title: mouse_mammary_Sham-irradiated_Wk12-post-IR_Rep1

status: Public on Nov 30 2013

type: RNA

city: Berkeley

first: Jonathan

last: Tang

state: CA

address: 1 Cyclotron Road, MS-977

department: Cancer and DNA Damage Response

country: USA

institute: Lawrence Berkeley National Laboratory

description:
Sham_Wk12_Rep1
mouse_mammary_Sham-irradiated_Wk12-post-IR

hyb_protocol: The labeled cDNA is added to the hybridization cocktail that is prepared according to the protocol included in the Affymetrix GeneTitan Hybridization Wash, and Stain kit.  The samples are then put onto a hybridization tray and loaded into the Affymetrix GeneTitan MC for hybridization, washing, and scanning. The samples are hybridized for 60 degrees C for 16 hours once all plates are loaded.

scan_protocol: Arrays are scanned in the  Affymetrix GeneTitan MC using a xenon light bulb and the image is captured using a camera.

data_processing: Raw CEL file data were imported into R for background subtraction and normalization using the Robust Multichip Average algorithm from the Bioconductor package oligo.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: total RNA of mammary tissue, BALB/c, 12WK post-IR, Sham Irradiated

label_protocol: 250 ng of total RNA is first amplified into cRNA and then made into cDNA using the Ambion WT Expression Kit. 5.5 ug of the cDNA is then fragmented using the Affymetrix GeneChip WT Terminal Labeling kit.  Fragmentation is confirmed by running each sample on the Agilent Bioanalyzer using the RNA 6000 kit.  The fragmented cDNA is then labeled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: 3 week old BALB/cJ female mice were purchased from Jackson Laboratory and housed in the Berg Animal Facility at NYUMC.  After acclimation, mice were cleared of the inguinal mammary gland on one side while the contra lateral inguinal mammary gland was kept intact.  The mice were allowed to recover and aged 6 additional weeks at the Berg Animal Facility at NYUMC.  Mice were given food and water ad libitum.  At 9 weeks of age, all mice were transported by courier to the Brookhaven National Lab Animal Facility.  After acclimation for one week, mice were irradiated or sham irradiated at 10 weeks of age.  Tissues are harvested 1 week, 4 weeks, and 12 weeks post IR.  The 4 and 12 week time points are collected after the mice are transported back to NYUMC.  This data submission is for the mammary tissue that was kept intact.  All procedures were done under protocols reviewed and approved by both IACUC committees at NYUMC and Brookhaven National Laboratories.

extract_protocol: Total RNA was extracted using Rneasy kit from Oiagen, according to manufacturer's instructions

treatment_protocol: Mice were either irradiated or not with high-LET silicon particles (350MeV/amu) or low-LET gamma-radiation

tag: gender

value: female

tag: strain

value: BALB/c

tag: stress

value: Sham Irradiated

tag: time

value: 12 weeks

tag: tissue

value: mammary tissue


title: mouse_mammary_irradiated_100cGy_Gamma_Wk12-post-IR_Rep2

description:
Gamma_100cGy_Wk12_Rep2
mouse_mammary_irradiated_100cGy_Gamma_Wk12-post-IR

source_name: total RNA of mammary tissue, BALB/c, 12WK post-IR, 100cGy Gamma Radiation

value: 100cGy Gamma Radiation


title: mouse_mammary_irradiated_30cGy_Si_Wk12-post-IR_Rep3

description:
Si_30cGy_Wk12_Rep3
mouse_mammary_irradiated_30cGy_Si_Wk12-post-IR

source_name: total RNA of mammary tissue, BALB/c, 12WK post-IR, 30cGy High-LET Si Particle Radiation (350 MeV/amu)


title: mouse_mammary_Sham-irradiated_Wk12-post-IR_Rep2

description:
Sham_Wk12_Rep2
mouse_mammary_Sham-irradiated_Wk12-post-IR


title: mouse_mammary_irradiated_100cGy_Gamma_Wk12-post-IR_Rep3

description:
Gamma_100cGy_Wk12_Rep3
mouse_mammary_irradiated_100cGy_Gamma_Wk12-post-IR


title: mouse_mammary_Sham-irradiated_Wk4-post-IR_Rep2

description:
Sham_Wk4_Rep2
mouse_mammary_Sham-irradiated_Wk4-post-IR

source_name: total RNA of mammary tissue, BALB/c, 4WK post-IR, Sham Irradiated

value: 4 weeks


title: mouse_mammary_irradiated_30cGy_Si_Wk12-post-IR_Rep1

description:
Si_30cGy_Wk12_Rep1
mouse_mammary_irradiated_30cGy_Si_Wk12-post-IR

value: 30cGy High-LET Si Particle Radiation (350 MeV/amu)


title: mouse_mammary_Sham-irradiated_Wk4-post-IR_Rep4

description:
Sham_Wk4_Rep4
mouse_mammary_Sham-irradiated_Wk4-post-IR


title: mouse_mammary_Sham-irradiated_Wk12-post-IR_Rep3

description:
Sham_Wk12_Rep3
mouse_mammary_Sham-irradiated_Wk12-post-IR


title: mouse_mammary_Sham-irradiated_Wk4-post-IR_Rep3

description:
Sham_Wk4_Rep3
mouse_mammary_Sham-irradiated_Wk4-post-IR


title: mouse_mammary_irradiated_10cGy_Si_Wk12-post-IR_Rep1

description:
Si_10cGy_Wk12_Rep1
mouse_mammary_irradiated_10cGy_Si_Wk12-post-IR

source_name: total RNA of mammary tissue, BALB/c, 12WK post-IR, 10cGy High-LET Si Particle Radiation (350 MeV/amu)


title: mouse_mammary_irradiated_10cGy_Si_Wk12-post-IR_Rep2

description:
Si_10cGy_Wk12_Rep2
mouse_mammary_irradiated_10cGy_Si_Wk12-post-IR

value: 10cGy High-LET Si Particle Radiation (350 MeV/amu)


title: mouse_mammary_irradiated_10cGy_Si_Wk4-post-IR_Rep3

description:
Si_10cGy_Wk4_Rep3
mouse_mammary_irradiated_10cGy_Si_Wk4-post-IR

source_name: total RNA of mammary tissue, BALB/c, 4WK post-IR, 10cGy High-LET Si Particle Radiation (350 MeV/amu)


title: mouse_mammary_irradiated_10cGy_Si_Wk4-post-IR_Rep2

description:
Si_10cGy_Wk4_Rep2
mouse_mammary_irradiated_10cGy_Si_Wk4-post-IR


title: mouse_mammary_irradiated_10cGy_Si_Wk4-post-IR_Rep1

description:
Si_10cGy_Wk4_Rep1
mouse_mammary_irradiated_10cGy_Si_Wk4-post-IR


title: mouse_mammary_irradiated_100cGy_Gamma_Wk12-post-IR_Rep1

description:
Gamma_100cGy_Wk12_Rep1
mouse_mammary_irradiated_100cGy_Gamma_Wk12-post-IR


title: mouse_mammary_irradiated_30cGy_Si_Wk4-post-IR_Rep3

description:
Si_30cGy_Wk4_Rep3
mouse_mammary_irradiated_30cGy_Si_Wk4-post-IR

source_name: total RNA of mammary tissue, BALB/c, 4WK post-IR, 30cGy High-LET Si Particle Radiation (350 MeV/amu)


title: mouse_mammary_irradiated_10cGy_Si_Wk12-post-IR_Rep3

description:
Si_10cGy_Wk12_Rep3
mouse_mammary_irradiated_10cGy_Si_Wk12-post-IR


title: mouse_mammary_Sham-irradiated_Wk4-post-IR_Rep1

description:
Sham_Wk4_Rep1
mouse_mammary_Sham-irradiated_Wk4-post-IR


title: mouse_mammary_irradiated_30cGy_Si_Wk12-post-IR_Rep2

description:
Si_30cGy_Wk12_Rep2
mouse_mammary_irradiated_30cGy_Si_Wk12-post-IR


title: mouse_mammary_irradiated_30cGy_Si_Wk4-post-IR_Rep2

description:
Si_30cGy_Wk4_Rep2
mouse_mammary_irradiated_30cGy_Si_Wk4-post-IR


title: mouse_mammary_irradiated_100cGy_Gamma_Wk4-post-IR_Rep3

description:
Gamma_100cGy_Wk4_Rep3
mouse_mammary_irradiated_100cGy_Gamma_Wk4-post-IR

source_name: total RNA of mammary tissue, BALB/c, 4WK post-IR, 100cGy Gamma Radiation


title: mouse_mammary_Sham-irradiated_Wk1-post-IR_Rep2

description:
Sham_Wk1_Rep2
mouse_mammary_Sham-irradiated_Wk1-post-IR

source_name: total RNA of mammary tissue, BALB/c, 1WK post-IR, Sham Irradiated

value: 1 week


title: mouse_mammary_irradiated_30cGy_Si_Wk4-post-IR_Rep1

description:
Si_30cGy_Wk4_Rep1
mouse_mammary_irradiated_30cGy_Si_Wk4-post-IR


title: mouse_mammary_irradiated_10cGy_Si_Wk1-post-IR_Rep3

description:
Si_10cGy_Wk1_Rep3
mouse_mammary_irradiated_10cGy_Si_Wk1-post-IR

source_name: total RNA of mammary tissue, BALB/c, 1WK post-IR, 10cGy High-LET Si Particle Radiation (350 MeV/amu)


title: mouse_mammary_irradiated_100cGy_Gamma_Wk4-post-IR_Rep1

description:
Gamma_100cGy_Wk4_Rep1
mouse_mammary_irradiated_100cGy_Gamma_Wk4-post-IR


title: mouse_mammary_Sham-irradiated_Wk1-post-IR_Rep3

description:
Sham_Wk1_Rep3
mouse_mammary_Sham-irradiated_Wk1-post-IR


title: mouse_mammary_irradiated_10cGy_Si_Wk1-post-IR_Rep2

description:
Si_10cGy_Wk1_Rep2
mouse_mammary_irradiated_10cGy_Si_Wk1-post-IR


title: mouse_mammary_irradiated_100cGy_Gamma_Wk4-post-IR_Rep2

description:
Gamma_100cGy_Wk4_Rep2
mouse_mammary_irradiated_100cGy_Gamma_Wk4-post-IR


title: mouse_mammary_irradiated_30cGy_Si_Wk1-post-IR_Rep2

description:
Si_30cGy_Wk1_Rep2
mouse_mammary_irradiated_30cGy_Si_Wk1-post-IR

source_name: total RNA of mammary tissue, BALB/c, 1WK post-IR, 30cGy High-LET Si Particle Radiation (350 MeV/amu)


title: mouse_mammary_Sham-irradiated_Wk1-post-IR_Rep1

description:
Sham_Wk1_Rep1
mouse_mammary_Sham-irradiated_Wk1-post-IR


title: mouse_mammary_irradiated_30cGy_Si_Wk1-post-IR_Rep3

description:
Si_30cGy_Wk1_Rep3
mouse_mammary_irradiated_30cGy_Si_Wk1-post-IR


title: mouse_mammary_irradiated_10cGy_Si_Wk1-post-IR_Rep1

description:
Si_10cGy_Wk1_Rep1
mouse_mammary_irradiated_10cGy_Si_Wk1-post-IR


title: mouse_mammary_irradiated_100cGy_Gamma_Wk1-post-IR_Rep2

description:
Gamma_100cGy_Wk1_Rep2
mouse_mammary_irradiated_100cGy_Gamma_Wk1-post-IR

source_name: total RNA of mammary tissue, BALB/c, 1WK post-IR, 100cGy Gamma Radiation


title: mouse_mammary_irradiated_100cGy_Gamma_Wk1-post-IR_Rep3

description:
Gamma_100cGy_Wk1_Rep3
mouse_mammary_irradiated_100cGy_Gamma_Wk1-post-IR


title: mouse_mammary_irradiated_30cGy_Si_Wk1-post-IR_Rep1

description:
Si_30cGy_Wk1_Rep1
mouse_mammary_irradiated_30cGy_Si_Wk1-post-IR


title: Wild type under dehydration stress, rep2

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

hyb_protocol: Hybridizaton was done according to the Affymetrix Expression Analysis Technical Manual; the wash followed the protocol EukGE-WS2v4_450 for Rice Genome Arrays.

scan_protocol: Scanning was done using the Gene Chip Operating System (GCOS) scanner.

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004, Genome Biology 5, R80) using gcRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and gives one value for each probe set instead of keeping probe level information (Wu et al., 2004, JASA). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

organism: Oryza sativa

source_name: Dongjin wild type, roots, dehydration stress

label_protocol: Labeling was done using biotinylated UTP (Bio-11-UTP) according to the MessageAmp™ II aRNA Amplification protocol (Life Technologies).

growth_protocol: Non-dehusked rice seeds were soaked with sterile water at 60°C for 10 min, rinsed with 40°C sterile water and subsequently germinated on wet  tissue paper in the dark for 5 d at 28°C. The seedlings were then transferred to a growth chamber set at 12 h day (600 µE m-2 s-1) at 26°C, and 12 h night at 22°C with 70% relative humidity for another four days. The seedlings were then grown in hydroponic medium by fixing them on polypropylene plates with a plant-to-plant distance of 10 cm, and placing them in boxes containing macro- and micro-elements (Yang et al., 1994, Plant Soil, 164: 1-7) under the above mentioned condition. Treatment was applied on 14-day-old seedlings.

extract_protocol: Total RNA was extracted from roots using the LiCl method reported by Moore et al. (2005) J. Exp. Bot, 56: 2885-2895.

treatment_protocol: Roots of  the 14-day-old rice plants grown in hydroponic culture were placed on filter paper in the same growth chamber for 90 min.

value: root

tag: genotype

value: Dongjin variety (wild type)

tag: age

value: 14-day-old seedlings


title: mouse_mammary_irradiated_100cGy_Gamma_Wk1-post-IR_Rep1

description:
Gamma_100cGy_Wk1_Rep1
mouse_mammary_irradiated_100cGy_Gamma_Wk1-post-IR


title: Wide type I-S plants biological rep3

city: Hangzhou

first: Yan

middle: Qiu

state: Zhejiang

address: Shiqiao Road 198#

department: Institute of Virology and Biotechnology

country: China

institute: Zhejiang Academy of Agricultural Sciences

description: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

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

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

data_processing: The data were analyzed with Agilent GeneSpring 11 using default analysis settings and global scaling as normalization method.

organism: Oryza sativa Japonica Group

source_name: leaf from WT, japonica rice (I-S)

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: Rice seeds were germinated at 37 ºC for 1 d. After germination, the plants were grown in a growth room under a photosynthetic photon flux density of approximately 200 μmol photons m-2s-1 with a 12 h light (32 ºC)/12 h dark (28 ºC) photoperiod. Humidity was controlled at 60%.

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

treatment_protocol: To evaluate of the function of OsXa5, rice plants overexpressing OsXa5 were developed. Plants overexpressing OsXa5 were used for RNA extraction from three repeats.

value: leaf

value: wild type

value: max tilling

tag: cultivar

value: Ishikari-shiroge (I-S)


title: Wide type I-S plants biological rep2

description: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).


title: OsXa5-overexpressing plants biological rep2

description: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2002, Affymetrix).

source_name: leaf from OsXa5-overexpressing plants

value: OsXa5 overexpressing


title: OsXa5-overexpressing plants biological rep3

description: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).


title: Knock-out line under dehydration stress, rep1

source_name: arid mutant, roots, dehydration stress

value: T-DNA insertion in gene Os02g31890 of Dongjin variety


title: Wide type I-S plants biological rep1

description: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).


title: OsXa5-overexpressing plants biological rep1

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


title: Wild type under control condition, rep1

source_name: Dongjin wild type, roots, control condition


title: Knock-out line under control condition, rep1

source_name: arid mutant, roots, control condition


title: HFF-Mockinfected-rep3

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

state: MI

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

hyb_protocol: Labeling, hybridization, and scanning were performed off-site at the Waynate State University Advanced Genomics Technology Center (AGTC)

scan_protocol: Chips were scanned using an Illumina iScan

data_processing: Unnormalized data is raw expression from the bead chip.  Normalization was conducted using the robust spline option within BRB array and is shown as log2 transformed expression.

organism: Homo sapiens

source_name: Human foreskin fibroblasts mock infected, total RNA extracted 96 hpi

label_protocol: Cy3 labeled

growth_protocol: Normal human foreskin fibroblasts were cultured and infected using  DMEM supplemented with minimal non-essential amino acids and 10% FBS

extract_protocol: Total RNA was extracted with Trizol reagent

treatment_protocol: Cells were infected with either HCMV AD169 or HCMV delted for US17 at a multiplicity of infection of 3.0

tag: cell type

value: Foreskin Fibroblasts


title: HFF-AD1699 96hpi-rep2

source_name: Human foreskin fibroblasts infected with HCMV strain AD169, total RNA extracted 96 hpi


title: Knock-out line under control condition, rep2


title: Wild type under control condition, rep2


title: HFF-Mockinfected-rep2


title: HFF-DeltaUS17 96hpi-rep2

source_name: Human foreskin fibroblasts infected with HCMV strain AD169 delta US17, total RNA extracted 96 hpi


title: HFF-AD169 96hpi-rep1


title: Wild type under dehydration stress, rep1


title: Knock-out line under dehydration stress, rep2


title: HFF-Mockinfected-rep1


title: HFF-DeltaUS17 96hpi-rep3


title: HFF-AD169 12hpi-rep2

source_name: Human foreskin fibroblasts infected with HCMV strain AD169, total RNA extracted 12 hpi


title: HFF-DeltaUS17 12hpi-rep1

source_name: Human foreskin fibroblasts infected with HCMV strain AD169 delta US17, total RNA extracted 12 hpi


title: HFF-DeltaUS17 96hpi-rep1


title: HFF-DeltaUS17 12hpi-rep2


title: HFF-AD169 12hpi-rep1


title: HFF-DeltaUS17 12hpi-rep3


title: C10_subcutaneous from C10-CSC_rep2

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: CSCs-like isolated from secondary tumor masses,originated after injectionof C10-CSC

hyb_protocol: standard Illumina hybridization protocol

scan_protocol: Standard scanning on a Illumina Beadstation 500

data_processing: Raw data were processed and cubic-spline normalized with Illumina Genome Studio

label: biotin-SA Cy3

source_name: secondary tumor grown SC

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s recommendations

growth_protocol: Breast CSCs-like and the bone metastatic cells were grown in DMEM F12  with 10ng/ml b-FGF, 20 ng/ml EGF, 5mg/ml insulin and 0,4% bovine serum albumine

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

treatment_protocol: Cells were grown as mammospheres before harvesting RNA.

tag: cell line

value: breast cancer stem-like cells (CSCs-like)

tag: cell hystology

tag: cell description

value: CSCs-like isolated from tumor masses in secondary mice


title: C10_subcutaneous from C10-CSC_rep1

description: CSCs-like isolated from secondary tumor masses,originated after injection of C10-CSC


title: C10_luciferase_rep1

description: parental luciferase-transduced breast CSCs-like

source_name: primary lobular infiltrating breast tumor

value: breast CSCs-like transduced with a luciferase-lentiviral expression vector


title: C10_boneMTS_rep1

description: bone isolated metastatic cells derived from C10 parental

source_name: metastasis in human implanted bone

value: metastatic cells isolated from the human implanted bone


title: C10_mammospheres_from_boneMTS_rep1

description: bone isolated metastatic cells derived from C10 and grown as mammospheres

value: metastatic cells isolated from the human implanted bone and cultured in vitro as spheroids


title: HFF-AD169 12hpi-rep3


title: barley_genotype:Rodnik_day21_pooled

city: Gatersleben

first: Athmer

last: Benedikt

address: Correnstrasse 3

institute: IPK Gatersleben

hyb_protocol: The filters were prehybridized for 4 h at 65°C with 100 µl salmon sperm (10 mg/ml, Stratagene) in 10 mL hybridization buffer (0.5 M Na-phosphate buffer pH 7.0, 2 mM EDTA pH 8.0, 1% BSA, 7% SDS) and then hybridized with denatured radioactive probes for 16 h at 65°C. Homologous barley probes were washed two times with 0.1% SDS + 0,1x SCC for 20 min. Heterologous rye and wheat probes were washed less stringent both for 20 min with solutions containing 0.1% SDS + 1x SSC and  0.1% SDS + 0.5x SCC.

scan_protocol: The filters were exposed for 48 h to an imaging screen (Fuji Film) ans signal were detected by the phosphor imaging system FLA-3000 (Fuji Film) at 16 bits/pixel with pixel size of 50 µm. Scanned images were processed with the ArrayVision software from GE Healthcare to quantify signal intensities.

data_processing: Background-substracted signals were normalized by the quantil normalization method proposed by Bolstad et al. (2003) and mean values were calculated from each double spot.

organism: Hordeum vulgare

source_name: primary shoot

label_protocol: RNA  was reserve-transcripted with SuperScript-II rerverse transcriptase kit (Invitrogen) according manufacture's instructions. The cDNA was labeled with MegaPrime random priming kit (Amersham GE Healthcare) and 10 Ci/mL 33-P dCTP (Hartmann-Analytik, Germany)

growth_protocol: After germination at room temperature for 3 days, the seedlings were cultivated for 10 days in hydroponic cultivation systems filled with half-strength modified Hoagland nutrient solution (in order to avoid the limited water availability to plants grown in soil at low temperature; Kocsy et al. 2000) placed in a growth chamber (Controlled Env. Ltd, Winnipeg, Canada) at 18/15°C day/night temperature and 75% relative humidity, with 16 h illumination at 270 µmol m-2 s-1 (Tischner et al. 1997).

extract_protocol: Total RNA was isolated from 200 µg by the TRIzol reagent (Invitrogen) and  mRNA was isolated from 36 µg total RNA with the Dynabeads mRNA purification kit (Dynal).

treatment_protocol: Cold treatment at 2°C was continued for 21 days without any change in the other growth conditions.

value: Rodnik

tag: frost tolerance grade

value: sensitive

tag: developmental stage

value: LP.03 three leaves visible


title: C10_boneMTS_rep2


title: C10_parental_rep1

description: parental breast CSCs-like

value: CSCs-like isolated from primary lobular infiltrating breast carcinoma (ER+, HER2-)


title: wheat_genotype:Capelle Desprez_day21_pooled

organism: Triticum aestivum

value: Capelle Desprez


title: barley_genotype:Barbinak_day21_pooled

value: Barbinak

value: tolerant


title: barley_genotype:Rex_day21_pooled

value: REX


title: barley_genotype:Kold_day21_pooled

value: Kold


title: barley_genotype:Baishishek_day21_pooled

value: Baishishek


title: C10_parental_rep2

description: parental breast CSCs-like


title: AAV-VEGF-B 6

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Chipster software (www.chipster.csc.fi)

label: Biotin

organism: Rattus norvegicus

source_name: Rat heart left ventricle

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

extract_protocol: Total RNA was isolated from left ventricular with TRIsure reagent (Bioline) and further purified with NucleoSpin RNA II (Macherey-Nagel). Quality control was performed with Agilent Bioanalyser.

value: heart left ventricle

tag: tranfection

value: AAV-VEGF-B

tag: genetic background

value: Wistar

tag: expression duration

value: 4 months

value: Male


title: AAV-HSA 6

value: AAV-HSA

value: 2 months

tag: gender

value: Female


title: AAV-HSA 4


title: wheat_genotype:Cheyenne izo_day21_pooled

value: Cheyenne izo


title: AAV-VEGF-B 4


title: AAV-HSA 5


title: barley_genotype:Hundred_day21_pooled

value: Hundred

value: LP.03 three leaves visible


title: wheat_genotype:Miranovszkaja_day21_pooled

value: Miranovszkaja 808


title: AAV-HSA 3


title: AAV-VEGF-B 5


title: AAV-VEGF-B 1


title: HFF-AD169 96hpi-rep3

value: Foreskin Fibroblasts


title: wheat_genotype:Martonvásári 8_day21_pooled

value: Martonvásári 8

value: sensitive


title: rye_genotype:LP5_day21_pooled

organism: Secale cereale


title: wheat_genotype:G.K. Tiszatáj_day21_pooled

value: G.K. Tiszatáj


title: wheat_genotype:Uljanovka_day21_pooled

value: Uljanovka izo

value: tolerant


title: rye_genotype:LP2_day21_pooled


title: Transgenic VEGF-B 6

value: heart left ventricle

tag: transgene

value: VEGF-B


title: AAV-VEGF-B 3

value: AAV-VEGF-B

value: Wistar


title: Transgenic VEGF-B 5

value: Male


title: rye_genotype:LP4_day21_pooled


title: AAV-HSA 1

value: AAV-HSA

value: 4 months


title: barley_genotype:Rodnik_day7_pooled

value: Rodnik


title: AAV-VEGF-B 2


title: AAV-HSA 2

value: 2 months

value: Female


title: barley_genotype:Baishishek_day7_pooled

value: Baishishek

value: LP.03 three leaves visible


title: rye_genotype:LP6_day21_pooled


title: rye_genotype:LP3_day21_pooled


title: Wildtype 6


title: Transgenic VEGF-B 2


title: Wildtype 4


title: Wildtype 1


title: Transgenic VEGF-B 4


title: wheat_genotype:Martonvásári 8_day7_pooled

value: Martonvásári 8


title: rye_genotype:LP1_day21_pooled


title: barley_genotype:Kold_day7_pooled

value: Kold


title: Wildtype 5


title: barley_genotype:Rex_day7_pooled

value: REX

value: sensitive


title: wheat_genotype:G.K. Tiszatáj_day7_pooled

value: G.K. Tiszatáj


title: barley_genotype:Hundred_day7_pooled

value: Hundred

value: tolerant


title: barley_genotype:Barbinak_day7_pooled

value: Barbinak


title: wheat_genotype:Uljanovka_day7_pooled

value: Uljanovka izo


title: wheat_genotype:Miranovszkaja_day7_pooled

value: Miranovszkaja 808


title: Wildtype 3

value: heart left ventricle

value: Wistar

value: Male


title: Transgenic VEGF-B 3

value: VEGF-B

value: 2 months


title: wheat_genotype:Capelle Desprez_day7_pooled

value: Capelle Desprez


title: Wildtype 2


title: wheat_genotype:Cheyenne izo_day7_pooled

value: Cheyenne izo

value: LP.03 three leaves visible


title: Transgenic VEGF-B 1


title: rye_genotype:LP4_day7_pooled


title: rye_genotype:LP6_day7_pooled


title: barley_genotype:Rodnik_day1_pooled

value: Rodnik


title: rye_genotype:LP1_day7_pooled


title: TDA3

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

data_processing: The data were normalised using lowess normalisation with oneChannelGUI 1.16.3 in R

source_name: TUBO cells grown in mammosphere medium in adherent conditions

label_protocol: Standard Illumina label protocol

growth_protocol: TUBO cells grown in adherent conditions as epithelial monolayer (TDA), were generated from a mammary carcinoma arising in a BALB-neuT female mouse, and cultured in epithelial medium, Dulbecco's Modified Eagle Medium supplemented with 20% fetal calf serum. TUBO cells grown in adherent conditions in mammosphere medium (TMA). Mammosphere medium, serum-free DMEM-F12 medium supplemented with 20 ng/ml basic-fibroblast growth factor (bFGF), 20 ng/ml epidermal growth factor (EGF), 5 μg/ml insulin, and 0.4% bovine serum albumin (BSA).

extract_protocol: Trizol total RNA extraction

value: TUBO

tag: origin tissue

value: breast cancer


title: rye_genotype:LP2_day7_pooled


title: TDA2


title: rye_genotype:LP5_day7_pooled

value: sensitive


title: TMA2

source_name: TUBO cells grown in DMEM in adherent conditions


title: rye_genotype:LP3_day7_pooled


title: TDA1


title: TMA1


title: TMA3


title: barley_genotype:Baishishek_day1_pooled

value: Baishishek


title: barley_genotype:Barbinak_day1_pooled

value: tolerant


title: barley_genotype:Kold_day1_pooled

value: Kold


title: wheat_genotype:Martonvásári 8_day1_pooled

value: Martonvásári 8


title: wheat_genotype:Capelle Desprez_day1_pooled


title: tubo exp 1 mammospheres p3

description: Detection of oncoantigens — proteins required for the neoplastic process — associated to breast cancer stem cells.

hyb_protocol: MouseWG-6 v2.0 Expression BeadChip hybridization, washing, and staining were also done, as suggested by the manufacturer.

scan_protocol: Arrays were scanned on Illumina BeadStation 500 as suggested by manufacturer.

data_processing: BeadChip array data quality control was done using Illumina BeadStudio software version 3. Probe average intensity signal was calculated with BeadStudio without background correction. Raw data were analyzed with Bioconductor [Gentleman et al. Genome Biol 2004;5:R80.] using the oneChannelGUI package [Sanges et al. Bioinformatics. 2007, 24, 3406-8]. Average probe intensities were log2 transformed and normalized by lowess method [Bolstad et al. Bioinformatics 2003;19:185–93]. To remove the non significant probes, i.e. not expressed Probes, all experimental groups were filtered to have an inter-quartile range for each probe ≥ 0.25. Differential expression between TuBo and mammospheres, was assessed using an empirical Bayes method [Smyth GK.  Stat Appl Genet Mol Biol. 2004;3:3] together with a false discovery rate (FDR) correction of the P-value.

source_name: non-adherent TuBo-derived mammospheres p3

label_protocol: cRNA was synthesized using Illumina RNA amplification kit (Ambion) starting from 500 ng of total RNA and following the procedure suggested by the manufacturer.

growth_protocol: Single TuBo cells were plated in ultra low attachment flasks (Corning Life Sciences, Chorges, France) at 6 x 104 viable cells/ml in serum-free DMEM-F12 medium (Cambrex BioScience, Venviers, Belgium) supplemented with 20 ng/ml basic fibroblast growth factor (bFGF), 20 ng/ml epidermal growth factor (EGF), 5 μg/ml insulin, and 0.4% bovine serum albumin (BSA), all from Sigma-Aldrich (St. Louis, MO). Nonadherent spherical clusters of cells, named mammospheres, were collected by gentle centrifugation after 7 days.

extract_protocol:
Mirvana kit (Ambion).
Quality and quantity of total RNA from samples was determined using Agilent 2100 Bioanalyzer and a Nanodrop spectrophotometer.

tag: strain

value: BALB/c

value: TuBo


title: barley_genotype:Rex_day1_pooled

value: REX


title: barley_genotype:Hundred_day1_pooled

value: Hundred


title: tubo exp 1 mammospheres p1

source_name: non-adherent TuBo-derived mammospheres p1


title: tubo exp 1 mammospheres p2

source_name: non-adherent TuBo-derived mammospheres p2


title: tubo exp 2 mammospheres p3

value: non-adherent TuBo-derived mammospheres p3


title: tubo exp 1 epithelial bulk

source_name: adherent TuBo epithelial cells

growth_protocol: The adherent TuBo epithelial cells were generated from a mammary carcinoma arising in a BALB/c mouse female transgenic for the activated rat ErbB2 oncogene (BALB-neuT) [Rovero et al. J Immunol, 2000. 165:5133-42] and were cultured in DMEM supplemented with 20% FCS (GIBCO, Grand Island, NY).

value: adherent TuBo epithelial cells


title: wheat_genotype:Miranovszkaja_day1_pooled

value: Miranovszkaja 808


title: tubo exp 2 mammospheres p2

value: non-adherent TuBo-derived mammospheres p2


title: wheat_genotype:Uljanovka_day1_pooled

value: Uljanovka izo

value: LP.03 three leaves visible


title: tubo exp 2 mammospheres p1

value: non-adherent TuBo-derived mammospheres p1


title: wheat_genotype:G.K. Tiszatáj_day1_pooled

value: G.K. Tiszatáj


title: wheat_genotype:Cheyenne izo_day1_pooled

value: Cheyenne izo


title: tubo exp 3 mammospheres p1


title: tubo exp 3 mammospheres p3


title: tubo exp 2 epithelial bulk


title: rye_genotype:LP5_day1_pooled

value: sensitive


title: rye_genotype:LP6_day1_pooled


title: tubo exp 3 epithelial bulk


title: tubo exp 3 mammospheres p2


title: barley_genotype:Kold_day0_pooled

value: tolerant


title: rye_genotype:LP4_day1_pooled


title: barley_genotype:Baishishek_day0_pooled

value: Baishishek


title: rye_genotype:LP3_day1_pooled


title: barley_genotype:Rex_day0_pooled


title: HSCs from female mice treated with E2, replicate 3

city: Houston

first: Daisuke

last: Nakada

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Gene expression data from HSCs isolated from female mice treated with E2
FE3 HSC

hyb_protocol: 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

scan_protocol: GeneChips were scanned using the Affymetrix’s GeneChip® Scanner 3000 and the GeneChip Command Console software v3.0

data_processing: The data were analyzed with dChip software using default analysis settings.

label_protocol: Biotinylated cDNA were prepared using Nugen Ovation Pico WTA V2 system and the Encore Biotin Module (NuGEN Technologies, San Carlos, CA)

growth_protocol: Young adult mice (2-3 month old) fed ad libitum

extract_protocol: 5000-7000 HSCs (CD150+ CD48- c-kit+ Sca-1+ lineage- cells) were sorted directly into Trizol reagent by flow cytometry.

treatment_protocol: Mice were either treated with control corn oil (100 micro L) or 2 micro gram estradiol in corn oil (100 micro L) subcutaneously.

value: female

tag: agent

value: Hematopoietic stem cells


title: HSCs from female mice treated with E2, replicate 2

description:
Gene expression data from HSCs isolated from female mice treated with E2
FE2 HSC


title: NOR6

description: asymptomatic individuals

data_processing: The data were normalized using the locally weighted scatterplot smoothing (LOWESS) algorithm. Analysis was performed using oneChannelGUI a package belonging to Bioconductor release 2.6.

source_name: colon biopsy

extract_protocol: Total RNA was extracted and purified from either surgical samples or five pooled pinch biopsies taken from the right colon using the RNA Purification Reagent (Promega, Madison, WI) as suggested by the manufacturer. RNAs were then quantified and inspected by Bioanalyzer (Agilent Technologies, Waldbrom, Germany) analysis

tag: tissue

value: colon biopsy

tag: disease status

value: asymptomatic individuals


title: NOR11

description: asymptomatic individuals


title: NOR10

description: asymptomatic individuals


title: M-CRC9

description: patient underwent curative large bowel resection for CRC


title: rye_genotype:LP1_day1_pooled

tag: genotype


title: rye_genotype:LP2_day1_pooled


title: HSCs from female mice treated with oil, replicate 3

description:
Gene expression data from HSCs isolated from female mice treated with oil
FO3 HSC

value: control

tag: cell type


title: barley_genotype:Rodnik_day0_pooled

value: Rodnik


title: HSCs from female mice treated with E2, replicate 1

description:
Gene expression data from HSCs isolated from female mice treated with E2
FE1 HSC


title: barley_genotype:Barbinak_day0_pooled

value: Barbinak


title: HSCs from female mice treated with oil, replicate 2

description:
Gene expression data from HSCs isolated from female mice treated with oil
FO2 HSC


title: NOR13

description: asymptomatic individuals


title: M-CRC38

value: patient underwent curative large bowel resection for CRC


title: barley_genotype:Hundred_day0_pooled

value: Hundred


title: M-CRC49


title: HSCs from female mice treated with oil, replicate 1

description:
Gene expression data from HSCs isolated from female mice treated with oil
FO1 HSC


title: wheat_genotype:Martonvásári 8_day0_pooled

value: Martonvásári 8


title: wheat_genotype:Cheyenne izo_day0_pooled

value: LP.03 three leaves visible


title: wheat_genotype:Miranovszkaja_day0_pooled

value: Miranovszkaja 808


title: HNORPC23

description: patient carrier of mutations predisposed to HNPCC


title: HSCs from male mice treated with E2, replicate 3

description:
Gene expression data from HSCs isolated from male mice treated with E2
ME3 HSC

value: male


title: wheat_genotype:Uljanovka_day0_pooled

value: Uljanovka izo


title: wheat_genotype:Capelle Desprez_day0_pooled

value: Capelle Desprez

value: sensitive


title: M-CRC50


title: rye_genotype:LP6_day0_pooled


title: wheat_genotype:G.K. Tiszatáj_day0_pooled

value: G.K. Tiszatáj


title: HSCs from male mice treated with E2, replicate 2

description:
Gene expression data from HSCs isolated from male mice treated with E2
ME2 HSC


title: HSCs from male mice treated with E2, replicate 1

description:
Gene expression data from HSCs isolated from male mice treated with E2
ME1 HSC


title: HNORPC22

value: female

value: patient carrier of mutations predisposed to HNPCC


title: rye_genotype:LP3_day0_pooled


title: HNORPC31

value: colon biopsy


title: rye_genotype:LP4_day0_pooled

value: tolerant


title: U937

type: genomic

city: Fitzroy

first: Ruth

middle: N

last: MacKinnon

state: Vic

address: PO Box 2900

department: Victorian Cancer Cytogenetics Service

country: Australia

institute: St Vincent's Hospital (Melbourne)

description:
Sample 2
Genomic DNA extracted from cell lines in culture was assayed using the CytoSNP 12 SNP array platform (Illumina). Reference Martin et al 1982 Science 216:1233-5

hyb_protocol: Illumina Infinium Assay Ultra

scan_protocol: Illumina BeadArray Reader

data_processing: Illumina Karyostudio

molecule: genomic DNA

source_name: myeloid leukemia cell line in log phase (fresh)

label_protocol: Illumina Infinium Assay Ultra

growth_protocol: Cultured in RPMI 1640 containing 10% FCS, glutamine, penicillin and streptomycin in air containing 5% CO2

extract_protocol: Qiagen DNeasy Cell and Tissue kit

value: Pleural effusion

tag: tumor

value: Large cell lymphoma

tag: primary tumor

value: Not applicable

tag: cell line

value: myeloid leukemia cell line U937

value: Male

tag: lineage

value: Myeloid


title: rye_genotype:LP5_day0_pooled

tag: frost tolerance grade

tag: developmental stage

value: LP.03 three leaves visible


title: HNORPC30


title: HEL

description:
Sample 1
Genomic DNA extracted from cell lines in culture was assayed using the CytoSNP 12 SNP array platform (Illumina). Reference Martin et al 1982 Science 216:1233-5

value: Peripheral blood mononuclear cells

value: Therapy-related erythroleukemia

value: Hodgkin's lymphoma

value: myeloid leukemia cell line HEL


title: HSCs from male mice treated with oil, replicate 2

description:
Gene expression data from HSCs isolated from male mice treated with oil
MO2 HSC

value: male

value: control

value: Hematopoietic stem cells


title: rye_genotype:LP1_day0_pooled


title: HSCs from male mice treated with oil, replicate 3

description:
Gene expression data from HSCs isolated from male mice treated with oil
MO3 HSC


title: rye_genotype:LP2_day0_pooled


title: tubo exp 2 mammospheres p3

description: Exon-level analysis: detecting the presence of isoforms specific of CSC derived by TuBo cell line. The analysis was done comparing TuBo cells grown in adherent conditions with respect to mammospheres derived by TuBo cells grown under no-adherent conditions.

hyb_protocol: Affimetrix GeneChip® Exon 1.0 ST hybridization, washing, and staining were also done, as suggested by the manufacturer.

scan_protocol: Arrays were scanned on Affymetrix Scanner 3000 7G as suggested by manufaturer

data_processing: GeneChip® Exon 1.0 ST arrays data quality control was done using Affymetrix Expression Console (www.affymetrix.com). Probe average intensity signal was calculated using oneChannelGUI package [Sanges et al. Bioinformatics. 2007, 24, 3406-8]. Probe set intensities were calculated using the RMA algorithm and normalized by the sketch quantile method [Irizarry et al. Biostatistics 2003, 4:249-264.]. Putative splicing events were detected using MiDAS (www.affymetrix.com) 2-way anova implemented in oneChannelGUI. Exons characterized by a p-value ≤ 0.05 in all three comparison (E vs P1, E vs P2 and E vs P3) were manually inspected using oneChannelGUI visualization tools.

label_protocol: cDNA was synthesized using Affymetrix kit starting from 100 ng of total RNA and following the procedure suggested by the manufacturer.

extract_protocol: Mirvana kit (Ambion)

value: BALB/c

value: TuBo

value: non-adherent TuBo-derived mammospheres p3


title: tubo exp 6 mammospheres p3


title: tubo exp 4 mammospheres p3


title: HFD-feeding Mouse exposed to arsenic, biological rep2

city: Nanjing

first: Bing

last: Wu

state: Jiangsu

address: NO.163 Xianlin Road

department: School of the Environment

institute: Nanjing University

hyb_protocol: Following fragmentation,  cRNA were hybridized in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Affymetrix Expression Console software (v.1.0) was applied to provides signal estimation and QC functionality

source_name: Mouse liver after 90-day exposure

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

growth_protocol: Male C57Bl/6J mice were housed in stainless-steel cages under controlled conditions (25±3 °C, 50±5 % humidity and 12/12 h light/dark cycle)  for 10 weeks

extract_protocol: Total RNA for each mouse was separately extracted using Trizol reagent protocol.10 mice per group were randomly divided into two sets (5 mice per set). Equal amounts of RNAs from 5 mice in the same set were pooled into one sample, and two samples per group were obtained.

treatment_protocol: A total of forty mice were randomly assigned to four groups. Mice were fed a control LFD (13% fat in calories) or HFD (42% fat in calories) and given deionized water with or without sodium arsenite (3 mg iAs/L) for 10 weeks.

tag: growth protocol

value: HFD

value: sodium arsenite

value: Liver


title: HFD-feeding Mouse exposed to arsenic, biological rep1


title: HSCs from male mice treated with oil, replicate 1

description:
Gene expression data from HSCs isolated from male mice treated with oil
MO1 HSC


title: tubo exp 2 mammospheres p2

hyb_protocol: Affimetrix GeneChipÂ® Exon 1.0 ST hybridization, washing, and staining were also done, as suggested by the manufacturer.

data_processing: GeneChipÂ® Exon 1.0 ST arrays data quality control was done using Affymetrix Expression Console (www.affymetrix.com). Probe average intensity signal was calculated using oneChannelGUI package [Sanges et al. Bioinformatics. 2007, 24, 3406-8]. Probe set intensities were calculated using the RMA algorithm and normalized by the sketch quantile method [Irizarry et al. Biostatistics 2003, 4:249-264.]. Putative splicing events were detected using MiDAS (www.affymetrix.com) 2-way anova implemented in oneChannelGUI. Exons characterized by a p-value â�€ 0.05 in all three comparison (E vs P1, E vs P2 and E vs P3) were manually inspected using oneChannelGUI visualization tools.

value: non-adherent TuBo-derived mammospheres p2


title: 60 d phosphorus deficiency (P2)

city: Guiyang

first: Fuhua

last: Fan

address: Xiahui Street, Huaxi

institute: Guizhou University

description: Analysis used phosphorus-sufficient treatment RNA as control samples for comparison to the experimental samples (P1 and P2) taken at 12, 24, 48 and 64 day.

hyb_protocol: Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath overnight at 42 °C. Arrays then washed in 2x SSC (+0.2 % SDS) and 0.2x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using an Agilent G2565CA microarray scanner and Feature Extraction software.

data_processing: Data analysis was carried out using Feature Extraction. The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental and biological repeats.

organism: Pinus massoniana

source_name: Masson pine seedlings P2 stressed for 60 days

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using cDNA Amplification Tag Kit (Jingxin, CapitalBio Corporation, China) as manufacturers instructions. Samples purified using NucleoSpinExtract II Kit (MN) before hybridization.

growth_protocol: The seeds were surface sterilized, rinsed in sterile water, and allowed to imbibe overnight in a tray containing warm sterile water (30℃). Then sterilized seeds were planted ten seedlings per pot in 12-inch pots containing quartz sand. Pots were placed in growth chambers at 25℃/16℃ with a 14-h photoperiod (2000Lx), and watered once per day until 10 d after emergence (DAE).

extract_protocol: Total RNA was extracted from the samples using Invitrogen Plant RNA Isolation Kit, following by RNA purification by RNeasy MiniElute Cleanup Kit (Qiagen) with on column DNAse digestion.

treatment_protocol: There were three treatments with different P levels: i) control nutrient solution (CK), composed of: 5.0 mM KNO3, 4.5 mM Ca(NO3)2•4H2O, 2.0 mM MgSO4•7H2O, 0.5 mM KH2PO4, 46 µM H3BO3, 10 µM MnCl2•4H2O, 0.8 µM ZnSO4•7H2O, 0.56 µM CuSO4•5H2O, 0.4 µM H2MoO4•4H2O, and 25 µM Fe-NaEDTA; ii) nutrient solution deficient in Pi (P1) in which 0.01 mM instead of 0.5 mM KH2PO4; iii) nutrient solution deficient in Pi (P2) in which 0.06 mM instead of 0.5 mM KH2PO4. KCl was added to Pi-deficient solution to maintain proper potassium concentrations.

value: whole seedlings

tag: stress

value: 60 d phosphorus deficiency

source_name: Masson pine seedlings in phosphorus-sufficiency for control


title: HFD-feeding Mouse, biological rep2

tag: gender


title: 48 d phosphorus deficiency (P2)

description: Analysis used phosphorus-sufficient treatment RNA as control samples for comparison to the experimental samples (P1 and P2) taken at 12, 24, 48 and 63 day.

source_name: Masson pine seedlings P2 stressed for 48 days

value: 48 d phosphorus deficiency


title: 12 d phosphorus deficiency (P2)

description: Analysis used phosphorus-sufficient treatment RNA as control samples for comparison to the experimental samples (P1 and P2) taken at 12, 24, 48 and 61 day.

source_name: Masson pine seedlings P2 stressed for 12 days

value: 12 d phosphorus deficiency


title: tubo exp 5 mammospheres p3


title: 24 d phosphorus deficiency (P2)

description: Analysis used phosphorus-sufficient treatment RNA as control samples for comparison to the experimental samples (P1 and P2) taken at 12, 24, 48 and 62 day.

source_name: Masson pine seedlings P2 stressed for 24 days

value: 24 d phosphorus deficiency


title: 60 d phosphorus deficiency (P1)

description: Analysis used phosphorus-sufficient treatment RNA as control samples for comparison to the experimental samples (P1 and P2) taken at 12, 24, 48 and 60 day.

source_name: Masson pine seedlings P1 stressed for 60 days


title: tubo exp 1 mammospheres p2


title: LFD-feeding Mouse exposed to arsenic, biological rep2

value: LFD


title: 12 d phosphorus deficiency (P1)

source_name: Masson pine seedlings P1 stressed for 12 days


title: 48 d phosphorus deficiency (P1)

source_name: Masson pine seedlings P1 stressed for 48 days


title: 24 d phosphorus deficiency (P1)

source_name: Masson pine seedlings P1 stressed for 24 days


title: LFD-feeding Mouse exposed to arsenic, biological rep1


title: J1 Thoc5 siRNA_rep2

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

hyb_protocol: Hybridization was carried out on Agilent Mouse GE 4x44K v2 Microarray (G2519F) accrording to Agilent protocol.

scan_protocol: Arrays were scanned on Agilent SureScan Microarray Scanner according to manufacturer's instructions using the one color scan setting.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 11.0 using default parameters to obtain background subtracted Processed Signal intensities.

source_name: mouse J1 ESC

label_protocol: Labeling was carried out with the Agilent Low Input Quick Amp Labeling Kit, one color, using 1 ug total RNA.

growth_protocol: J1 cell were maintianed in ESGRO medium. Cell were cultured in M10 medium when transfection or infection was performed.

extract_protocol: Total RNA were prepared using Therno RNA kit according to the manufacturer's instructions.

treatment_protocol: Cell were transfected with siRNAs against NT, Thoc2 and Thoc5. Total RNA was harvested 96 hours after transfection.

value: embryonic cell line

tag: transfection

value: Thoc5 siRNA


title: HFD-feeding Mouse, biological rep1

value: male

value: control


title: J1 Thoc5 siRNA_rep1


title: tubo exp 4 mammospheres p2

value: BALB/c


title: J1 Thoc2 siRNA_rep2

value: Thoc2 siRNA


title: LFD-feeding Mouse, biological rep2


title: J1 Thoc2 siRNA_rep1


title: tubo exp 2 mammospheres p1

value: TuBo

value: non-adherent TuBo-derived mammospheres p1


title: tubo exp 1 mammospheres p1


title: tubo exp 3 mammospheres p1


title: J1 NT siRNA_rep2

value: non-targeting siRNA


title: BH1-Bcl2-Ik1ER cells 24h, -IL-7, +4OHT, exp2

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

hyb_protocol: 1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix)

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: CEL files were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

growth_protocol: Cell lines were cultured in Iscove's medium supplemented with 10% FCS, 100 U/ml penicillin-streptomycin, 2 mM Glutamine, 50 µM 2-mercaptoethanol and 8% conditioned medium from a J558L cell line stably overexpressing murine IL-7 (Winkler et al., 1995)

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy micro kit

treatment_protocol: 4OHT was used at 100 nM. Cells cultured in IL-7 withdrawal conditions were cultured without J558L-conditionned medium


title: tubo exp 4 mammospheres p1


title: patient underwent curative large bowel resection for CRC MCRC12

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Genechip HGU133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Microarray quality control and statistical validation were performed using oneChannelGUI a package belonging to Bioconductor release 2.6. The presence of hybridization/construction artifacts was evaluated with the fitPLM function (Bioconductor package affyPLM). The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of RMA and normalization was done according to quantiles method.

label_protocol: Biotinylated cRNA target was produced starting from 1 microg of total RNA in according to Affymetrix (Santa Clara, CA)  instructions and for each sample 15 microg were fragmented to a length of 20–200 bp before hybridization to Genechip HGU133 plus2.0 arrays

value: female

tag: disease state

value: CRC

value: colon mucosa


title: tubo exp 5 mammospheres p1

tag: strain


title: asymptomatic individual NOR26

value: asymptomatic


title: patient underwent curative large bowel resection for CRC MCRC33


title: ROX370_2

city: Kawasaki

first: Takashi

last: Osanai

state: Kanagawa

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

country: Japan

institute: Meiji University

description: rre37 overexpression strain

hyb_protocol: Labeling cDNAs are spotted onto CyanoChip (slide glass), and covered by slide glass, followed by incubation at 60 degree for overnight

scan_protocol: Hybridization signals were measured with a 428 Array scanner (Affymetrix) and a software Affymetrix 428 array scanner version 1.1. Cy3 or Cy5 signals were scanned with 532 nm or 635 nm laser. Resolution were 2200 x 5760 pixels. Scanned pictures were saved as 16-bit TIFF files.

data_processing: Normalization was performed for adjusting total signal intensities between cy3 and cy5 by Excel (Microsoft).

organism: Synechocystis sp. PCC 6803

label_protocol: cDNAs were synthetized from total RNA by RNA Fluorescence Labeling Core Kit （M-MLV Version） Ver.2.0 (Takara Bio).

growth_protocol: Cells grown in modified BG-11 liquid medium (5 mM NH4Cl as nitrogen sources) under 50-70 micromolphotons/m2s.

extract_protocol: Total RNAs were isolated by hot-phenol method.

tag: growth phase

value: log-phage


title: Wild-type GT3

description: Glucose-tolerant Synechocystis strain


title: tubo exp 6 mammospheres p1


title: LFD-feeding Mouse, biological rep1

tag: agent

tag: tissue

value: Liver


title: BH1-Bcl2-Ik1ER cells 24h, -IL-7, -4OHT, exp2


title: BH1-Bcl2-Ik1ER cells 24h, +IL-7, +4OHT, exp2


title: ROX370_3

description: rre37 overexpression strain


title: patient underwent curative large bowel resection for CRC MCRC17


title: patient underwent curative large bowel resection for CRC MCRC7


title: BH1-Bcl2-Ik1ER cells 24h, +IL-7, -4OHT, exp2


title: patient underwent curative large bowel resection for CRC MCRC4


title: Wild-type GT2

description: Glucose-tolerant Synechocystis strain


title: asymptomatic individual NORL


title: J1 NT siRNA_rep1


title: tubo exp 2 epithelial bulk

value: adherent TuBo epithelial cells


title: Wild-type GT1

description: Glucose-tolerant Synechocystis strain


title: tubo exp 1 epithelial bulk


title: BH1-Bcl2-Ik1ER cells 6h, +IL-7, +4OHT, exp2


title: tubo exp 3 epithelial bulk


title: BH1-Bcl2-Ik1ER cells 6h, -IL-7, +4OHT, exp2


title: asymptomatic individual NORM


title: BH1-Bcl2-Ik1ER cells at time 0, exp2

source_name: BH1-Bcl2-Ik1ER cells at time 0, exp2


title: ROX370_1

description: rre37 overexpression strain


title: tubo exp 6 epithelial bulk


title: tubo exp 5 epithelial bulk


title: asymptomatic individual NORE


title: asymptomatic individual NORI


title: asymptomatic individual NORB


title: BH1-Bcl2-Ik1ER cells 24h, -IL-7, +4OHT, exp1


title: BH1-Bcl2-Ik1ER cells 24h, +IL-7, +4OHT, exp1


title: asymptomatic individual NOR29


title: asymptomatic individual NORA


title: tubo exp 4 epithelial bulk


title: asymptomatic individual NOR28


title: lb_vs_glu_2

first: Lydia

last: Freddolino

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description: Transposon footprinting comparing fitness of the secondary library in glucose minimal media to LB

hyb_protocol: Samples were hybridized to custom Agilent arrays using the manufacturer's instructions

scan_protocol: Scanned using an Agilent microarray scanner

data_processing: Data were processed and analyzed using Agilent Feature Extraction v. 9.5 with default settings

organism: Escherichia coli

source_name: Glucose selection

label_protocol: Transposon insertions were amplified via ligation mediated PCR, and then in vitro transcribed using a T7 promoter in the presence of appropriate dye-labeled nucleotide analogue

growth_protocol: The transposon library was thawed, washed, and then diluted 500-fold into fresh media under the condition of interest and grown for 16 hours

extract_protocol: Genomic DNA was extracted using a Qiagen DNEasy Blood and Tissue kit

tag: condition

value: Transposon footprinting from secondary library grown in MOPS/glucose (Footprinted regions from strain K12 substr. MG1655, in an ATCC8739 background)

source_name: LB selection

value: Transposon footprinting from secondary library grown in LB (Footprinted regions from strain K12 substr. MG1655, in an ATCC8739 background)


title: BH1-Bcl2-Ik1ER cells 24h, -IL-7, -4OHT, exp1

tag: cell type


title: ella_vs_glu_2

description: Transposon footprinting comparing fitness of the secondary library in glucose minimal media to glucose minimal media with ellagic acid added

source_name: ELLA selection

value: Transposon footprinting from secondary library grown in MOPS/glucose + ellagic acid (Footprinted regions from strain K12 substr. MG1655, in an ATCC8739 background)


title: BH1-Bcl2-Ik1ER cells 6h, +IL-7, +4OHT, exp1


title: BH1-Bcl2-Ik1ER cells 24h, +IL-7, -4OHT, exp1


title: BH1-Bcl2-Ik1ER cells 6h, -IL-7, +4OHT, exp1


title: asymptomatic individual NOR27

source_name: colon biopsy


title: U937_fixed

description:
Sample 3
Genomic DNA extracted from cell lines in culture was assayed using the CytoSNP 12 SNP array platform (Illumina). Reference Martin et al 1982 Science 216:1233-5

source_name: Carnoy's fixed metaphase preparation from myeloid leukemia cell line

treatment_protocol: Standard cytogenetic harvest:pre- treated with 0.2ug/mL colcemid (37°C, 30min) and hypotonic solution (0.075M Kl, 37°C, 40min), then fixed and stored in Carnoy's fixative, 3:1 methanol:acetic acid. Washed and resuspended in PBS before DNA extraction.

value: Pleural effusion

tag: tumor

value: Large cell lymphoma

value: Not applicable

value: myeloid leukemia cell line U937

value: Male

value: Myeloid


title: ella_vs_glu_1


title: K38

status: Public on Nov 29 2013

city: Odense C

first: Kristina

middle: P

last: Sørensen

address: Srd. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

hyb_protocol: Hybridization and washing were performed according to manufacturer’s recommendations in a low ozone environment.

scan_protocol: Scanned using a Agilent G2565CA Microarray scanner

data_processing: Scanned images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).

source_name: Breast tumor tissue

label_protocol: RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).

value: postmenopausal

tag: age

tag: who

value: Carcinoma with metaplasia

tag: grade

source_name: Universal Human Reference RNA (Stratagene)

tag: sample type

value: reference


title: M37a

value: Invasive ductal carcinoma


title: A38

value: premenopausal


title: asymptomatic individual NOR24

value: female

value: asymptomatic

value: colon mucosa


title: RP11B


title: RP11A


title: lb_vs_glu_1

value: Transposon footprinting from secondary library grown in MOPS/glucose (Footprinted regions from strain K12 substr. MG1655, in an ATCC8739 background)


title: RP14A(D11)


title: M37b(K36)


title: RP14B(nyN11)


title: BH1-Bcl2-Ik1ER cells at time 0, exp1

source_name: BH1-Bcl2-Ik1ER cells at time 0, exp1


title: kdg_vs_glu_2

description: Transposon footprinting comparing fitness of the secondary library in glucose minimal media to 5-keto D-gluconate minimal media

source_name: KDG selection

value: Transposon footprinting from secondary library grown in MOPS/KDG(Footprinted regions from strain K12 substr. MG1655, in an ATCC8739 background)


title: kdg_vs_glu_1

value: Transposon footprinting from secondary library grown in MOPS/KDG (Footprinted regions from strain K12 substr. MG1655, in an ATCC8739 background)


title: RP7B

value: Invasive lobular carcinoma


title: RP6A

value: Papillary carcinoma


title: RP6B


title: RP4B


title: RP7A


title: RP10B


title: RP3A


title: RP5A

value: Mucinous carcinoma


title: RP5B


title: RP4A(ny)


title: RP2B


title: 31Bny


title: RP10A


title: RP1B


title: RP3B


title: RP2A


title: RP1A


title: 33A


title: K18(N20ny)


title: 33B


title: 9A


title: 27A


title: D20


title: 27Bny(N14)


title: D21


title: 9B


title: 31A


title: N21


title: 7A


title: D18


title: N19


title: 7B


title: K41(N18ny)


title: K51(N15ny)


title: D13

value: Unknown


title: N08


title: asymptomatic individual NORC


title: D17


title: N17


title: D19


title: K56(N16ny)


title: D16


title: N09


title: D12


title: D15


title: K52(N13ny)


title: D09


title: D08


title: D04


title: N12


title: N05


title: M44


title: D07


title: D05


title: N02


title: N07


title: C48


title: D02


title: K29(N04ny)


title: M42


title: M40


title: M37ny(L07)


title: C40


title: M35ny(L08)


title: M36


title: C33


title: C42


title: C35


title: C37


title: C38


title: C44


title: M32


title: M38


title: M39


title: C31


title: M29


title: C36


title: M27


title: C39


title: M33


title: M30ny(M58)


title: C30


title: M28


title: K33(M31ny)


title: C32


title: C27


title: C28


title: microRNA profile of case 5N

city: Guangzhou

first: Zhenhua

last: Chen

address: NO.58,ZhongShan 2nd Road

department: Urology

institute: The First Affiliated Hospital,Sun Yat-sen University

description:
Co-hybridized: 5T and 5N
Raw data file: 120914-S9-up_5T_5N.gpr

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

source_name: adjacent normal tissues

label_protocol:
2.5 μg of total RNA of colon tumor tissues was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight
2.5 μg of total RNA of adjacent normal tissues was employed with 100 nmol/L of pCp-DY547 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: sample name

tag: paired sample name

value: adjacent normal tissues


title: microRNA profile of case 13N

description:
Co-hybridized: 13T and 13N
Raw data file: 120914-S9-low_13T_13N.gpr


title: microRNA profile of case 3N

description:
Co-hybridized: 3T and 3N
Raw data file: 120914-S10-low_3T_3N.gpr


title: microRNA profile of case 22N

description:
Co-hybridized: 22T and 22N
Raw data file: 120914-S12-low_22T_22N.gpr


title: microRNA profile of case 43N

description:
Co-hybridized: 43T and 43N
Raw data file: 120914-S13-low_43T_43N.gpr


title: microRNA profile of case 246N

description:
Co-hybridized: 246T and 246N
Raw data file: 120914-S14-low_246T_246N.gpr


title: C29


title: M25


title: M22


title: C25


title: M24


title: Primary Myelofibrosis PMF Transformed to Acute Myeloid Leukaemia AML sample 3

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

country: Spain

institute: CIMA

description:
Peripheral Blood.Karyotype:46,XX,-7,+mar[30]; JAK2: JAK2V617F; TET2: No Information; EZH2:No Information
Transformed PMF Sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Peripheral blood of PMF Transformed to LMA patient

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA from PBMCs was extracted using QIAmp DNA Mini Kit following the manufacturer´s instructions (Qiagen, Hilden, Germany).

value: peripheral blood

value: mononuclear cells

value: Female

value: No information

tag: karyotype

value: No Information

value: NoInformation

value: PMF Transformed to LMA


title: Primary Myelofibrosis PMF Transformed to Acute Myeloid Leukaemia AML sample 1

description:
Bone Marrow.Karyotype:46,XY,del(1)(p33) [23]/ 46,XY[7]; JAK2: Wild Type; TET2: No Information; EZH2:No Information
Transformed PMF Sample

source_name: Bone Marrow of PMF Transformed to LMA patient

tag: gender

value: Male

value: WildType


title: microRNA profile of case 566N

description:
Co-hybridized: 566T and 566N
Raw data file: 120914-S14-up_566T_566N.gpr


title: Essential Thrombocythaemia Transformed to Acute Myeloid Leukaemia AML sample 3

description:
Bone Marrow.Karyotype:46,XX,del(5)(q15q31),del(20)(q11)[50]; JAK2: Wild Type; TET2: No Information; EZH2:No Information
Transformed ET Sample

source_name: Bone Marrow sample of TE Transformed to LMA patient

value: ET Transformed to LMA


title: Primary Myelofibrosis PMF Transformed to Acute Myeloid Leukaemia AML sample 2

description:
Bone Marrow.Karyotype:46,XY,add(12)(p13) [12]/ 46,XY[18]; JAK2: Wild Type; TET2: No Information; EZH2:No Information
Transformed PMF Sample


title: C24

value: postmenopausal

value: Invasive ductal carcinoma

value: reference


title: Primary Myelofibrosis PMF Transformed to Acute Myeloid Leukaemia AML sample 5

description:
Peripheral Blood.Karyotype: 46,XY,+der(1)del(1)(p21),-7[30]; JAK2: Wild Type; TET2: No Information; EZH2:No Information
Transformed PMF Sample


title: Primary Myelofibrosis PMF Transformed to Acute Myeloid Leukaemia AML sample 4

description:
Bone Marrow.Karyotype:46,XY,del(1)(p32),-7,-8,-12,add(16)(q24),+3mar [24]/ 46,XY[6]; JAK2: Wild Type; TET2: No Information; EZH2:No Information
Transformed PMF Sample


title: C22


title: microRNA profile of case 163N

description:
Co-hybridized: 163T and 163N
Raw data file: 120914-S33-LOW_163T_163N.gpr


title: M18


title: Essential Thrombocythaemia Transformed to Acute Myeloid Leukaemia AML sample 4

description:
Karyotype:47,XX,del(5)(q13q32),-13,-17,+21,+2mar [17]/ 46,XX [13]; JAK2: JAK2V617F; TET2: No Information; EZH2:No Information
Transformed ET Sample


title: Essential Thrombocythaemia Transformed to Acute Myeloid Leukaemia AML sample 2

description:
Bone Marrow.Karyotype:47,XX,del(20)(q13)x2[3]/ 46,XX[27]; JAK2: JAK2V617F; TET2: No Information; EZH2:No Information
Transformed ET Sample


title: Essential Thrombocythaemia Transformed to Acute Myeloid Leukaemia AML sample 1

description:
Bone Marrow.Karyotype: 46,XY,-5,add(6)(p25),+mar[20]; JAK2: JAK2V617F; TET2: No Information; EZH2:No Information
Transformed ET Sample


title: Polycythemia Vera PV Transformed to Acute Myeloid Leukaemia AML sample 3

description:
Peripheral Blood.Karyotype:44,X,-Y,-17,der(19)t(17;19)(p13;q12) [27]/ 45,X,-Y [23] ; JAK2: JAK2V617F; TET2: No Information; EZH2:No Information
Transformed PV Sample

source_name: Peripheral Blood sample of PV Transformed to LMA patient

value: PV Transformed to LMA


title: Polycythemia Vera PV Transformed to Acute Myeloid Leukaemia AML sample 4

description:
Bone Marrow.Karyotype:44,XY,del(2)(q?),-4,del(5)(q13q32)-17 [13]/ 45,XY,del(5)(q13q32),del(12)(p13)-17 [14]/ 46,XY [3]; JAK2:No Information ; TET2: No Information; EZH2:No Information
Transformed PV Sample

source_name: Bone Marrow sample of PV Transformed to LMA patient


title: Polycythemia Vera PV Transformed to Acute Myeloid Leukaemia AML sample 1

description:
Peripheral Blood.Karyotype: 59,X,-Y,+1,+2,+6,+8,+9,+13,+14,+15,+19,+20,+4mar  [40]/45,X,-Y  [10]; JAK2: JAK2V617F; TET2: No Information; EZH2:No Information
Transformed PV Sample


title: Polycythemia Vera PV Transformed to Acute Myeloid Leukaemia AML sample 2

description:
Bone Marrow.Karyotype: 46,XY,der(20)t(1;20)(q21,q1)[30]; JAK2: JAK2V617F; TET2: No Information; EZH2:No Information
Transformed PV Sample


title: microRNA profile of case 100N

description:
Co-hybridized: 100T and 100N
Raw data file: 120914-S33-up_100T_100N.gpr


title: microRNA profile of case 7N

description:
Co-hybridized: 7T and 7N
Raw data file: 120914-S34-up_7T_7N.gpr


title: microRNA profile of case 1N

description:
Co-hybridized: 1T and 1N
Raw data file: 120914-S34-low_1T_1N.gpr


title: microRNA profile of case 15N

description:
Co-hybridized: 15T and 15N
Raw data file: 120914-S35-low_15T_15N.gpr


title: microRNA profile of case 21N

description:
Co-hybridized: 21T and 21N
Raw data file: 120914-S36-low_21T_21N.gpr


title: Primary Myelofibrosis sample 21

description:
Bone Marrow.Karyotype: 46, XY; JAK2: Wild type; TET2: Wild type; EZH2:Wild type
PMF Sample

source_name: Bone Marrow sample of Primary Myelofibrosis patient

value: Wildtype

value: Primary Myelofibrosis


title: Primary Myelofibrosis sample 22


title: Primary Myelofibrosis sample 24

description:
Bone Marrow.Karyotype: 47,XY,+8 [1]/ 46,XY[29]; JAK2: Wild type; TET2: No Information; EZH2:Wild type
PMF Sample


title: C18


title: M53(M17ny)


title: Primary Myelofibrosis sample 23


title: L06


title: microRNA profile of case 20N

description:
Co-hybridized: 20T and 20N
Raw data file: 120914-S35-up_20T_20N.gpr

value: adjacent normal tissues


title: microRNA profile of case 26N

description:
Co-hybridized: 26T and 26N
Raw data file: 120914-S36-up_26T_26N.gpr


title: Primary Myelofibrosis sample 18

description:
Peripheral Blood.Karyotype:No Information; JAK2: Wild type; TET2: Wild type; EZH2:Wild type
PMF Sample

source_name: Peripheral Blood sample of PMF patient

value: peripheral blood


title: Primary Myelofibrosis sample 14

description:
Bone Marrow. Karyotype: 46, XX; JAK2: Wild type; TET2: Wild type; EZH2:Wild type
PMF Sample

value: mononuclear cells


title: microRNA profile of case 27N

description:
Co-hybridized: 27T and 27N
Raw data file: 120914-S37-low_27T_27N.gpr


title: microRNA profile of case 52N

description:
Co-hybridized: 52T and 52N
Raw data file: 120914-S37-up_52T_52N.gpr


title: B06


title: Primary Myelofibrosis sample 20


title: Primary Myelofibrosis sample 17

description:
Bone Marrow.Karyotype: 47,XX,del(13)(q12q21) [37%]/ 46,XX [63%]; JAK2: Wild type; TET2: Wild type; EZH2:Wild type
PMF Sample

value: Female


title: L04


title: Primary Myelofibrosis sample 16

description:
Peripheral Blood.Karyotype: No Information; JAK2: Wild type; TET2: Wild type; EZH2:Wild type
PMF Sample


title: Primary Myelofibrosis sample 13

description:
Peripheral Blood. Karyotype: No Information; JAK2: Wild type; TET2: No information; EZH2:Wild type
PMF Sample

value: No information


title: Primary Myelofibrosis sample 12

description:
Peripheral Blood. Karyotype: No Information; JAK2:JAKV617F-HET; TET2: Wild Type; EZH2:Wild Type
PMF Sample

value: No Information


title: C17


title: B04


title: Primary Myelofibrosis sample 15

description:
Peripheral Blood.Karyotype:No Information; JAK2: Wild Type; TET2: Wild type; EZH2:Wild type
PMF Sample


title: Primary Myelofibrosis sample 19


title: Primary Myelofibrosis sample 11


title: B03


title: Primary Myelofibrosis sample 10

description:
Peripheral Blood. Karyotype: 46,XY; JAK2:JAKV617F-HET; TET2: Wild Type; EZH2:Wild Type
PMF Sample


title: L03


title: B02


title: microRNA profile of case 609N

description:
Co-hybridized: 609T and 609N
Raw data file: 120914-S49-up_609T_609N.gpr


title: microRNA profile of case 40N

description:
Co-hybridized: 40T and 40N
Raw data file: 120914-S40-up_40T_40N.gpr


title: L02


title: microRNA profile of case 604N

description:
Co-hybridized: 604T and 604N
Raw data file: 120914-S49-low_604T_604N.gpr


title: microRNA profile of case 611N

description:
Co-hybridized: 611T and 611N
Raw data file: 120914-S50-low_611T_611N.gpr


title: microRNA profile of case 54N

description:
Co-hybridized: 54T and 54N
Raw data file: 120914-S50-up_54T_54N.gpr


title: Primary Myelofibrosis sample 9


title: microRNA profile of case 622N

description:
Co-hybridized: 622T and 622N
Raw data file: 120914-S50-up_622T_622N.gpr


title: microRNA profile of case 104N

description:
Co-hybridized: 104T and 104N
Raw data file: 20121120-S10-low_104T_104N.gpr


title: microRNA profile of case 110N

description:
Co-hybridized: 110T and 110N
Raw data file: 20121120-S11-low_110T_110N.gpr


title: microRNA profile of case 595N

description:
Co-hybridized: 595T and 595N
Raw data file: 20121120-S13-low_595T_595N.gpr


title: Primary Myelofibrosis sample 8


title: A64


title: K64


title: Primary Myelofibrosis sample 7

description:
Peripheral Blood. Karyotype: 46,XX [37%];47,XX,+8 [63%]; JAK2:JAKV617F-HET; TET2: Wild Type; EZH2:Wild Type
PMF Sample


title: microRNA profile of case 1026N

description:
Co-hybridized: 1026T and 1026N
Raw data file: 20121120-S14-low_1026T_1026N.gpr


title: Primary Myelofibrosis sample 4

description:
Bone Marrow. Karyotype: 46, XY; JAK2: JAKV617F-HET; TET2: Wild Type; EZH2:Wild Type
PMF Sample

source_name: Bone Marrow sample of PMF patient


title: Primary Myelofibrosis sample 3

description:
Peripheral Blood. Karyotype: 46, XY; JAK2: JAKV617F-HET; TET2: Wild Type; EZH2:Wild Type
PMF Sample


title: K63


title: Primary Myelofibrosis sample 2

description:
Peripheral Blood. Karyotype: No Information; JAK2: JAKV617F-HET; TET2: Wild TypeI; EZH2:73980T>TG;660L>L/V
PMF Sample


title: Primary Myelofibrosis sample 6

description:
Peripheral Blood. Karyotype: 46, XY; JAK2: JAKV617F-HET; TET2: ins/del; EZH2:Wild Type
PMF Sample

value: ins/del


title: Primary Myelofibrosis sample 5


title: K35(K62ny)


title: Primary Myelofibrosis sample 1

description:
Peripheral Blood. Karyotype: No Information; JAK2: JAKV617F-HET; TET2:  T1372I; EZH2:Wild Type
PMF Sample

source_name: Peripheral Blood sample of ET patient


title: Essential Thrombocythemia sample 23

description:
Peripheral Blood. Karyotype: No Information; JAK2: JAK2:JAKV617F-HET; TET2:  Wild Type; EZH2:No Information
ET Sample

value: NoInformation

value: Essential Thrombocythemia


title: A62


title: Essential Thrombocythemia sample 22

description:
Peripheral Blood. Karyotype: 46, XY; JAK2:JAKV617F-HET; TET2:  Wild Type; EZH2:No Information
ET Sample

value: WildType


title: K55


title: A63


title: microRNA profile of case 1065N

description:
Co-hybridized: 1065T and 1065N
Raw data file: 20121120-S14-up_1065T_1065N.gpr


title: microRNA profile of case 1070N

description:
Co-hybridized: 1070T and 1070N
Raw data file: 20121120-S15-low_1070T_1070N.gpr


title: K34(K50ny)


title: A55


title: Essential Thrombocythemia sample 21

description:
Peripheral Blood. Karyotype: No Information;  JAK2:JAKV617F-HET; TET2:  Wild Type; EZH2:No Information
ET Sample


title: Essential Thrombocythemia sample 20

description:
Bone Marrow. Karyotype: No Information; JAK2: Wild type; TET2:  Wild Type; EZH2:No Information
ET Sample

source_name: Bone Marrow sample of ET patient


title: Essential Thrombocythemia sample 19

description:
Peripheral Blood. Karyotype: No Information; JAK2: Wild type; TET2:  Wild Type; EZH2:No Information
ET Sample

value: Male


title: A50

value: postmenopausal


title: microRNA profile of case 6N

description:
Co-hybridized: 6T and 6N
Raw data file: 20121120-S16-low_6T_6N.gpr


title: microRNA profile of case 1075N

description:
Co-hybridized: 1075T and 1075N
Raw data file: 20121120-S15-up_1075T_1075N.gpr


title: microRNA profile of case 30N

description:
Co-hybridized: 30T and 30N
Raw data file: 20121120-S16-up_30T_30N.gpr


title: microRNA profile of case 41N

description:
Co-hybridized: 41T and 41N
Raw data file: 20121120-S17-low_41T_41N.gpr


title: microRNA profile of case 85N

description:
Co-hybridized: 85T and 85N
Raw data file: 20121120-S19-low_85T_85N.gpr


title: microRNA profile of case 563N

description:
Co-hybridized: 563T and 563N
Raw data file: 20121120-S21-up_563T_563N.gpr


title: microRNA profile of case 98N

description:
Co-hybridized: 98T and 98N
Raw data file: 20121120-S20-low_98T_98N.gpr


title: microRNA profile of case 554N

description:
Co-hybridized: 554T and 554N
Raw data file: 20121120-S21-low_554T_554N.gpr


title: K49

value: premenopausal

value: Invasive ductal carcinoma


title: Essential Thrombocythemia sample 16

description:
Bone Marrow. Karyotype: No Information; JAK2: JAKV617F-HET; TET2: Wild Type; EZH2:No Information
ET Sample


title: A48

value: reference


title: K48


title: Essential Thrombocythemia sample 18

description:
Peripheral Blood. Karyotype: 46,XY; JAK2: JAKV617F-HET; TET2: ins/del; EZH2:No Information
ET Sample


title: Essential Thrombocythemia sample 14

description:
Peripheral Blood. Karyotype: No Information; JAK2:Wild type; TET2: Wild Type; EZH2:No Information
ET Sample

value: Wildtype


title: A44


title: Essential Thrombocythemia sample 13

description:
Peripheral Blood. Karyotype: No Information; JAK2: Wild Type; TET2: Wild Type; EZH2:No Information
ET Sample


title: Essential Thrombocythemia sample 15

description:
Peripheral Blood. Karyotype: No Information; JAK2:JAKV617F- HOMO; TET2: Wild Type; EZH2:No Information
ET Sample


title: K40


title: A49


title: A40


title: K44


title: Essential Thrombocythemia sample 17

description:
Peripheral Blood. Karyotype: No Information; JAK2: JAKV617F-HET; TET2: Wild Type; EZH2:No Information
ET Sample


title: microRNA profile of case 564N

description:
Co-hybridized: 564T and 564N
Raw data file: 20121120-S22-low_564T_564N.gpr


title: Essential Thrombocythemia sample 12


title: Essential Thrombocythemia sample 11

description:
Peripheral Blood. Karyotype: No information; JAK2:Wild type; TET2: No information; EZH2:No Information
ET Sample


title: Essential Thrombocythemia sample 10

description:
Peripheral Blood. Karyotype: 46, XY; JAK2:Wild type; TET2: Wild Type; EZH2:No Information
ET Sample


title: microRNA profile of case 572N

description:
Co-hybridized: 572T and 572N
Raw data file: 20121120-S22-up_572T_572N.gpr


title: microRNA profile of case 593N

description:
Co-hybridized: 593T and 593N
Raw data file: 20121120-S23-low_593T_593N.gpr


title: A30


title: microRNA profile of case 5T

description:
Co-hybridized: 5T and 5N
Raw data file: 120914-S9-up_5T_5N.gpr

source_name: colon tumor tissues

value: colon tumor

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case 13T

description:
Co-hybridized: 13T and 13N
Raw data file: 120914-S9-low_13T_13N.gpr


title: Essential Thrombocythemia sample 9

tag: disease state


title: K30


title: microRNA profile of case 3T

description:
Co-hybridized: 3T and 3N
Raw data file: 120914-S10-low_3T_3N.gpr

tag: tissue


title: microRNA profile of case 43T

description:
Co-hybridized: 43T and 43N
Raw data file: 120914-S13-low_43T_43N.gpr


title: Essential Thrombocythemia sample 8

description:
Peripheral Blood. Karyotype: No information; JAK2:JAKV617F- HOMO; TET2: Wild Type; EZH2:No Information
ET Sample


title: microRNA profile of case 22T

description:
Co-hybridized: 22T and 22N
Raw data file: 120914-S12-low_22T_22N.gpr


title: K28

value: Papillary carcinoma


title: A28


title: microRNA profile of case 566T

description:
Co-hybridized: 566T and 566N
Raw data file: 120914-S14-up_566T_566N.gpr


title: A25


title: K26


title: microRNA profile of case 246T

description:
Co-hybridized: 246T and 246N
Raw data file: 120914-S14-low_246T_246N.gpr


title: Essential Thrombocythemia sample 6

description:
Bone Marrow. Karyotype: 46,XY; JAK2:JAKV617F- HOMO; TET2: Wild Type; EZH2:No Information
ET Sample

value: peripheral blood


title: Essential Thrombocythemia sample 7

value: mononuclear cells


title: microRNA profile of case 163T

description:
Co-hybridized: 163T and 163N
Raw data file: 120914-S33-LOW_163T_163N.gpr


title: microRNA profile of case 100T

description:
Co-hybridized: 100T and 100N
Raw data file: 120914-S33-up_100T_100N.gpr


title: Essential Thrombocythemia sample 5

description:
Karyotype: No Information; JAK2:Wild type; TET2: Wild Type; EZH2:No Information
ET Sample

value: Female


title: microRNA profile of case 1T

description:
Co-hybridized: 1T and 1N
Raw data file: 120914-S34-low_1T_1N.gpr


title: A26


title: Essential Thrombocythemia sample 4

description:
Peripheral Blood. Karyotype: No Information; JAK2:Wild type; TET2: Wild Type; EZH2:No Information
ET Sample


title: microRNA profile of case 7T

description:
Co-hybridized: 7T and 7N
Raw data file: 120914-S34-up_7T_7N.gpr


title: K25


title: microRNA profile of case 15T

description:
Co-hybridized: 15T and 15N
Raw data file: 120914-S35-low_15T_15N.gpr


title: Essential Thrombocythemia sample 2


title: A19

value: Unknown


title: A21


title: K17


title: microRNA profile of case 20T

description:
Co-hybridized: 20T and 20N
Raw data file: 120914-S35-up_20T_20N.gpr


title: Essential Thrombocythemia sample 3

value: No Information


title: Essential Thrombocythemia sample 1

description:
Peripheral Blood. Karyotype: No Information; JAK2:JAKV617F- HOMO; TET2: Wild Type; EZH2:No Information
ET Sample


title: K21


title: K19


title: microRNA profile of case 21T

description:
Co-hybridized: 21T and 21N
Raw data file: 120914-S36-low_21T_21N.gpr


title: Polycythemia Vera sample 22

description:
Peripheral Blood. Karyotype: No Information; JAK2:JAKV617F- HET; TET2: Wild Type; EZH2:No Information
PV sample

source_name: Peripheral Blood sample of PV patient

value: Polycythemia Vera


title: Polycythemia Vera sample 24

description:
Peripheral Blood. Karyotype: No Information; JAK2:JAKV617F- HET; TET2:  V1395L; EZH2:No Information
PV sample

value: NoInformation


title: Polycythemia Vera sample 23


title: A17

source_name: Breast tumor tissue


title: Polycythemia Vera sample 21

description:
Bone Marrow. Karyotype: 46XY; JAK2:JAKV617F- HET; TET2: Wild Type; EZH2:No Information
PV sample

source_name: Bone Marrow sample of PV patient


title: K13

source_name: Universal Human Reference RNA (Stratagene)


title: Polycythemia Vera sample 20

value: No information


title: K14

value: Carcinoma with metaplasia


title: microRNA profile of case 26T

description:
Co-hybridized: 26T and 26N
Raw data file: 120914-S36-up_26T_26N.gpr


title: A14


title: Polycythemia Vera sample 19

value: Male

value: WildType


title: A13

value: postmenopausal


title: microRNA profile of case 27T

description:
Co-hybridized: 27T and 27N
Raw data file: 120914-S37-low_27T_27N.gpr


title: microRNA profile of case 52T

description:
Co-hybridized: 52T and 52N
Raw data file: 120914-S37-up_52T_52N.gpr


title: microRNA profile of case 40T

description:
Co-hybridized: 40T and 40N
Raw data file: 120914-S40-up_40T_40N.gpr


title: microRNA profile of case 604T

description:
Co-hybridized: 604T and 604N
Raw data file: 120914-S49-low_604T_604N.gpr


title: microRNA profile of case 609T

description:
Co-hybridized: 609T and 609N
Raw data file: 120914-S49-up_609T_609N.gpr


title: microRNA profile of case 611T

description:
Co-hybridized: 611T and 611N
Raw data file: 120914-S50-low_611T_611N.gpr


title: microRNA profile of case 54T

description:
Co-hybridized: 54T and 54N
Raw data file: 120914-S50-up_54T_54N.gpr


title: Polycythemia Vera sample 18


title: Polycythemia Vera sample 14


title: Polycythemia Vera sample 16


title: Polycythemia Vera sample 15

description:
Bone Marrow. Karyotype: No Information; JAK2:JAKV617F- HET; TET2: Wild Type; EZH2:No Information
PV sample


title: A12

value: Invasive ductal carcinoma


title: microRNA profile of case 622T

description:
Co-hybridized: 622T and 622N
Raw data file: 120914-S50-up_622T_622N.gpr


title: Polycythemia Vera sample 17


title: Polycythemia Vera sample 13


title: K12

value: reference


title: K08


title: Polycythemia Vera sample 11

description:
Peripheral Blood. Karyotype:No Information; JAK2:JAKV617F- HOMO; TET2: Wild Type; EZH2:No Information
PV sample


title: K06


title: K04

value: premenopausal


title: A06


title: Polycythemia Vera sample 10


title: microRNA profile of case 104T

description:
Co-hybridized: 104T and 104N
Raw data file: 20121120-S10-low_104T_104N.gpr

value: colon tumor


title: A04


title: Polycythemia Vera sample 9


title: K03


title: microRNA profile of case 110T

description:
Co-hybridized: 110T and 110N
Raw data file: 20121120-S11-low_110T_110N.gpr


title: microRNA profile of case 1026T

description:
Co-hybridized: 1026T and 1026N
Raw data file: 20121120-S14-low_1026T_1026N.gpr


title: microRNA profile of case 1065T

description:
Co-hybridized: 1065T and 1065N
Raw data file: 20121120-S14-up_1065T_1065N.gpr


title: microRNA profile of case 6T

description:
Co-hybridized: 6T and 6N
Raw data file: 20121120-S16-low_6T_6N.gpr


title: microRNA profile of case 595T

description:
Co-hybridized: 595T and 595N
Raw data file: 20121120-S13-low_595T_595N.gpr


title: A08


title: microRNA profile of case 1070T

description:
Co-hybridized: 1070T and 1070N
Raw data file: 20121120-S15-low_1070T_1070N.gpr


title: Polycythemia Vera sample 8

description:
Peripheral Blood. Karyotype:46,XY; JAK2:JAKV617F- HOMO; TET2: Wild Type; EZH2:No Information
PV sample


title: microRNA profile of case 1075T

description:
Co-hybridized: 1075T and 1075N
Raw data file: 20121120-S15-up_1075T_1075N.gpr


title: Polycythemia Vera sample 7

description:
Bone Marrow. Karyotype:46,XY; JAK2:JAKV617F- HOMO; TET2: Wild Type; EZH2:No Information
PV sample


title: microRNA profile of case 30T

description:
Co-hybridized: 30T and 30N
Raw data file: 20121120-S16-up_30T_30N.gpr


title: A02


title: Polycythemia Vera sample 6


title: microRNA profile of case 41T

description:
Co-hybridized: 41T and 41N
Raw data file: 20121120-S17-low_41T_41N.gpr


title: K01


title: Polycythemia Vera sample 4


title: Polycythemia Vera sample 2

description:
Bone Marrow. Karyotype:46,XY;JAK2: JAKV617F- HOMO; TET2: Wild Type;EZH2:No Information
PV sample


title: A03


title: Polycythemia Vera sample 12

description:
Bone Marrow. Karyotype:46,XY; JAK2:JAKV617F- HOMO; TET2: R1516X; EZH2:No Information
PV sample


title: Polycythemia Vera sample 5


title: Polycythemia Vera sample 3


title: K02


title: microRNA profile of case 98T

description:
Co-hybridized: 98T and 98N
Raw data file: 20121120-S20-low_98T_98N.gpr


title: microRNA profile of case 554T

description:
Co-hybridized: 554T and 554N
Raw data file: 20121120-S21-low_554T_554N.gpr


title: microRNA profile of case 85T

description:
Co-hybridized: 85T and 85N
Raw data file: 20121120-S19-low_85T_85N.gpr


title: microRNA profile of case 564T

description:
Co-hybridized: 564T and 564N
Raw data file: 20121120-S22-low_564T_564N.gpr


title: microRNA profile of case 572T

description:
Co-hybridized: 572T and 572N
Raw data file: 20121120-S22-up_572T_572N.gpr


title: C19


title: Polycythemia Vera sample 1

description:
Peripheral Blood. Karyotype:46,XX,del(20)(q12); JAK2:JAKV617F- HOMO;TET2: Wild Type;EZH2:No Information
PV sample


title: DIA4

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description:
Replicate 4 of 4, DIA vs NON-DIA
Sample 4

hyb_protocol: Cy3 and Cy5 labeled cRNA were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65°C; Slides were washed using the Gene Expression Wash Buffer Kit (also provided by Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Data were normalized by the Agilent Feature Extraction software, using the GE2_107_Sep09 protocol. This protocol uses a Linear and Lowess algorithm for normalization. See also page 35 in the reference guide of the Agilent Feature extraction software (http://www.chem.agilent.com/Library/usermanuals/Public/G4460-90026_FE_Reference.pdf).

organism: Tetranychus urticae

source_name: diapausing mite_whole organism

label_protocol: 100 ng of total RNA (+ RNA-spike in control) was used to generate Cy3 or Cy5 labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies)

growth_protocol: Larvae of the LS-VL strain were kept in diapause inducing conditions (17±0.5 °C, 80% RH and 8:16h light:dark photoperiod) until reaching the adult female life stage.

extract_protocol: Total RNA was extracted from adult female spider mites using RNEasy Mini Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: By letting mites develop in diapause inducing conditions, some mites entered into diapause, while others did not.

tag: developmental stage

value: adult

value: female

source_name: non-diapausing mite_whole organism


title: 6dN BORIS IP biological rep 2

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

country: United Kingdom

institute: Barts & The London School of Medicine & Dentistry

description: BORIS-bound transcripts in hNP1 cells differentiated for 6 days

hyb_protocol: Following fragmentation, cRNA were hybridized to Affymetrix GeneChip Human Genome 2.0 arrays for 16 hr at 45C

scan_protocol: Affymetrix scan protocol

data_processing: The data were analyzed with Partek Genomics Suiteversion 6.5

source_name: 6 day differentaited neuronal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using between 1.5 - 5 ug total RNA

growth_protocol: Cells were cultured in Neurobasal medium supplemented with B27 and 10 ng/ml FGF

extract_protocol: RNA was extracted using RNeasy mini kit, Qiagen. Immunoprecipitation was carried out using BORIS antibody (Abcam, ab18337)

treatment_protocol: Differentiation was induced by the removal of FGF

tag: cell type

value: Neural progenitor cells

tag: differentiation

value: 6 days differentiation

tag: antibody

value: BORIS antibody (Abcam, ab18337)


title: DIA3

description:
Replicate 3 of 4, DIA vs NON-DIA
Sample 3


title: hNP1 BORIS IP biological rep 1

description: BORIS-bound transcripts in hNP1 cells

source_name: Neural progenitor cells Day 0


title: Control IP_rep 2

city: Montpellier

first: johann

last: Soret

address: 1919, route de Mende

department: Institut de Genetique Moleculaire

institute: CNRS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse GeneChip 1,0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning and data collection were done by GeneChip Scanner 3000 7G (Affymetrix) and GeneChip Operating Software.

data_processing: The data were analyzed with a specific R script (v.2.13.1) which contains some methods coming from the Bioconductor (v.2.12.2, Biobase) tools package called affy. Probes intensities have been extracted from CEL files with the “expresso” function. Correction of the background noise was performed by the RMA method. Z-scores and ratios with associated pValues have been calculated according to Cheadle et al. (J. Mol. Diagn., 5, 2003).

source_name: IP from NSC34 cells expressing no 3X flag-SMN protein

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300-500 ng of immunoprecipitated RNA

growth_protocol: NSC-34 cells were maintained in DMEM supplemented with 10% fetal bovine serum (tetracycline-free, Biowest) and penicillin-streptomycin. Differentiation of the cells was obtained by growing them in the presence of low serum concentration (1%) for 3 days.

extract_protocol: Following lysis of the cells in the recommended buffer, immuno-precipitation was performed with anti-FLAG M2 magnetic beads (Sigma) according to the manufacturer’s instructions. Immuno-precipitated proteins were eluted with 3X-Flag peptide (Sigma) and digested with proteinase K before purification of co-immuno-precipitated RNAs by phenol-chloroform extraction.

treatment_protocol: 3XFLAG-flSMN NSC-34 cells and NSC-34 cells not containing a 3XFLAG construct were induced to differentiate for 48 hours and then incubated in the presence of doxycycline (3 microg/ml) for 3 days. Treated cells were resuspended in PBS, placed in a UV Crosslinker (Amersham Life Science) and irradiated one time for 400mJ/cm2.

tag: cell line

value: murine motor neuron-like cells

tag: genotype/variation

value: control (no FLAG construct)

tag: immunoprecipiated with

value: anti-FLAG M2 magnetic beads (Sigma)


title: DIA1

description:
Replicate 1 of 4, DIA vs NON-DIA
Sample 1


title: 6dN expression biological rep 2

description: Gene expression data from hNP1 cells differentiated for 6 days


title: DIA2

description:
Replicate 2 of 4, DIA vs NON-DIA
Sample 2


title: microRNA profile of case 593T

description:
Co-hybridized: 593T and 593N
Raw data file: 20121120-S23-low_593T_593N.gpr

tag: sample name


title: hNP1 expression biological rep 2

description: Gene expression data from neural progenitor cells hNP1


title: hNP1 expression biological rep 1


title: FlSMN IP_rep 3

source_name: IP from NSC34 cells expressing a 3X flag-FlSMN protein

value: contains 3XFLAG-flSMN construct


title: 6dN expression biological rep 1


title: FlSMN IP_rep 2


title: 6dN BORIS IP biological rep 1


title: hNP1 BORIS IP biological rep 2

description: BORIS-bound transcripts in hNP1 cells


title: hNP1 expression biological rep 3


title: Control IP_rep 1


title: D19_antimiR_rep1

status: Public on Nov 28 2013

city: Sheffield

first: Keith

middle: David

last: Hunter

state: South Yorkshire

address: Claremont Crescent

department: School of Clinical Dentistry

institute: University of Sheffield

description: Gene expression in oral keratinocytes

hyb_protocol: 25µl of labelled and fragmented cRNA was hybridised onto Aglient Sureprint G3 60K arrays (8 per slide). The slides were placed in a hybridization rotator set to rotate at 10 rpm inside a 65 °C hybridization oven. After 17 hours, hybridized slides were disassembled and washed.

scan_protocol: The arrays were scanned at 3 μm resolution using Agilent C Microarray Scanner pre-set with the default settings for a 8x60K G3 Microarray Format.

data_processing: Agilent Feature Extraction Software (version 10.5) was used to process the generated image files and create exportable data files containing all the parameters, computed statistical analysis, and feature results.  The raw data (.txt) file was loaded into Qlucore Omics Explorer software, before normalisation by the 75th percentile shift method as implemented in the program

source_name: Oral keratinocyte

label_protocol: sample RNA together with the internal control transcripts were labelled with Cyanine 3-CTP (Cy3) dye during an amplification reaction using the Agilent Low Input Quick Amp Kit. The generated fluorescent cRNA (complimentary RNA) products were then purified using Qiagen’s RNeasy Mini Kit. Next,   the yield of the linearly amplified cRNA and the Cy3 specific activity were quantified using the Microarray Measurement function of the NanoDrop spectrophotometer. To reduce its structure complexity, 600 ng cRNA of each sample were fragmented into approximately 50-200 bases long. The fragmentation step took place at 60 ºC for 30-min using a Fragmentation Mix for 8-pack microarray format.

growth_protocol: All cells were grown in KGM/Greens medium, as per standard protocols, to 60% confluence before trypsinisation

extract_protocol: Total RNA was extracted from cell pellets using RNEasy minikit (Qiagen), before quantificaiton and QC on an Agilent Bioanalyser

value: Oral keratinocyte

tag: native mir196a expression

value: high

tag: treatment


title: microRNA profile of case 563T

description:
Co-hybridized: 563T and 563N
Raw data file: 20121120-S21-up_563T_563N.gpr

tag: paired sample name


title: D19_control_rep2

description: Gene expression in oral keratinocytes

value: control


title: OKF4_control_rep1

description: Gene expression in oral keratinocytes

value: low


title: OKF4_control_rep2

description: Gene expression in oral keratinocytes


title: OKF4_premiR_rep1

description: Gene expression in oral keratinocytes


title: D19_antimiR_rep2

description: Gene expression in oral keratinocytes


title: B16_antimiR_rep3

description: Gene expression in oral keratinocytes


title: FlSMN IP_rep 1


title: OKF4_premiR_rep2

description: Gene expression in oral keratinocytes


title: B16_control_rep3

description: Gene expression in oral keratinocytes


title: D19_control_rep3

description: Gene expression in oral keratinocytes


title: B16_antimiR_rep2

description: Gene expression in oral keratinocytes


title: B16_control_rep2

description: Gene expression in oral keratinocytes


title: B16_control_rep1

description: Gene expression in oral keratinocytes


title: D19_antimiR_rep3

description: Gene expression in oral keratinocytes


title: CAL27 replicate 1

description: miRNA expression data malignant oral keratinocytes

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the miRNA-1.0 Affymetrix miRNA Array in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: The data were normalised using RMAExpress before further anlaysis in TIGR MeV

source_name: oral cancer cell line CAL27

label_protocol: Biotinylation of antisense miRNA carried out according to Affymetrix protocol

extract_protocol: Total RNA was extracted from cell pellets using RNEasy minikit (Qiagen)

value: oral cancer cell line CAL27


title: B56 replicate 1

source_name: oral cancer cell line BICR56

value: oral cancer cell line BICR56


title: CAL27 replicate 2


title: B16_antimiR_rep1

description: Gene expression in oral keratinocytes


title: D19_control_rep1

description: Gene expression in oral keratinocytes


title: M48

value: postmenopausal

tag: age

tag: who

value: Invasive ductal carcinoma

tag: grade

tag: sample type

value: reference


title: B56 replicate 2