title: Breast cancer cell line HCC1403

value: Unknown


title: T00333360

status: Public on Aug 17 2010

type: RNA

city: Seattle

first: Changkyu

last: Lee

state: WA

address: 551 N 34th St

country: USA

institute: Allen Institute for Brain Science

description: sample barcode: T00333360

hyb_protocol: Samples were applied to CodeLink Mouse Whole Genome Bioarrays (formerly supplied by GE Healthcare, Piscataway, NJ; now supplied by Applied Microarrays, Inc, Tempe, AZ) in hybridization buffer. Arrays were hybridized (37°C for 18 h) in a shaking incubator, washed in 0.75X Tris-buffered saline (pH 7.6) at 46°C for 1 h, and stained with Cy5-Streptavidin dye conjugate for 30 min.

scan_protocol: Rinsed and dried arrays were scanned with a GenePixTM 4000B scanner [Molecular Devices, (formerly Axon Instruments), Sunnyvale, CA] at 5 µm resolution.

data_processing: Codelink Expression Analysis software (Applied Microarrays, Inc, Tempe, AZ) was used for gridding and feature intensity extraction from the scanned array images. quantile normalization followed by COMBAT

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Following the second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP. Purified cRNA (10 µg) was fragmented to uniform size (~0.1 kb).

extract_protocol: Laser microdissection using the Leica LMD6000 was carried out on tissue sections (10 um) lightly stained with cresyl violet. Tissue was isolated into RLT buffer (Qiagen) and purified using the RNeasy kit (Qiagen). Using 5 ng total RNA as starting material, a two-round RNA amplification (Ambion MessageAmp II kit) was used to produce sufficient cDNA for biotin-labeling and hybridization to microarrays.

tag: strain

tag: age

tag: tissue region

value: Hcrt

tag: region name

value: Hypocretin area

tag: condition

value: RS

tag: specimen

tag: time of day


title: T00320628

description: sample barcode: T00320628

value: RSC


title: Parental RCC cell line, non-metastatic

type: genomic

city: New York

first: Venkata

middle: J

last: Thodima

state: NY

department: Cell Biology

institute: Memorial Sloan-Kettering Cancer Center

description: SN12C non-metastatic RCC cell line as experimental DNA and Promega reference DNA as control

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B US45103030. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human RCC cell line SN12C

label_protocol: genomic DNA samples were labeled using the BioPrime Array CGH Labeling kit (Invitrogen catalog #18095-012) according to the manufacturer's protocol, except 10μg of amplified DNA was used in each reaction instead of 4μg.

extract_protocol: Extraction of genomic DNA was performed using Qiagen DNeasy kit according to the manufacturer's instructions.

tag: cell line

tag: metastasis

value: non-metastatic

source_name: Promega reference human genome DNA from normal male

tag: sample type


title: Breast cancer cell line HCC1397

city: Boston

first: Qiyuan

last: Li

state: MA

address: 44 Binney street

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Gene expression data from breast cancer tumor cell line

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: Raw gene expression values were obtained using Affymetrix GeneChip software and further analyzed using the DNA-Chip Analyzer (dChip).

source_name: Cell line

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc).

treatment_protocol: Primary tumor samples were collagenase digested then sorted for epithelial cells using BerEp4 antibody coated magnetic beads

tag: cell type

value: Breast cancer cell line

tag: genotype

value: wt

tag: invasive tumour type

value: Ductal

tag: invasive b-r grade

value: III

tag: er status

value: neg

tag: pr status

tag: her2 status

value: pos


title: patient 1, dye swap

city: Houston

first: zhishuo

last: ou

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of medicine

description: Chromosomal microarray analysis with BAC V5 array discovered chromosome 4p deletion and 11p gain of this patient

hyb_protocol: Labeled probes hybridized onto the arrays at 37°C for 24 hours.

scan_protocol: The slides were washed and fluorescent signals on the slides were scanned into image files using an Axon microarray scanner and ScanArray software (GenePix 4000B from Axon Instruments, Union City, CA).

data_processing: Individual microarray LogRatio values were normalized using lowess smoothing to correct for intensity and spatially structured variation in the logRatio values.  The logRatio values for replicate spots were then averaged within each array.  These within array averaged values were then scaled by array using the median absolute deviation (MAD) of the smoothed, averaged  logRatios.  The scale factor for each array is determined to make the post scaling MAD values equivalent in between arrays using the geometric mean method.  Finally, the dye-reversed pair of arrays are sign corrected and averaged to create a final statistic for determing segmental events and a final combined log-ratio value -- and this value is reported as the combined logRatio.

source_name: blood

label_protocol: Genomic DNAs from patient samples and controls were differentially labeled with cyanin-3 (Cy3) and Cy5 (Perkin Elmer,Boston, MA) using a Bioprime DNA direct labeling kit (Invitrogen, Carlsbad, CA)

extract_protocol: Genomic DNA was extracted  from peripheral blood  using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: gender

value: Male

tag: patient

source_name: Blood

tag: reference

value: gender matched normal reference sample


title: Lung metastatic cell line generation 2 in RCC, biological rep 2

description: LM2 metastatic RCC cell line as experimental DNA, biological rep2 and Promega reference DNA as control

source_name: Human RCC cell line LM2

value: Metastatic

value: Promega reference human genome DNA from normal male


title: Lung metastatic cell line generation 2 in RCC, biological rep 1

description: LM2 metastatic RCC cell line as experimental DNA, biological rep1 and Promega reference DNA as control


title: T00321669

description: sample barcode: T00321669

tag: strain

tag: age

tag: tissue region

tag: region name


title: Lung metastatic cell line generation 1 in RCC

description: LM1 metastatic RCC cell line as experimental DNA and Promega reference DNA as control

source_name: Human RCC cell line LM1

tag: cell line


title: AJ_MU2_RP2E11

status: Public on Aug 16 2010

city: Atlanta

first: Steven

middle: M

last: Bray

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University School of Medicine

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Genotype data was extracted from CEL files using Affymetrix birdseed v2.0.  We removed SNPs that failed the Hardy-Weinberg exact test P < 0.000001 and had a call rate <95% across all samples
primary data description: Genotype data is in PLINK ped and map formats - GSE23636_AJ_471_732k.ped and GSE23636_AJ_471_732k.map (see readme file for description). The PLINK version: 1.06.

source_name: DNA extraced from blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extraced from blood using theGentra PureGene DNA extraction kit or the Qiagen DNA extraction kit

tag: population

value: Ashkenazi Jew

tag: individual id


title: AJ_AP9F3


title: AJ_AP9F6


title: T00320670

description: sample barcode: T00320670

value: LC

value: Locus Coeruleus

tag: condition

tag: specimen

tag: time of day


title: patient 1


title: T00320760

description: sample barcode: T00320760

value: Hcrt

value: Hypocretin area


title: AJ_MU2_RP2E10


title: AJ_AP9E11


title: AJ_MU2_RP2E7


title: AJ_MU2_RP2E6


title: T00321797

description: sample barcode: T00321797

value: RS


title: AJ_MU2_RP2E1


title: Breast cancer cell line HCC1396

tag: cell type

tag: genotype

tag: invasive tumour type

tag: invasive b-r grade


title: AJ_AP9D10


title: AJ_AP9D9


title: Breast cancer cell line HCC1395

tag: er status

tag: pr status

tag: her2 status


title: AJ_MU2_RP2E3


title: AJ_AP9D6


title: AJ_MU2_RP2D12


title: Breast cancer cell line HCC1400


title: AJ_AP9C8


title: AJ_AP9C3


title: AJ_RP2D10


title: AJ_RP2D8


title: AJ_AP9B12


title: AJ_AP9D8


title: AJ_AP9B6


title: AJ_AP9B9


title: AJ_AP9B8


title: AJ_AP9B5


title: AJ_AP9D5


title: AJ_AP9D3


title: AJ_RP2D4


title: AJ_AP9A9


title: AJ_AP9A8


title: AJ_RP2D2


title: AJ_AP9A12


title: AJ_AP9C11


title: AJ_RP2D3


title: AJ_AP9B3


title: AJ_AP8H6


title: AJ_AP9A3


title: AJ_AP9A2


title: AJ_AP8G6


title: AJ_AP8G12


title: AJ_AP8H2


title: AJ_AP8G5


title: AJ_AP8G3


title: AJ_AP8F2


title: AJ_AP8F11


title: AJ_AP8F3


title: AJ_AP8F9


title: AJ_AP8E11


title: AJ_AP8E12


title: AJ_AP8E8


title: AJ_AP8G8


title: AJ_MU1_AP8D12


title: AJ_MU1_AP8D11


title: AJ_AP8F6


title: AJ_AP8_2_D7


title: AJ_RP2D1


title: AJ_AP8_2_D6


title: AJ_AP8E2


title: AJ_AP8_2_D5


title: AJ_AP8E6


title: AJ_AP8_2_B12


title: AJ_AP8_2_C11


title: AJ_RP2C12


title: AJ_AP8_2_B6


title: AJ_AP8_2_B5


title: AJ_AP8_2_B2


title: AJ_RP2C6


title: AJ_RP2C9


title: AJ_AP8_2_B3


title: AJ_AP8_2_A9


title: AJ_AP8_2_A8


title: AJ_AP8_2_B9


title: AJ_AP8_2_A2


title: AJ_AP8_2_A3


title: AJ_AP8_2_A5


title: AJ_RP2C1


title: AJ_RP2B12


title: AJ_AP7H10


title: AJ_RP2B11


title: AJ_AP7H4


title: AJ_RP2B7


title: AJ_RP2B5


title: AJ_RP2B4


title: AJ_AP7G8


title: AJ_AP7G4


title: patient 4 [SNP]

description: Breakpoints of chromosomal translocations were fine mapped with the Affymetrix Genome-Wide SNP Array 6.0 arrays

scan_protocol: The Arrays were  scanned using a GeneChip® Scanner 3000 7G (Affymetrix, Inc.)

data_processing:
Data were analyzed using Genotyping Console version 2.1 software.
primary data description: Copy number state

label: Biotin

tag: gender

tag: patient


title: AJ_AP7G3


title: AJ_RP2A7


title: AJ_RP2A8


title: AJ_RP2A10


title: AJ_AP7G1


title: AJ_RP2A6


title: AJ_AP7F5


title: AJ_MU1_AP7E11


title: AJ_AP7E7_h2


title: AJ_AP7E6_h2


title: patient 6 [SNP]

value: Female


title: AJ_RP2A4


title: patient 5 [SNP]


title: AJ_AP7G10


title: patient 2 [SNP]


title: AJ_AP7D9


title: AJ_AP8G11


title: AJ_AP7D4_h2


title: AJ_AP7E3


title: AJ_AP7E1_h2


title: AJ_AP7D12


title: AJ_MU2_RP1H12


title: AJ_AP7D1_h2


title: AJ_AP7C12_h2


title: AJ_RP1H9


title: AJ_RP1H8


title: AJ_AP7C6_h2


title: AJ_AP7C2_h2


title: AJ_RP1H6


title: AJ_AP7B11_h2


title: AJ_AP7C3_h2


title: AJ_AP7B8_h2


title: AJ_AP7B12_h2


title: AJ_AP7B2


title: patient 1 [SNP]


title: AJ_AP7A3


title: AJ_AP7A5


title: AJ_RP1G12


title: AJ_AP6H11


title: AJ_AP7A2


title: AJ_AP6H8


title: AJ_AP6H7


title: AJ_RP1H1


title: AJ_AP6H1


title: AJ_AP6H3


title: AJ_AP6G11


title: AJ_AP6G7


title: AJ_AP6G10


title: AJ_AP6H4


title: AJ_AP6G5


title: AJ_AP7A12


title: AJ_AP6G6


title: AJ_AP6H2


title: AJ_AP7A11


title: AJ_AP6G4


title: AJ_RP1G9


title: AJ_RP2B8


title: AJ_RP1G8


title: AJ_AP8_2_B11


title: AJ_AP6F10


title: AJ_AP6G1


title: AJ_AP6E10


title: AJ_AP6H10


title: AJ_AP6F3


title: AJ_AP6E6


title: AJ_AP6G2


title: AJ_AP6F2


title: AJ_AP6E2


title: AJ_AP6E5


title: AJ_RP1G3


title: AJ_AP6D5


title: AJ_AP6D4


title: AJ_AP6D1


title: AJ_AP6F4


title: AJ_AP6D8


title: AJ_AP6C12


title: AJ_AP6C7


title: AJ_AP6C11


title: AJ_AP8_2_B8


title: AJ_AP6D7


title: AJ_AP8F8


title: AJ_AP6C10


title: AJ_AP6C4


title: patient 3 [SNP]


title: AJ_RP2B2


title: AJ_RP2A5


title: AJ_AP6C1


title: AJ_AP6C3


title: AJ_AP6B12


title: AJ_AP6B7


title: AJ_AP6B10


title: AJ_AP6B11


title: AJ_AP6A9


title: AJ_AP6A11


title: AJ_AP6A6


title: AJ_AP6A8


title: AJ_RP1F9


title: AJ_AP6F7


title: AJ_AP5G9


title: AJ_AP6A2


title: AJ_AP5G10


title: AJ_AP5H1


title: AJ_AP5G3


title: AJ_RP1F7


title: AJ_AP5H9


title: AJ_AP5H10


title: AJ_AP5F11


title: AJ_AP5G12


title: AJ_AP5F9


title: AJ_AP5F8


title: AJ_AP5F3


title: AJ_AP5E12


title: AJ_AP5F2


title: AJ_AP5H4


title: AJ_RP2C11


title: AJ_AP5F5


title: AJ_AP5E6


title: AJ_AP5E3


title: AJ_MU2_AP5E5


title: AJ_AP6C8


title: AJ_RP2A9


title: AJ_AP5E8


title: AJ_AP5E2


title: AJ_AP5D12


title: AJ_AP5E9


title: AJ_AP5D9


title: AJ_AP5D6


title: AJ_AP5D5


title: AJ_AP5D11


title: AJ_AP5C6


title: AJ_AP5C5


title: AJ_AP5D3


title: AJ_AP5C9


title: AJ_AP5E11


title: AJ_RP1F4


title: AJ_AP5C8


title: AJ_AP5C2


title: AJ_AP5B11


title: AJ_AP5D2


title: AJ_AP5B8


title: AJ_RP1F3


title: AJ_RP1F1


title: AJ_AP5A11


title: AJ_RP1E7


title: AJ_RP1E10


title: AJ_RP1E6


title: AJ_AP6F1


title: AJ_AP5A6


title: AJ_AP5B9


title: AJ_AP5A8


title: AJ_RP1E4


title: AJ_AP5A5


title: AJ_RP1E3


title: AJ_AP4H8


title: AJ_MU2_RP1D12


title: AJ_AP4H1


title: AJ_AP4G5


title: AJ_AP4F11


title: AJ_AP4G10


title: AJ_AP4G1


title: AJ_AP4G4


title: AJ_AP4F10


title: AJ_AP4G2


title: AJ_RP1E1


title: AJ_RP1D9


title: AJ_AP4F5


title: AJ_AP5A2


title: AJ_AP4F7


title: AJ_AP4H11


title: AJ_AP4D9


title: AJ_AP4D7


title: AJ_RP1D7


title: AJ_AP4D12


title: AJ_AP4G8


title: AJ_AP4E1


title: AJ_RP1D10


title: AJ_AP4E11


title: AJ_MU2_RP1D11


title: AJ_AP4E6_2


title: AJ_RP1D8


title: AJ_AP4B4


title: AJ_AP4B3


title: AJ_AP4D4


title: AJ_AP4C7


title: AJ_AP4C6


title: AJ_AP4B8


title: AJ_AP4C10


title: AJ_AP4D1


title: AJ_AP4C12


title: AJ_AP4C3


title: AJ_AP4B12


title: AJ_AP4A6


title: AJ_AP4B1


title: AJ_AP4A9


title: AJ_AP4A12


title: AJ_AP3_2_H10


title: AJ_AP3_2_H1


title: AJ_AP3_2_H7


title: AJ_AP3_2_H6


title: AJ_AP3_2_H4


title: AJ_AP3_2_H3


title: AJ_MU1_AP3G12


title: AJ_AP4A10


title: AJ_MU1_AP3G10


title: AJ_MU1_AP3G3


title: AJ_AP4D10


title: AJ_MU1_AP3G2


title: AJ_AP4C1


title: AJ_AP3_2_F9


title: AJ_AP3_2_F3


title: AJ_AP3_2_E12


title: AJ_AP3_2_E9


title: AJ_AP3_2_F12


title: AJ_AP3_2_E8


title: AJ_AP3_2_E6


title: AJ_AP3_2_F2


title: AJ_AP3_2_E11


title: AJ_AP3_2_E2


title: AJ_MU1_AP3D12


title: AJ_AP3_2_E3


title: AJ_AP3_2_E5


title: AJ_MU1_AP3D11


title: AJ_AP3_2_D8


title: AJ_AP3_2_D3


title: AJ_AP3_2_D9


title: AJ_AP3_2_C11


title: AJ_AP3_2_D5


title: AJ_AP3_2_D6


title: AJ_AP3_2_D2


title: AJ_AP3_2_C6


title: AJ_AP3_2_A12


title: AJ_MU1_AP2H8


title: AJ_AP3_2_B8


title: AJ_AP3_2_C5


title: AJ_AP3_2_A3


title: AJ_MU1_AP2H7


title: AJ_AP3_2_A2


title: AJ_AP3_2_B6


title: AJ_AP3_2_B9


title: AJ_AP3_2_C8


title: AJ_AP3_2_C2


title: AJ_AP3_2_A11


title: AJ_AP3_2_A5


title: AJ_AP3_2_C9


title: AJ_AP3_2_B12


title: AJ_AP3_2_C3


title: AJ_AP3_2_B11


title: AJ_AP3_2_A8


title: AJ_MU1_AP2H10


title: AJ_AP3_2_A9


title: AJ_AP2G7


title: AJ_AP2G5


title: AJ_MU1_AP2H5


title: AJ_MU1_AP2H2


title: AJ_AP2G10


title: AJ_MU1_AP2H11


title: AJ_MU1_AP2H4


title: AJ_MU1_AP2H1


title: AJ_MU1_AP2G11


title: AJ_AP2G4


title: AJ_AP2G1


title: AJ_AP2G2


title: AJ_AP2F10


title: AJ_AP2F7


title: AJ_AP2F11


title: AJ_AP2F4


title: AJ_AP2F6


title: AJ_AP2D10


title: AJ_AP2D3


title: AJ_RP1C6


title: AJ_RP1C5


title: AJ_RP1C3


title: AJ_AP2E1


title: AJ_AP2E12


title: AJ_AP2F3


title: AJ_AP2E3


title: AJ_AP2D9


title: AJ_AP2E4


title: AJ_AP2C4


title: AJ_RP1C1


title: AJ_RP1C2


title: AJ_AP2B5


title: AJ_RP1B10


title: AJ_MU1_AP2A12


title: AJ_AP2C6


title: AJ_AP2C9


title: AJ_AP2C3


title: AJ_MU1_AP2A9


title: AJ_AP2B2


title: AJ_AP2B9


title: AJ_AP2C7


title: AJ_MU1_AP2A11


title: AJ_AP2C10


title: AJ_AP2A3


title: AJ_RP1B7


title: AJ_APH7


title: AJ_MU1_AP1H10


title: AJ_AP2A2


title: AJ_APH9


title: AJ_AP2A5


title: AJ_AP2A8


title: AJ_RP1B9


title: AJ_APH6


title: AJ_APH4


title: AJ_APH1


title: AJ_APH3


title: AJ_APG9


title: AJ_APG12


title: AJ_RP1B6


title: AJ_APG4


title: AJ_APG6


title: AJ_RP1B5


title: AJ_APF9


title: AJ_APF10


title: AJ_APE10


title: AJ_APC3


title: AJ_APD4


title: AJ_APD1


title: AJ_APB12


title: AJ_APD6


title: AJ_APC9


title: AJ_APE12


title: AJ_APC7


title: AJ_APE6


title: AJ_MU1_AP1D10


title: AJ_APE1


title: AJ_APB6


title: AJ_MU1_AP1D9


title: AJ_APF3


title: AJ_APD7


title: AJ_APB11


title: AJ_APF7


title: AJ_APB9


title: AJ_APE7


title: AJ_APF1


title: AJ_APD3


title: AJ_MU1_AP1D12


title: AJ_APE9


title: AJ_APC10


title: AJ_APB8


title: AJ_APC12


title: AJ_RP1A12


title: AJ_APF6


title: AJ_APC6


title: AJ_APB5


title: AJ_APA12


title: AJ_APA11


title: AJ_APA9


title: AJ_APA6


title: AJ_APA8


title: AJ_1H9


title: AJ_1G2


title: AJ_1H6


title: AJ_1F3


title: AJ_RP1A3


title: AJ_1H2


title: AJ_1H5


title: AJ_RP1A5


title: AJ_1G6


title: AJ_1F2


title: AJ_1F11


title: AJ_1F8


title: AJ_1H8


title: AJ_1F6


title: AJ_1H3


title: AJ_1G9


title: AJ_1G8


title: AJ_P1E8


title: AJ_P1E2


title: AJ_1D11


title: AJ_1G11


title: AJ_1D9


title: AJ_1D8


title: AJ_1D5


title: AJ_1D3


title: AJ_1C3


title: AJ_1D2


title: AJ_1B11


title: AJ_1C2


title: AJ_1C5


title: AJ_1B9


title: AJ_1B8


title: AJ_1B6


title: AJ_1B5


title: AJ_1B3


title: AJ_1A12


title: AJ_1B2


title: IL12-4, biological rep 2, 2007, low pmt

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

country: Italy

institute: University of Naples Federico II

description: IL12-4_2 low

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20 min at 95 °C.  Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).  Hybridization washings were performed as the following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST wash solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing:
Data extraction was carried out using CombiMatrix Microarray Imager software, and a median normalization of raw medians and log2 transformation were performed using SPSS v.15.0 software. Further statistical processing was performed using the two-factor ANOVA module in the TIGR Multiple Experiment Viewer Software v4.0 (http://www.tigr.org/software/tm4/).

Hybridization signals with a variability coefficient higher than 0.5 were filtered out. A 10% cut off was applied to remove the lower tail from the low PMT distribution. Also, a 5% cut off on both tails was applied to the high PMT distribution.

label: Alexa Fluor 647

organism: Solanum lycopersicum

source_name: Red ripe fruit from tomato IL12-4 variety, trial 2007

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating Alexa Fluor 647 Reactive Dye according to manufacturer's instructions.

growth_protocol: The introgression line 12-4 (IL 12-4) and its parental genotype (cv. M82) were cultivated over consecutive years in a greenhouse at the Department of Soil, Plant, Environmental and Animal Production Sciences at the University of Naples (Portici, Italy). Six plants from IL 12-4 and the parental cv. M82 were transferred into 20-cm pots containing a 1:1 mixture of medium sandy soil and compost at the beginning of March. Pots were distributed randomly 15 cm apart in rows 1 separated by a 50-cm 2 channel, and were supplemented with Nitrophoska Blu Spezial 12-12-17 (+2+20) (Compu) slow release fertilizer (5 g). Plants were watered twice daily using an automated irrigation device with 4 individual drip lines. Prior to flowering, the plants were supplied every two weeks with 30-10-10 liquid fertilizer (Grow More, USA). Fruits were collected at red-ripe stage.

extract_protocol: Total RNA was extracted from frozen, homogenized and powdered tomato fruit tissue using the CTAB (hexadecyltrimethylammonium bromide) method (Griffiths et al. J Exp Bot 50: 793–798 1999). Samples were taken from IL 12-4 and M82 using three plants per genotype in the 2007 and 2008 growing trials.

treatment_protocol: Fruits were collected from IL 12-4 and its cultivated parent when 75% were full sized and red-ripe, softening had increased and the inside of the columella was completely red. Samples were generated by pooling ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Samples were frozen under liquid nitrogen and stored at –80°C prior to homogenization in a Waring blender and processing for the extraction of ascorbic acid and total RNA.

value: Introgression Line 12-4

tag: tissue

value: epicarp and mesocarp

tag: trial

tag: plant replica

tag: scan pmt

value: low


title: IL12-4, biological rep 5, 2008, high pmt

description: IL12-4_5 high

source_name: Red ripe fruit from tomato IL12-4 variety, trial 2008

value: high


title: IL12-4, biological rep 4, 2008, high pmt

description: IL12-4_4 high


title: AJ_1A8

tag: population

tag: individual id


title: IL12-4, biological rep 5, 2008, low pmt

description: IL12-4_5 low


title: IL12-4, biological rep 2, 2007, high pmt

description: IL12-4_2 high


title: IL12-4, biological rep 4, 2008, low pmt

description: IL12-4_4 low


title: IL12-4, biological rep 3, 2007, high pmt

description: IL12-4_3 high


title: AJ_1A6


title: IL12-4, biological rep 1, 2007, low pmt

description: IL12-4_1 low


title: AJ_1C11


title: IL12-4, biological rep 1, 2007, high pmt

description: IL12-4_1 high


title: miR155-/- dendritic cells + LPS

city: Pasadena

first: Aadel

last: Chaudhuri

state: CA

address: 1200 E California Blvd

institute: Caltech

description:
KO LPS
gene expression from miR-155-/- bone marrow derived dendritic cells incubated in lipopolysaccharide

hyb_protocol: Standard Affymetrix hyb protocol.

scan_protocol: Standard Affymetrix scan protocol.

data_processing:
Standard Affymetrix data analysis protocol.
Algorithm: ExpressionStat 5.0

source_name: dendritic cells, miR-155-/- C57Bl/6 mice

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

growth_protocol: Bone marrow derived macrophages were incubated in a 37 degree sterile incubator in complete RPMI media containing 20ng/ml of recombinant murine GM-CSF.

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

treatment_protocol: After 7 days of incubation, media was replaced with complete RPMI media containing 10ng/ml of lipopolysaccharide.

tag: strain

value: dendritic cells (differentiated from bone marrow using GMCSF)

tag: protocol

value: miR155 knockout

tag: stress

value: LPS challenge


title: IL12-4, biological rep 6, 2008, high pmt

description: IL12-4_6 high

tag: genotype


title: IL12-4, biological rep 3, 2007, low pmt

description: IL12-4_3 low


title: wild type dendritic cells + LPS

description:
WT LPS
gene expression from wild type bone marrow derived dendritic cells incubated in lipopolysaccharide

source_name: dendritic cells, wildtype C57Bl/6 mice

tag: cell type

value: control


title: sirna-treated under tension, biological rep2

city: Mannheim

first: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

description: Gene expression data from cultured endothelial cells treate with SiRNA against Zyxin, under tension

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133_plus2. GeneChips were washed and stained in a Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with JMP Genomics, version 3.2 (SAS). Signal densities of perfect matches were log2-transformed, quantile normlized and analyzed with ANOVA.

source_name: sirna-treated endothelial cells under tension

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

growth_protocol: Endothelial cells (Huvec) isolated from umbilical cord veins was cultured on BioFlexÔ collagen I elastomers (Flexercell Inc., Hillsborough, NC, USA) till confluence (typically 4 days post isolation).

treatment_protocol: To simulate hypertension, cells were exposed to cyclic stretch (elongation 10% at 0.5 Hz with a sinusoidal profile). SiRNA-transfection was performed with magnet-assisted transfection  (IBA, Göttingen, Germany),  using Hs_ZYX_1_HP and the AllStars Negative Control (Qiagen, Hilden, Germany).

value: primary Huvec cells


title: sirna-treated under normal condition, biological rep2

description: Gene expression data from cultured endothelial cells treate with SiRNA against Zyxin, under normal conditions.

source_name: sirna-treated endothelial cells under normal condition


title: sirna-treated under tension, biological rep1


title: AJ_1A3


title: AJ_1A2


title: IL12-4, biological rep 6, 2008, low pmt

description: IL12-4_6 low


title: AJ_1A5


title: Glomerular endothelial cells of diabetic mice, biological rep2

city: Cincinnati

first: Eric

middle: W

last: Brunskill

state: OH

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

description: Gene expression data from the glomerular endothelium of diabetic mice

hyb_protocol: Affymetrix standard protocol

scan_protocol: The arrays were washed and and stained  using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.  Probe arrays were scanned using a Affymetrix GeneChip Scanner 3000 7G and    Affymetrix scanning software Genechip Operating Software Version 1.4

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: Glomerular endothelial cells from the kidneys of diabetic mice

label_protocol: The FL-Ovation cDNA Biotin Module V2 (NuGEN) is used to chemically  modify fragments and label target sense cDNA.

extract_protocol: RNA was isolated using a Qiagen RNeasy RNA isolation kit according to manufacturer's instructions.

value: Glomerular endothelial cell

value: Tie2-GFP/ DB/DB

tag: age

value: 7 month old


title: sirna-treated under normal condition, biological rep3


title: wild type under tension, biological rep3

description: Gene expression data from cultured wild type endothelial cells under tension.


title: wild type under tension, biological rep2

source_name: wild type endothelial cells under tension


title: Glomerular endothelial cells of diabetic mice, biological rep3


title: sirna-treated under tension, biological rep3


title: Glomerular endothelial cells of normal mice, biological rep3

description: Gene expression data from the glomerular endothelium of normal mice

source_name: Glomerular endothelial cells from the kidneys of normal mice

value: Tie2-GFP/ +/+


title: Glomerular endothelial cells of diabetic mice, biological rep1


title: wild type under normal condition, biological rep2

description: Gene expression data from cultured wild type endothelial cells under normal conditions.


title: Glomerular endothelial cells of normal mice, biological rep2


title: wild type under tension, biological rep1


title: sirna-treated under normal condition, biological rep1


title: wild type under normal condition, biological rep1

source_name: wild type endothelial cells under normal condition


title: Glomerular endothelial cells of normal mice, biological rep1


title: wild type under normal condition, biological rep3


title: Metastatic RCC tumor pair 14

status: Public on Aug 15 2010

description: Expression data from RCC Human tumors to study metastasis progression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Scanner GSC3000 M10 type.

data_processing: The data were analyzed with Partek Genomic Suite 6.5 using default analysis settings and RMA as normalization method.

source_name: Human tumor

extract_protocol: Extraction of total RNA was performed using Qiagen miRNeasy kit according to the manufacturer's instructions.

value: Metastatic RCC tumor

tag: sample type

value: pair 14


title: Primary RCC tumor pair 14

value: Primary RCC tumor


title: Primary RCC tumor pair 16

value: pair 16


title: Metastatic RCC tumor pair 15

value: pair 15


title: Metastatic RCC tumor pair 16


title: Primary RCC tumor pair 12

value: pair 12


title: Metastatic RCC tumor pair 13

value: pair 13


title: Primary RCC tumor pair 15


title: Primary RCC tumor pair 13


title: Metastatic RCC tumor pair 11

value: pair 11


title: Metastatic RCC tumor pair 8

value: pair 8


title: Primary RCC tumor pair 8


title: Primary RCC tumor pair 6

value: pair 6


title: Primary RCC tumor pair 11


title: Metastatic RCC tumor pair 7

value: pair 7


title: Metastatic RCC tumor pair 12


title: Metastatic RCC tumor pair 9

value: pair 9


title: Primary RCC tumor pair 9


title: Primary RCC tumor pair 10

value: pair 10


title: Primary RCC tumor pair 7


title: Metastatic RCC tumor pair 4

value: pair 4


title: Metastatic RCC tumor pair 5

value: pair 5


title: Primary RCC tumor pair 4


title: Primary RCC tumor  pair 5


title: Metastatic RCC tumor pair 6


title: Metastatic RCC tumor pair 2

value: pair 2


title: Primary RCC tumor pair 2


title: Metastatic RCC tumor pair 1

value: pair 1


title: Primary RCC tumor pair 3

value: pair 3


title: Metastatic RCC tumor pair 3

value: Metastatic RCC tumor


title: RCC Lung metastatic Genration 2, biological rep 2

description: Expression data from RCC cell lines to study metastasis progression

source_name: Cell line

tag: cell line


title: Primary RCC tumor pair 1

value: Primary RCC tumor


title: RCC Lung metastatic Genration 2, biological rep 1


title: RCC Lung metastatic Genration 1


title: RCC parental cell line (non-metastatic), biological rep2


title: RCC parental cell line (non-metastatic), biological rep1


title: BY4741_ypd_r2

type: mixed

city: Cambridge

first: Joshua

middle: Z

last: Levin

address: 320 Charles Street

institute: Broad Institute of MIT & Harvard

scan_protocol: Standard Agilent protocols for Agilent-015072 Yeast Oligo Microarray 4x44K G2519F with dye rank correlation normalization disabled

data_processing: Agilent Feature Extraction version 10.5.1.1 with dye rank correlation normalization disabled.

organism: Saccharomyces cerevisiae

source_name: BY4741 YPD

label_protocol: Indirect total RNA labeling

extract_protocol: Qiagen Yeast RNA extraction

source_name: BY4741 DNA

value: progenitor


title: BY4741_ypd_r1

hyb_protocol: Standard Agilent protocols for Agilent-015072 Yeast Oligo Microarray 4x44K G2519F


title: Metastatic RCC tumor pair 10


title: E146vsE264

city: SINGAPORE

first: BERNICE

middle: MENGQI

last: SIM

state: SINGAPORE

address: 60 Biopolis Street, Genome; #02-01

department: INFECTIOUS DISEASES 2

country: Singapore

institute: GENOME INSTITUTE OF SINGAPORE

hyb_protocol: 2 µg of labeled gDNA per strain was hybridized to the BPGA at 52°C for 16 hours in a MAUI hybridization system.

scan_protocol: After hybridization and washing, arrays were scanned on an Axon 4000B scanner (Molecular Devices, Sunnyvale, Ca, USA).

data_processing: Arrays were normalized using Loess in R package Limma

organism: Burkholderia thailandensis

source_name: Bt E146

label_protocol: Genomic DNAs were labeled with either Cy3 or Cy5 flouresence dyes using a BAC array labeling kit (Kreatech, USA).

growth_protocol: Rich media (LB)

extract_protocol: Bacterial cultures were grown in LB media and genomic DNA was extracted using the Qiagen Genomic DNA kit.

tag: test strain

source_name: Bt E264

tag: reference strain


title: E131vsE264

source_name: Bt E131


title: CDC2721121vsE264


title: E049vsE264

source_name: Bt E049


title: E004vsE264

source_name: Bt E004


title: E128vsE264

source_name: Bt E128


title: E158vsE264

source_name: Bt E158


title: E161vsE264

source_name: Bt E161


title: E174vsE264

source_name: Bt E174


title: E119vsE264

source_name: Bt E119


title: E177vsE264

source_name: Bt E177


title: E153vsE264

source_name: Bt E153


title: E159vsE264

source_name: Bt E159


title: E260vsE264

source_name: Bt E260


title: CDC3015869vsE264


title: E032vsE264

source_name: Bt E032


title: E188vsE264

source_name: Bt E188


title: MPP_FLpos_rep3

city: Stanford

first: Jun

last: Seita

address: Lokey Stem Cell Building #G3101, 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G with GCOS version 1.4.0.036.

data_processing: The data were analyzed with R/Bioconductor.

source_name: bone marrow

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

tag: progenitor population

value: MMPFL+

value: 2 month

tag: gender

value: male


title: CMP_rep1

value: CMP


title: E169vsE264

source_name: Bt E169


title: E257vsE264

source_name: Bt E257

source_name: Bt E264


title: E017vsE264

source_name: Bt E017


title: E202vsE264

source_name: Bt E202


title: E112vsE264

source_name: Bt E112


title: E207vsE264

source_name: Bt E207


title: E234vsE264

source_name: Bt E234


title: E048vsE264

source_name: Bt E048


title: Flk2_neg_MPP_2a methyl-depleted

city: Baltimore

first: Hong

last: Ji

state: MD

address: 855 N Wolfe Street, Rangos 580

department: Medicine

institute: Johns hopkins school of Medicine

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

source_name: Methyl-depleted fraction from Flk2_neg_MPP_2a

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 1~5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

value: Flow sorted MPPFL- cells  from mouse bone marrow (Lin- Il7ra- c-Kit+ Sca-1+ CD34+ Flk2-)

source_name: Input fraction from Flk2_neg_MPP_2a


title: E192vsE264

source_name: Bt E192


title: Flk2_neg_MPP_3 methyl-depleted

source_name: Methyl-depleted fraction from Flk2_neg_MPP_3

source_name: Input fraction from Flk2_neg_MPP_3


title: Flk2_neg_MPP_2b methyl-depleted

source_name: Methyl-depleted fraction from Flk2_neg_MPP_2b

source_name: Input fraction from Flk2_neg_MPP_2b


title: Flk2_neg_MPP methyl-depleted

source_name: Methyl-depleted fraction from Flk2_neg_MPP

source_name: Input fraction from Flk2_neg_MPP


title: E285vsE264

source_name: Bt E285


title: E253vsE264

source_name: Bt E253

source_name: Bt E264


title: E263vsE264

source_name: Bt E263


title: E274vsE264

source_name: Bt E274


title: E291vsE264

source_name: Bt E291


title: E246vsE264

source_name: Bt E246


title: E440vsE264

source_name: Bt E440


title: GMP_3 methyl-depleted

source_name: Methyl-depleted fraction from GMP_3

value: Flow sorted GMP cells  from mouse bone marrow (Lin- Il7ra- c-Kit+  Sca-1- CD34+ FcγRII/III+)

source_name: Input fraction from GMP_3


title: E444vsE264

source_name: Bt E444


title: CLP_2b methyl-depleted

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software (methylation_userguide_v5p0.pdf). The values are quantile normalized p(percent methylation) value.

source_name: Methyl-depleted fraction from CLP_2b

value: Flow sorted CLP cells  from mouse bone marrow  (Lin- CD27+ Flk2+ Il7ra+ Ly6D-)

source_name: Input fraction from CLP_2b


title: E287vsE264

source_name: Bt E287


title: DN3_3 methyl-depleted

source_name: Methyl-depleted fraction from DN3_3

value: Flow sorted DN3 cells  from mouse thymocyte(Lin- CD4- CD8- c-Kit- CD44- CD25+)

source_name: Input fraction from DN3_3


title: GMP_3 methyl-depleted


title: DN3_2 methyl-depleted

source_name: Methyl-depleted fraction from DN3_2

source_name: Input fraction from DN3_2


title: Flk2_neg_MPP_3 methyl-depleted

source_name: Methyl-depleted fraction from Flk2_neg_MPP_3

source_name: Input fraction from Flk2_neg_MPP_3


title: Flk2_pos_MPP_2b methyl-depleted

source_name: Methyl-depleted fraction from Flk2_pos_MPP_2b

value: Flow sorted MPPFL+ cells  from mouse bone marrow (Lin- Il7ra- c-Kit+ Sca-1+  CD34+ Flk2+)

source_name: Input fraction from Flk2_pos_MPP_2a


title: Flk2_pos_MPP_2a methyl-depleted

source_name: Methyl-depleted fraction from Flk2_pos_MPP_2a

source_name: Input fraction from Flk2_pos_MPP_2b


title: Flk2_pos_MPP_3 methyl-depleted

source_name: Methyl-depleted fraction from Flk2_pos_MPP_3

source_name: Input fraction from Flk2_pos_MPP_3


title: CLP methyl-depleted

source_name: Methyl-depleted fraction from CLP

source_name: Input fraction from CLP


title: E433vsE264

source_name: Bt E433

source_name: Bt E264


title: CLP_2a methyl-depleted

source_name: Methyl-depleted fraction from CLP_2a

source_name: Input fraction from CLP_2a


title: GMP_2 methyl-depleted

source_name: Methyl-depleted fraction from GMP_2

source_name: Input fraction from GMP_2


title: Flk2_pos_MPP methyl-depleted

source_name: Methyl-depleted fraction from Flk2_pos_MPP

source_name: Input fraction from Flk2_pos_MPP


title: GMP_2 methyl-depleted


title: GMP methyl-depleted

source_name: Methyl-depleted fraction from GMP

source_name: Input fraction from GMP


title: GMP methyl-depleted


title: Aspergillus nidulans reoxygenation 3 h

status: Public on Aug 14 2010

city: tsukuba

first: masuo

last: shunsuke

address: 1-1-1 tennodai

country: Japan

institute: university of tsukuba

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

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

data_processing: The data were analyzed with GCOS program (version 1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Aspergillus nidulans

source_name: Aspergillus nidulans grown under normoxic condition for 3h after reoxygenation.

label_protocol: Biotinylated cRNA were prepared from 250 ng total RNA using GeneChip 3' IVT Express Kit.

growth_protocol: Conidia were incubated for 16 h at 30oC and 120 rpm in 500-ml Erlenmeyer flasks containing 100 ml of MM medium (1% glucose, 0.6% NaNO3, 10 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 0.2 µg l-1 biotin and 0.2% Hutner’s trace metals (v/v)) (Barratt et al. 1965), and plugged with cotton (normoxic conditions). The head space in the flasks was replaced with nitrogen gas by purging the air for 15 min. The flasks were sealed with butyl rubber stoppers and rotated at 30oC at 120 rpm (hypoxic conditions). The stoppers were removed 6 h later and the culture broth was re-oxidized by vigorously shaking the flasks, which were incubated once again under the normoxic conditions described above.

extract_protocol: Mycelia were immediately frozen in liquid nitrogen and powdered to prepare total RNA using the RNeasy plant mini kit (Qiagen, Venlo, Netherlands).

treatment_protocol: Mycelia were harvested by filtration and washed by ddH2O.

tag: treatment

value: reoxygenation

tag: time

value: 3 h

value: Aspergillus nidulans A26 (biA1)


title: Aspergillus nidulans reoxygenation 6 h

source_name: Aspergillus nidulans grown under normoxic condition for 6h after reoxygenation.

value: 6 h


title: Aspergillus nidulans hypoxic 6 h

source_name: Aspergillus nidulans grown under hypoxic condition for 6h after exposure to hypoxia.

value: hypoxic


title: E421vsE264

source_name: Bt E421


title: Aspergillus nidulans hypoxic 3 h

source_name: Aspergillus nidulans grown under hypoxic condition for 3h after exposure to hypoxia.


title: Aspergillus nidulans normoxic

source_name: Aspergillus nidulans grown under normoxic condition for 16 h before exposure to hypoxia.

value: normoxic

value: control


title: DN3 methyl-depleted

source_name: Methyl-depleted fraction from DN3

source_name: Input fraction from DN3


title: ovarian epithelial cells T80A2-11_with HMGA2_rep 1

city: Chicago

first: Jingjing

last: Wu

state: IL

address: 303 E. Chicago Avenue

department: pathology

institute: northwestern university

hyb_protocol: The array was hybridized by using OneArray Hybridization Buffer (Phalanx) for 14 to 16h at 420C which was followed by washing two times per manufacturer’s protocol.

scan_protocol: The chips were scanned by Axon 4000 scanner (Molecular Devices).

data_processing: Hierarchical clustering the expression profiles was done by software Cluster 3.0. The genes which have different expression with fold>2 were further analyzed by Pathway-Express.

source_name: immortalized ovarian surface epithelial cells

label_protocol: The labeling was accomplished by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to manufacturer’s protocol. Firstly, cDNA were synthesized by reverse transcription, including first and second strand synthesis. Then the purified cDNA became the template for in vitro transcription with T7 RNA polymerase. In this step, the modified nucleotide, 5-(3-aminoallyl)-UTP (aaUTP) were incorporated into the aRNA which would be subsequently labeled by Cy5 dye.

growth_protocol: Cells were maintained at 37oC in 5% CO2.

extract_protocol: Total RNA was isolated by miRNA isolation kit from Ambion according to manufacturer’s protocol.

value: immortalized ovarian epithelial cell line T80A2-11

tag: transfection


title: E346vsE264

source_name: Bt E346

source_name: Bt E264


title: E365vsE264

source_name: Bt E365


title: E555vsE264

source_name: Bt E555


title: E352vsE264

source_name: Bt E352


title: E447vsE264

source_name: Bt E447


title: ovarian epithelial cells T29A2-15_with HMGA2_rep 1

value: immortalized ovarian epithelial cell line T29A2-15


title: E305vsE264

source_name: Bt E305


title: E336vsE264

source_name: Bt E336


title: ovarian epithelial cells T29A2-8_with HMGA2_rep 2

value: immortalized ovarian epithelial cell line T29A2-8


title: ovarian epithelial cells T80A2-11_with HMGA2_rep 2


title: E360vsE264

source_name: Bt E360


title: ovarian epithelial cells T29A2-15_with HMGA2_rep 2


title: BM2

city: New Haven

last: Lu

state: CT

address: 10 Amistad St

department: Yale Stem Cell Center and Department of Genetics

institute: Yale University

description: Population definition: none

hyb_protocol: microRNA hybridization was performed according to Lu et al. Nature 2005, PubMed 15944708

data_processing:
Data processing was performed according to Lu et al. Nature 2005, PubMed 15944708
Analysis was performed using MATLAB custom computational "pipeline" (publicly available GenePattern Analysis Suite).

source_name: unfractionated bone marrow cells

label_protocol: microRNA labeling was performed according to Lu et al. Dev Cell 2008, PubMed 18539114.  microRNAs were labeled by a new plate-capture method, through ligation-mediated amplification

growth_protocol: mice 6-8 weeks in age was used. Regular maintenance condition.

extract_protocol: Bone marrow cells of the corresponding populations were FACS-sorted. Total RNA was prepared by Trizol.

treatment_protocol: No treatment after sorting

value: 6-8 weeks

value: unfractionated bone marrow cells


title: BM1

description: Population definition: none

scan_protocol: microRNA hybridization was performed according to Lu et al. Nature 2005, PubMed 15944708


title: ovarian epithelial cells T29A2-8_with HMGA2_rep 1


title: E367vsE264

source_name: Bt E367


title: ovarian epithelial cells T80_without HMGA2_rep 2

label_protocol: The labeling was accomplished by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to manufacturer’s protocol. Firstly, cDNA was synthesized by reverse transcription, including first and second strand synthesis. Then the purified cDNA became the template for in vitro transcription with T7 RNA polymerase. In this step, the modified nucleotide, 5-(3-aminoallyl)-UTP (aaUTP) will be incorporated into the aRNA which would be subsequently labeled by Cy5 dye.

value: immortalized ovarian epithelial cell line T80


title: E438vsE264

source_name: Bt E438


title: Sca2

description: Population definition: Lin-Kit-Sca+

source_name: Lin-Kit-Sca+ bone marrow cell

value: Lin-Kit-Sca+ bone marrow cell


title: Kit1

description: Population definition: Lin-Kit+Sca-

source_name: Lin-Kit+Sca- bone marrow cell

value: Lin-Kit+Sca- bone marrow cell


title: ovarian epithelial cells T80_without HMGA2_rep 1


title: ovarian epithelial cells T29-2_without HMGA2_rep 2

value: immortalized ovarian epithelial cell line T29-2


title: Sca1.2

description: Population definition: Lin-Kit-Sca+


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 24 hour, replicate 1

city: Harbin

first: Yanming

last: Zhu

state: Heilongjiang

address: Wood Street 59

department: Life sciences

country: China

institute: Northeast Agriculture University

description: Gene expression data from Glycine soja roots of 21 days old after 24h NaHCO3 stress

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The computation of expression values were conducted using dChip software. Sample wise normalization to the median probe cell intensity (CEL) of all 14 arrays. Model-based gene expression was obtained from normalized CEL intensities based on a Perfect Match-only model.

organism: Glycine soja

source_name: root after 24h stress

growth_protocol: Glycine soja seeds were grown in a culture room with 60 % relative humidity, 24℃ and a light regime of 12h light/12h dark. Germinated seedlings were grown in the growth boxes containing 1/4 strength Hoagland's solution.

extract_protocol: Total RNA was extracted from frozen roots with TRIzol (Invitrogen, Carlsbad, CA) according to the instructions from the manufacturer.

treatment_protocol: 21 days old seedlings were transferred into the growth boxes containing 1/4 strength Hoagland’s solution with 50mmol/L NaHCO3 (pH 8.5).

tag: line

value: 21 days after germination


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 24 hour, replicate 2


title: ovarian epithelial cells T29-1_without HMGA2_rep 1

hyb_protocol: The array was hybridized by using OneArray Hybridization Buffer (Phalanx) for 14 to 16h at 42oC which was followed by washing two times per manufacturer’s protocol.

value: immortalized ovarian epithelial cell line T29-1


title: E430vsE264

source_name: Bt E430


title: normal Post ECP, biological rep6

first: Carole

middle: L.

last: Berger

address: 333 Cedar Street

department: Dermatology

description: this sample involved data from two arrays

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

scan_protocol: GCOS 1.2

data_processing: Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2.  Data was normalized using Robust Multi-Array.  Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.

source_name: normal Post ECP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols

extract_protocol: Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).

treatment_protocol: Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum

tag: disease state

value: normal

tag: dose

value: post ECP

tag: peripheral blood

value: Treated with ECP and Incubated overnight


title: CMP_3 methyl-depleted

source_name: Methyl-depleted fraction from CMP_3

value: Flow sorted CMP cells  from mouse bone marrow (Lin- Il7ra- c-Kit+ Sca-1- CD34+ FcγRII/IIIlow)

source_name: Input fraction from CMP_3


title: ovarian epithelial cells T29-2_without HMGA2_rep 1

source_name: immortalized ovarian surface epithelial cells


title: E426vsE264

source_name: Bt E426

source_name: Bt E264


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 12 hour, replicate 2

description: Gene expression data from Glycine soja roots of 21 days old after 12h NaHCO3 stress

source_name: root after 12h stress


title: KLS1

description: Population definition: Lin-Kit+Sca+

source_name: Lin-Kit+Sca+ bone marrow cell

tag: strain

value: Lin-Kit+Sca+ bone marrow cell


title: normal Post ECP, biological rep5

description: Gene expression data


title: DN3 methyl-depleted

source_name: Methyl-depleted fraction from DN3

value: Flow sorted DN3 cells  from mouse thymocyte(Lin- CD4- CD8- c-Kit- CD44- CD25+)

source_name: Input fraction from DN3


title: normal Post ECP, biological rep3

description: Gene expression data


title: normal Post ECP, biological rep2

description: Gene expression data


title: CMP methyl-depleted

source_name: Methyl-depleted fraction from CMP

source_name: Input fraction from CMP


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 6 hour, replicate 2

description: Gene expression data from Glycine soja roots of 21 days old after 6h NaHCO3 stress

source_name: root after 6h stress


title: normal Post ECP, biological rep4


title: MPP3

description: Population definition: Lin-Kit+Sca+CD34+Flk2+

source_name: Multipotent progenitor

value: Multipotent progenitor


title: Sca1

description: Population definition: Lin-Kit-Sca+

source_name: Lin-Kit-Sca+ bone marrow cell


title: KLS2

description: Population definition: Lin-Kit+Sca+


title: MPP2


title: CMP_2 methyl-depleted

source_name: Methyl-depleted fraction from CMP_2

source_name: Input fraction from CMP_2


title: ovarian epithelial cells T29-1_without HMGA2_rep 2

value: control


title: normal Pre ECP, biological rep4

description: Gene expression data

source_name: normal Pre ECP

value: pre ECP

value: blood harvested with the Therakos machine


title: MPP1

value: 6-8 weeks


title: normal Pre ECP, biological rep2

description: Gene expression data


title: DN1_2 methyl-depleted

source_name: Methyl-depleted fraction from DN1_2

value: Flow sorted DN1 cells  from mouse thymocyte (Lin- CD4- CD8-  c-Kit+ CD44+ CD25-)

source_name: Input fraction from DN1_2


title: normal Post ECP, biological rep1

description: Gene expression data

source_name: normal Post ECP

value: Leukapheresis


title: DN2 methyl-depleted

source_name: Methyl-depleted fraction from DN2

value: Flow sorted DN2 cells  from mouse thymocyte(Lin- CD4- CD8- c-Kit+ CD44+ CD25+)

source_name: Input fraction from DN2


title: ST2

description: Population definition: Lin-Kit+Sca+CD34+Flk2-

source_name: Short term hematopoietic stem cell

value: Short term hematopoietic stem cell


title: normal Pre ECP, biological rep3

description: Gene expression data


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 3 hour, replicate 2

description: Gene expression data from Glycine soja roots of 21 days old after 3h NaHCO3 stress

source_name: root after 3h stress

value: 21 days after germination


title: DN3_3 methyl-depleted

source_name: Methyl-depleted fraction from DN3_3

source_name: Input fraction from DN3_3


title: normal Pre ECP, biological rep1

description: Gene expression data


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 6 hour, replicate 1


title: ST3


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 3 hour, replicate 1


title: patient Post ECP, biological rep4

description: Gene expression data

source_name: GVHD patient Post ECP

value: graft-versus host disease


title: patient Post ECP, biological rep3

description: Gene expression data

source_name: CTCL patient Post ECP

value: cutaneous T cell lymphoma


title: normal Pre ECP, biological rep5

description: Gene expression data

value: normal


title: ST1


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 1 hour, replicate 2

description: Gene expression data from Glycine soja roots of 21 days old after 1h NaHCO3 stress

source_name: root after 1h stress


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 12 hour, replicate 1

source_name: root after 12h stress


title: patient Post ECP, biological rep6

description: Gene expression data

value: post ECP

value: Treated with ECP and Incubated overnight


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 1 hour, replicate 1


title: DN2_2 methyl-depleted

source_name: Methyl-depleted fraction from DN2_2

source_name: Input fraction from DN2_2


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 30 minutes, replicate 2

description: Gene expression data from Glycine soja roots of 21 days old after 0.5h NaHCO3 stress

source_name: root after 0.5h stress


title: DN3_2 methyl-depleted

source_name: Methyl-depleted fraction from DN3_2

source_name: Input fraction from DN3_2


title: LT1

description: Population definition: Lin-Kit+Sca+CD34-Flk2-

source_name: Long term hematopoietic stem cell

value: Long term hematopoietic stem cell


title: LT3


title: DN2_3 methyl-depleted

source_name: Methyl-depleted fraction from DN2_3

source_name: Input fraction from DN2_3


title: patient Post ECP, biological rep2

description: Gene expression data


title: DN1_3 methyl-depleted

source_name: Methyl-depleted fraction from DN1_3

source_name: Input fraction from DN1_3


title: patient Pre ECP, biological rep4

description: Gene expression data

source_name: GVHD patient Pre ECP


title: patient Pre ECP, biological rep6

description: Gene expression data


title: DN1 methyl-depleted

source_name: Methyl-depleted fraction from DN1

source_name: Input fraction from DN1


title: patient Pre ECP, biological rep1

description: Gene expression data

source_name: CTCL patient Pre ECP


title: patient Pre ECP, biological rep5

description: Gene expression data


title: SCV_SaureusVsParent_replicate_1

status: Public on Aug 13 2010

city: Heidelberg

first: Benjamin

middle: Peter

last: Howden

state: Victoria

address: Studley Rd

department: Infectious Diseases

country: Australia

institute: Austin Health

description: Biological replicate 1 of 4

hyb_protocol: 50 ul of cDNA hybridisation mixture was applied to array slide and covered with LifterSlip coverslips (Erie Scienctific), then incubated overnight at 42°C.

scan_protocol: GMS418 Array Scanner

data_processing: Images were combined and quantified using ImaGene ver 5.1 (Biodiscovery) and then imported into BASE and analysed using Bioconductor and Limma. After global lowess normalization the log-ratios for each array sclaed so that the median absolute deviation was the same between arrays. The fold ratio for gene expression for the SCV strain (JKD6229) compared to the parent (JKD6210) was calculated.

organism: Staphylococcus aureus

label_protocol: 5 µg of total RNA was reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 0.5 mM each dATP, dCTP, dGTP, with 0.2 mM dTTP, 0.3 mM aa-dUTP. After cDNA collection, aminoallyl-labelled cDNA was resuspended in 0.1 M sodium bicarbonate buffer (pH 9.3), then incubated with cy3 or cy5 for 2 hours at room temperature.

growth_protocol: Isolates grown in BHI broth to exponential phase (OD600 = 0.5)

extract_protocol: Total RNA extracted using Rneasy kit from Qiagen following manufacturer's instructions

treatment_protocol: 1 ml of culture was added to 0.5 ml of RNA stabilization reagent (RNAlater, Qiagen) and allowed to stand for 10 min after mixing

tag: phenotype

value: SCV strain, active stringent response

value: Normal phenotype


title: SCV_SaureusVsParent_replicate_2

description: Biological replicate 2 of 4


title: SCV_SaureusVsParent_replicate_4

description: Biological replicate 4 of 4


title: patient Post ECP, biological rep1

description: Gene expression data

source_name: CTCL patient Post ECP


title: Glycine soja, roots from 3cm root apex, 50 mM NaHCO3, 30 minutes, replicate 1


title: Glycine soja, roots from 3cm root apex, standard condition, replicate 1

description: Gene expression data from Glycine soja roots of 21 days old without stress

source_name: root at 0h as control

value: control


title: LT2

tag: cell type


title: patient Pre ECP, biological rep3

description: Gene expression data

value: pre ECP


title: SCV_SaureusVsParent_replicate_3

description: Biological replicate 3 of 4


title: patient Pre ECP, biological rep2

description: Gene expression data


title: Tissue_BC_Tamoxifen_A101

city: Woburn

first: Christos

last: Hatzis

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

description: FL1094 A101.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A or Plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX (MDA) or 3000 (JBI).

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html). MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 1322 breast cancer specific genes.

source_name: tissue from breast tumor excision

label_protocol: A single-round of T7 amplification was used to generate biotin-labeled cRNA for hybridization.  At least 1 ug of RNA was used for cRNA synthesis.

extract_protocol: Total RNA was extracted from fresh frozen tissue specimens from breast cancer patients using Qiagen RNeasy columns.

tag: patient id

tag: profiling lab

value: MDA

tag: tissue

value: breast cancer

tag: estrogen receptor (er) status

value: ER+

tag: endocrine therapy

value: Tamoxifen treatment for 5 years

tag: nodal status (0=negative, 1=positive, na=not applicable)

tag: distant relapse (1=dr, 0 censored)

tag: event time (years)


title: Tissue_BC_Tamoxifen_A100

description: FL1093 A100.CEL


title: Mature mushrooms

type: SAGE

anchor: DpnII

city: Utrecht

last: Wösten

address: Padualaan 8

country: Netherlands

institute: Utrecht University

description: Anchoring enzyme: DpnII

data_processing: Tags of 16 bp were identified using custom scripts. Note that the restriction site of DpnII (GATC) is not included in these 16 bp.

organism: Schizophyllum commune

source_name: Mushrooms

growth_protocol: Mature mushrooms of 3 days old were picked from dikaryotic cultures that had grown for 8 days in the light.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified over a column (Qiagen RNeasy Mini). PolyA RNA was isolated using oligo-dT beads.

tag: developmental stage

value: mature mushrooms

value: Dikaryon, resulting from a cross of the co-isogenic monokaryotic strains 4-40 (CBS 340.81) and 4-39 (CBS 341.81)


title: Stage_I_Aggregates

description: Anchoring enzyme: DpnII

source_name: Stage I Aggregates

growth_protocol: A 7-day-old dikaryotic colony grown on solid mnimal medium at 30 degrees C in the dark was homogenized in 200 ml Minimal Medium using a Waring blender for 1 min at low speed. 2 ml of the homogenized mycelium was spread out over a polycarbonate membrane that was placed on top of solidified minimal medium. The dikaryon was grown for 2 days in the light at 25 degrees C.

value: stage I aggregates

value: Dikaryon, resulting from a cross of the monokaryotic co-isogenic strains 4-40 (CBS 340.81) and 4-39 (CBS 341.81)


title: Stage_II_Primordia

description: Anchoring enzyme: DpnII

source_name: Stage II Primordia

growth_protocol: A 7-day-old dikaryotic colony grown on solid mnimal medium at 30 degrees C in the dark was homogenized in 200 ml Minimal Medium using a Waring blender for 1 min at low speed. 2 ml of the homogenized mycelium was spread out over a polycarbonate membrane that was placed on top of solidified minimal medium. The dikaryon was grown for 4 days in the light at 25 degrees C.

value: stage II primordia


title: Glycine soja, roots from 3cm root apex, standard condition, replicate 2

tag: age

value: 21 days after germination

tag: treatment

tag: time


title: Monokaryon_vegetative_mycelium

description: Anchoring enzyme: DpnII

source_name: Monokaryon, vegetative mycelium

growth_protocol: A 7-day-old colony grown on solid mnimal medium at 30 degrees C in the dark was homogenized in 200 ml Minimal Medium using a Waring blender for 1 min at low speed. 2 ml of the homogenized mycelium was spread out over a polycarbonate membrane that was placed on top of solidified minimal medium. Vegetative monokaryotic mycelium was grown for 4 days in the light at 25 degrees C.

value: vegetative mycelium

value: Monokaryon, strain 4-40 (CBS 340.81)


title: Tissue_BC_Tamoxifen_A99

description: FL1092 A99.CEL


title: Tissue_BC_Tamoxifen_A98

description: FL1091 A98.CEL


title: patient Post ECP, biological rep5

description: Gene expression data

source_name: GVHD patient Post ECP

tag: disease state

value: graft-versus host disease

tag: dose

value: post ECP

value: Treated with ECP and Incubated overnight


title: Tissue_BC_Tamoxifen_A97

description: FL1090 A97.CEL


title: Tissue_BC_Tamoxifen_A95

description: FL1088 A95.CEL


title: Tissue_BC_Tamoxifen_A94

description: FL1102 A94.CEL


title: Tissue_BC_Tamoxifen_A91

description: FL1099 A91.CEL


title: Tissue_BC_Tamoxifen_A92

description: FL1100 A92.CEL


title: Tissue_BC_Tamoxifen_A90

description: FL1098 A90.CEL


title: Tissue_BC_Tamoxifen_A89

description: FL1097 A89.CEL


title: Tissue_BC_Tamoxifen_A88

description: FL1096 A88.CEL


title: Tissue_BC_Tamoxifen_A85

description: FL1086 A85.CEL


title: Tissue_BC_Tamoxifen_A79

description: FL1080 A79.CEL


title: Tissue_BC_Tamoxifen_A83

description: FL1084 A83.CEL


title: Tissue_BC_Tamoxifen_A77

description: FL1078 A77.CEL


title: Tissue_BC_Tamoxifen_A87

description: FL1095 A87.CEL


title: Tissue_BC_Tamoxifen_A72

description: FL1073 A72.CEL


title: Tissue_BC_Tamoxifen_A73

description: FL1074 A73.CEL


title: Tissue_BC_Tamoxifen_A76

description: FL1077 A76.CEL


title: Tissue_BC_Tamoxifen_A71

description: FL1072 A71.CEL


title: Tissue_BC_Tamoxifen_A69

description: FL1070 A69.CEL


title: Tissue_BC_Tamoxifen_A68

description: FL1069 A68.CEL


title: Tissue_BC_Tamoxifen_A67

description: FL1068 A67.CEL


title: Tissue_BC_Tamoxifen_A66

description: FL1067 A66.CEL


title: Tissue_BC_Tamoxifen_A65

description: FL1066 A65.CEL


title: Tissue_BC_Tamoxifen_A64

description: FL1065 A64.CEL


title: Tissue_BC_Tamoxifen_A60

description: FL1061 A60.CEL


title: Tissue_BC_Tamoxifen_A57

description: FL1058 A57.CEL


title: Tissue_BC_Tamoxifen_A58

description: FL1059 A58.CEL


title: Tissue_BC_Tamoxifen_A53

description: FL1053 A52.CEL


title: Tissue_BC_Tamoxifen_A49

description: FL1050 A49.CEL


title: Tissue_BC_Tamoxifen_A78

description: FL1079 A78.CEL


title: Tissue_BC_Tamoxifen_A40

description: FL1042 A40.CEL


title: Tissue_BC_Tamoxifen_A86

description: FL1087 A86.CEL


title: Tissue_BC_Tamoxifen_A80

description: FL1081 A80.CEL


title: Tissue_BC_Tamoxifen_A81

description: FL1082 A81.CEL


title: Tissue_BC_Tamoxifen_A51

description: FL1052 A51.CEL


title: Tissue_BC_Tamoxifen_A47

description: FL1048 A47.CEL


title: Tissue_BC_Tamoxifen_A50

description: FL1051 A50.CEL


title: Tissue_BC_Tamoxifen_A74

description: FL1075 A74.CEL


title: Tissue_BC_Tamoxifen_A45

description: FL999 A45.CEL


title: Tissue_BC_Tamoxifen_A63

description: FL1064 A63.CEL


title: Tissue_BC_Tamoxifen_A55

description: FL1056 A55.CEL


title: Tissue_BC_Tamoxifen_A62

description: FL1063 A62.CEL


title: Tissue_BC_Tamoxifen_A42

description: FL 1044 A42.CEL


title: Tissue_BC_Tamoxifen_A96

description: FL1089 A96.CEL


title: Tissue_BC_Tamoxifen_A54

description: FL1055 A54.CEL


title: Tissue_BC_Tamoxifen_A84

description: FL1085 A84.CEL


title: Tissue_BC_Tamoxifen_A70

description: FL1071 A70.CEL


title: Tissue_BC_Tamoxifen_A59

description: Fl1060 A59.CEL


title: Tissue_BC_Tamoxifen_A31

description: FL1033 A31.CEL


title: Tissue_BC_Tamoxifen_A56

description: FL1057 A56.CEL


title: Tissue_BC_Tamoxifen_A61

description: FL1062 A61.CEL


title: Tissue_BC_Tamoxifen_A93

description: FL1101 A93.CEL


title: Tissue_BC_Tamoxifen_A36

description: FL 1038 A36.CEL


title: Tissue_BC_Tamoxifen_A41

description: FL1043 A41.CEL


title: Tissue_BC_Tamoxifen_A46

description: FL1047 A46.CEL


title: Tissue_BC_Tamoxifen_A37

description: FL 1039 A37.CEL


title: Tissue_BC_Tamoxifen_A44

description: FL1046 A44.CEL


title: Tissue_BC_Tamoxifen_A82

description: FL1083 A82.CEL


title: Tissue_BC_Tamoxifen_A34

description: FL 1036 A34.CEL


title: Tissue_BC_Tamoxifen_A29

description: FL1031 A29.CEL


title: Tissue_BC_Tamoxifen_A23

description: FL1025 A23.CEL


title: Tissue_BC_Tamoxifen_A43

description: FL1045 A43.CEL


title: Tissue_BC_Tamoxifen_A48

description: FL1049 A48.CEL


title: Tissue_BC_Tamoxifen_A24

description: FL1026 A24.CEL


title: Tissue_BC_Tamoxifen_A35

description: FL 1037 A35.CEL


title: Tissue_BC_Tamoxifen_A38

description: FL 1040 A38.CEL


title: Tissue_BC_Tamoxifen_A19

description: FL1021 A19.CEL


title: Tissue_BC_Tamoxifen_A39

description: FL1041 A39.CEL


title: Tissue_BC_Tamoxifen_A16

description: FL1019 A16.CEL


title: Tissue_BC_Tamoxifen_A33

description: FL 1035 A33.CEL


title: Tissue_BC_Tamoxifen_A32

description: FL 1034 A32.CEL


title: Tissue_BC_Tamoxifen_A12

description: FL1015 A12.CEL


title: Tissue_BC_Tamoxifen_A18

description: FL1020 A18.CEL


title: Tissue_BC_Tamoxifen_A25

description: FL1027 A25.CEL


title: Tissue_BC_Tamoxifen_A30

description: FL1032 A30.CEL


title: Tissue_BC_Tamoxifen_F95


title: Tissue_BC_Tamoxifen_F98


title: Tissue_BC_Tamoxifen_A09

description: FL1012 A09.CEL


title: Tissue_BC_Tamoxifen_A28

description: FL1030 A28.CEL


title: Tissue_BC_Tamoxifen_A04

description: FL1008 A04.CEL


title: Tissue_BC_Tamoxifen_A01

description: FL1005 A01.CEL


title: Tissue_BC_Tamoxifen_A06

description: FL1003 A06.CEL


title: Tissue_BC_Tamoxifen_F99


title: Tissue_BC_Tamoxifen_F94


title: Tissue_BC_Tamoxifen_A11

description: FL1014 A11.CEL


title: Tissue_BC_Tamoxifen_A22

description: FL1024 A22.CEL


title: Tissue_BC_Tamoxifen_A14

description: FL1017 A14.CEL


title: Tissue_BC_Tamoxifen_A17

description: FL1004 A17.CEL


title: Tissue_BC_Tamoxifen_A26

description: FL1028 A26.CEL


title: Tissue_BC_Tamoxifen_A10

description: FL1013 A10.CEL


title: Tissue_BC_Tamoxifen_A02

description: FL1006 A02.CEL


title: Tissue_BC_Tamoxifen_A08

description: FL1011 A08.CEL


title: Tissue_BC_Tamoxifen_A15

description: FL1018 A15.CEL


title: Tissue_BC_Tamoxifen_A05

description: FL1009 A05.CEL


title: Tissue_BC_Tamoxifen_A20

description: FL1022 A20.CEL


title: Tissue_BC_Tamoxifen_A21

description: FL1023 A21.CEL


title: Tissue_BC_Tamoxifen_F93


title: Tissue_BC_Tamoxifen_A07

description: FL1010 A07.CEL


title: Tissue_BC_Tamoxifen_F97


title: Tissue_BC_Tamoxifen_A03

description: FL1007 A03.CEL


title: Tissue_BC_Tamoxifen_A27

description: FL1029 A27.CEL


title: Tissue_BC_Tamoxifen_F89


title: Tissue_BC_Tamoxifen_F82


title: Tissue_BC_Tamoxifen_F91


title: Tissue_BC_Tamoxifen_F85


title: Tissue_BC_Tamoxifen_F81


title: Tissue_BC_Tamoxifen_F80


title: Tissue_BC_Tamoxifen_F83


title: Tissue_BC_Tamoxifen_F84


title: Tissue_BC_Tamoxifen_F90


title: Tissue_BC_Tamoxifen_F78


title: Tissue_BC_Tamoxifen_A13

description: FL1016 A13.CEL


title: Tissue_BC_Tamoxifen_F96


title: Tissue_BC_Tamoxifen_F88


title: Tissue_BC_Tamoxifen_F74


title: Tissue_BC_Tamoxifen_F76


title: Tissue_BC_Tamoxifen_F69


title: Tissue_BC_Tamoxifen_F72


title: Tissue_BC_Tamoxifen_F77


title: Tissue_BC_Tamoxifen_F75


title: Tissue_BC_Tamoxifen_F65


title: Tissue_BC_Tamoxifen_F73


title: Tissue_BC_Tamoxifen_F70


title: Tissue_BC_Tamoxifen_F67


title: Tissue_BC_Tamoxifen_F71


title: Tissue_BC_Tamoxifen_F66


title: Tissue_BC_Tamoxifen_F79


title: Tissue_BC_Tamoxifen_F55


title: Tissue_BC_Tamoxifen_F54


title: Tissue_BC_Tamoxifen_F59


title: Tissue_BC_Tamoxifen_F50


title: Tissue_BC_Tamoxifen_F64


title: Tissue_BC_Tamoxifen_F68


title: Tissue_BC_Tamoxifen_F56


title: Tissue_BC_Tamoxifen_F51


title: Tissue_BC_Tamoxifen_F61


title: Tissue_BC_Tamoxifen_F48


title: Tissue_BC_Tamoxifen_F63


title: Tissue_BC_Tamoxifen_F53


title: Tissue_BC_Tamoxifen_F45


title: Tissue_BC_Tamoxifen_F47


title: Tissue_BC_Tamoxifen_F86


title: Tissue_BC_Tamoxifen_F44


title: Tissue_BC_Tamoxifen_F62


title: Tissue_BC_Tamoxifen_F58


title: Tissue_BC_Tamoxifen_F38


title: Tissue_BC_Tamoxifen_F92


title: Tissue_BC_Tamoxifen_F39


title: Tissue_BC_Tamoxifen_F40


title: Tissue_BC_Tamoxifen_F57


title: Tissue_BC_Tamoxifen_F37


title: Tissue_BC_Tamoxifen_F52


title: Tissue_BC_Tamoxifen_F46


title: Tissue_BC_Tamoxifen_F36


title: Tissue_BC_Tamoxifen_F43


title: ZT21_rep2

city: Boston

first: Jonathan

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

description: AG16 (ZT21)/control (ZT0) = Hy5/Hy3

hyb_protocol: Hybridization was performed according to the Exiqon miRCURY LNA array manual using a Tecan hybridization station (Tecan, Austria). Samples were hybridized against a reference sample consisting of RNA pooled from HALO 0 rats.

scan_protocol: Scanning was done using a GenePix 4000B scanner and quantified with GenePix Pro 6.0.1.25.

data_processing: Data was background corrected and loess normalized using the R / Bioconductor package limma. Each spot is printed in quadruplicate on the arrays, and the median of each of these 4 spots is given here.

organism: Rattus norvegicus

source_name: control (ZT0)

label_protocol: Samples were labeled as Hy5 or Hy3 using the Exiqon miRCURY LNA microRNA Array labeling kit according to manufacturer's protocols.

extract_protocol: Total RNA from jejunum was extracted using the mirVana kit (Ambion; Austin, TX).

value: jejunum


title: ZT21_rep1

description: control (ZT0)/AG16 (ZT21) = Hy5/Hy3


title: ZT21_rep3

description: control (ZT0)/AG7 (ZT21) = Hy5/Hy3


title: ZT18_rep2

description: control (ZT0)/MD23 (ZT18) = Hy5/Hy3


title: ZT18_rep3

description: MD23 (ZT18)/control (ZT0) = Hy5/Hy3


title: ZT15_rep2

description: AG14 (ZT15)/control (ZT0) = Hy5/Hy3


title: ZT18_rep1

description: control (ZT0)/MD26 (ZT18) = Hy5/Hy3


title: Tissue_BC_Tamoxifen_F30


title: Tissue_BC_Tamoxifen_F19


title: Tissue_BC_Tamoxifen_F17


title: Tissue_BC_Tamoxifen_F22


title: Tissue_BC_Tamoxifen_F23


title: Tissue_BC_Tamoxifen_F27


title: Tissue_BC_Tamoxifen_F29


title: Tissue_BC_Tamoxifen_F34


title: Tissue_BC_Tamoxifen_F28


title: Tissue_BC_Tamoxifen_F35


title: Tissue_BC_Tamoxifen_F33


title: Tissue_BC_Tamoxifen_F25


title: Tissue_BC_Tamoxifen_F31


title: Tissue_BC_Tamoxifen_F20


title: ZT12_rep2

description: MD19 (ZT12)/control (ZT0) = Hy5/Hy3


title: ZT12_rep3

description: control (ZT0)/MD19 (ZT12) = Hy5/Hy3


title: ZT12_rep1

description: control (ZT0)/MD15 (ZT12) = Hy5/Hy3


title: Tissue_BC_Tamoxifen_F21


title: Tissue_BC_Tamoxifen_F15


title: Tissue_BC_Tamoxifen_F14


title: Tissue_BC_Tamoxifen_F13


title: Tissue_BC_Tamoxifen_F16


title: ZT15_rep1

description: control (ZT0)/AG6 (ZT15) = Hy5/Hy3


title: ZT15_rep3

description: control (ZT0)/AG14 (ZT15) = Hy5/Hy3


title: ZT6_rep2

description: control (ZT0)/MD11 (ZT6) = Hy5/Hy3


title: ZT3_rep3

description: AG17 (ZT3)/control (ZT0) = Hy5/Hy3


title: ZT9_rep1

description: control (ZT0)/AG27 (ZT9) = Hy5/Hy3


title: ZT9_rep2

description: AG27 (ZT9)/control (ZT0) = Hy5/Hy3


title: Tissue_BC_Tamoxifen_F12


title: ZT6_rep1

description: control (ZT0)/MD7 (ZT6) = Hy5/Hy3


title: ZT6_rep3

description: MD11 (ZT6)/control (ZT0) = Hy5/Hy3


title: ZT3_rep2

description: AG1 (ZT3)/control (ZT0) = Hy5/Hy3


title: ZT9_rep3

description: AG20 (ZT9)/control (ZT0) = Hy5/Hy3


title: Tissue_BC_Tamoxifen_F08


title: Tissue_BC_Tamoxifen_F07


title: Tissue_BC_Tamoxifen_F11


title: Tissue_BC_Tamoxifen_F10


title: Tissue_BC_Tamoxifen_F05


title: ZT3_rep1

description: control (ZT0)/AG1 (ZT3) = Hy5/Hy3


title: Tissue_BC_Tamoxifen_F06


title: Tissue_BC_Tamoxifen_F09


title: Tissue_BC_Tamoxifen_F04


title: Tissue_BC_Tamoxifen_F60


title: Tissue_BC_Tamoxifen_F01


title: Tissue_BC_Tamoxifen_F02


title: Tissue_BC_Tamoxifen_F18


title: Tissue_BC_Tamoxifen_F03


title: MDG 185 - breast - cancer

city: Oslo

first: Vilde

middle: Drageset

last: Haakensen

address: Montebello

department: Dept of Genetics

country: Norway

institute: The Norwegian Radium Hospital

description: 240507_MDG185_251239152517_S01_GE2-SSPE_91_2.txt

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (Surehyb enables/SSPE)

scan_protocol: Agilent scanner (Agilent Technologies, Santa Clara, CA)

data_processing: Feature Extraction 9.1.3.1 software and lowess normalization was used.

source_name: Biopsy from breast tumor

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit Protocol

extract_protocol: RNeasy Mini protocol, Qiagen, Valencia, CA

value: breast

tag: clinical characteristic/disease status

value: breast tumor

source_name: Universal reference

tag: reference source

value: Stratagene, LaJolla, CA


title: MDG 181 - breast - non-cancer

description: 220507_MDG181_251239152513_S01_GE2-SSPE_91_2.txt

source_name: Biopsy from benign lesion/irregularity

value: benign lesion/irregularity


title: MDG 183 - breast - non-cancer

description: 300507_MDG183_251239152485_S02_GE2-SSPE_91_2.txt

source_name: Biopsy from area with some mammographic density

value: area with some mammographic density


title: Tissue_BC_Tamoxifen_F32

value: MDA

value: breast cancer

value: ER+

value: Tamoxifen treatment for 5 years


title: MDG 184 - breast - cancer

description: 300507_MDG184_251239152518_S01_GE2-SSPE_91_2.txt


title: MDG 186 - breast - cancer

description: 300507_MDG186_251239152496_S02_GE2-SSPE_91_2.txt


title: Tissue_BC_Tamoxifen_F42


title: MDG 176 - breast - cancer

description: 210507_MDG176_251239152526_S01_GE2-SSPE_91_2.txt


title: MDG 171 - breast - cancer

description: 220507_MDG171_251239152515_S01_GE2-SSPE_91_2.txt


title: MDG 169 - breast - cancer

description: 061206-MDG169_251239138480_S01_GE2-SSPE_91_2.txt


title: MDG 170 - breast - cancer

description: 071107_MDG170_251239138171_S01_GE2-SSPE_91_2.txt


title: MDG 177 - breast - non-cancer

description: 240407_MDG177_251239138778_S01_GE2-SSPE_91_2.txt


title: MDG 175 - breast - non-cancer

description: 160507_MDG175_251239152669_S01_GE2-SSPE_91_2.txt


title: MDG 172 - breast - non-cancer

description: 210507_MDG172_251239152525_S01_GE2-SSPE_91_2.txt


title: MDG 180 - breast - non-cancer

description: 180407_MDG180_251239125706_S01_GE2-SSPE_91_2.txt


title: MDG 174 - breast - cancer

description: 101007_MDG174_251239138057_S02_GE2-SSPE_91_2.txt


title: MDG 179 - breast - cancer

description: 220507_MDG179_251239152512_S01_GE2-SSPE_91_2.txt


title: Tissue_BC_Tamoxifen_F26


title: MDG 178 - breast - non-cancer

description: 150507_MDG178_251239152494_S01_GE2-SSPE_91_2.txt


title: MDG 173 - breast - cancer

description: 030507_MDG173_251239138777_S01_GE2-SSPE_91_2.txt


title: MDG 168 - breast - cancer

description: 201206_MDG168_251239125718_S01_GE2-SSPE_91_2.txt


title: MDG 165 - breast - non-cancer

description: 180407_MDG165_251239126224_S02_GE2-SSPE_91_2.txt


title: MDG 166 - breast - non-cancer

description: 131206_MDG166_251239137849_S01_GE2-SSPE_91_2.txt


title: MDG 164 - breast - cancer

description: 131206_MDG164_251239137848_S01_GE2-SSPE_91_2.txt


title: MDG 162 - breast - non-cancer

description: 300507_MDG162_251239152497_S02_GE2-SSPE_91_2.txt


title: MDG 163 - breast - non-cancer

description: 190607_MDG163_251239138789_S01_GE2-SSPE_91_2.txt


title: MDG 159 - breast - cancer

description: 030107-mdg159_251239125705_S01_GE2-SSPE_91_2.txt


title: MDG 161 - breast - cancer

description: 081206_MDG161_251239138489_S01_GE2-SSPE_91_2.txt


title: MDG 154 - breast - cancer

description: 131206_MDG154_251239137847_S01_GE2-SSPE_91_2.txt


title: MDG 158 - breast - non-cancer

description: 240407_MDG158_251239138767_S01_GE2-SSPE_91_2.txt


title: MDG 157 - breast - cancer

description: 030107-mdg157_251239125704_S01_GE2-SSPE_91_2.txt


title: MDG 155 - breast - cancer

description: 240407_MDG155_251239138755_S01_GE2-SSPE_91_2.txt


title: MDG 153 - breast - cancer

description: 221107_MDG153_251239138040_S01_GE2-SSPE_91_2.txt


title: Tissue_BC_Tamoxifen_F24


title: MDG 151 - breast - cancer

description: 030107-mdg151_251239125703_S01_GE2-SSPE_91_2.txt


title: MDG 149 - breast - cancer

description: 281206-MDG149_251239126229_S01_GE2-SSPE_91_2.txt


title: MDG 152 - breast - cancer

description: 180407_MDG152_251239126223_S01_GE2-SSPE_91_2.txt


title: MDG 143 - breast - cancer

description: 240507_MDG143_251239152509_S01_GE2-SSPE_91_2.txt


title: MDG 137 - breast - cancer

description: 221107_MDG137_251239138042_S01_GE2-SSPE_91_2.txt


title: MDG 148 - breast - non-cancer

description: 240507_MDG148_251239152510_S01_GE2-SSPE_91_2.txt


title: MDG 146 - breast - non-cancer

description: 081206_MDG146_251239138485_S01_GE2-SSPE_91_2.txt


title: MDG 144 - breast - cancer

description: 281206-MDG144_251239126228_S01_GE2-SSPE_91_2.txt


title: MDG 139 - breast - non-cancer

description: 061206-MDG139_251239138478_S01_GE2-SSPE_91_2.txt


title: MDG 182 - breast - non-cancer

description: 210507_MDG182_251239152527_S01_GE2-SSPE_91_2.txt


title: MDG 145 - breast - non-cancer

description: 030507_MDG145_251239138776_S01_GE2-SSPE_91_2.txt


title: MDG 142 - breast - cancer

description: 160507_MDG142_251239152668_S01_GE2-SSPE_91_2.txt


title: MDG 141 - breast - cancer

description: 160507_MDG141_251239152667_S01_GE2-SSPE_91_2.txt


title: MDG 167 - breast - cancer

description: 081206_MDG167_251239138486_S01_GE2-SSPE_91_2.txt


title: MDG 150 - breast - non-cancer

description: 131206_MDG150_251239137846_S01_GE2-SSPE_91_2.txt


title: MDG 156 - breast - non-cancer

description: 240507_MDG156_251239152516_S01_GE2-SSPE_91_2.txt


title: MDG 130 - breast - non-cancer

description: 030507_MDG130_251239138774_S01_GE2-SSPE_91_2.txt


title: MDG 160 - breast - non-cancer

description: 081206_MDG160_251239138487_S01_GE2-SSPE_91_2.txt


title: MDG 135 - breast - cancer

description: 281206-MDG135_251239126227_S01_GE2-SSPE_91_2.txt


title: MDG 129 - breast - cancer

description: 190607_MDG129_251239138788_S01_GE2-SSPE_91_2.txt


title: MDG 147 - breast - non-cancer

description: 150507_MDG147_251239152491_S01_GE2-SSPE_91_2.txt


title: MDG 132 - breast - cancer

description: 150507_MDG132_251239152495_S01_GE2-SSPE_91_2.txt


title: MDG 125 - breast - non-cancer

description: 210507_MDG125_251239152523_S01_GE2-SSPE_91_2.txt


title: MDG 140 - breast - non-cancer

description: 061206-MDG140_251239138479_S01_GE2-SSPE_91_2.txt


title: MDG 133 - breast - cancer

description: 281106_MDG133_251239138474_S01_GE2-SSPE_91_2.txt


title: MDG 131 - breast - cancer

description: 210507_MDG131_251239152524_S01_GE2-SSPE_91_2.txt


title: MDG 118 - breast - non-cancer

description: 121206_MDG118_251239137882_S01_GE2-SSPE_91_2.txt


title: MDG 124 - breast - non-cancer

description: 201206_MDG124_251239125716_S01_GE2-SSPE_91_2.txt


title: MDG 123 - breast - cancer

description: 081206_MDG123_251239138484_S01_GE2-SSPE_91_2.txt


title: MDG 122 - breast - cancer

description: 061206-MDG122_251239138477_S01_GE2-SSPE_91_2.txt


title: MDG 134 - breast - cancer

description: 121206_MDG134_251239137884_S01_GE2-SSPE_91_2.txt


title: MDG 121 - breast - cancer

description: 061206-MDG121_251239138476_S01_GE2-SSPE_91_2.txt


title: MDG 119 - breast - non-cancer

description: 121206_MDG119_251239137883_S01_GE2-SSPE_91_2.txt


title: MDG 127 - breast - non-cancer

description: 030507_MDG127_251239138773_S01_GE2-SSPE_91_2.txt


title: MDG 126 - breast - cancer

description: 281106_MDG126_251239137999_S01_GE2-SSPE_91_2.txt


title: MDG 109 - breast - non-cancer

description: 091007_MDG109_251239138785_S01_GE2-SSPE_91_2.txt


title: MDG 117 - breast - cancer

description: 131206_MDG117_251239137845_S01_GE2-SSPE_91_2.txt


title: MDG 113 - breast - non-cancer

description: 150507_MDG113_251239152492_S01_GE2-SSPE_91_2.txt


title: MDG 110 - breast - non-cancer

description: 201206_MDG110_251239125702_S01_GE2-SSPE_91_2.txt


title: MDG 104 - breast - cancer

description: 061206-MDG104_251239138475_S01_GE2-SSPE_91_2.txt


title: MDG 108 - breast - non-cancer

description: 071107_MDG108_251239138058_S01_GE2-SSPE_91_2.txt


title: MDG 111 - breast - non-cancer

description: 300507_MDG111_251239152484_S01_GE2-SSPE_91_2.txt


title: MDG 114 - breast - non-cancer

description: 180407_MDG114_251239126222_S01_GE2-SSPE_91_2.txt


title: MDG 106 - breast - cancer

description: 081206_MDG106_251239138483_S01_GE2-SSPE_91_2.txt


title: MDG 112 - breast - cancer

description: 121206_MDG112_251239138144_S01_GE2-SSPE_91_2.txt


title: MDG 101 - breast - non-cancer

description: 160507_MDG101_251239152535_S01_GE2-SSPE_91_2.txt


title: MDG 107 - breast - non-cancer

description: 131206_MDG107_251239138141_S01_GE2-SSPE_91_2.txt


title: MDG 116 - breast - cancer

description: 300507_MDG116_251239152482_S01_GE2-SSPE_91_2.txt


title: MDG 100 - breast - cancer

description: 091007_MDG100_251239138784_S01_GE2-SSPE_91_2.txt


title: MDG 098 - breast - cancer

description: 190607_MDG098_251239152501_S01_GE2-SSPE_91_2.txt


title: MDG 103 - breast - cancer

description: 210507_MDG103_251239152522_S01_GE2-SSPE_91_2.txt


title: MDG 120 - breast - non-cancer

description: 281106_MDG120_251239137998_S01-2_GE2-SSPE_91_2.txt


title: MDG 091 - breast - cancer

description: 161106_MDG091_251239137996_S01_GE2-SSPE_91_2.txt


title: MDG 086 - breast - non-cancer

description: 281106_MDG086_251239137997_S01_GE2-SSPE_91_2.txt


title: MDG 093 - breast - non-cancer

description: 201206_MDG093_251239126226_S01_GE2-SSPE_91_2.txt


title: MDG 084 - breast - non-cancer

description: 200407_MDG084_251239138759_S01_GE2-SSPE_91_2.txt


title: MDG 085 - breast - cancer

description: 081206_MDG085_251239138481_S01_GE2-SSPE_91_2.txt


title: MDG 082 - breast - cancer

description: 131206_MDG082_251239137896_S01_GE2-SSPE_91_2.txt


title: MDG 092 - breast - non-cancer

description: 081206_MDG092_251239138482_S01_GE2-SSPE_91_2.txt


title: MDG 083 - breast - cancer

description: 200407_MDG083_251239138758_S01_GE2-SSPE_91_2.txt


title: MDG 128 - breast - cancer

description: 160507_MDG128_251239152666_S01_GE2-SSPE_91_2.txt


title: MDG 081 - breast - non-cancer

description: 121206_MDG081_251239138142_S01_GE2-SSPE_91_2.txt


title: MDG 090 - breast - cancer

description: 121206_MDG090_251239138143_S01_GE2-SSPE_91_2.txt


title: MDG 073 - breast - cancer

description: 240507_MDG073_251239152508_S01_GE2-SSPE_91_2.txt


title: MDG 078 - breast - non-cancer

description: 131206_MDG078_251239137895_S01_GE2-SSPE_91_2.txt


title: MDG 070 - breast - non-cancer

description: 030507_MDG070_251239138780_S01_GE2-SSPE_91_2.txt


title: MDG 069 - breast - cancer

description: 300507_MDG069_251239152481_S01_GE2-SSPE_91_2.txt


title: MDG 066 - breast - non-cancer

description: 160507_MDG066_251239152534_S01_GE2-SSPE_91_2.txt


title: MDG 077 - breast - non-cancer

description: 221107_MDG077_251239138043_S01_GE2-SSPE_91_2.txt


title: MDG 068 - breast - non-cancer

description: 240407_MDG068_251239138765_S01_GE2-SSPE_91_2.txt


title: MDG 063 - breast - non-cancer

description: 220507_MDG063_251239152511_S01_GE2-SSPE_91_2.txt


title: MDG 079 - breast - non-cancer

description: 030107-mdg079_251239125949_S01_GE2-SSPE_91_2.txt


title: Human_Cortex_Control_1

first: Kazue

last: Hashimoto-Torii

address: 333 Cedar St.

hyb_protocol: Samples were hybridized according to Affymetrix protocols

scan_protocol: Standard Affymetrix scan protocol for gene expression profiling

data_processing: Data were processed (RMA) using Partek Genomics Suite.

label_protocol: standard Affymetrix 3’ IVT labeling protocol

extract_protocol: total RNA was extracted using Qiagen RNeasy Mini kit

tag: agent

value: Control

tag: stage


title: Tissue_F98_JBI_U133A

description: F98 A.CEL

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

extract_protocol: Total RNA was extracted from fresh frozen breast cancer tissue using Qiagen RNeasy columns.

tag: patient id

tag: lab

value: JBI

tag: array platform_id


title: Human_Cortex_Ethanol_2

value: Ethanol


title: Tissue_F91_JBI_U133A

description: F91 A.CEL

tag: tissue


title: MDG 060 - breast - non-cancer

description: 180407_MDG060_251239126221_S01_GE2-SSPE_91_2.txt


title: Tissue_F93_JBI_PLUS2

description: F93 Plus.CEL


title: Tissue_F98_JBI_PLUS2

description: F98 Plus.CEL


title: Tissue_F90_JBI_PLUS2

description: F90 Plus.CEL


title: MDG 105 - breast - cancer

description: 20040_MDG105_251239138760_S01_GE2-SSPE_91_2.txt


title: Human_Cortex_Ethanol_1


title: MDG 059 - breast - non-cancer

description: 190607_MDG059_251239152499_S01_GE2-SSPE_91_2.txt


title: Tissue_F90_JBI_U133A

description: F90 A.CEL


title: Tissue_F91_JBI_PLUS2

description: F91 Plus.CEL


title: Tissue_F76_JBI_PLUS2

description: F76 Plus.CEL


title: MDG 062 - breast - non-cancer

description: 240507_MDG062_251239152506_S01_GE2-SSPE_91_2.txt


title: Tissue_F93_JBI_U133A

description: F93 A.CEL


title: MDG 064 - breast - non-cancer

description: 240507_MDG064_251239152507_S01_GE2-SSPE_91_2.txt


title: Human_Cortex_Control_2


title: Tissue_F68_JBI_PLUS2

description: F68 Plus.CEL


title: Tissue_F80_JBI_U133A

description: F80 A.CEL


title: Tissue_F71_JBI_PLUS2

description: F71 Plus.CEL


title: Tissue_F63_JBI_PLUS2

description: F63 Plus.CEL


title: Tissue_F74_JBI_PLUS2

description: F74 Plus.CEL


title: Tissue_F80_JBI_PLUS2

description: F80 Plus.CEL


title: Tissue_F76_JBI_U133A

description: F76 A.CEL


title: MDG 058 - breast - cancer

description: 071107_MDG058_251239138172_S01_GE2-SSPE_91_2.txt


title: Tissue_F59_JBI_PLUS2

description: F59 Plus.CEL


title: MDG 057 - breast - cancer

description: 190607_MDG057_251239152498_S01_GE2-SSPE_91_2.txt


title: MDG 099 - breast - non-cancer

description: 150507_MDG099_251239152493_S01_GE2-SSPE_91_2.txt


title: MDG 056 - breast - cancer

description: 220507_MDG056_251239152530_S01_GE2-SSPE_91_2.txt


title: MDG 115 - breast - cancer

description: 030507_MDG115_251239138782_S01_GE2-SSPE_91_2.txt


title: Tissue_F19_JBI_PLUS2

description: F19 Plus.CEL


title: Tissue_F71_JBI_U133A

description: F71 A.CEL


title: Tissue_F35_JBI_PLUS2

description: F35 Plus.CEL


title: Tissue_F55_JBI_PLUS2

description: F55 Plus.CEL


title: Tissue_F68_JBI_U133A

description: F68 A.CEL


title: MDG 055 - breast - cancer

description: 071107_MDG055_251239138059_S01_GE2-SSPE_91_2.txt


title: Tissue_F13_JBI_PLUS2

description: F13 Plus.CEL


title: MDG 051 - breast - non-cancer

description: 030107-mdg051_251239125948_S01_GE2-SSPE_91_2.txt


title: Tissue_F93_MDA_PLUS2

description: U133 plus 2.0_80_FL_271_04_08_08.CEL


title: Tissue_F98_MDA_PLUS2

description: U133 plus 2.0_80_FL_272_04_08_08.CEL


title: Tissue_F90_MDA_PLUS2

description: U133 plus 2.0_80_FL_270_04_08_08.CEL


title: MDG 052 - breast - non-cancer

description: 180407_MDG052_251239126220_S01_GE2-SSPE_91_2.txt


title: MDG 054 - breast - cancer

description: 240407_MDG054_251239138764_S01_GE2-SSPE_91_2.txt


title: Tissue_F59_JBI_U133A

description: F59 A.CEL


title: Tissue_F74_JBI_U133A

description: F74 A.CEL


title: Tissue_F74_MDA_PLUS2

description: U133 plus 2.0_80_FL_257_03_19_08.CEL


title: Tissue_F80_MDA_PLUS2

description: U133 plus 2.0_80_FL_258_03_19_08.CEL


title: Tissue_F91_MDA_PLUS2

description: U133 plus 2.0_80_FL_259_03_19_08.CEL


title: Tissue_F55_JBI_U133A

description: F55 A.CEL


title: Tissue_F63_JBI_U133A

description: F63 A.CEL


title: Tissue_F38_JBI_U133A

description: F38 A.CEL


title: S.pombe_mis4-367_37°C_rep3

city: Bordeaux

first: Sonia

last: Dheur

address: 1, Rue Camille Saint-Saëns

department: Université Bordeaux 2

country: France

institute: IBGC CNRS UMR5095

description: Gene expression data from G1-arrested cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Yeast Genome 2.0 microarrays. Microarrays were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G System.

data_processing: The data processing (background correction, normalization and probe summarization) was performed using the RMA algorithm with the Stratagene ArrayAssist Expression Software.

organism: Schizosaccharomyces pombe

source_name: S. pombe, mis4-367 at 37°C

label_protocol: Biotinylated cRNA were prepared from 5 ug total RNA using the GeneChip One-Cycle Target Labelling Kit from Affymetrix

growth_protocol: Cells bearing ura4+-pREP2-res1 were grown in cycling conditions at 25°C in EMM2 containing 20 mg thiamine to repress expression of the C-terminal fragment of Res1.

extract_protocol: Total RNA was extracted using standard hot phenol method followed by a DNAse I treatment and a cleanup step on a QIAGEN RNeasy mini Kit column

treatment_protocol: Cells were harvested, washed and inoculated into fresh EMM2 without thiamine at a density of 3x105 cells/ml. Cell proliferation ceased after seven doublings. Once arrested, cells were shifted to 37°C for 2 hours.

tag: genotype

value: h- ura4+-pREP2-res1 mis4-367

tag: temperature

tag: biological replicate


title: Tissue_F71_MDA_PLUS2

description: U133 plus 2.0_80_FL_256_03_19_08.CEL


title: MDG 047 - breast - non-cancer

description: 091105_MDG047_251239126089_S01_Green_A01_GE2-SSPE_91_2.txt


title: Tissue_F76_MDA_PLUS2

description: U133 plus 2.0_80_FL_265_03_28_08.CEL


title: MDG 048 - breast - non-cancer

description: 281206-MDG048_251239125933_S01_GE2-SSPE_91_2.txt


title: MDG 043 - breast - non-cancer

description: 281206-MDG043_251239125932_S01_GE2-SSPE_91_2.txt


title: S.pombe_mis4-367_37°C_rep1


title: Tissue_F19_JBI_U133A

description: F19 A.CEL


title: Tissue_F63_MDA_PLUS2

description: U133 plus 2.0_80_FL_254_03_18_08.CEL


title: S.pombe_mis4-367_25°C_rep3

source_name: S. pombe, mis4-367 at 25°C


title: S.pombe_mis4-367_37°C_rep2


title: MDG 040 - breast - non-cancer

description: 221107_MDG040_251239138174_S01_GE2-SSPE_91_2.txt


title: S.pombe_mis4-367_25°C_rep1


title: Tissue_F55_MDA_PLUS2

description: U133 plus 2.0_80_FL_253_03_18_08.CEL


title: Tissue_F93_MDA_U133A


title: S.pombe_mis4-367_25°C_rep2


title: Tissue_F68_MDA_PLUS2

description: U133 plus 2.0_80_FL_264_03_28_08.CEL


title: Tissue_F59_MDA_PLUS2

description: U133 plus 2.0_80_FL_263_03_28_08.CEL


title: MDG 035 - breast - non-cancer

description: 160507_MDG035_251239152533_S01_GE2-SSPE_91_2.txt


title: Tissue_F98_MDA_U133A


title: S.pombe_mis4+_37°C_rep2

source_name: S. pombe, mis4+ at 37°C

value: h- ura4+-pREP2-res1 mis4+


title: Tissue_F91_MDA_U133A

description: FL1213 F91.CEL


title: MDG 036 - breast - non-cancer

description: 081105_MDG036_251239126086_S01_Green_A01_GE2-SSPE_91_2.txt


title: Tissue_F38_MDA_PLUS2

description: U133 plus 2.0_80_FL_262_03_28_08.CEL


title: Tissue_F35_MDA_PLUS2

description: U133 plus 2.0_80_FL_252_03_18_08.CEL


title: MDG 031 - breast - non-cancer

description: 081105_MDG031_251239125939_S01_Green_A01_GE2-SSPE_91_2.txt


title: Tissue_F13_JBI_U133A

description: F13 A.CEL


title: Tissue_F90_MDA_U133A


title: MDG 030 - breast - non-cancer

description: 201206_MDG030_251239126225_S06_GE2-SSPE_91_2.txt


title: S.pombe_mis4+_37°C_rep1


title: Tissue_F80_MDA_U133A

description: FL1212 F80.CEL


title: S.pombe_mis4+_37°C_rep3


title: S.pombe_mis4+_25°C_rep3

source_name: S. pombe, mis4+ at 25°C


title: Tissue_F76_MDA_U133A


title: MDG 027 - breast - non-cancer

description: 011105_MDG027_251239125712_S01_Green_A01_GE2-SSPE_91_2.txt


title: MDG 020 - breast - non-cancer

description: 210507_MDG020_251239152670_S01_GE2-SSPE_91_2.txt


title: Tissue_F74_MDA_U133A

description: FL1211 F74.CEL


title: Tissue_F71_MDA_U133A

description: FL1210 F71.CEL


title: S.pombe_mis4+_25°C_rep1


title: MDG 028 - breast - non-cancer

description: 300507_MDG028_251239152520_S01_GE2-SSPE_91_2.txt


title: Tissue_F68_MDA_U133A


title: Tissue_F35_JBI_U133A

description: F35 A.CEL


title: MDG 019 - breast - non-cancer

description: 031105_MDG019_251239126219_S01_Green_A01_GE2-SSPE_91_2.txt


title: MDG 015 - breast - non-cancer

description: 220507_MDG015_251239152529_S01_GE2-SSPE_91_2.txt