title: WT-Saline-2 [gene expression]


title: WT-Veh-4 [expression]

status: Public on May 23 2016

type: RNA

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

department: Pathology

country: USA

institute: Emory University

hyb_protocol: Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001) following their standard operating protocol.

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Mus musculus

source_name: Heart, WT, Vehicle treated

label_protocol: DNA labeling was completed using NimbleGen labeling Kit (Cat # 06370438001) following their standard operating protocol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc.) and cDNA was synthesized using Superscript Double-Stranded cDNA Synthesis kit (Invitrogen/Life Technologies). cDNA quality was determined using a Spectramax 190 plate reader for A260 and A280 absorbance determination along with gel electrophoresis.

treatment_protocol: All heart samples were obtained fresh. Each sample was quickly flash frozen in liquid nitrogen and stored at -80°C until needed.

tag: strain/background

tag: genotype/variation

value: wild-type

tag: tissue

value: left ventricle

tag: treatment

value: vehicle (1%CMC)


title: miR-204 overexpressed MCF10A

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

country: South Korea

institute: dongguk unversity

description:
SAMPLE 2
Mammary gland; breast

hyb_protocol: Following fragmentation, 0.75ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina Genomestudio v2011.1 (Gene Expresion Module v1.9.0)

label: biotin

organism: Homo sapiens

source_name: miR-204 overexpressed MCF10A

label_protocol: Biotinylated cRNA were prepared from 0.55ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

extract_protocol: RNA was extracted with QIAzol Lysis reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: female

value: breast

tag: cell line

value: normal breast cell line MCF10A

tag: cell type

value: epithelial

value: miR-204 overexpression


title: miR-204 overexpressed MCF7

description:
SAMPLE 5
mammary gland, breast; derived from metastatic site: pleural

source_name: miR-204 overexpressed MCF7

value: breast cancer cell line MCF-7


title: miR-NC overexpressed MCF7

description:
SAMPLE 4
mammary gland, breast; derived from metastatic site: pleural

source_name: miR-NC overexpressed MCF7

value: control


title: dyskeratosis congenita sample 4

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing:
Data pre-processing of DNA methylation arrays was performed with BeadStudio Methylation Module (Genomestudio 2011.1 (Modul M Version 1.9.0)). The data are normalized to the internal controls (beta-values of at least 3 beads [technical replica] - otherwise no beta-value is provided) as suggested by Illumina s Standard Procedure (page 49 of GenomeStudio_M_Module_v1.8.pdf; Normalization to Internal Controls).
the non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

source_name: dyskeratosis congenita_whole blood

label_protocol: Standard Illumina labelling protocol

extract_protocol: Genomic DNA was isolated with the QIAamp DNA Blood Midi Kit (Qiagen, Hilden, Germany). DNA quality was assessed with a NanoDrop ND-1000 spectrometer and by gel electrophoresis.

tag: disease

value: dyskeratosis congenita

tag: age (yrs)

value: whole blood


title: WT-Veh-2 [expression]


title: WT-AZT-2 [expression]

source_name: Heart, WT, AZT treated

value: AZT


title: miR-211 overexpressed MCF10A

description:
SAMPLE 3
Mammary gland; breast

source_name: miR-211 overexpressed MCF10A

value: miR-211 overexpression


title: dyskeratosis congenita sample 2


title: miR-NC overexpressed MCF10A

description:
SAMPLE 1
Mammary gland; breast

source_name: miR-NC overexpressed MCF10A


title: WT-Veh-1 [expression]


title: WT-Veh-3 [expression]


title: dyskeratosis congenita sample 3


title: 2102EP in vivo 6w

status: Public on May 22 2016

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

institute: University Hospital Düsseldorf

description:
Sample 8
Tumor tissue from 2102EP 6 weeks after xenografting

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with Bioconductor R. Normalized values were tranformed into log2-values.
Expression values were quantile normalized using the 'limma'-software-package.

source_name: Tumor tissue from 2102EP_6 wks after xenografting

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol:
cultivation protocol: TCam-2 and 2102EP cells were cultivated as published (Nettersheim et al., 2013, PubMed ID: 24386123)
xenografting protocol: TCam-2 and 2102EP cells were xenografted in CD1 nude mice as published previously (Nettersheim et al., 2012, Pubmed ID: 22489004)

extract_protocol: RNA was extracted with Trizol reagent (Sigma-Aldrich) as already published (Nettersheim et al., 2012, Pubmed ID: 22489004), followed by clean-up  treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: host strain

value: CD1 nude mice

tag: xenografted with

value: 2120EP embryonal carcinoma

tag: time point

value: 6 weeks after xenografting

tag: tissue type

value: Embryonal carcinoma-like

tag: tissue/cell type

value: Tumor tissue from 2102EP


title: dyskeratosis congenita sample 1


title: SOX2 -/- clone 5

description:
Sample 6
Tumor tissue from TCam-2 SOX2 -/- clone 5 6 weeks after xenografting

source_name: Tumor tissue from TCam-2 SOX2 -/- clone_6 wks after xenografting

value: TCam-2 SOX2 -/- clone 5

value: Seminoma-like

value: tumors of TCam-2 (SOX2 -/- clone)


title: SOX2 -/- clone 1

description:
Sample 2
Tumor tissue from TCam-2 SOX2 -/- clone 1 6 weeks after xenografting

value: TCam-2 SOX2 -/- clone 1


title: SOX2 -/- clone 4

description:
Sample 5
Tumor tissue from TCam-2 SOX2 -/- clone  6 weeks after xenografting

value: TCam-2 SOX2 -/- clone 4


title: TCam-2 in vivo 6w

description:
Sample 7
Tumor tissue from TCam-2 6 weeks after xenografting

source_name: Tumor tissue from TCam-2_6 wks after xenografting

value: parental TCam-2 cells

value: tumors of TCam-2 (parental clone)


title: NHDF_stimulated with IBS17_rep3

city: Strasbourg

first: Frédéric

last: Schramm

address: 3, rue Koeberlé

department: University of Strasbourg

country: France

institute: EA 7290 Early Bacterial Virulence

scan_protocol: Standard Illumina scanning protocol with Illumina Iscan

data_processing: The data were normalised using quantile normalisation with Genomestudio software

source_name: NHDF cells batch 1011801_2, stimulated with IBS17

label_protocol: Biotinylated cRNA were prepared with the ambion amp Kit for Illumina Beadchip

growth_protocol: NHDF cells at passage 5 are maintained in FGM2 medium in a 24-well plate. At confluence and one day before Borrelia activation, FGM2 medium is replaced by FGM medium without fetal calf serum.

extract_protocol: After removal of the supernatant, fibroblasts are directly suspended in Trizol and stored at -80°C until use, followed by clean-up with Qiagen Rneasy Mini kit. Quality control was performed with 2100 Agilent Bioanalyzer

treatment_protocol: Fibroblasts are stimulated with B. burgdorferi spirochetes at MOI of 100:1 in FGM for 24 hours; unstimulated cells are maintened in FGM alone for 24 hours.

tag: agent

value: Borrelia garinii strain IBS17

value: male

tag: age

tag: race

value: caucasian

tag: anatomical region

value: temple


title: Distal_Colon Wild_Type_a1line_rep1

city: Riverside

first: Eugene

middle: L

last: Bolotin

state: CA

address: 900 university ave

department: Cell Biology and Neuroscience

institute: UC Riverside

description: WT controls for a1 HMZ line: express P1- and P2-HNF4a in the colon

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized to Affymetrix Mouse Exon 1.0 Arrays as per the GeneChip Expression Analysis Technical Manual (2005-2009); Affymetric Fluidics Station 450 was used for staining and washing

scan_protocol: Affymetrix GeneChip Workstation with a Scanner 3000

data_processing: Bioconductor packages: RMA, exonmap, affy

source_name: Distal colon from WTa1 mice

label_protocol: Sense strand cDNA probes were prepared using Agilent Whole Transcript Expression Assay

growth_protocol: RNA from distal colon of young adult male mice (12-16 weeks old) on standard lab chow fed ad libitum, harvested between11 am and 4 pm

extract_protocol: Total RNA extracted (Trizol Reagent and Qiagen RNA Extraction kit)

treatment_protocol: RNA was pooled from two to three mice per genotype per array; results from duplicate arrays were averaged for a total of 4-6 mice assayed per genotype

value: distal colon

tag: genotype

value: 129/Sv/C57Bl6 mixed background WT for Hnf4a locus

value: Male

value: Young adult (12-16 weeks)


title: NHDF_stimulated with IBS17_rep2

source_name: NHDF cells batch 3022702, stimulated with IBS17

value: female

value: eyelid


title: NHDF_stimulated with IBS6_rep4

source_name: NHDF cells batch 1021506_1, stimulated with IBS6

value: Borrelia garinii strain IBS6

value: cheek


title: SOX2 -/- clone 2

description:
Sample 3
Tumor tissue from TCam-2 SOX2 -/- clone 2 6 weeks after xenografting

value: CD1 nude mice

value: TCam-2 SOX2 -/- clone 2

value: 6 weeks after xenografting

value: Seminoma-like

value: tumors of TCam-2 (SOX2 -/- clone)


title: NHDF_stimulated with IBS17_rep1

source_name: NHDF cells batch 3021904, stimulated with IBS17

value: Borrelia garinii strain IBS17

value: breast


title: SOX2 -/- clone 3

description:
Sample 4
Tumor tissue from TCam-2 SOX2 -/- clone 3 6 weeks after xenografting

value: TCam-2 SOX2 -/- clone 3


title: TCam-2 in vitro culture

description:
Sample 1
in vitro cultivated TCam-2

source_name: in vitro cultivated TCam-2

value: in vitro cultivated, Seminoma-like

value: cultivated TCam-2


title: NHDF_stimulated with IBS17_rep4

source_name: NHDF cells batch 1021506_1, stimulated with IBS17

value: caucasian


title: Distal_Colon_Wild_Type_a7line_rep1

description: WT controls for a7 HMZ line: express P1- and P2-HNF4a in colon

source_name: Distal colon from WTa7 mice

tag: tissue

value: distal colon

value: 129/Sv/C57Bl6 mixed background WT for Hnf4a locus

value: Male


title: WT-AZT-1 [expression]

tag: strain/background

tag: genotype/variation

value: wild-type

value: left ventricle

tag: treatment

value: AZT


title: Distal_Colon_Wild_Type_a7line_rep2

tag: gender

value: Young adult (12-16 weeks)


title: Distal_Colon Homozygous_HNF4a7_rep1

description: Express only P2-HNF4a in colon (and other HNF4a expressing tissues)

source_name: Distal colon from a7HMZ mice

value: a7 HMZ in 129/Sv/C57Bl6 mixed background


title: Distal_Colon Wild_Type_a1line_rep2


title: NHDF_stimulated with IBS6_rep3

source_name: NHDF cells batch 1011801_2, stimulated with IBS6

value: Borrelia garinii strain IBS6

value: male

value: temple


title: Distal_Colon Homozygous_HNF4a1_rep1

description: Express only P1-HNF4a in colon (and other HNF4a expressing tissues)

source_name: Distal colon from a1HMZ mice

value: a1 HMZ in 129/Sv/C57Bl6 mixed background


title: MCAT-Veh-4 [expression]

source_name: Heart, MCAT overexpressing, Vehicle treated

value: MCAT transgenic

value: vehicle (1%CMC)


title: Distal_Colon Homozygous_HNF4a7_rep2


title: NHDF_stimulated with IBS6_rep2

source_name: NHDF cells batch 3022702, stimulated with IBS6

value: female

value: eyelid


title: NHDF_stimulated with IBS6_rep5

source_name: NHDF cells batch 2061206_2, stimulated with IBS6

value: caucasian

value: cheek


title: NHDF_stimulated with IBS17_rep5

source_name: NHDF cells batch 2061206_2, stimulated with IBS17

value: Borrelia garinii strain IBS17


title: NHDF_stimulated with IBS19_rep6

source_name: NHDF cells batch 7071106_1, stimulated with IBS19

value: Borrelia burgdorferi sensu stricto strain IBS19

value: lip


title: NHDF_stimulated with IBS19_rep4

source_name: NHDF cells batch 1021506_1, stimulated with IBS19


title: NCCIT

description: In vitro cultivated NCCIT

data_processing: The data were normalised using quantile normalisation with Bioconductor R (limma package). Normalized values were tranformed into log2-values.

source_name: Embryonal carcinoma-like cell line

growth_protocol: TCam-2, 2102EP, NCCIT and JAR cells were cultivated as published (Nettersheim et al., 2013, PubMed ID: 24386123)

extract_protocol: RNA was isolate by the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Embryonal carcinoma-like

tag: cell line

value: NCCIT


title: NHDF_stimulated with IBS19_rep5

source_name: NHDF cells batch 2061206_2, stimulated with IBS19


title: 2102EP

description: In vitro cultivated 2102EP


title: NHDF_stimulated with IBS19_rep2

source_name: NHDF cells batch 3022702, stimulated with IBS19


title: NHDF_stimulated with IBS6_rep6

source_name: NHDF cells batch 7071106_1, stimulated with IBS6


title: NHDF_stimulated with IBS19_rep3

source_name: NHDF cells batch 1011801_2, stimulated with IBS19


title: NHDF_stimulated with IBS19_rep1

source_name: NHDF cells batch 3021904, stimulated with IBS19

value: breast


title: sh-A 3

description: TCam-2 PRAME shRNA cells without ATRA treatment 3

source_name: Seminoma-like cell line

value: Seminoma-like


title: JAR

description: In vitro cultivated JAR

source_name: Choriocarcinoma-like cell line

value: Choriocarcinoma-like

value: JAR


title: TCam-2 +A

description: TCam-2 treated with ATRA


title: NHDF_unstimulated_rep1

source_name: NHDF cells batch 3021904, unstimulated


title: NHDF_unstimulated_rep3

source_name: NHDF cells batch 1011801_2, unstimulated

value: male

value: temple


title: sh+A 2

description: TCam-2 PRAME shRNA cells with ATRA treatment 2


title: sh+A 3

description: TCam-2 PRAME shRNA cells with ATRA treatment 3


title: NHDF_stimulated with IBS17_rep6

source_name: NHDF cells batch 7071106_1, stimulated with IBS17


title: NHDF_unstimulated_rep6

source_name: NHDF cells batch 7071106_1, unstimulated


title: TCam-2

description: In vitro cultivated TCam-2


title: NHDF_unstimulated_rep4

source_name: NHDF cells batch 1021506_1, unstimulated


title: Distal_Colon Homozygous_HNF4a1_rep2

source_name: Distal colon from a1HMZ mice

value: distal colon

value: a1 HMZ in 129/Sv/C57Bl6 mixed background

value: Male

value: Young adult (12-16 weeks)


title: NHDF_unstimulated_rep5

source_name: NHDF cells batch 2061206_2, unstimulated

value: caucasian


title: TCam-2-deltaSOX2 clone 2 1w

description:
Tumor tissue from TCam-2-deltaSOX2 clone 2 1 weeks after xenografting
TCam-2, TCam-2-deltaSOX2 and 2102EP cells were cultivated as published (Nettersheim et al., 2013, PubMed ID: 24386123)
TCam-2, TCam-2-deltaSOX2 and 2102EP cells were xenografted in CD1 nude mice as published previously (Nettersheim et al., 2012, Pubmed ID: 22489004)

data_processing: The data were normalised using quantile normalisation with Bioconductor R. Normalized values were tranformed into log2-values.

tag: strain

value: CD1 nude mice

value: 1 week after xenografting


title: NHDF_unstimulated_rep2

source_name: NHDF cells batch 3022702, unstimulated

value: female

value: eyelid


title: NHDF_stimulated with IBS6_rep1

source_name: NHDF cells batch 3021904, stimulated with IBS6

value: Borrelia garinii strain IBS6


title: sh+A 1

description: TCam-2 PRAME shRNA cells with ATRA treatment 1


title: TCam-2 DMSO

description: TCam-2 treated with DMSO


title: HCC1954_DMSO_2

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
04902_14
Gene expression data from HCC1954 cells treated for 4h with DMSO.

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner.

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

label: Biotin

source_name: HCC1954 cells, DMSO

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

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

tag: cell type

value: breast cancer cell line

value: DMSO


title: HCC1954_DMSO_1

description:
04902_13
Gene expression data from HCC1954 cells treated for 4h with DMSO.


title: HCC1954_GSK70_1

description:
04902_19
Gene expression data from HCC1954 cells treated for 4h with 1 uM GSK2334470.


title: JIMT1_COMBO_2

description:
04902_11
Gene expression data from JIMT1 cells treated for 4h with 1 uM BYL719 and 1 uM GSK2334470.

source_name: JIMT1 cells, BYL719 and GSK2334470


title: sh-A 2

description: TCam-2 PRAME shRNA cells without ATRA treatment 2

value: Seminoma-like


title: HCC1954_COMBO_2

description:
04902_23
Gene expression data from HCC1954 cells treated for 4h with 1 uM BYL719 and 1 uM GSK2334470.

source_name: HCC1954 cells, BYL719 and GSK2334470


title: JIMT1_COMBO_3

description:
04902_12
Gene expression data from JIMT1 cells treated for 4h with 1 uM BYL719 and 1 uM GSK2334470.


title: JIMT1_BYL719_3

description:
04902_06
Gene expression data from JIMT1 cells treated for 4h with 1 uM BYL719.

source_name: JIMT1 cells, BYL719


title: JIMT1_GSK70_2

description:
04902_08
Gene expression data from JIMT1 cells treated for 4h with 1 uM GSK2334470.

source_name: JIMT1 cells, GSK2334470


title: JIMT1_COMBO_1

description:
04902_10
Gene expression data from JIMT1 cells treated for 4h with 1 uM BYL719 and 1 uM GSK2334470.


title: JIMT1_GSK70_3

description:
04902_09
Gene expression data from JIMT1 cells treated for 4h with 1 uM GSK2334470.


title: TCam-2 pS.r

description: TCam-2 cells infected with pSUPER.retro-vector


title: JIMT1_BYL719_2

description:
04902_05
Gene expression data from JIMT1 cells treated for 4h with 1 uM BYL719.


title: HCC1954_BYL719_1

description:
04902_16
Gene expression data from HCC1954 cells treated for 4h with 1 uM BYL719.

source_name: HCC1954 cells, BYL719


title: JIMT1_GSK70_1

description:
04902_07
Gene expression data from JIMT1 cells treated for 4h with 1 uM GSK2334470.


title: HCC1954_GSK70_3

description:
04902_21
Gene expression data from HCC1954 cells treated for 4h with 1 uM GSK2334470.


title: JIMT1_BYL719_1

description:
04902_04
Gene expression data from JIMT1 cells treated for 4h with 1 uM BYL719.


title: HCC1954_DMSO_3

description:
04902_15
Gene expression data from HCC1954 cells treated for 4h with DMSO.


title: HCC1954_COMBO_1

description:
04902_22
Gene expression data from HCC1954 cells treated for 4h with 1 uM BYL719 and 1 uM GSK2334470.


title: JIMT1_DMSO_3

description:
04902_03
Gene expression data from JIMT1 cells treated for 4h with DMSO.

source_name: JIMT1 cells, DMSO


title: HCC1954_BYL719_2

description:
04902_17
Gene expression data from HCC1954 cells treated for 4h with 1 uM BYL719.


title: sh-A 1

description: TCam-2 PRAME shRNA cells without ATRA treatment 1

source_name: Seminoma-like cell line


title: JIMT1_DMSO_2

description:
04902_02
Gene expression data from JIMT1 cells treated for 4h with DMSO.


title: HCC1954_BYL719_3

description:
04902_18
Gene expression data from HCC1954 cells treated for 4h with 1 uM BYL719.


title: JIMT1_DMSO_1

description:
04902_01
Gene expression data from JIMT1 cells treated for 4h with DMSO.


title: Tempranillo_pericarp_NaCl-immersion_watering_block3_rep3

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

description:
Sample name: NaCl W3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 1:30 pm from the watering block 3. It is the third of five replicates for NaCl immersion treatment.

hyb_protocol: If the quality control was correct, then 4 µg of labelled cDNA were hybridized. Hybridization solution (NimbleGen Hybridization kit) was added to each labelled cDNA and hybridization was performed for 16 h at 42ºC in a HS 4 Hybridization station (NimbleGen-Roche).

scan_protocol: Hybridized microarrays were washed with Wash buffer kit (NimbleGen-Roche) and scanned at 532 nm and 2 µm resolution in a DNA Microarray Scanner with Surescan High-Resolution Technology (Agilent Technologies).

data_processing: After evaluation of hybridization quality by Experimental metrics report implemented in NimbleScan Software version 2.6 (NimbleGen-Roche), probeset signal values from all the microarray hybridizations were background corrected and normalized together using Robust Microarray Average (RMA) (Irizarry et al., 2003) in NimbleScan Software, which produces a calls file for each sample with normalized expression data for each gene.

organism: Vitis vinifera

source_name: Vitis vinifera cv. Tempranillo berry pericarp, watering block 3, NaCl-immersed sample

label_protocol: cDNA was synthesized from 10 µg of total RNA using cDNA Synthesis System Kit (NimbleGen-Roche). The cDNA preparation (1 µg) was amplified and labelled with Cy3-random nonamers using One color labeling kit (NimbleGen-Roche).

growth_protocol: V. vinifera cv. Tempranillo plants grafted on rootstock 110 Richter at the Tira Agustín vineyard (Haro, La Rioja, Spain) belonging to Bodegas Roda S. A. winery were used. Six independent randomly localised blocks were considered in this vineyard, three with dropper irrigation (W condition) and three without irrigation (NW condition). Each block comprised at least 60 plants. The irrigation rate was established according to the evapotranspiration rate (ETc), which was calculated as a proportional relation between the ET0 and the crop coefficient (kc) using the formula: ETc= Kc•ET0. The final amount of water provided was calculated as: W= (ETc - Rainfall)•Watering efficiency (0.9).

extract_protocol: Tempranillo frozen berries were de-seeded. About 10-15 berries were used for RNA extraction on each sample. Total RNA was extracted from frozen Tempranillo berry pericarp as described by Reid et al. (2006). DNase digestion of contaminating DNA in the RNA samples was carried out with the RNase-Free DNase Set (QIAGEN). Final RNA purification was carried out using the SpektrumTM Plant Total RNA kit (Sigma-Aldrich) according to standard protocols.

treatment_protocol: Tempranillo bunches at mid-véraison (~50% of coloured grapes) were harvested on 12/08/2011 from the Tira Agustín vineyard. Six replicates were independently collected (three W and three NW condition blocks). For each block, 6 to 8 bunches were randomly sampled, from different plants each. Berries at the same ripening state were visually selected according to ~50% coloured skin surface. Berries were separated from the bunches by cutting the pedicel and individualised berries from each growth condition were submitted to the treatment. NaCl-treated berries (NaCl) were immersed in a highly concentrated NaCl solution (170 g•L-1) during a relatively long time lapse (1 h) simulating the density sorting procedure. Control berries (C) were kept at room air 1 h prior to sample freezing. NaCl-treated and control berries from each replicate were immediately rinsed in distilled H2O, dried, frozen in liquid nitrogen and kept at -80ºC until further analysis. Pairs of NW and W blocks were processed simultaneously, the first harvested at 9:00 am, the second at 11 am and the third at 1:30 pm (solar time).

tag: cultivar

value: Tempranillo

value: NaCl-immersed

tag: growth condition

value: irrigation

value: berry pericarp


title: Tempranillo_pericarp_NaCl-immersion_no-watering_block3_rep5

description:
Sample name: NaCl NW3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 1:30 pm from the no-watering block 3. It is the fifth of five replicates for NaCl immersion treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, no-watering block 3, NaCl-immersed sample

value: no-irrigation


title: HCC1954_GSK70_2

description:
04902_20
Gene expression data from HCC1954 cells treated for 4h with 1 uM GSK2334470.


title: Tempranillo_pericarp_NaCl-immersion_no-watering_block1_rep4

description:
Sample name: NaCl NW1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 9:00 am from the no-watering block 1. It is the fourth of five replicates for NaCl immersion treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, no-watering block 1, NaCl-immersed sample


title: HCC1954_COMBO_3

description:
04902_24
Gene expression data from HCC1954 cells treated for 4h with 1 uM BYL719 and 1 uM GSK2334470.


title: Tempranillo_pericarp_control_no-watering_block3_rep6

description:
Sample name: C NW3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 1:30 pm from the no-watering block 3. It is the sixth of six replicates for control treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, no-watering block 3, control sample

value: control


title: Tempranillo_pericarp_NaCl-immersion_watering_block2_rep2

description:
Sample name: NaCl W2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 11:00 am from the watering block 2. It is the second of five replicates for NaCl immersion treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, watering block 2, NaCl-immersed sample


title: Tempranillo_pericarp_control_watering_block1_rep1

description:
Sample name: C W1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 9:00 am from the watering block 1. It is the first of six replicates for control treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, watering block 1, control sample


title: Albariño_pericarp_over-ripe_berry_class_watering_south_orientation_rep3

description:
Sample name: Over-ripe_W_S3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within watered block 3. It is the 8th of eight replicates for over-ripe (160-180 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, over-ripe berry class, south orientation from watering block 3

growth_protocol: V. vinifera cv. Albariño plants grafted on rootstock Millardet et de Grasset 420 A at Finca Pé Redondo experimental vineyard located at Meis (Galicia, Spain), which was planted in 2003 and belongs to Bodegas Martín Códax winery, were used. Six independent randomly localised blocks were considered in this vineyard, three with dropper irrigation (W condition) and three without irrigation (NW condition). Each block comprised at least 60 plants. The irrigation rate was established according to the evapotranspiration rate (ETc), which was calculated as a proportional relation between the ET0 and the crop coefficient (kc) using the formula: ETc= Kc•ET0. The final amount of water provided was calculated as: W= (ETc - Rainfall)•Watering efficiency (0.9).

extract_protocol: Albariño frozen berries were de-seeded. About 10-15 berries were used for RNA extraction on each sample. Total RNA was extracted from frozen Albariño berry pericarp as described by Reid et al. (2006). DNase digestion of contaminating DNA in the RNA samples was carried out with the RNase-Free DNase Set (QIAGEN). Final RNA purification was carried out using the SpektrumTM Plant Total RNA kit (Sigma-Aldrich) according to standard protocols.

treatment_protocol: Albariño bunches from Finca Pé Redondo, a vineyard with East-West oriented rows, were simultaneously harvested at maturity on 22/09/2010. Twelve samples were independently analysed: samples from the north and the south side of the rows were processed separately for three W and three NW blocks. On each sample, 20-22 bunches were randomly collected, each from a different plant, and all the berries were densimetrically-sorted. Berries of the three density ranges 120-140, 140-160 and 160-180 g NaCl•L-1 from each replicate were transcriptomically compared. Densimetrically sorted berries were immediately rinsed in distilled H2O, dried, frozen in liquid nitrogen and kept at -80ºC until further analysis. Sampling started at 8:00 am (solar time) and time lapse from bunch collection to berry freezing ranged between 3-5 h. Water supplied to W blocks throughout the season was 204 mm (from 23/06/2010 to 26/09/2010). Gene expression differences among the three selected density classes were specifically searched.

value: Albarino

tag: berry density class

value: over-ripe (160-180 g NaCl/L)

tag: vineyard row side orientation

value: south


title: Albariño_pericarp_over-ripe_berry_class_no-watering_south_orientation_rep3

description:
Sample name: Over-ripe_NW_S3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 3. It is the sixth of eight replicates for over-ripe (160-180 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, over-ripe berry class, south orientation from no-watering block 3


title: Tempranillo_pericarp_control_no-watering_block1_rep4

description:
Sample name: C NW1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 9:00 am from the no-watering block 1. It is the fourth of six replicates for control treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, no-watering block 1, control sample


title: Tempranillo_pericarp_control_watering_block2_rep2

description:
Sample name: C W2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 11:00 am from the watering block 2. It is the second of six replicates for control treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, watering block 2, control sample


title: Tempranillo_pericarp_control_no-watering_block2_rep5

description:
Sample name: C NW2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 11:00 am from the no-watering block 2. It is the fifth of six replicates for control treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, no-watering block 2, control sample


title: Tempranillo_pericarp_control_watering_block3_rep3

description:
Sample name: C W3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 1:30 pm from the watering block 3. It is the third of six replicates for control treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, watering block 3, control sample


title: Albariño_pericarp_over-ripe_berry_class_no-watering_north_orientation_rep3

description:
Sample name: Over-ripe_NW_N3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 3. It is the fifth of eight replicates for over-ripe (160-180 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, over-ripe berry class, north orientation from no-watering block 3

value: north


title: Albariño_pericarp_over-ripe_berry_class_no-watering_north_orientation_rep2

description:
Sample name: Over-ripe_NW_N2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 2. It is the third of eight replicates for over-ripe (160-180 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, over-ripe berry class, north orientation from no-watering block 2


title: Albariño_pericarp_Ripe_berry_class_watering_south_orientation_rep3

description:
Sample name: Ripe_W_S3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within watered block 3. It is the 12th of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, south orientation from watering block 3

value: ripe (140-160 g NaCl/L)


title: Albariño_pericarp_Ripe_berry_class_watering_south_orientation_rep2

description:
Sample name: Ripe_W_S2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within watered block 2. It is the 10th of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, south orientation from watering block 2


title: Albariño_pericarp_Ripe_berry_class_watering_north_orientation_rep2

description:
Sample name: Ripe_W_N2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within watered block 2. It is the 9th of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, north orientation from watering block 2


title: Albariño_pericarp_over-ripe_berry_class_no-watering_north_orientation_rep1

description:
Sample name: Over-ripe_NW_N1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 1. It is the first of eight replicates for over-ripe (160-180 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, over-ripe berry class, north orientation from no-watering block 1


title: Albariño_pericarp_Ripe_berry_class_no-watering_north_orientation_rep2

description:
Sample name: Ripe_NW_N2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 2. It is the third of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, north orientation from no-watering block 2


title: Albariño_pericarp_Ripe_berry_class_no-watering_south_orientation_rep1

description:
Sample name: Ripe_NW_S1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 1. It is the second of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, south orientation from no-watering block 1


title: Albariño_pericarp_Ripe_berry_class_no-watering_south_orientation_rep2

description:
Sample name: Ripe_NW_S2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 2. It is the fourth of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, south orientation from no-watering block 2


title: Albariño_pericarp_Ripe_berry_class_watering_north_orientation_rep3

description:
Sample name: Ripe_W_N3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within watered block 3. It is the 11th of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, north orientation from watering block 3


title: Albariño_pericarp_over-ripe_berry_class_no-watering_south_orientation_rep2

description:
Sample name: Over-ripe_NW_S2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 2. It is the fourth of eight replicates for over-ripe (160-180 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, over-ripe berry class, south orientation from no-watering block 2


title: Albariño_pericarp_over-ripe_berry_class_watering_south_orientation_rep1

description:
Sample name: Over-ripe_W_S1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within watered block 1. It is the 7th of eight replicates for over-ripe (160-180 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, over-ripe berry class, south orientation from watering block 1


title: Albariño_pericarp_Ripe_berry_class_no-watering_south_orientation_rep3

description:
Sample name: Ripe_NW_S3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 3. It is the sixth of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, south orientation from no-watering block 3


title: Albariño_pericarp_Ripe_berry_class_watering_north_orientation_rep1

description:
Sample name: Ripe_W_N1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within watered block 1. It is the 7th of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, north orientation from watering block 1


title: Albariño_pericarp_over-ripe_berry_class_no-watering_south_orientation_rep1

description:
Sample name: Over-ripe_NW_S1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 1. It is the second of eight replicates for over-ripe (160-180 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, over-ripe berry class, south orientation from no-watering block 1


title: Keratocystic Odontogenic Tumor Replicate 19

city: Chapel Hill

first: Shijia

last: Hu

state: NC

address: 228 Brauer Hall Campus Box 7450

department: Pediatric Dentistry

institute: University of North Carolina

description: Biological replicate 19 of 20. Microdissected Keratocystic Odontogenic Tumor.

hyb_protocol: Equal amounts of Cy3 and Cy5-labeled cRNA (825 ng) from two different samples were hybridized to Agilent Human Whole Genome Oligonucleotide Microarrays.  The hybridized array was then washed and scanned.

scan_protocol: Scanned on an Agilent G2500 Scanner and data was extracted from the scanned image using Feature Extraction version 9.5 (Agilent Technologies).

source_name: Keratocystic Odontogenic Tumor

label_protocol: The TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnologies, Madison, WI, USA) was used for the linear amplification process. 5 µg of amplified aRNA from the laser-captured tissue was labeled with the Cy5 dye and hybridized to the arrays with a Cy3-labeled Stratagene Human Universal Reference(Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated from the microdissected cells with the PicoPure RNA Isolation kit (Arcturus Bioscience, Santa Clara, CA, USA).

tag: sample condition

value: FFPE

value: Keratocystic Odontogenic Tumor

tag: recurrence

value: No

source_name: Stratagene Human Universal Reference

tag: type

value: Reference RNA


title: Keratocystic Odontogenic Tumor Replicate 20

description: Biological replicate 20 of 20. Microdissected Keratocystic Odontogenic Tumor.

data_processing: Feature Extraction version 9.5 (Agilent Technologies)


title: Albariño_pericarp_Ripe_berry_class_no-watering_north_orientation_rep3

description:
Sample name: Ripe_NW_N3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 3. It is the fifth of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, north orientation from no-watering block 3


title: Albariño_pericarp_Ripe_berry_class_watering_south_orientation_rep1

description:
Sample name: Ripe_W_S1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within watered block 1. It is the 8th of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, south orientation from watering block 1


title: Albariño_pericarp_Ripe_berry_class_no-watering_north_orientation_rep1

description:
Sample name: Ripe_NW_N1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 1. It is the first of twelve replicates for ripe (140-160 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, ripe berry class, north orientation from no-watering block 1


title: Albariño_pericarp_under-ripe_berry_class_watering_south_orientation_rep3

description:
Sample name: Under-ripe_W_S3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within watered block 3. It is the 12th of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, south orientation from watering block 3

value: under-ripe (120-140 g NaCl/L)


title: Albariño_pericarp_under-ripe_berry_class_watering_north_orientation_rep3

description:
Sample name: Under-ripe_W_N3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within watered block 3. It is the 11th of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, north orientation from watering block 3


title: Albariño_pericarp_under-ripe_berry_class_watering_south_orientation_rep2

description:
Sample name: Under-ripe_W_S2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within watered block 2. It is the 10th of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, south orientation from watering block 2


title: Albariño_pericarp_under-ripe_berry_class_watering_south_orientation_rep1

description:
Sample name: Under-ripe_W_S1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within watered block 1. It is the 8th of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, south orientation from watering block 1


title: Keratocystic Odontogenic Tumor Replicate 16

description: Biological replicate 16 of 20. Microdissected Keratocystic Odontogenic Tumor.

value: Yes


title: Albariño_pericarp_under-ripe_berry_class_watering_north_orientation_rep2

description:
Sample name: Under-ripe_W_N2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within watered block 2. It is the 9th of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, north orientation from watering block 2


title: Keratocystic Odontogenic Tumor Replicate 18

description: Biological replicate 18 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Albariño_pericarp_under-ripe_berry_class_watering_north_orientation_rep1

description:
Sample name: Under-ripe_W_N1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within watered block 1. It is the 7th of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, north orientation from watering block 1


title: Keratocystic Odontogenic Tumor Replicate 15

description: Biological replicate 15 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Keratocystic Odontogenic Tumor Replicate 17

description: Biological replicate 17 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Keratocystic Odontogenic Tumor Replicate 13

description: Biological replicate 13 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Keratocystic Odontogenic Tumor Replicate 12

description: Biological replicate 12 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Albariño_pericarp_under-ripe_berry_class_no-watering_south_orientation_rep3

description:
Sample name: Under-ripe_NW_S3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 3. It is the sixth of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, south orientation from no-watering block 3


title: Albariño_pericarp_under-ripe_berry_class_no-watering_south_orientation_rep2

description:
Sample name: Under-ripe_NW_S2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 2. It is the fourth of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, south orientation from no-watering block 2


title: Keratocystic Odontogenic Tumor Replicate 14

description: Biological replicate 14 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: BS07_PreRYGB_Muscle_Basal

city: Tucson

first: Dawn

middle: K

last: Coletta

state: AZ

address: 1501 N. Campbell Ave

department: Medicine

institute: UNIVERSITY OF ARIZONA

description:
BS07 PRE
Gene expression pre-RYGB surgery.

hyb_protocol: Cy3-labeled aRNA was fragmented using Agilent Gene Expression Hybridization kit and hybridized to the Agilent-039494 SurePrint G3 Human Gene Expression 8x60K v2 Microarray at 65C for 17 hours.

scan_protocol: After washing, slides were scanned with an Agilent DNA microarray scanner.

data_processing:
Feature Extraction software version 10.5.1.1 (Agilent) was used for generating the raw data files.
Quantile-normalized log2 signal intensities were obtained from the raw data files using the package LIMMA in R.

source_name: Vastus lateralis muscle, pre-surgery, basal

label_protocol: Total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit, and quantified for Cy3 dye labeled aRNA concentration, RNA absorbance ratio, A260, Adye, and dye/probe values.

extract_protocol: Muscle biopsy specimens were homogenized in TRIzol solution using a Polytron homogenizer, and total RNA was purified with RNeasy MinElute Cleanup Kit.

treatment_protocol: Patients before and 3 months after Roux-en-Y gastric bypass (RYGB) (n=7, age 45.1±3.6 years) had glucose clamps (Rd) and a basal muscle biopsy (Bx). Muscle biopsies were frozen in liquid nitrogen.

value: female

tag: phenotype

value: obese

tag: age (yr)

value: vastus lateralis muscle

tag: subject identifier


title: Albariño_pericarp_under-ripe_berry_class_no-watering_north_orientation_rep3

description:
Sample name: Under-ripe_NW_N3
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 3. It is the fifth of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, north orientation from no-watering block 3

tag: tissue

value: berry pericarp


title: Albariño_pericarp_under-ripe_berry_class_no-watering_south_orientation_rep1

description:
Sample name: Under-ripe_NW_S1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the south side of vineyard rows within non-watered block 1. It is the second of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, south orientation from no-watering block 1

value: no-irrigation


title: Keratocystic Odontogenic Tumor Replicate 11

description: Biological replicate 11 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Keratocystic Odontogenic Tumor Replicate 8

description: Biological replicate 8 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Keratocystic Odontogenic Tumor Replicate 7

description: Biological replicate 7 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Keratocystic Odontogenic Tumor Replicate 9

description: Biological replicate 9 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: BS07_PostRYGB_Muscle_Basal

description:
BS07 POST
Gene expression post-RYGB surgery.

source_name: Vastus lateralis muscle, post-surgery, basal

value: Roux-en-Y gastric bypass (RYGB) surgery


title: Keratocystic Odontogenic Tumor Replicate 10

description: Biological replicate 10 of 20. Microdissected Keratocystic Odontogenic Tumor.

source_name: Keratocystic Odontogenic Tumor


title: Albariño_pericarp_under-ripe_berry_class_no-watering_north_orientation_rep2

description:
Sample name: Under-ripe_NW_N2
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 2. It is the third of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, north orientation from no-watering block 2

value: Albarino


title: Keratocystic Odontogenic Tumor Replicate 5

description: Biological replicate 5 of 20. Microdissected Keratocystic Odontogenic Tumor.

value: Fresh frozen

source_name: Stratagene Human Universal Reference


title: BS06_PreRYGB_Muscle_Basal

description:
BS06 PRE
Gene expression pre-RYGB surgery.


title: Keratocystic Odontogenic Tumor Replicate 1

description: Biological replicate 1 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: BS05_PostRYGB_Muscle_Basal

description:
BS05 POST
Gene expression post-RYGB surgery.


title: BS06_PostRYGB_Muscle_Basal

description:
BS06 POST
Gene expression post-RYGB surgery.


title: BS05_PreRYGB_Muscle_Basal

description:
BS05 PRE
Gene expression pre-RYGB surgery.


title: Keratocystic Odontogenic Tumor Replicate 3

description: Biological replicate 3 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: TT_CTL_1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing, followed by quantile normalization and statistical analysis with limma - Bioconductor package in R

molecule: polyA RNA

label_protocol: Agilent - Low RNA input QuickAmp

growth_protocol: Nthy ORI 3.1 (non tumoral follicular cell line, ECACC, catalogue number 90011609) and TT cells (medullary carcinoma cell line, ATCC® CRL-1803™) were grown in RPMI 1640 and Dulbecco's Modified Eagle Medium /F12 respectively supplemented with 5% fetal calf serum, sodium pyruvate and penicillin/streptomycin (Life Technologies).

extract_protocol: Trizol+RNeasy+Minelute

treatment_protocol: Cells were plated at 100.000 cells/well in a six-well plate and transfected for 48h with synthetic premiRs or antagomiRs using Lipofectamine RNAiMAX reagent (Life Technologies), following the manufacturer's instructions at a final concentration of 5 and 20nM respectively.

value: thyroid

value: TT

tag: transfection protocol

value: CTL

tag: amount in (µg)

tag: rin number


title: Keratocystic Odontogenic Tumor Replicate 6

description: Biological replicate 6 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: BS04_PostRYGB_Muscle_Basal

description:
BS04 POST
Gene expression post-RYGB surgery.

tag: gender

tag: treatment


title: Keratocystic Odontogenic Tumor Replicate 2

description: Biological replicate 2 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: Keratocystic Odontogenic Tumor Replicate 4

description: Biological replicate 4 of 20. Microdissected Keratocystic Odontogenic Tumor.


title: BS03_PostRYGB_Muscle_Basal

description:
BS03 POST
Gene expression post-RYGB surgery.


title: ORI_premiR-375_2

tag: cell line

value: ORI


title: ORI_CTL_1


title: BS04_PreRYGB_Muscle_Basal

description:
BS04 PRE
Gene expression pre-RYGB surgery.


title: Albariño_pericarp_under-ripe_berry_class_no-watering_north_orientation_rep1

description:
Sample name: Under-ripe_NW_N1
This sample is of Vitis vinifera cv. Albariño berry pericarp collected on 2010/09/22 at 8:00 am from the north side of vineyard rows within non-watered block 1. It is the first of twelve replicates for under-ripe (120-140 g NaCl•L-1) berry class.

source_name: Vitis vinifera cv. Albariño berry pericarp, under-ripe berry class, north orientation from no-watering block 1

tag: cultivar

value: north


title: BS02_PostRYGB_Muscle_Basal

description:
BS02 POST
Gene expression post-RYGB surgery.


title: BS03_PreRYGB_Muscle_Basal

description:
BS03 PRE
Gene expression pre-RYGB surgery.


title: TT_AntagomiR-375_1


title: ORI_CTL_2


title: ORI_premiR-375_1


title: Tempranillo_pericarp_NaCl-immersion_watering_block1_rep1

description:
Sample name: NaCl W1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected on 2011/08/12 at 9:00 am from the watering block 1. It is the first of five replicates for NaCl immersion treatment.

source_name: Vitis vinifera cv. Tempranillo berry pericarp, watering block 1, NaCl-immersed sample

value: Tempranillo

value: NaCl-immersed

tag: growth condition

value: irrigation


title: BS02_PreRYGB_Muscle_Basal

description:
BS02 PRE
Gene expression pre-RYGB surgery.


title: BS01_PreRYGB_Muscle_Basal

description:
BS01 PRE
Gene expression pre-RYGB surgery.


title: GABA exporter 1

status: Public on May 21 2016

city: Bielefeld

first: João

middle: M. P.

last: Jorge

address: Universitätsstraße 25

institute: University of Bielefeld

description: Technical replicate 1 of 3

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the microarray data was done with the software package EMMA 2 (Dondrup, M., Albaum, S. P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Küster, H., Linke, B., Mertens, D., et al. (2009). EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50.). Genes which were up- or downregulated in GABA4 in at least two of the three replicates were taken into account for further analysis (p-value < 0.05, mRNA value > 2). The supplementary excel files contain fold changes and statistics.

organism: Corynebacterium glutamicum

source_name: Growth of ABAL4 in minimal medium supplemented with 4% glucose

label_protocol: cDNA synthesis from total RNA and labeling were performed as described previously (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ).

growth_protocol: LB seed culture was inoculated from an agar plate and grown overnight. The cells were harvested by centrifugation (4000 x g, 10 min) and washed once with CGXII medium lacking the carbon source. Finally, 50 mL of CGXII medium containing 4% of glucose, the necessary supplements were inoculated to an OD600 of 1.0. Cells were grown until mid-exponential phase (OD between 16 and 22) and were spilled in two falcons (half filled with ice) and centrifuged (4000 x g, 10 minutes, 4ºC). Supernatant was discarded and cells were kept at -80ºC.

extract_protocol: RNA isolation was performed as described previously with some modification (Wendisch, V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104, 273–285.). Total RNA was isolated using the RNeasy Mini   Kit(Qiagen). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality. The RNA sample was stored at −80 °C until further use.

treatment_protocol: Two different strains were used ABAL4 (does not produce GABA) and GABA4 (produces GABA4)

tag: strain

source_name: Growth of GABA4 in minimal medium supplemented with 4% glucose


title: GABA exporter 2

description: Technical replicate 2 of 3


title: Co-culture between tumor cells and mMDSC (Tumor 4T1)

city: Lyon

first: Anne-Pierre

last: Morel

state: Rhone-Alpes

address: 28, rue Laennec, Cheney D 2nd floor

institute: Cancer Research Center of Lyon

description: Gene expression data from co-cultured tumor cells

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45C on Mouse transcriptome 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files were processed with Gene Level-SST-RMA algorithm of the Expression Console 1.4.  Differential expressions were calculated on Transcriptome Analysis Console, TAC (Affymetrix) using CHP files and CEL files.

source_name: co-culture

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 2 ng total RNA (GeneChip WT Pico Reagent kit, Affymetrix).

growth_protocol: Murine breast cancer cells expressing the luciferase gene were implanted into the fat pads of 5-week –old BALB/c or C57BL/J6 mice.

extract_protocol: Extraction of total RNA was performed with Qiagen RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Single cell suspensions were prepared from bone marrows, lungs and tumor tissues. Bone marrow cells were obtained by flushing bones with PBS using a 28G 1/2 syringe. Tumor and lung tissues were dissociated and digested with collagenase  for 1hr at 37°C. Red blood cells were lysed by ACK lysis buffer. These cells were labeled with fluorescence-conjugated Ly6C, Ly6G and CD11b antibodies andsorted with a FACS Aria cell sorter. Sorted cells were lysed using RLT lysis buffer from Qiagen RNeasy Mini Kit.

tag: cell type

value: Tumor cell+mMDSC (Tumor 4T1)


title: GABA exporter 3

description: Technical replicate 3 of 3


title: BS01_PostRYGB_Muscle_Basal

description:
BS01 POST
Gene expression post-RYGB surgery.

value: female


title: gMDSC- Ly6g+CD11b+ flow sorted from bone marrow of 4T1 tumor-bearing mice

description: Gene expression data from sorted gMDSC

source_name: gMDSC

value: gMDSC (Bone Marrow 4T1)


title: Co-culture between tumor cells and mMDSC (Lung 4T1)

value: Tumor cell+mMDSC (Lung 4T1)


title: mMDSC- Ly6c+CD11b+ flow sorted from tumor of 4T1 tumor-bearing mice

description: Gene expression data from sorted mMDSC

source_name: mMDSC

value: mMDSC (Tumor 4T1)


title: Co-culture between tumor cells and gMDSC (Lung 4T1)

value: Tumor cell+gMDSC (Lung 4T1)


title: 4T1 tumor- CD45-flow cytometry sorted

description: Gene expression data from sorted tumor cells

source_name: tumor

value: CD45- 4T1 Tumor


title: mMDSC- Ly6c+CD11b+ flow sorted from bone marrow of 4T1 tumor-bearing mice

description: Gene expression data from sorted mMDSC

value: mMDSC (Bone Marrow 4T1)


title: TT_CTL_2


title: Co-culture between tumor cells and mMDSC (Bone Marrow 4T1)

value: Tumor cell+mMDSC ( Bone Marrow 4T1)


title: 4T1 cell line- in vitro culture

description: Gene expression data from cell line

source_name: cell line

value: 4T1 cell line


title: EMT6 tumor- CD45-flow cytometry sorted

value: CD45-EMT6 Tumor


title: EMT6 cell line- in vitro culture

description: Gene expression data from cell line

value: EMT6 cell line


title: Co-culture between tumor cells and gMDSC (Tumor 4T1)

value: Tumor cell+gMDSC (Tumor 4T1)


title: TT_AntagomiR-375_2

value: thyroid

value: TT


title: Co-culture between tumor cells and gMDSC (Bone Marrow 4T1)

value: Tumor cell+gMDSC (Bone Marrow 4T1)


title: WT_10wk_3

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

hyb_protocol: Ten micrograms of biotin-labeled and fragmented cDNAs were hybridized onto 1.0 ST GeneChip arrays (Affymetrix) for 16 hours at 45°C. Post-hybridization staining and washing was done according to the manufacturer's protocols using a Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChip Scanner 3000 laser confocal slide scanner. The images were quantified using GCOS 1.0 software (GeneChip Operating Software, Affymetrix).

data_processing: Average signal intensities for each probeset within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.2) software using the RMA method which incorporates convolution background correction, quantile-normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm. Pairwise comparisons were used to statistically resolve gene expression differences between sample groups using the R/MAANOVA analysis package. Specifically, differentially expressed genes were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/MAANOVA package. Statistical significance levels of the pairwise comparisons were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method. Differentially expressed genes were declared at an FDR q-value threshold of 0.05.

source_name: skin, wildtype, 10wk

label_protocol: In an in vitro transcription (IVT) reaction with T7 RNA polymerase, the cDNA was amplified and labeled with biotinylated nucleotides (Affymetrix).

extract_protocol: Total RNA was isolated by standard TRIzol methods, and quality assessed using a 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA). Following reverse transcription with an oligo(dT)-T7 primer (Affymetrix, Santa Clara, CA), double-stranded cDNA was synthesized with the GeneChip Expression 3’–Amplification One-cycle kit (Affymetix).

treatment_protocol: Skin samples were stored in RNAlater (Ambion, Austin, TX) per the manufacturer’s instructions and homogenized in TRIzol (Life Technologies, Carlsbad, CA).

tag: age


title: WT_10wk_1


title: WT_10wk_2


title: CPDM_10wk_1

source_name: skin, cpdm, 10wk


title: WT_8wk_3

source_name: skin, wildtype, 8wk


title: CPDM_10wk_3


title: WT_8wk_2


title: gMDSC- Ly6g+CD11b+ flow sorted from tumor of 4T1 tumor-bearing mice

description: Gene expression data from sorted gMDSC

value: gMDSC (Tumor 4T1)


title: TcellcloneIGRP7

city: Utrecht

first: Bobby

last: Koeleman

address: Universiteitsweg 100

department: Genetics

country: Netherlands

institute: UMC Utrecht

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Data has been generated using Illumina Genome Studio v2010 in combination with the GX (Gene Expression) v.1.9.0 module. Beadstudio's Rank Invariant Normalization was used to normalize data (http://www.illumina.com/documents/products/technotes/technote_beadstudio_normalization.pdf). Data was then exported and post processed in Microsoft Excel (taking into account Fold Change values)

source_name: T cell clone IGRP7, post-antigen stimulation

label_protocol: standard Illumina protocol

growth_protocol: All T cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM) with 10% human serum (Sanquin, Leiden, the Netherlands), supplemented with IL-2 and IL-15. Restimulation was performed in the presence of   irradiated, cognate peptide loaded JY-cells and irradiated, pooled third-party PBMCs. All cells used are routinely tested for mycoplasma before freezing

extract_protocol: Total RNA, including the miRNA fraction, was purified from cytotoxic T cell clone derived from T1D patient and healthy donor by the miRNeasy isolation kit (Qiagen, Venlo, the Netherlands).

tag: subject status

value: T1D patient

tag: clone id

value: T cell clone IGRP7

value: T1D patient derived IGRP-specific T cell clones


title: TcellcloneIGRP32

source_name: T cell clone IGRP32, post-antigen stimulation

value: T cell clone IGRP32


title: pool of embryos 3, RFP+ GFP+ sorted population

city: barcelona

first: Elisa

last: Martí

state: Not Listed

address: Baldiri i Reixac, 15-21

institute: IBMB-CSIC

description:
Gene expression data from chick neuroepithelial cells  at HH10/11 + 24 hpe , that activate Bone Morphogenetic Protein- responsive element.
c.BRE3

hyb_protocol: The quality and quantity  of purified RNA was verified by measuring with nanodrop,  and subsequently the RNA was hybridized to  microarrays and processed in accordance to the manufacturer’s  instructions (Affymetrix). Two-cycle cDNA synthesis  was performed on 35–50 ng of total RNA and  hybridized to the GeneChip Chicken Genome Array  (Affymetrix)

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

data_processing: For statistical analysis, the data from four biological replicates of each experiment were averaged and microarray data was analyzed using Bioconductor software, and a false discovery rate (FDR) with a p value <0.05. The quality of the data was assessed, normalized with the “rma” algorithm and differentially expressed genes were selected. The results were filtered using thresholds of [log2FC]>0.5849 and a p value <0.05.  The excel file on the series record (BREvsCTRL_array_processed_data.xlsx) contains the statistical analysis.

organism: Gallus gallus

source_name: Chick neuroepithelial cells  at HH10/11 + 24 hpe , that activate BRE-reporter

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: Fertilized eggs  of white Leghorn chickens were windowed after a 36/40-h incubation at 38C at 70% humidity, at which time the embryos have developed to HH stages (St) 10/11 (Hamburger and Hamilton, 1951).

extract_protocol: Nearly 30 electroporated embryos were pooled, and a single cell suspension was obtained. GFP and RFP fluorescent cells were sorted using a MoFlo flow cytometer (DakoCytomation, Fort Collins, Colorado, USA). At least 100,000 RFP+ cells and 20,000 GFP+ cells were obtained per pool, and total RNA was extracted from the resulting cell sorted populations, 90% of RFP+/GFP+ cells or 90% of RFP+/GFP- cells, using a standard Trizol (Promega) protocol.

treatment_protocol: A solution of plasmid DNA diluted in H2O and 0.2% Fast Green (Sigma) was microinjected into the lumen of the embryos’ NT and electrodes were placed either side of the NT, at trunk levels. Electroporation was carried out in ovo using a Intracel Dual Pulse TSS-100 electroporator, delivering five 50-ms pulses of 20 V, after which embryos were allowed to develop before harvesting at the time points indicated.

value: embryonic neuroepithelial cells

tag: breed

value: white Leghorn chicken

value: HH10/11 + 24hours post-electroporation


title: pool of embryos 4, RFP+ GFP+ sorted population

description:
Gene expression data from chick neuroepithelial cells  at HH10/11 + 24 hpe , that activate Bone Morphogenetic Protein- responsive element.
c.BRE4


title: CPDM_8wk_1

source_name: skin, cpdm, 8wk


title: WT_6wk_4

source_name: skin, wildtype, 6wk


title: pool of embryos 4, RFP+ GFP- sorted population

description:
Gene expression data from chick neuroepithelial cells  at HH10/11 + 24 hpe , that do not activate Bone Morphogenetic Protein- responsive element.
c.CTL4

source_name: Chick neuroepithelial cells  at HH10/11 + 24 hpe , that do not activate BRE-reporter


title: TcellcloneFSB

description: FSB

source_name: T cell clone FSB, post-antigen stimulation

value: Healthy donor

value: T cell clone FSB

value: Healthy donor derived IGRP specific T cell clone


title: pool of embryos 1, RFP+ GFP+ sorted population

description:
Gene expression data from chick neuroepithelial cells  at HH10/11 + 24 hpe , that activate Bone Morphogenetic Protein- responsive element.
c.BRE1


title: WT_8wk_1


title: pool of embryos 2, RFP+ GFP+ sorted population

description:
Gene expression data from chick neuroepithelial cells  at HH10/11 + 24 hpe , that activate Bone Morphogenetic Protein- responsive element.
c.BRE2


title: CPDM_8wk_2


title: pool of embryos 2, RFP+ GFP- sorted population

description:
Gene expression data from chick neuroepithelial cells  at HH10/11 + 24 hpe , that do not activate Bone Morphogenetic Protein- responsive element.
c.CTL2


title: WT_6wk_2


title: CPDM_10wk_2


title: pool of embryos 1, RFP+ GFP- sorted population

description:
Gene expression data from chick neuroepithelial cells  at HH10/11 + 24 hpe , that do not activate Bone Morphogenetic Protein- responsive element.
c.CTL1


title: pool of embryos 3, RFP+ GFP- sorted population

description:
Gene expression data from chick neuroepithelial cells  at HH10/11 + 24 hpe , that do not activate Bone Morphogenetic Protein- responsive element.
c.CTL3


title: CPDM_8wk_3


title: CPDM_6wk_1

source_name: skin, cpdm, 6wk


title: CPDM_6wk_2


title: WT_6wk_1


title: WT_6wk_3


title: WT_4wk_2

source_name: skin, wildtype, 4wk


title: CPDM_6wk_3


title: WT_4wk_1


title: WT_2wk_3

source_name: skin, wildtype, 2wk


title: WT_2wk_1


title: CPDM_4wk_2

source_name: skin, cpdm, 4wk


title: WT_4wk_3


title: CPDM_4wk_1


title: CPDM_4wk_3


title: CPDM_2wk_1

source_name: skin, cpdm, 2wk


title: CPDM_2wk_2


title: WT_2wk_2


title: Cartilage_Control_Rep3

status: Public on May 20 2016

city: toronto

first: benjamin

last: alman

state: ontario

address: 555 university avenue

department: Developmental and stem cell biology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Each 5.5ug cDNA sample was hybridized to the Affymetrix Human Gene 1.0 ST array, and processed in the Affymetrix Fluidics Station 450 by TCAG

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, by TCAG

data_processing: CHP data were generated using Expression Console with RMA processing algorithm and default analysis settings

source_name: Osteoarthritic articular cartilage, control

label_protocol: Samples were prepared from 200ng total RNA using the Affymetrix WT kit, by The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children

growth_protocol: Articular cartilage explants were dissected from the subchondral bone of the femoral condyle and maintained as described in Ali & Alman, 2012, Analytical Biochemistry

extract_protocol: Total RNA was extracted as described in Ali & Alman, 2012, Analytical Biochemistry

treatment_protocol: Explants were divided into control or treatment groups, and treated with pharmacologic Hh antagonist

value: articular cartilage

value: female


title: Cartilage_Hhantag_Rep3

source_name: Osteoarthritic articular cartilage, treated with Hh inhibitor

value: treated with Hh inhibitor


title: Cartilage_Hhantag_Rep2

value: male


title: Cartilage_Hhantag_Rep1


title: Cartilage_Control_Rep1


title: Sample_64247_Veh_TAM

type: SRA

city: Philadelphia

first: Robert

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

library_source: transcriptomic

data_processing:
FASTQ files were mapped to mouse genome mm10 using STAR 2.3.0e (default parameters)
BAM files were generated, sorted, indexed, and duplicate reads were removed using SAMTOOLs.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of counts

source_name: Mouse vehicle treated tumor TAMs

growth_protocol: XFM mice were intracranially injected with DF-1:PDGFB cells at 5-6 weeks of age.  Mice were monitored weekly for tumor growth and were enrolled on trial when the tumors reached reached 20-40 mm3.

extract_protocol:
Mice were anesthetized with Avertin, and transcardially perfused with PBS.  The tumor was isolated, macro dissected, and a single cell suspension was generated with a papain digestion.  PDGFRA+ tumor cells were sorted along side Cd11b+ Gr.1 - TAMs.  Cells were sorted directly into TriZOL and RNA was isolated.
RNA-sequencing libraries were prepared using the SMART-Seq library preparation kit and 2x50 base pair sequencing was performed on an Illumina HISeq 2000.

treatment_protocol: Mice were treated daily with Vehicle or BLZ945 untill they developed symptoms or reached the trial endpoint of 26 weeks of age.

tag: mouse id

tag: Stage

value: Vehicle

value: TAM

tag: agent


title: Sample_57682_Veh_TC

source_name: Mouse vehicle treated tumor cells

value: TC


title: Sample_57682_Veh_TAM


title: ABCs, biological rep 5

first: Michael

middle: P

last: Cancro

address: 284 JMB / 2360 Hamilton Walk

department: Pathology & Laboratory Medicine

institute: University of Pennsylvania

description: gene expression data for FACS-sorted ABCs from aged (22-24-month) C57BL/6 mouse

hyb_protocol: 5.5 ug of labeled cDNA was added to Affymetrix hybridization cocktails and hybridized for 16 hrs at 45C to Mouse Gene 1.0 ST GeneChips (Affymetrix, Inc.) followed by staining with SA-PE.

scan_protocol: Signal was read with a GeneChip 3000 7G scanner.

data_processing: RMA normalization was calculated form .cel files using Partek Genomics Suite version 6.6 (Partek, Inc., St. Louis, MO)

source_name: ABCs from aged mouse 6

label_protocol: 25 ng of total RNA was converted to first-strand cDNA; second-strand cDNA synthesis was followed by ribo-SPIA amplification; biotinylation was by terminal transferase end labeling.

growth_protocol: Aged (22-24 mo.) and young (3 mo.) mice were obtained from the NIA Aged Rodent Colony.

extract_protocol: RNA extraction from sorted ABC, AFO, and YFO cells was performed with the Qiagen RNeasy Kit according to manufacturer instructions.

treatment_protocol: Mice were euthanized, spleens harvested, and splenocytes isolated and stained with surface markers as described in Hao et al., Blood (2011) vol. 118 pp. 1294-1304.  ABC, AFO, and YFO subsets were sorted with a BD FACS Aria II.

value: ABCs from aged mouse

tag: tissue

value: spleen


title: Sample_54363_Veh_TC


title: ABCs, biological rep 3

source_name: ABCs from aged mouse 4


title: ABCs, biological rep 1

source_name: ABCs from aged mouse 1


title: Sample_54363_Veh_TAM


title: aged FO B cells, biological rep 5

description: gene expression data for FACS-sorted follicular B cells from aged (22-24-month) C57BL/6 mouse

source_name: follicular B cells from aged mouse 6

value: follicular B cells from aged mouse


title: ABCs, biological rep 2

source_name: ABCs from aged mouse 2


title: Sample_57098_Veh_TAM


title: aged FO B cells, biological rep 4

source_name: follicular B cells from aged mouse 5


title: Sample_57098_Veh_TC


title: aged FO B cells, biological rep 2

source_name: follicular B cells from aged mouse 2


title: young FO B cells, biological rep 4

description: gene expression data for FACS-sorted follicular B cells from young (3-month) C57BL/6 mouse

source_name: follicular B cells from young mouse 4

value: 3 months


title: aged FO B cells, biological rep 1

source_name: follicular B cells from aged mouse 1


title: aged FO B cells, biological rep 3

source_name: follicular B cells from aged mouse 4


title: ABCs, biological rep 4

source_name: ABCs from aged mouse 5


title: Sample_54359_Veh_TAM


title: CSF-1R inhibitor resistant neurospheres replicate 2

hyb_protocol: All hybridization steps were performed by the MSKCC genomics core facility per the manufacturers instructions

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent feature extraction was used for background correction and LOWESS normalization.  Subsequent data was processed in the DNACopy packages in R

label_protocol: All labeling was performed by the MSKCC genomics core facility per the manufacturers instructions

growth_protocol: Neurosphere lines were derived from CSF-1R inhibitor resistant tumors and cultured in mouse neurostem cell media from neurocult for no more than 3 passages.

extract_protocol: Genomic DNA was isolated using the Qiagen Dneasy blood and tissue kit

tag: source

value: Neurosphere line

value: mouse liver


title: young FO B cells, biological rep 3

source_name: follicular B cells from young mouse 3


title: Sample_49843_EP_TAM

source_name: Mouse dormant tumor TAMs

value: EndPoint


title: young FO B cells, biological rep 5

source_name: follicular B cells from young mouse 5


title: young FO B cells, biological rep 2

source_name: follicular B cells from young mouse 2


title: Sample_64247_Veh_TC


title: Sample_54359_Veh_TC


title: CSF-1R inhibitor resistant neurospheres replicate 3


title: Sample_49849_Reb_TAM

source_name: Mouse Rebound tumor TAMs

value: Rebound


title: Sample_49830_EP_TAM


title: Sample_49845_EP_TC

source_name: Mouse dormant tumor cells


title: Sample_49830_EP_TC


title: Sample_49831_EP_TAM


title: Sample_49843_EP_TC


title: CPDM_2wk_3

source_name: skin, cpdm, 2wk


title: Sample_49041_Reb_TC

source_name: Mouse Rebound tumor cells


title: Sample_49849_Reb_TC


title: Sample_49825_EP_TAM


title: Sample_49041_Reb_TAM


title: Sample_49834_Reb_TAM


title: Sample_49059_Reb_TAM


title: Sample_49823_EP_TC


title: young FO B cells, biological rep 1

source_name: follicular B cells from young mouse 1


title: Sample_49059_Reb_TC


title: Sample_49845_EP_TAM


title: Sample_49692_Reb_TC


title: Sample_49825_EP_TC


title: CSF-1R inhibitor resistant neurospheres replicate 1


title: Sample_49831_EP_TC


title: Sample_49827_Reb_TAM


title: Sample_49823_EP_TAM


title: ZR75.16wk.3

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data were transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

extract_protocol: mRNA from cultured cells was extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Expert Software version B.02.03) with RNA Nano LabChip Kits (Agilent Technologies).

value: estrogen receptor positive (ER+) breast cancer (BC) cell lines

tag: cultured in

value: 2D on plastic

tag: treated with

value: 10% dextran charcoal-stripped bovine serum (DCC) for 16 wks

tag: sample group

value: long-term estrogen deprivation (LTED)


title: Sample_49827_Reb_TC


title: ZR75.1wk.3

tag: cell line

value: 10% dextran charcoal-stripped bovine serum (DCC) for 1 wk


title: ZR75.16wk.2


title: ZR75.16wk.1


title: T47D.20wk.3

value: 10% dextran charcoal-stripped bovine serum (DCC) for 20 wks


title: ZR75.1wk.2


title: ZR75.1wk.1


title: ZR75.9E2.3

value: phenol red-free RPMI+ 10% FBS+ 1nM E2

value: control


title: T47D.9E2.1


title: HCC1428.20wk.2


title: ZR75.9E2.2


title: HCC1428.9E2.2


title: HCC1428.1wk.3


title: HCC1428.1wk.2


title: T47D.20wk.2


title: T47D.20wk.1


title: T47D.1wk.3


title: HCC1428.9E2.3


title: T47D.9E2.3


title: HCC1428.20wk.1


title: HCC1428.9E2.1


title: T47D.1wk.2


title: HCC1428.1wk.1


title: T47D.9E2.2


title: T47D.1wk.1


title: Sum44.20wk.3


title: ZR75.9E2.1


title: Sum44.9E2.2


title: Sum44.20wk.1


title: Cartilage_Control_Rep2

source_name: Osteoarthritic articular cartilage, control

value: articular cartilage

tag: treatment

tag: gender

value: male


title: Sum44.20wk.2


title: HCC1428.20wk.3


title: MCF7.3D.20wk.3

value: 3D on collagen


title: Sum44.1wk.2


title: Sum44.1wk.3


title: MCF7.3D.9E2.1


title: MCF7.3D.20wk.1


title: MCF7.3D.20wk.2


title: Sum44.9E2.3


title: MCF7.3D.9E2.2


title: Sum44.9E2.1


title: MCF7.3D.1wk.2


title: MCF7.2D.22wk.3

value: 10% dextran charcoal-stripped bovine serum (DCC) for 22 wks


title: MCF7.3D.1wk.3


title: MCF7.2D.1wk.1


title: MCF7.3D.1wk.1


title: MCF7.2D.1wk.2


title: Sum44.1wk.1


title: MCF7.2D.22wk.1


title: MCF7.2D.1wk.3


title: MCF7.2D.9E2.1


title: MCF7.2D.9E2.3


title: MCF7.2D.22wk.2


title: MCF7.2D.9E2.2


title: HEK293T-99021-2

first: Charlotte

last: Bevan

address: South Kensington Campus

department: Department of Surgery & Cancer

institute: Imperial College London

description: HEK293T cells teated with 99021

hyb_protocol: Hybridisation was achieved as instructed by the basic Agilent microRNA microarray protocol.

scan_protocol: Microarray scanning was achieved using the Agilent C scanner using default conditions.

data_processing: Data was processed using Agilent feature extraction and Genespring.

label: Cyanine 3-pCp

label_protocol: Labeling was achieved using the Agilent microRNA labeling kit.

extract_protocol: RNA was extracted using Trizol.


title: HEK293T-99021-3

description: HEK293T cells teated with 99021


title: BP138

first: Thomas

middle: W

last: Battaglia

address: 423 E 23rd Street

institute: NYU School of Medicine

description: PAT-Male

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: Terminal Ileum

label_protocol: Affymetrix GeneChip IVT Labeling Kit, according to manufactuer's protocol (GeneChip Expression Analysis Technical Manual)

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers protocols

value: Terminal Ileum

value: pulsed therapeutic doses of antibiotics

tag: Sex

value: Male

tag: disease state

value: NOD Mice


title: HEK293T-Ctrl-1

description: HEK293T cells treated with a vehicle control

value: Control


title: BP127

description: PAT-Male


title: HEK293T-Ctrl-3


title: BS146

description: STAT-Male

value: Sub-therapeutic antibiotic treatment


title: BS145

description: STAT-Male


title: BC141

description: Control-Male


title: BP126

description: PAT-Male


title: HEK293T-99021-1

description: HEK293T cells teated with 99021


title: HEK293T-Ctrl-2


title: BC111

description: Control-Male


title: BP124

description: PAT-Male


title: BC140

description: Control-Male


title: BS119

description: STAT-Male


title: BP128

description: PAT-Male


title: BP125

description: PAT-Female

value: Female


title: BP129

description: PAT-Female


title: lung tumor of large size, biological rep1

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for pharmacology and toxicology

institute: Hanover Medical School

description: Mice aged between 9 – 13 months were anesthetized by an overdose of CO2 and the lungs were explanted and rinsed with ice cold physiological saline. The tumors were inspected macroscopically, separated from the surrounding lung tissue and frozen immediately in liquid nitrogen. The tumors were divided into groups according to size (1 mm, 5 mm, and >10 mm). Because of low yield in RNA small tumors were pooled into groups of n=3 whereas medium and large size tumors were obtained from n= 4 and n = 3 individual animals, respectively. Normal lung from n= 4 non-transgenic mice of the same age was used as control.

hyb_protocol: 10 µg of the biotinylated fragmented cRNA was hybridized onto Affymetrix MG U74Av2 microarrays containing 12,488 probe sets representing over 6000 annotated sequences. Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a Bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

scan_protocol: The arrays were scanned using the Agilent GeneChip® Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250. Data from replicate samples were evaluated and compared using statistical analyses with the Affymetrix Data Mining Tool 2 (DMT-2). To summarize the expression level (the signal values) for each transcript across the replicates we used the average and standard deviation statistics. Mean fold change values were calculated as the ratio of the average expression levels for each gene between two tissue sets. To determine significance of change in mean gene expression level between comparison groups the unpaired two-sided T-Test was used, with the p-value cutoff determined as 0.05. Additionally to parametric T-test, which uses for analysis numeric expression values (signal intensities), comparison ranking analysis was done to study the concordance between  „Increase“ or „Decrease“ calls for tumors in one set. The results are shown as % of concordance between all comparisons, e.g. 16 analyses (4 tumors versus 4 controls) for tumors of median size and 12 (3 tumors versus 4 controls) for tumors of large size. Three pools of small tumors (1mm) were compared with the 4 individual controls, resulting in 12 comparisons. We restricted the group of differently regulated genes in tumors to those genes, which were detected ("Present" call) in all samples of a tumor sets for the up regulated genes and in all control lungs for the down regulated genes. Further criteria were FC> 3, p-value in T-test < 0,05 and 100% of "Increase" call in comparative ranking analysis for one or more sets of tumors versus control lungs for up regulated genes and FC<- 3, p-value in T-test < 0,05 and 100% of "Decrease" call accordingly for down regulated genes.

source_name: c-Myc transgenic lung tumor of large size (  ≥10 mm)

label_protocol: 10 µg of total RNA was used to prepare  cRNA-samples  following the Affymetrix Gene Chipâ Expression Analysis Technical Manual (Santa Clara, CA).

growth_protocol: SPC/myc transgenic mice (Ehrhardt et al., 2001) were maintained as hemizygotes in the CD2F1-(DBA/2xBalb/C) background.

extract_protocol: RNA-extraction was performed with the RNeasy Midi Kit (RNeasy MidiKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Mice were anasthesized by an overdose of CO2  at the age of 9 – 13 months. The tumors were inspected macroscopically, separated from the surrounding lung tissue of SPC/myc transgenic mice and frozen immediately in liquid nitrogen.

tag: strain

tag: genotype/variation

value: c-Myc transgenic

tag: tumor

value: large size (  ≥10 mm)


title: BC107

description: Control-Female


title: lung tumor of large size, biological rep3


title: BS117

description: STAT-Female


title: BS116

description: STAT-Female


title: BS142

description: STAT-Female


title: BP121

description: PAT-Female


title: BC109

description: Control-Male


title: BC110

description: Control-Male


title: lung tumor of large size, biological rep2


title: BC100

description: Control-Female


title: lung tumor of middle  size, biological rep4

source_name: c-Myc transgenic lung tumor of middle size (about 4-5mm)

value: middle size (about 4-5mm)


title: lung tumor of middle  size, biological rep2


title: BC101

description: Control-Female


title: GSC-811 baseline

city: Houston

first: Dimpy

last: Koul

state: TX

address: 1515 Holcombe Ave

department: Neuro-Oncology

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human HGU133Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 by Expression Analysis, Inc.   GeneChips were scanned using the Affymetrix 3000 7G Scanner.

data_processing: The CEL files were preprocessed with the aroma package (http://aroma-project.org/) using the CDF file from GPL5356 and quantile normalization.

source_name: GSC811 without treatment

label_protocol: Complementary RNA synthesis and labeling/hybridization/scanning of U133A 2.0 microarrays using GeneChip products (Affymetrix) was done as described in the GeneChip manual (see below fields) by Expression Analysis, Inc.

growth_protocol: These GBM neurospheres were cultured in DMEM/F12 medium containing B27 supplement (Invitrogen, Carlsbad, CA), basic fibroblast growth factor, and epidermal growth factor (20 ng/ml each).

extract_protocol: We extracted total RNA at 24 hour after treatment with control, BEZ235, DS7423, from 3 independent experiments. RNA was harvested using RNeasy mini Kits (Qiagen), DNase I digestion, and RNeasy MinElute Cleanup Kit (Qiagen) following manufacturer’s protocols. We performed synthesis of complementary RNA from total RNA and hybridization/scanning of U133 plus 2.0 microarrays using GeneChip products (Affymetrix) as described in the GeneChip manual.

treatment_protocol: Cells were treated with or without 100nM BEZ235, 100nM DS7423 for 24 hours.

tag: cell type

value: Glioma initiating cells


title: GSC-25 BEZ treated

source_name: GSC25 treated with BEZ235 at 100 nM for 24 hours


title: GSC-811 DS treated

source_name: GSC811 treated with DS7423 at 100nM for 24 hours


title: GSC 7-10 DS treated

source_name: GSC7-10 treated with DS7423 at 100nM for 24 hours


title: GSC-811 BEZ treated

source_name: GSC811 treated with BEZ235 at 100nM for 24 hours


title: lung tumor of middle  size, biological rep3


title: GSC-42 baseline

source_name: GSC-42 without treatment


title: GSC-42 DS treated

source_name: GSC-42 treated with DS7423 at 100nM for 24 hours


title: lung tumor of middle  size, biological rep1


title: Turbot_Gonad_Femalejuvenile_6

city: Santiago de Compostela

first: Diego

last: Robledo

address: Rúa Lope Gómez de Marzoa s/n CIBUS building

institute: University of Santiago de Compostela

hyb_protocol: Samples were hybridized individually in a custom 4x44K Agilent platform at the Universidad de Santiago de Compostela (USC) in the Functional Genomics Platform. cRNA was prepared for overnight hybridization with the corresponding buffers during 17 h at 65°C and washed on the following day.

scan_protocol: slides were scanned using an Agilent G2565B microarray scanner (Agilent Technologies, USA). The scanner images were segmented with the Agilent Feature and the Agilent software was applied to avoid saturation in the highest intensity range. Agilent feature extraction produced the raw data for further pre-processing. The processed signal (gProcessed-Signal) value was chosen as statistics for the absolute hybridization signal.

data_processing: Normalization using all microarray data was done by the Aquantile method implemented in the Limma R package (R version 3.0.2).

organism: Scophthalmus maximus

source_name: Gonad

label_protocol: 50 ng of total RNA were labeled (1 color) using the Low Input Quick Amp Labeling Kit, One-Color (Cy3) (Agilent Technologies, USA).

growth_protocol: Turbot were grown at the facilities of CETGA (Centro Tecnológico Gallego de Acuicultura; NW Spain)

extract_protocol: RNA was individually extracted by RNeasy Mini Kit (Qiagen, Germany) following the manufacturer’s instructions. Quantity was determined using a Nanodrop spectrophotometer (Nanodrop Technologies, US). Quality (RNA integrity number, RIN) was determined in a Bioanalizer (Agilent Technologies, US). RNA samples with RIN>8.1 were further processed for microarray analysis.

treatment_protocol: Gonads were dissected and they were rapidly flash frozen in liquid nitrogen

tag: age (dph)

tag: size (cm)

tag: weight (g)

value: gonad

tag: gonad development stage

value: Female juveniles


title: lung tumor of small size, biological rep3

source_name: c-Myc transgenic lung tumor of small size (about 1mm), pool of 3-4 tumors

value: small size (about 1mm)


title: GSC-25 DS treated

source_name: GSC25 treated with DS7423 at 100 nM for 24 hours


title: Turbot_Gonad_Femalejuvenile_5

tag: tissue


title: GSC 7-10 BEZ treated

source_name: GSC7-10 treated with BEZ235 at 100nM for 24 hours


title: GSC-42 BEZ treated

source_name: GSC-42 treated with BEZ235 at 100nM for 24 hours


title: lung tumor of small size, biological rep1


title: GSC 7-10 baseline

source_name: GSC7-10 without treatment


title: lung tumor of small size, biological rep2


title: GSC-25 baseline

source_name: GSC25 without treatment


title: non-transgenic (control) lung, biological rep4

source_name: lung of non-transgenic mouse

value: non-transgenic


title: Turbot_Gonad_Femalejuvenile_3


title: non-transgenic (control) lung, biological rep1


title: Turbot_Gonad_Femalejuvenile_2


title: non-transgenic (control) lung, biological rep2


title: Turbot_Gonad_Differentiating_8

value: Differentiating


title: non-transgenic (control) lung, biological rep3


title: Turbot_Gonad_Femalejuvenile_1


title: Turbot_Gonad_Femalejuvenile_4


title: Turbot_Gonad_Malejuvenile_4

value: Male juveniles


title: Turbot_Gonad_Differentiating_6


title: Turbot_Gonad_Malejuvenile_6


title: Turbot_Gonad_Malejuvenile_5


title: Turbot_Gonad_Malejuvenile_1


title: MCF7.3D.9E2.3

hyb_protocol: Standard Illumina hybridization protocol

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

value: estrogen receptor positive (ER+) breast cancer (BC) cell lines

tag: cultured in

value: 3D on collagen

value: phenol red-free RPMI+ 10% FBS+ 1nM E2

value: control


title: Turbot_Gonad_Differentiating_1


title: Turbot_Gonad_Malejuvenile_3


title: Turbot_Gonad_Differentiating_4


title: Primary Mouse_Pravastatin treated_Replicate3

city: Detroit

last: Kocarek

state: MI

address: 6135 Woodward Ave

department: Institute of Environmental Health Sciences

institute: Wayne State University

description: Mo Prav7

hyb_protocol: 0.825µg of Alexa 555 labeled Aminoallyl-aRNA and 0.825µg of Alexa 647 labeled Aminoallyl-aRNA were mixed together and allowed to co-hybridize on the array for 17 hours at 65°C at 10rpm in the hybridization rotator.   After hybridization the slide was washed with Agilent GE Wash Buffers following the Agilent’s protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: primary hepatocytes_Pravastatin

label_protocol: 500ng of total RNA was input to the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, Madison, WI)  to produce aminoallyl-aRNA according to the vendor’s protocol. Five ug of each aminoallyl-aRNA sample was labeled with Alexa 555 or Alexa 647 (Molecular probes/ Life Technologies, Foster City, CA).

growth_protocol: Primary hepatocytes plated at density and maintained in Williams Medium E.

extract_protocol: Total RNA was extracted using Qiagen lysis buffer following manufacturer's instructions

treatment_protocol: 48 hours after plating, hepatocytes were left untreated or treated with 100 µM SQ1 or 30 µM pravastatin for 48 hours.

value: male

value: Primary cultured Mouse Hepatocytes

tag: treated with

value: Pravastatin

source_name: primary hepatocytes_untreated control

value: none (untreated control)