in darkness.  Seeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.  150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.  Seedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.  Autoclaved.  20 seedlings clumped together. 19 C average, 19 C day, 19 C night. 50 % average, 50 % day, 50 % night. Murashige & Skoog basal salt mixture. Constant light.

value: seedlings, aerial tissue

value: EMS-induced mutation in At5g61380

value: toc1 mutant

tag: treatment

tag: time


title: Robertson_1-70_toc1-1-85hr_Rep2_ATH1

description: The seeds were stratified at 4C for 48 hours in darkness.  Seeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.  150-200 Seeds were plated in 10 clusters (app 20 seeds per cluster) on 1/2 MS 0.8% agar plates.  Seedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s. Autoclaved.  20 seedlings clumped together. 19 C average, 19 C day, 19 C night. 50 % average, 50 % day, 50 % night. Murashige & Skoog basal salt mixture. Constant light.


title: Robertson_1-62_toc1-1-53hr_Rep2_ATH1


title: Robertson_1-66_toc1-1-69hr_Rep2_ATH1


title: Robertson_1-65_toc1-1-65hr_Rep2_ATH1


title: Robertson_1-72_toc1-1_93hr_Rep2_ATH1


title: Robertson_1-64_toc1-1-61hr_Rep2_ATH1


title: Robertson_1-71_toc1-1-89hr_Rep2_ATH1


title: Marco_3-27_KO-Pip3-3_Rep3_ATH1


title: Robertson_1-63_toc1-1-57hr_Rep2_ATH1


title: Robertson_1-69_toc1-1-81hr_Rep2_ATH1


title: Robertson_1-61_toc1-1-49hr_Rep2_ATH1


title: Robertson_1-55_Nicotinamide-treated-73hr_Rep2_ATH1

description: The seeds were stratified at 4C for 48 hours in darkness.  Seeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.  70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.  Seedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s. Autoclaved.  20 seedlings clumped together. 19 C average, 19 C day, 19 C night. 50 % average, 50 % day, 50 % night. Murashige & Skoog basal salt mixture. Constant light.

source_name: C24, nicotinamide, 73hr

value: nicotinamide


title: Robertson_1-58_Nicotinamide-treated-85hr_Rep2_ATH1

source_name: C24, nicotinamide, 85hr


title: Robertson_1-37_WT-untreated-49hr_Rep2_ATH1

source_name: C24, untreated, 49hr


title: Robertson_1-57_Nicotinamide-treated-81hr_Rep2_ATH1

source_name: C24, nicotinamide, 81hr


title: Robertson_1-56_Nicotinamide-treated-77hr_Rep2_ATH1

source_name: C24, nicotinamide, 77hr


title: Robertson_1-38_WT-untreated-53hr_Rep2_ATH1

source_name: C24, untreated, 53hr


title: Robertson_1-41_WT-untreated-65hr_Rep2_ATH1

source_name: C24, untreated, 65hr


title: Robertson_1-60_Nicotinamide-treated-93hr_Rep2_ATH1

source_name: C24, nicotinamide, 93hr


title: Robertson_1-43_WT-untreated-73hr_Rep2_ATH1

source_name: C24, untreated, 73hr


title: Robertson_1-42_WT-untreated-69hr_Rep2_ATH1

source_name: C24, untreated, 69hr


title: Robertson_1-68_toc1-1-77hr_Rep2_ATH1


title: Robertson_1-39_WT-untreated-57hr_Rep2_ATH1

source_name: C24, untreated, 57hr


title: Robertson_1-44_WT-untreated-77hr_Rep2_ATH1

source_name: C24, untreated, 77hr


title: Marco_3-26_pGli-69-24-3_Rep3_ATH1


title: Robertson_1-40_WT-untreated-61hr_Rep2_ATH1

source_name: C24, untreated, 61hr


title: Robertson_1-59_Nicotinamide-treated-89hr_Rep2_ATH1

source_name: C24, nicotinamide, 89hr


title: Ethanol 90

description: Head RNA extracted 60' after Drosophila exposed for 30' to ethanol.

source_name: Ethanol 90

value: head

value: Ethanol


title: Robertson_1-47_WT-untreated-89hr_Rep2_ATH1

source_name: C24, untreated, 89hr


title: Robertson_1-50_Nicotinamide-treated-53hr_Rep2_ATH1

source_name: C24, nicotinamide, 53hr


title: Robertson_1-17_Nicotinamide-treated-65hr_Rep1_ATH1_2

description: The seeds were stratified at 4C for 48 hours in darkness.  Seeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.  70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates. Seedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.  10-20 seeds clumped together. 19 C average, 19 C day, 19 C night. 50 % average, 50 % day, 50 % night. Murashige & Skoog basal salt mixture. 12 hour days, 12 hour nights.

source_name: C24, nicotinamide, 65hr

value: aerial tissue


title: Robertson_1-45_WT-untreated-81hr_Rep2_ATH1

source_name: C24, untreated, 81hr


title: Robertson_1-52_Nicotinamide-treated-61hr_Rep2_ATH1

source_name: C24, nicotinamide, 61hr


title: Robertson_1-36_toc1-1-93hr_Rep1_ATH1


title: Robertson_1-28_toc1-1-61hr_Rep1_ATH1


title: Robertson_1-46_WT-untreated-85hr_Rep2_ATH1

source_name: C24, untreated, 85hr


title: Robertson_1-53_Nicotinamide-treated-65hr_Rep2_ATH1_2


title: Robertson_1-24_Nicotinamide-treated-93hr_Rep1_ATH1


title: Robertson_1-25_toc1-1-49hr_Rep1_ATH1


title: Robertson_1-20_Nicotinamide-treated-77hr_Rep1_ATH1

source_name: C24, nicotinamide, 77hr


title: Robertson_1-27_toc1-1-57hr_Rep1_ATH1


title: Robertson_1-33_toc1-1-81hr_Rep1_ATH1


title: Robertson_1-31_toc1-1-73hr_Rep1_ATH1


title: Robertson_1-34_toc1-1-85hr_Rep1_ATH1


title: Robertson_1-29_toc1-1-65hr_Rep1_ATH1


title: Robertson_1-35_toc1-1-89hr_Rep1_ATH1


title: Robertson_1-51_Nicotinamide-treated-57hr_Rep2_ATH1

source_name: C24, nicotinamide, 57hr


title: Robertson_1-49_Nicotinamide-treated-49hr_Rep2_ATH1

source_name: C24, nicotinamide, 49hr


title: Robertson_1-32_toc1-1-77hr_Rep1_ATH1


title: Robertson_1-30_toc1-1-69hr_Rep1_ATH1


title: Robertson_1-54_Nicotinamide-treated-69hr_Rep2_ATH1

source_name: C24, nicotinamide, 69hr


title: Robertson_1-21_Nicotinamide-treated-81hr_Rep1_ATH1

source_name: C24, nicotinamide, 81hr


title: Robertson_1-48_WT-untreated-93hr_Rep2_ATH1

source_name: C24, untreated, 93hr


title: Robertson_1-22_Nicotinamide-treated-85hr_Rep1_ATH1

source_name: C24, nicotinamide, 85hr


title: Robertson_1-26_toc1-1-53hr_Rep1_ATH1


title: Robertson_1-23_Nicotinamide-treated-89hr_Rep1_ATH1


title: Marco_3-7_pGli-69-31_Rep1_ATH1_2


title: Robertson_1-7_WT-untreated-73hr_Rep1_ATH1

source_name: C24, untreated, 73hr


title: Robertson_1-13_Nicotinamide-treated-49hr_Rep1_ATH1_2


title: Robertson_1-3_WT-untreated-57hr_Rep1_ATH1

source_name: C24, untreated, 57hr


title: Robertson_1-18_Nicotinamide-treated-69hr_Rep1_ATH1


title: Robertson_1-12_WT-untreated-93hr_Rep1_ATH1


title: Robertson_1-15_Nicotinamide-treated-57hr_Rep1_ATH1


title: Robertson_1-6_WT-untreated-69hr_Rep1_ATH1

source_name: C24, untreated, 69hr


title: Robertson_1-19_Nicotinamide-treated-73hr_Rep1_ATH1

source_name: C24, nicotinamide, 73hr


title: Robertson_1-11_WT-untreated-89hr_Rep1_ATH1

source_name: C24, untreated, 89hr


title: Robertson_1-9_WT-untreated-81hr_Rep1_ATH1


title: Robertson_1-16_Nicotinamide-treated-61hr_Rep1_ATH1


title: Robertson_1-2_WT-untreated-53hr_Rep1_ATH1

source_name: C24, untreated, 53hr


title: Robertson_1-10_WT-untreated-85hr_Rep1_ATH1


title: Robertson_1-5_WT-untreated-65hr_Rep1_ATH1

source_name: C24, untreated, 65hr


title: Robertson_1-4_WT-untreated-61hr_Rep1_ATH1

source_name: C24, untreated, 61hr


title: Robertson_1-14_Nicotinamide-treated-53hr_Rep1_ATH1

source_name: C24, nicotinamide, 53hr


title: Robertson_1-8_WT-untreated-77hr_Rep1_ATH1

source_name: C24, untreated, 77hr


title: Song_1-9_Ler_8.9.10_Rep2_ATH1

description: Growth Room Commercial soil: a mixture of Levington M3 (The Scotts Company, UK), John Innes No.3 (E A Groundrey & Son Ltd. UK), vermiculite and perlite in the proportion 6:6:1:1

source_name: Glabra, PMII

growth_protocol: Plants were grown in growth rooms at 22h of daylight at 22 C and 2h of night at 22 C

value: wild-type control

value: anther and filament

value: pollen mitosis II (PMII)


title: Song_1-3_Ler_8.9.10_Rep1_ATH1


title: Song_1-6_MS35_8.9.10_Rep1_ATH1

source_name: ms35, PMII

value: ms35 mutant


title: Song_1-8_Ler_6.7_Rep2_ATH1

source_name: Glabra, bicellular

value: bicellular


title: Song_1-1_Ler_3.4.5_Rep1_ATH1

source_name: Glabra, PMI

value: pollen mitosis I (PMI)


title: Song_1-12_MS35_8.9.10_Rep2_ATH1


title: Song_1-2_Ler_6.7_Rep1_ATH1


title: Robertson_1-1_WT-untreated-49hr_Rep1_ATH1

description: The seeds were stratified at 4C for 48 hours in darkness.  Seeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times.  70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates.  Seedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s.  10-20 seeds clumped together. 19 C average, 19 C day, 19 C night. 50 % average, 50 % day, 50 % night. Murashige & Skoog basal salt mixture. 12 hour days, 12 hour nights.

source_name: C24, untreated, 49hr


title: Song_1-10_MS35_3.4.5_Rep2_ATH1

source_name: ms35, PMI


title: Song_1-5_MS35_6.7_Rep1_ATH1

source_name: ms35, bicellular


title: Song_1-4_MS35_3.4.5_Rep1_ATH1


title: Song_1-7_Ler_3.4.5_Rep2_ATH1


title: Brownfield_1-18_24hr-induced_Rep3_ATH1

description: 3 days at 4C on agar plate. 70% Ethanol/0.05% Tritin X-100 for 5 min. 100% Ethanol for 10 min. Air dry before plating Phytagar Growth room 22C 95% Murashige & Skoog basal salt mixture.

source_name: pMDC7DUO1, induced, 24hr

growth_protocol: Seeds were sterilized by washing for 5 min with 70% (w/v) ethanol/0.05% (w/v) triton-X 100 and then 10 min with 100% ethanol. Approximately 200 dry seeds were then spread on a 14cm Petri dish containing 1 X Murashige and Skoog basal salts, 0.8% phytagar and 20 ug/ml hyromycin with no carbon source. Plates were placed at 4C for 3 days then plants grown under constant light at 22C for 12 days before treatment began.

value: whole plant

value: T-DNA mutation

tag: duo1 induction

value: yes


title: Brownfield_1-10_12hr-induced_Rep1_ATH1

source_name: pMDC7DUO1, induced, 12hr


title: Brownfield_1-13_24hr-not-induced_Rep1_ATH1

source_name: pMDC7DUO1, not induced, 24hr

value: no


title: Brownfield_1-16_24hr-induced_Rep1_ATH1


title: Brownfield_1-15_24hr-not-induced_Rep3_ATH1


title: Brownfield_1-12_12hr-induced_Rep3_ATH1


title: Brownfield_1-17_24hr-induced_Rep2_ATH1


title: Brownfield_1-8_12hr-not-induced_Rep2_ATH1

source_name: pMDC7DUO1, not induced, 12hr


title: Brownfield_1-11_12hr-induced_Rep2_ATH1


title: Brownfield_1-9_12hr-not-induced_Rep3_ATH1


title: Brownfield_1-5_6hr-induced_Rep2_ATH1

source_name: pMDC7DUO1, induced, 6hr


title: Brownfield_1-4_6hr-induced_Rep1_ATH1


title: Brownfield_1-7_12hr-not-induced_Rep1_ATH1


title: Brownfield_1-14_24hr-not-induced_Rep2_ATH1


title: Brownfield_1-6_6hr-induced_Rep3_ATH1


title: Brownfield_1-3_6hr-not-induced_Rep3_ATH1

source_name: pMDC7DUO1, not induced, 6hr


title: Brownfield_1-2_6hr-not-induced_Rep2_ATH1


title: Brownfield_1-1_6hr-not-induced_Rep1_ATH1


title: Truman_2-22_12h-hrpA_Rep3_ATH1

description: Growth Room Levingtons F2 compost (Fisons, Ipswich, UK). 2 days in fridge at 4oC.

source_name: Col-5, hrpA, 12hr

growth_protocol: A. thaliana was sown in Levingtons F2 compost and vernalised for 2 days at 4C. Plants were grown under short day conditions in a controlled environment chamber (10 h light, 100?150 microEinsteins at 22C day, 20C night) for 4-5 weeks before use.

tag: strain

value: leaves

tag: p. syringae pv tomato strain

value: DC3000 hrpA mutant


title: Truman_2-23_12h-DC3000_Rep3_ATH1

source_name: Col-5, wildtype, 12hr

tag: tissue

value: DC3000 wildtype


title: Truman_2-25_21h-hrpA_Rep3_ATH1

source_name: Col-5, hrpA, 21hr


title: Truman_2-27_21h-avrRpm1_Rep3_ATH1

source_name: Col-5, avrRpm1, 21hr

value: DC3000 carrying avrRpm1


title: Truman_2-20_8h-DC3000_Rep3_ATH1

source_name: Col-5, wildtype, 8hr


title: Truman_2-21_8h-avrRpm1_Rep3_ATH1

source_name: Col-5, avrRpm1, 8hr


title: Truman_2-26_21h-DC3000_Rep3_ATH1

source_name: Col-5, wildtype, 21hr


title: Truman_2-19_8h-hrpA_Rep3_ATH1

source_name: Col-5, hrpA, 8hr


title: Truman_2-24_12h-avrRpm1_Rep3_ATH1

source_name: Col-5, avrRpm1, 12hr


title: U937 cells infected with empty pSICO-R vector - Replica 2

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: U937 is a human cell line established from a diffuse histiocytic lymphoma and displaying monocytic characteristics.

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

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

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

source_name: U937 myelomonocytic cell line, control

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

growth_protocol: U937 cell lines were maintained in RPMI-1640 supplemented with 10% FCS and 2mM glutamine at 37°C in a humidified atmosphere containing 5% CO2.

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

tag: pir knock-down


title: Truman_2-15_12h-avrRpm1_Rep2_ATH1


title: Truman_2-17_21h-DC3000_Rep2_ATH1


title: Truman_2-16_21h-hrpA_Rep2_ATH1


title: Truman_2-14_12h-DC3000_Rep2_ATH1


title: U937 cells with knock-down of Pirin - Replica 2

source_name: U937 myelomonocytic cell line, PIR knock-down


title: primary sc preadipocytes.48h CNTRL.replicate 1

city: Calgary

first: Robert

last: Haché

state: Alberta

address: 2500 University Drive NW

country: Canada

institute: University of Calgary

description: gene expression data from primary preadipocytes treated with vehicle (EtOH) for 48 hours

hyb_protocol: Samples were processed and hybridized accoring to the standard small sample protocol from Affymetrix (Expression Analysis Technical Manual, 2001, Affymetrix)

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

data_processing: Normalized expression data has been produced by Robust Multichip Average (RMA) using the software ArrayAssist from Stratagene (originally Iobion).  Log2 expression values are automatically unlogged by this software.

source_name: Primary preadipocytes; vehicle control (EtOH) - 48 hours

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

growth_protocol: Human subcutaneous primary preadipocytes were purchased from Zen-Bio Inc.  Preadipocytes from 5 female donors (average BMI 22.5±0.2kg/m2) were pooled prior to the initial seeding in Nunc brand T75 flasks.  Cells were maintained at 5% CO2 in DMEM with 1.0g/L glucose, 20% calf serum, 100U/ml penicillin, 100mg/ml streptomycin and 50U/ml nystatin.  Media was replaced every 2 days.  Cells were expanded once (1:2 dilution) prior to seeding in Nunc-brand 12-well dishes at which point they were allowed to reach confluence (occurred within 24h) and were treated as described.

extract_protocol: RNA was extracted using the Qiagen Rneasy Mini Kit as per manufacturer's instuctions.  For each sample, 3 wells of the 12-well dish were pooled.  The quality of the samples was verified using the Agilent  Bioanalyzer 2100 (Nano Chips).

treatment_protocol: Confluent preadipocytes (12-well dish) were stimulated with vehicle (EtOH) or 1uM dex for 48 hours in growth media (above) containing 3% calf serum.

value: Cultured primary preadipocytes


title: primary sc preadipocytes.48h CNTRL.replicate 2


title: primary sc preadipocytes.48h DEX.replicate 2

description: gene expression data from primary preadipocytes treated with 1uM DEX for 48 hours

source_name: Primary preadipocytes; DEX treated (1uM) - 48 hours


title: Truman_2-13_12h-hrpA_Rep2_ATH1


title: Truman_2-18_21h-avrRpm1_Rep2_ATH1


title: primary sc preadipocytes.48h DEX.replicate 1


title: Truman_2-12_8h-avrRpm1_Rep2_ATH1


title: U937 cells infected with empty pSICO-R vector - Replica 1


title: U937 cells with knock-down of Pirin - Replica 1


title: NPC_5-8F_rep1 (U133 Plus 2.0 Array)

city: Guangzhou

first: Zhong-Xi

last: Huang

address: Tonghe

department: Cancer Institute

country: China

institute: Southern Medical University

description:
gene expression analysis
Cells are cultured and harvested at two different time points. Thus it is biological repeats.

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

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

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

source_name: Nasopharyngeal carcinoma cell line 5-8F

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

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

value: nasopharyngeal carcinoma cell line 5-8F

tag: biological replicate


title: NPC_6-10B_rep3 (U133 Plus 2.0 Array)

description:
gene expression analysis
Cells are cultured and harvested at three different time points. Thus it is biological repeats.

source_name: Nasopharyngeal carcinoma cell line 6-10B

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

value: nasopharyngeal carcinoma cell line 6-10B


title: NPC_5-8F_rep2 (U133 Plus 2.0 Array)


title: NPC_6-10B_rep2 (U133 Plus 2.0 Array)


title: NPC_6-10B_rep1 (U133 Plus 2.0 Array)


title: Truman_2-11_8h-DC3000_Rep2_ATH1


title: NPC_5-8F (U133 Plus 2.0 Array)

description: gene expression analysis


title: Song_1-11_MS35_6.7_Rep2_ATH1

source_name: ms35, bicellular


title: Truman_2-6_12h-avrRpm1_Rep1_ATH1


title: Truman_2-9_21h-avrRpm1_Rep1_ATH1


title: Truman_2-4_12h-hrpA_Rep1_ATH1


title: Truman_2-10_8h-hrpA_Rep2_ATH1


title: Truman_2-3_8h-avrRpm1_Rep1_ATH1


title: Truman_2-2_8h-DC3000_Rep1_ATH1


title: Truman_2-1_8h-hrpA_Rep1_ATH1


title: Truman_2-5_12h-DC3000_Rep1_ATH1


title: Edwards_4-15_cca1-lhy30m_Rep2_ATH1

description: 4 days at 4degC in dark (on Murashige-Skoog media containing 2% Agar and 3% Sucrose). 1-2 minutes in 70% Ethanol. 8 mins 50% bleach. 3 rinses in sterile distilled water. Growth chamber Agar Murashige and Skoog (4.4g per Litre). All seedlings on sample plate were harvested into RNAlater. They were homogenized using a mixer mill in RLT buffer and RNA was extracted using Qiagen RNeasy plant kits.

growth_protocol: Seedlings were grown for 9 days at 22degC on MS media in sealed petri-dishes under 18h:6h Light:Dark cycles of 60-65 uEINSTEINS cool white fluorescent light. Samples were taken at time intervals relative to time zero at dawn on the 9th day of growth.

value: whole seedlings

value: Wassilewskija

value: T-DNA gene knock out


title: CD14+ after 2 wk quercetin supplementation, biological replicate 1

city: Kiel

first: Frank

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

country: Germany

institute: Christian-Albrechts-University Kiel

description: gene expression data from peripheral blood mononuclear cells (PBMC) isolated from (fasting) blood samples before and after a 2 wk supplementation of 150mg quercetin per day

hyb_protocol: Human Genome U133+ 2.0 GeneChip® microarrays were hybridized for 16h at 45°C with 15µg fragmented, biotin-labeled cRNA. Arrays were washed and stained using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and the Fluidics Station 450 (FS450_0004 script) .

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The data was analysed with Bioconductor software package for R using the simpleaffy package (2.16.0-1) and normalisation method was gcrma (slow) with the gcrma package (2.12.1).

source_name: CD14+ monocytes, by positive selection

label_protocol: Biotinylated cRNA was prepared from 2µg total RNA with MessageAmp™ II-Biotin Enhanced Kit (Ambion).

extract_protocol: Total RNA isolation including an on-column DNA-digestion step was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: CD14+ monocytes were isolated by density centrifugation (LymphoPrep) and successive positive selection with magnetic beads (Miltenyi).

tag: female


title: Truman_2-8_21h-DC3000_Rep1_ATH1


title: Edwards_4-16_cca1-lhy60m_Rep2_ATH1


title: CD14+ after 2 wk quercetin supplementation, biological replicate 2

tag: male


title: CD14+ after 2 wk quercetin supplementation, biological replicate 3


title: CD14+ at baseline, biological replicate 2


title: Edwards_4-14_cca1-lhy15m_Rep2_ATH1


title: CD14+ at baseline, biological replicate 1


title: Truman_2-7_21h-hrpA_Rep1_ATH1


title: Edwards_4-13_cca1-lhy-15m_Rep2_ATH1


title: Edwards_4-11_cca1-lhy30m_Rep1_ATH1


title: Edwards_4-12_cca1-lhy60m_Rep1_ATH1


title: CD14+ at baseline, biological replicate 3


title: Edwards_4-8_WS60m_Rep2_ATH1

source_name: WS, +60min

value: wild type


title: Edwards_4-7_WS30m_Rep2_ATH1

source_name: WS, +30min


title: Edwards_4-9_cca1-lhy-15m_Rep1_ATH1


title: Edwards_4-6_WS15m_Rep2_ATH1

source_name: WS, +15min


title: Edwards_4-5_WS-15m_Rep2_ATH1

source_name: WS, -15min


title: Edwards_4-4_WS60m_Rep1_ATH1


title: Edwards_4-10_cca1-lhy15m_Rep1_ATH1


title: Edwards_4-3_WS30m_Rep1_ATH1


title: SNT-8 duplicate 1

status: Public on Dec 09 2009

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

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

department: Intractable Immune System Diseases Research Center

country: Japan

institute: Tokyo Medical University

description: nasal T cell lymphoma

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

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

source_name: Sample

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

extract_protocol: RNeasy kit

tag: Gamma-delta T cell line derived from patient with nasal T cell lymphoma


title: SKOV3 Cell line

status: Public on Dec 08 2009

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133_Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Probe set intensities were calculated using the Microarray Analysis Suite (MAS v5.0, Affymetrix). Data analysis and exploration of probe set intensities levels were performed using Bioconductor open source (http://www.bioconductor.org/) under the R software environment. The reading of probe level data, background correction, normalization by MAS5 “global scaling” procedure and summarizing the probe set values into one expression measure were performed using the affy package.

source_name: Cell line

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Quality of total RNA was first analyzed by Agilent Bioanalyzer 2100.

tag: cell line


title: OV1 Tumor

source_name: Tumor

tag: age at diagnosis

tag: histotype

value: serous

tag: grade


title: SNT-13 duplicate 2

description: chronic active Epstein-Barr virus (EBV) infection

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

tag: Gamma-delta T cell line derived from patient with chronic active EBV infection


title: SNT-8 duplicate 2

description: nasal T cell lymphoma


title: TM105 Tumor


title: normal gamma-delta T cell duplicate 2

description: Normal control

source_name: Control

growth_protocol: IL2 150 U/ml

treatment_protocol: ZOL 1 uM for 14 days

tag: Gamma-delta T cells obtained from a healthy voulenter.


title: 04 065 Tumor


title: SNT-15 duplicate 2


title: SNT-15 duplicate 1


title: Pool Ovarian surface epithelium cells

source_name: Ovarian surface epithelium cells

tag: cell type

value: Ovarian surface epithelium cells


title: OSE112 Ovarian surface epithelium cells


title: IGROV1 Cell line


title: OVCA432 Cell line


title: normal gamma-delta T cell duplicate 1

description: Normal control


title: OC23 Tumor


title: OVCAR3 Cell line


title: CABA Cell line

value: CABA


title: SNT-13 duplicate 1


title: OAW42 Cell line


title: Edwards_4-2_WS15m_Rep1_ATH1

tag: developmental stage

tag: stock code

tag: genotype

tag: time


title: Edwards_4-1_WS-15m_Rep1_ATH1

tag: tissue


title: TM0116 Tumor


title: 04 007 Tumor


title: 02 024 Tumor


title: 02 035 Tumor

value: mullerian


title: OC26 Tumor


title: 271TC Tumor


title: 273PE Tumor


title: 02 039 Tumor


title: 116TM Tumor


title: 05 022 Tumor

value: mixed


title: 129LC Tumor


title: TMO110 Tumor


title: 118BML Tumor


title: 138PI Tumor


title: 132DM Tumor

value: undiff


title: mock-infected, biological rep1

city: Orange

first: Philip

middle: Hitchins

last: Schwartz

address: 455 South Main Street

department: Research Institute

institute: Children's Hospital of Orange County

description: Gene expression data from mock-infected cells

hyb_protocol: Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450

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

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

source_name: Human neural stem cell culture

label_protocol: First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).

growth_protocol: Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]

extract_protocol: RNA was extracted using the SV Total RNA Isolation kit (Promega).

treatment_protocol: HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).

value: Post-mortem, fetal, human brain-derived neural stem cells

value: Normal

tag: age

value: no more than passage 15


title: 24 hours post-infection, biological rep2

description: Gene expression data from cells 24 hours after HCMV infection


title: 4 hours post-infection, biological rep2

description: Gene expression data from cells 4 hours after HCMV infection


title: Lopez-Juez_1-16_Cotyledons-6hr-light_Rep2_ATH1

status: Public on Dec 05 2009

description: Imbibed (after sterilisation) in 0.1% agar for 3 days at 4 C in the dark. With ethanol, then dilute bleach, then rinses with sterile water. Growth chamber Agar 50-80 Murashige and Skoog basal salt mixture MES, pH 5.7

source_name: Landsberg erecta, cotyledon, 6hr light

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were transferred back to white light for 6 h before harvesting.

extract_protocol: Seedlings were immersed in RNAlater (Ambion) for 1 h (the harvesting and immersion being under green safelight), and stored at 4°C. Within one week seedlings were dissected on a chilled platform under a stereomicroscope, by slicing below the meristem and at the base of each cotyledon ('meristem' or M samples) or near the base and tip of each cotyledon ('cotyledon' or C samples), before flash-freezing and storing at -80°C. Only one tissue was obtained per seedling and the number of seedlings per sample ranged from ca.1500 (72 h samples) to over 4000 (0 h samples). Each sample contained material from multiple plates and several separate experiments. RNA was extracted using an RiboPure kit (Ambion), essentially according to manufacturer's instructions.

tag: strain

value: Landsberg erecta

value: Cotyledon, with both the cotyledon petiole and the cotyledon tip removed

tag: treatment

value: 6hr light


title: 12 hours post-infection, biological rep1

description: Gene expression data from cells 12 hours after HCMV infection


title: mock-infected, biological rep2


title: 121FM Tumor


title: 24 hours post-infection, biological rep1


title: 12 hours post-infection, biological rep2


title: 4 hours post-infection, biological rep1


title: Lopez-Juez_1-14_Cotyledons-1hr-light_Rep2_ATH1

source_name: Landsberg erecta, cotyledon, 1hr light

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were transferred back to white light for 1 h before harvesting.

value: 1hr light


title: Lopez-Juez_1-15_Cotyledons-6hr-light_Rep1_ATH1


title: Lopez-Juez_1-13_Cotyledons-1hr-light_Rep1_ATH1


title: CD16- 1

status: Public on Dec 07 2009

city: Gauting

first: Loems

last: Ziegler-Heitbrock

address: Robert-Koch Allee 29

department: Asklepios-Fachklinik and Helmholtz Zentrum München

institute: German Research Center for Environmental Health

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: All arrays were analysed with ArrayAssist (Stratagene). We used GC-RMA, and then in conjunction with MAS5 analysis to determine present or absent genes we compared the two subsets within each species (eg: we compared human CD16- and CD16+ monocytes) using an unpaired T test with asymptotic P value computation and Benjamini-Hochburg correction.

source_name: human CD16- monocytes

label_protocol: Per human monocyte sample, 1 µg total RNA was processed using Ambions MessageAmp II Biotin Enhanced labeling kit according to the manufacterers instruction.

extract_protocol: Three to four x 10^6 cells per sample were lysed with TRI-reagent (Sigma) and stored at -80°C.  Ten µg linear acrylamide (Ambion) was added to lysates and RNA was isolated by phenol/chloroform extraction and precipitation.

tag: monocyte subsets

value: CD16- monocytes


title: CD16+ 3

source_name: human CD16+ monocytes

value: CD16+ monocytes


title: CD16- 3


title: CD16+ 2


title: CD16- 2


title: Lopez-Juez_1-12_Cotyledons-dark_Rep2_ATH1

source_name: Landsberg erecta, cotyledon, dark

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were harvested.

value: dark


title: Lopez-Juez_1-9_Shoot-apex-48hr-light_Rep1_ATH1

source_name: Landsberg erecta, shoot apex, 48hr light

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were transfered back to white light for 48 h before harvesting.

value: shoot apical meristem region and developing leaf primordia

value: 48 light


title: Lopez-Juez_1-6_Shoot-apex-6hr-light_Rep1_ATH1

source_name: Landsberg erecta, shoot apex, 6hr light

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were transfered back to white light for 6 h before harvesting.

value: shoot apical meristem region


title: Lopez-Juez_1-1_Shoot-apex-dark_Rep1_ATH1

source_name: Landsberg erecta, shoot apex, dark

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time the seedlings were harvested under a green safelight.


title: Lopez-Juez_1-7_Shoot-apex-6hr-light_Rep2_ATH1


title: Lopez-Juez_1-2_Shoot-apex-dark_Rep2_ATH1


title: Weise_1-12_Sex1-3_Rep3_ATH1

description: Growth chamber Levington F2 (Fine peat/with intercept an insecticide) with extra grit 4mm at 40%. 75% 20oC. Three leaves from 8 different plants of each genotype were harvested using a green safe lamp 0.5 hours before the lights came on in the morning and immediately frozen in LN2.

growth_protocol: Plants were sewn in flats of modified commercial soil and grown in a growth chamber with a 12 hour photoperiod, quantum flux of 100 micromol m-2s-1, relative humidity was at least 75%, and a constant temperature of 20 degrees Celsius

extract_protocol: Leaf material was powered using a mortar and pestle and RNA was extracted using a Purescript RNA isolation kit (Gentra Systems, MN, USA)according to kit directions. Samples were then treated with DNaseI (Invitrogen, CA, USA) according to manufactures directions

value: sex1-3 mutation

value: leaves

tag: genetic background

tag: genetic variation


title: CD16+ 1


title: Lopez-Juez_1-5_Shoot-apex-2hr-light_Rep1_ATH1

source_name: Landsberg erecta, shoot apex, 2hr light

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were transfered back to white light for 2 h before harvesting.

value: 2hr light


title: Lopez-Juez_1-3_Shoot-apex-1hr-light_Rep1_ATH1

source_name: Landsberg erecta, shoot apex, 1hr light

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were transfered back to white light for 1 h before harvesting.


title: Lopez-Juez_1-11_Cotyledons-dark_Rep1_ATH1


title: Lopez-Juez_1-4_Shoot-apex-1hr-light_Rep2_ATH1


title: Lopez-Juez_1-8_Shoot-apex-24hr-light_Rep1_ATH1

source_name: Landsberg erecta, shoot apex, 24hr light

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were transfered back to white light for 24 h before harvesting.

value: 24hr light


title: Weise_1-11_Sex1-3_Rep2_ATH1


title: Weise_1-6_ptpks_Rep3_ATH1

value: ptpkis2 mutation


title: Weise_1-7_Sex4-3_Rep1_ATH1

value: sex4-3 mutation


title: Weise_1-4_ptpks_Rep1_ATH1


title: Weise_1-9_Sex4-3_Rep3_ATH1


title: Weise_1-8_Sex4-3_Rep2_ATH1


title: Weise_1-3_Col-WT_Rep3_ATH1

value: wild type


title: Weise_1-10_Sex1-3_Rep1_ATH1


title: Weise_1-5_ptpks_Rep2_ATH1


title: Weise_1-1_Col-WT_Rep1_ATH1


title: Foreman_1-13_L16-4hrs_Rep2_ATH1

description: Seeds were suspended in water and individually pipetted onto the soil surface. Trays were stratified at 4C in the dark for 5 days. Commercial Soil: 3 parts Levington's F2 soil, 1 part sand. Growth room 16C 50%

source_name: Ler, 16C

growth_protocol: Seedlings were grown on soil at 16C for 11 days, then transferred to 22C for 21 days.

value: whole plant excluding roots


title: Foreman_1-16_B16-10hrs_Rep2_ATH1

source_name: phyB-1, 16C


title: Foreman_1-14_L16-10hrs_Rep2_ATH1


title: Foreman_1-10_L22-10hrs_Rep2_ATH1

source_name: Ler, 22C


title: Foreman_1-9_L22-4hrs_Rep2_ATH1


title: Foreman_1-15_B16-4hrs_Rep2_ATH1


title: Foreman_1-12_B22-10hrs_Rep2_ATH1

source_name: phyB-1, 22C


title: Foreman_1-6_L16-10hrs_Rep1_ATH1


title: Foreman_1-5_L16-4hrs_Rep1_ATH1


title: Foreman_1-7_B16-4hrs_Rep1_ATH1


title: Foreman_1-8_B16-10hrs_Rep1_ATH1


title: Yun_1-15_sid2-treated-avrB-6h_Rep1_ATH1

status: Public on Dec 04 2009

description: Growth Room 20'C

source_name: sid2, avrB

growth_protocol: The seeds were germinated on commercial compost. The plants were grown in a growth room with a temperature of 20C and a relative humidity of 65%. The photoperiod was 18 h of light and 6 h of dark

value: 4 weeks old

value: leaf tissue

value: avrB


title: Yun_1-14_atgsnor1-3-treated-avrB-6h_Rep2_ATH1

description: Growth Room 20'C

source_name: atgsnor1-3, avrB


title: Foreman_1-1_L22-4hrs_Rep1_ATH1


title: Yun_1-9_Col-0-treated-avrB-6h_Rep1_ATH1

description: Growth Room 20'C

source_name: Col-0, avrB


title: Yun_1-16_sid2-treated-avrB-6h_Rep1_Rep2_ATH1

description: Growth Room 20'C


title: Foreman_1-4_B22-10hrs_Rep1_ATH1


title: Foreman_1-11_B22-4hrs_Rep2_ATH1


title: Yun_1-10_Col-0-treated-avrB-6h_Rep2_ATH1

description: Growth Room 20'C


title: Foreman_1-3_B22-4hrs_Rep1_ATH1


title: Yun_1-12_atgsnor1-1-treated-avrB-6h_Rep2_ATH1

description: Growth Room 20'C

source_name: atgsnor1-1, avrB


title: Foreman_1-2_L22-10hrs_Rep1_ATH1


title: Yun_1-11_atgsnor1-1-treated-avrB-6h_Rep1_ATH1

description: Growth Room 20'C


title: Yun_1-7_sid2-untreated-control_Rep1_ATH1

description: Growth Room 20'C

source_name: sid2, untreated

value: untreated


title: Yun_1-13_atgsnor1-3-treated-avrB-6h_Rep1_ATH1

description: Growth Room 20'C


title: Yun_1-4_atgsnor1-1-untreated-control_Rep2_ATH1

description: Growth Room 20'C

source_name: atgsnor1-1, untreated


title: Yun_1-8_sid2-untreated-control_Rep2_ATH1

description: Growth Room 20'C


title: Yun_1-3_atgsnor1-1-untreated-control_Rep1_ATH1

description: Growth Room 20'C


title: Yun_1-2_Col-0-untreated-control_Rep2_ATH1

description: Growth Room 20'C

source_name: Col-0, untreated


title: Yun_1-5_atgsnor1-3-untreated-control_Rep1_ATH1

description: Growth Room 20'C

source_name: atgsnor1-3, untreated


title: Yun_1-1_Col-0-untreated-control_Rep1_ATH1

description: Growth Room 20'C


title: sample 7a zero 33--1, biological rep2, technical rep1

city: Bethesda

first: Jung

middle: S

last: Byun

state: MD

address: 37 convent drive, Bldg 37,  Rm 1042

institute: NCI/NIH

description: Mitogen stimulated Jurkat T-cells were harvest at 0, 30 min, 1hr, 2hr, 4hr, and 6hr and RNA was collected.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 plus 2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: Jurkat T-cells were harvest at 0

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion MessageAmp II Biotin-enhanced protocol from 1 ug total RNA (Message Amp II Biotin-Enhanced Technical Manual, 2006, Ambion).

growth_protocol: Jurkat Cells were treated with P/I for 45 min.

extract_protocol: Human promoter microarray from NimbleGen Systems, Inc., was co-hybridized with either antibody precipitated and total imput control or an IgG-precipitated sample with the total imput control.

tag: Jurkat T-cells were harvest at 0


title: sample 3b 1hr 32--4, technical rep2

source_name: Jurkat T-cells were harvest at 1hr

tag: Jurkat T-cells were harvest at 1hr


title: sample 1B zero 32--2, technical rep2


title: sample 9b 1hr 33--4, biological rep2, technical rep2