title: LPS 24hr C

city: South San Francisco

first: Jason

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

description: Biological replicate 3 of 3: BMDCs stimulated with LPS for 24hr

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Raw intensity data were background subtracted using the normal + exponential method from the limma Bioconductor package. The test/reference ratio was log2 transformed and normalized using loess normalization for each array. Loess normalized log2 ratios were then subjected to quantiles normalization across all arrays in the dataset.

source_name: LPS 24hr C

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

growth_protocol: Bone marrow was harvested from mouse femur and tibia.  B and T cells were depleted using biotinylated antibody cocktail and streptavidin magnetic beads.  Non-depleted cells were cultured in RPMI supplemented with 10ng/ml GM-CSF and 5ng/ml IL-4 recombinant cytokines for 5 days.  One half culture medium was replaced with fresh growth medium every other day.

extract_protocol: Total RNA was extracted from collected cells using RNeasy Plus Kit (Qiagen) following manufacturers protocol.

treatment_protocol: Day 5 BMDCs were stimulated with 100ng/ml LPS (Sigma) for 0, 1, 6, or 24 hours.  DCs were then collected by repeated pipetting.

value: LPS

tag: timepoint

tag: donor

value: C

source_name: Universal mouse reference (UMR) from Stratagene

tag: sample type

value: pooled mouse reference RNA


title: Differentiating Day 3 embryoid bodies, non treated, biological rep1

status: Public on May 21 2015

type: RNA

city: Cologne

first: Dina

last: Ivaniuk

address: Robert Koch Str.39

country: Germany

institute: Istitute for Neurophysiology University of Cologne

description: Gene expression data from Day 3 of differentiation of mESC

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Gene-Chip Scanner-3000-7G

data_processing: Robust Multi-array Analysis algorithm (RMA) did background correction, summarization and normalization.Quantile normalization  method was employed to normalize the raw dataset at probe feature level

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Differentiating murine embryonic stem cells at day 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: murine embryonic stem cells CGR8 were differentiated in hanging drop method.First cell were dissociated and grown in hanging drop with 500 cells per 25 μL .After Day 2 formed embryoid bodies were transfered to shaker and cultured addtional 3 days upon horizontal agitation. At chosen time points samples were collected

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

treatment_protocol: samples at different stages of differentiation were collected. Embryoid bodies were collected and washed 1 time in PBS and placed into TRIzol(Gibco)

tag: tissue

value: mESC

tag: cell line

tag: age

value: day 3

tag: differentiation medium

value: 20% IMDM


title: Repl.2_Area17 Inner Subventricular Zone

city: San Juan de Alicante

first: Victor

last: Borrell

state: Alicante

address: Av Ramon y Cajal s/n

department: Institute of Neuroscience

country: Spain

institute: CSIC

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-036832 Ferret_44K_v3 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mustela putorius furo

source_name: Repl.2_Area17 Inner Subventricular Zone

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy  Mini  RNA Purification kit (QUIAGEN, Cat. No. 74104) following the manufacturer's recommendations.  The protocol includes  cell lysis  and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: area

tag: zone

value: inner subventricular

value: Cerebral cortex

value: Postnatal day 2


title: LPS 24hr A

middle: A

state: CA

country: USA

description: Biological replicate 1 of 3: BMDCs stimulated with LPS for 24hr

source_name: LPS 24hr A

tag: treatment

value: A


title: Differentiating Day 3 embryoid bodies, non treated, biological rep2


title: Repl.1_Area19 Ventricular Zone

source_name: Repl.1_Area19 Ventricular Zone

value: ventricular


title: Differentiating Day 2 embryoid bodies, ascorbic acid treated, biological rep3

description: Gene expression data from Day 2 of differentiation of mESC

source_name: Differentiating murine embryonic stem cells at day 2

value: day 2

value: 20% IMDM+Ascorbic acid(100 μM, Wako Pure Chemicals Industry, Japan)


title: LPS 6hr C

description: Biological replicate 3 of 3: BMDCs stimulated with LPS for 6hr

source_name: LPS 6hr C


title: Repl.1_Area19 Outer Subventricular Zone

source_name: Repl.1_Area19 Outer Subventricular Zone

value: outer subventricular


title: Repl.1_Area19 Inner Subventricular Zone

source_name: Repl.1_Area19 Inner Subventricular Zone


title: Empty vector transfected cells, biological  rep2

city: Stanford

first: Julien

last: Sage

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

description: Ctrl #2

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16 hour (overnight) hybridization at 45°C at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed using Robust Multichip Average (RMA) Express (v.1.0.4) using Affymetrix default analysis settings and quantile as normalization method.

source_name: Mouse SCLC cells_empty vector control_48 hrs

label_protocol: Affymetrix WT Plus kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Affymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: The mouse SCLC cell line, KP1, was grown and maintained at 37°C and 5% CO2 in RPMI media supplemented with 10% bovine growth serum and 1% penicillin-streptomycin.

extract_protocol: Total RNA was extracted using the Qiagen AllPrep DNA/RNA micro kit.

treatment_protocol: Cells were transfected with either an empty ires-GFP vector control or Notch1-ICD-ires-GFP and GFP+ cells were FACS sorted after 48 hours.

tag: cell type

value: small cell lung cancer (SCLC) cell line

tag: cell line info.

value: mouse SCLC cells derived from Rb/p53/p130 triple knockout mouse model

tag: transfected with

value: empty vector; ires-GFP

tag: cell subtype

value: FACS sorted for GFP+ cells

tag: time point

value: 48 hours after transfection


title: LPS 24hr B

description: Biological replicate 2 of 3: BMDCs stimulated with LPS for 24hr

source_name: LPS 24hr B

value: LPS

value: B

value: pooled mouse reference RNA


title: Repl.1_Area17 Outer Subventricular Zone

source_name: Repl.1_Area17 Outer Subventricular Zone


title: Differentiating Day 2 embryoid bodies, ascorbic acid treated, biological rep1

value: mESC


title: LPS 6hr B

description: Biological replicate 2 of 3: BMDCs stimulated with LPS for 6hr

source_name: LPS 6hr B


title: Repl.1_Area17 Inner Subventricular Zone

source_name: Repl.1_Area17 Inner Subventricular Zone

value: inner subventricular


title: LPS 6hr A

description: Biological replicate 1 of 3: BMDCs stimulated with LPS for 6hr

source_name: LPS 6hr A


title: LPS 1hr C

description: Biological replicate 3 of 3: BMDCs stimulated with LPS for 1hr

source_name: LPS 1hr C

value: C


title: Differentiating Day 2 embryoid bodies, ascorbic acid treated, biological rep2


title: LPS 1hr B

description: Biological replicate 2 of 3: BMDCs stimulated with LPS for 1hr

source_name: LPS 1hr B


title: Repl.1_Area17 Ventricular Zone

source_name: Repl.1_Area17 Ventricular Zone

value: Cerebral cortex

value: Postnatal day 2


title: Differentiating Day 2 embryoid bodies, non treated, biological rep3

value: 20% IMDM


title: Unstimulated B

description: Biological replicate 2 of 3: unstimulated BMDCs

source_name: Unstimulated B

value: Unstimulated

source_name: Universal mouse reference (UMR) from Stratagene


title: Differentiating Day 2 embryoid bodies, non treated, biological rep1

value: day 2


title: LPS 1hr A

description: Biological replicate 1 of 3: BMDCs stimulated with LPS for 1hr

source_name: LPS 1hr A

value: A


title: undifferentiated embryonic stem cells, biological rep3

description: Gene expression data from undifferentiated mESC

source_name: undifferentiated murine embryonic stem cells

value: day 0

value: 10% GMEM


title: Unstimulated A

description: Biological replicate 1 of 3: unstimulated BMDCs

source_name: Unstimulated A


title: Unstimulated C

description: Biological replicate 3 of 3: unstimulated BMDCs

source_name: Unstimulated C


title: undifferentiated embryonic stem cells, biological rep1


title: 35B1_Untreated_A498

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Frozen A498 Untreated

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).

data_processing: The data was normalised using Robust Multichip Average (RMA), Dchip and MAS5 algorithms

organism: Homo sapiens

source_name: Frozen A498 Xenograft Tumors

label_protocol: Standard Affymetrix Protocol

growth_protocol: Female athymic nude/beige mice (Charles River Laboratories, MA) were used for subcutaneous xenograft tumor models. All experiments were approved by the Beth Israel Deaconess Medical Center Institutional Animal Care and Use Committee. To establish RCC tumor xenografts, 1 x 10^7 786-O or A498 tumor cells were prepared and injected subcutaneously into the flanks of 6-8 week old mice. To ensure a consistent size at the outset of treatment, tumors were measured with calipers daily once they reached a diameter of 3-5 mm. Sunitinib (additive-free, 53.6 mg/kg) was administered 6 out of 7 days per week by gavage beginning when the tumors had grown to a diameter of 12 mm. Sorafenib (80 mg/kg, Bayer) was administered 6 out of 7 days per week by gavage beginning when the tumors had grown to a diameter of 12 mm. Treated and control tumors were again measured daily during therapy.

extract_protocol: Trizol extraction was performed after tumor were excised and frozen

treatment_protocol: biopsy specimens were snap frozen at time of mouse surgery, then stored at -80C until time of total RNA extraction

value: Frozen A498 Untreated Sorafenib

tag: host organism

value: Mus musculus

value: renal cell carcinoma


title: Differentiating Day 2 embryoid bodies, non treated, biological rep2

source_name: Differentiating murine embryonic stem cells at day2


title: undifferentiated embryonic stem cells, biological rep2


title: Fat line chicken 272

status: Public on May 20 2015

type: genomic

city: Harbin

first: Hui

last: Zhang

state: Heilongjiang

address: Mucai street No. 59

department: College of Animal Science and Technology

country: China

institute: Northeast Agricultural University

description: Genomic DNA extracted from blood was genotyped using chicken 60k SNP chip.

hyb_protocol: DNA samples were hybridized onto the Illumina chicken 60k SNPchip containing 57,636 SNPs.

scan_protocol: Genotyping data were generated using BeadStudio (Version 3.2.2) and after quality control procedures, a total of 475 birds and 48,034 SNPs  on 28 autosomes and the Z sex chromosome were kept for CNV detection.

data_processing: Genomic DNA extracted from the blood was genotyped using the Illumina chicken 60k SNPchip and PennCNV software was used to identify chicken CNVs.

molecule: genomic DNA

organism: Gallus gallus

source_name: chicken in the fat line

label_protocol: DNA sample quality was determined by spectrophotometry and agarose gel electrophoresis.

extract_protocol: Genomic DNA samples were extracted from the blood using the standard phenol/chloroform method

value: blood

tag: gender

value: Male


title: Fat line chicken 271


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title: 35A3_Untreated_786-O

description: Frozen 786-O Untreated

source_name: Frozen 786-O Xenograft Tumors

value: Frozen 786-O Untreated Sunitinb


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title: Lean line chicken 202

source_name: chicken in the lean line


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title: cKO mouse 6 Exp 1

city: Madrid

first: Miguel

last: Foronda

state: Select a State or Province

address: Calle Melchor Fernández Almagro

institute: CNIO

description: Gene expression 12 days after plucking

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Total RNA samples were analyzed on Agilent’s Mouse Genome DNA microarray by following manufacturer instructions. Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1).

data_processing: Microarray background subtraction was carried out using normexp method. Normalization was performed using quantiles. Differentially expressed genes were obtained by applying linear models with R limma package {Smyth, 2005 #1166} (Bioconductor project, http://www.bioconductor.org). To account for multiple hypotheses testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.

label_protocol: Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore.

extract_protocol: Total RNA was extracted with Trizol. QIAGEN kit was employed for purification.  RNA Integrity Numbers were in the range 6,5 to 8,5 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer

tag: genotype

value: Sox4 conditional knockout in skin

value: skin

tag: age (weeks)

value: male

tag: strain

value: Mice were of mixed background with C57Bl6/129Sv contribution (75:25)


title: cKO mouse 4 Exp 2

description: Gene expression 12 days after plucking

tag: tissue


title: WT_no_Treated_Replicate3

description: Gene expression in Telogen

value: wildtype


title: Lean line chicken 18


title: Lean line chicken 9


title: cKO mouse 5 Exp 1

description: Gene expression 12 days after plucking


title: KO_no_Treated_Replicate2

description: Gene expression in Telogen


title: WT_no_Treated_Replicate2

description: Gene expression in Telogen


title: Lean line chicken 8


title: KO_no_Treated_Replicate3

description: Gene expression in Telogen


title: cKO mouse 2 Exp 1

description: Gene expression 12 days after plucking


title: Lean line chicken 7


title: WT_no_Treated_Replicate1

description: Gene expression in Telogen


title: Lean line chicken 6


title: KO_no_Treated_Replicate1

description: Gene expression in Telogen


title: cKO mouse 3 Exp 2

description: Gene expression 12 days after plucking


title: Lean line chicken 1


title: cKO mouse 1 Exp 2

description: Gene expression 12 days after plucking


title: WT mouse 6 Exp 2

description: Gene expression 12 days after plucking


title: WT mouse 5 Exp 2

description: Gene expression 12 days after plucking


title: WT mouse 2 Exp 1

description: Gene expression 12 days after plucking


title: WT mouse 4 Exp 2

description: Gene expression 12 days after plucking


title: WT mouse 3 Exp 1

description: Gene expression 12 days after plucking


title: HIVAN-CHE-DD3.9

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Hybriziation was performed by following Affymetrix standard procedure.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Gene-level intensity data were extracted and normalized by RMA stretch in Affymetrix Expression Console (v.1.4.1) and Batch effects from different labeling protocols were adjusted using the ComBat R package (in the SVA package, v.3.14.0).

source_name: HIV-1 transgenic_Tg26_ serious kidney injury

label_protocol: ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to the first batch of samples starting with approximately 100ng of total RNA to generate biotin-labeled RNA fragments for hybridization to the chip. For samples with a low RNA concentration, the Nugen Ovation PICO amplification kit (NuGen, San Carlos, CA) was applied

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from percutaneous allograft biopsy samples obtained at 3 month after transplantation using All prep kit (QIAGEN-ALLprep kit, Valencia, CA USA). RNA quality was assessed using Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: not applicable

tag: strain background

value: FVB/N

tag: genotype/variation

value: HIV-1 transgenic; Tg26

tag: kidney injury

value: serious

value: Kidney


title: WT mouse 1 Exp 1

description: Gene expression 12 days after plucking


title: HIVAN-CHE-DD7

source_name: WT mice

value: WT


title: HIVAN-CHE-dd3


title: HIVAN-CHE-CC1

source_name: HIV-1 transgenic_Tg26_mild kidney injury

value: mild


title: HUVEC pretreated with DHA followed by IL-1 replicate 3

city: Baronissi (SA)

first: Rosanna

last: Martinelli

address: Via Allende

department: Medicine and Surgery

country: Italy

institute: Salerno University

hyb_protocol: The hybridization procedure was conducted according to the Two-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Tecnologies ). Briefly, 825ng of the correspondiing Cy3- and Cy5-labeled cRNA were combined and hybridized overnight (17 hours at 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44K (G4112F, Part No. G4112-60520; Batch No. 0006060953) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 4x44k array slides. Microarray slides were scanned at 5 uM resolution using an extended dynamic range (XDR)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE12_107_Sep09 and Grid: 014850_D_F_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HUVEC Untreated

label_protocol: 300ng of total RNA  per each condition was amplified and labeled in the presence of cyanine 3-CTP and cyanine 5-CTP using the Agilent Low RNA Input Linear Amp Kit following the manufacturer's protocol. Dye-incorporation rate and cRNA output were quantified with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were isolated from segments of umbilical cords from normal-term deliveries, and cultured in Medium 199

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, Milan, Italy) according to manufacturer’s instructions. RNA quality and integrity were assessed using the Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, U.S.A) and 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) respectively. Samples with ratios of absorbance at 280/260 nm between 1.8 and 2.0 and at 280/230 nm between 2.0 and 2.2, and with RNA integrity number (RIN) of ≥ 9 were judged to be of acceptable quality and integrity to be used for microarray labelling.

treatment_protocol: Three condition experiment: DHA treated HUVEC  cells (25 µmol/L DHA for 48 hours) vs control; IL-1 treated HUVEC  cells (5ng/ml for 3 hours)  vs control; HUVEC treated with 25 µmol/L DHA for 48 hours and then stimulated with 5 ng/mL IL-1β for 3 hours. For each condition, 3 replicates

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: treaetd with

value: none (untreated control)

tag: treated with

value: 25 µmol/L DHA for 48 hrs and then stimulated with 5 ng/mL IL-1β for 3 hrs


title: HIVAN-CHE-8


title: HIVAN-CHE-2


title: HIVAN-CHE-CC3


title: HIVAN-CHE-CC9


title: HUVEC treated with IL-1  replicate 1

source_name: HUVEC treated with IL-1

value: 5ng/ml iL-1 for 3 hrs


title: HUVEC pretreated with DHA followed by IL-1 replicate 1


title: HUVEC pretreated with DHA followed by IL-1 replicate 2


title: HUVEC treated with IL-1  replicate 2


title: HUVEC treated with IL-1  replicate 3


title: HUVEC treated with DHA  replicate 3

source_name: HUVEC treated with DHA

value: 25 µmol/L DHA for 48 hrs


title: HUVEC treated with DHA  replicate 1


title: HIVAN-CHE-DD4


title: HUVEC treated with DHA  replicate 2


title: EvgSc_ompR_2

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

country: United Kingdom

institute: University of Liverpool

description: EvgSc ompR double mutant

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was hybridized to Agilent E. coli Gene Expression Microarrays (Agilent-020097) for 17 hours at 65°C according to the manufacturers instructions.  After hybridization, microarrays were washed according to the manufacturers instructions for washing steps including stabilisation and drying solution.

scan_protocol: Slides were scanned immediately after washing on an Agilent SureScan microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: EvgSc ompR double mutant rep 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low Input Quick-Amp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LB media

extract_protocol: RNA was extracted using RNAeasy columns (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: EvgSc ompR KO


title: ompR_2

description: ompR mutant

source_name: ompR mutant rep 2

value: ompR KO


title: ompR_1

description: ompR mutant

source_name: ompR mutant rep 1


title: EvgSc_ompR_1

description: EvgSc ompR double mutant

source_name: EvgSc ompR double mutant rep 1


title: EvgSc_2

description: EvgSc mutant

source_name: EvgSc mutant rep 2

value: EvgSc KO


title: WT_1

description: Wild Type

source_name: wild type rep 1

value: Wild Type


title: EvgSc_1

description: EvgSc mutant

source_name: EvgSc mutant rep 1


title: WT_2

description: Wild Type

source_name: wild type rep 2


title: Red1-Flag-TEV-protein A(FTP) -2

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

hyb_protocol: Hybridization, blocking, and washing was performed following the Agilent instructions

scan_protocol: Scanning of arrays was performed using Agilent DNA Microarray Scanner and Agilent Scan control software (v A.8.4.1.)

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1) Protocol: GE2_107_Sep09 with modifications; Background Substraction Method - Local Background; Detrend on Replicates Only - False; Robust Neg Ctrl Stats? - True; Choose universal error, or the most conservative - Use Universal Error Model; Dye Normalization Probe Selection Method/Variable Rank Tolerance - True; Max Number Ranked Probes - -1; Normalization Correction Method - Lowess Only; Spikein Target Used - False
p-value filtering (p<=0.05) and background filtering (BG=median of negative control probes for green channel and red channel, probes with gProcessedSignal < 2x gBG AND rProcessedSignal < 2x rBG are filtered out) Filtered probes value set to 1

organism: Schizosaccharomyces pombe

source_name: Protein binding RNA of Red1-FTP

label_protocol: The cDNAs from IPed and WCE sample were labeled with Cy5 and Cy3 (GE Healthcare)

growth_protocol: Flag-TEV-protein A (FTP)-tagged strains were grown in YEA at 30°C to OD 1.8-2.2.

extract_protocol: The IPed RNAs and WCE RNAs were then treated with Turbo DNase (Life Technologies) to remove potential DNA contamination. Reverse transcription was performed using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with random hexamers.

treatment_protocol: Total RNAs from the whole cell extract (WCE) were extracted using TRI Reagent (Sigma Aldrich) according to the manufacturer’s instructions. Immunoprecipited (IPed) RNA-protein complexes were eluted from anti-Flag beads after tandem affinity purifications , followed by the phenol/chloroform/isoamyl alcohol extraction of RNAs.

tag: protein tag

value: Tagged strain with Flag-TEV-protein A in C-terminal

tag: fraction

value: Protein binding RNA

source_name: Total RNA of Red1-FTP

value: total RNA


title: Mtl1-Flag-TEV-protein A(FTP) -1

source_name: Protein binding RNA of Mtl1-FTP

source_name: Total RNA of Mtl1-FTP


title: Red5-Flag-TEV-protein A(FTP) -2

source_name: Protein binding RNA of Red5-FTP

source_name: Total RNA of Red5-FTP


title: rmn1Δ

source_name: rRNA depleted RNA of rmn1Δ

label_protocol: The cDNAs from WT and mutant strains were labeled with Cy3(WT) and Cy5(mutant) (GE Healthcare)

growth_protocol: WT and gene deletion strains were grown in YEA at 30°C to OD 0.5~0.8. Temperature sensitive strains were grown in YEA at 23°C to OD 0.3~0.4 and then moved to 37°C and grown for 4 h to OD<0.8.

extract_protocol: Ribosomal RNA was depleted from total RNA extracts of all strains using a mixture of 5' biotinylated rRNA probes. The rRNA-depleted samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20 and random hexamers.

treatment_protocol: RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions

source_name: rRNA depleted RNA of wildtype

value: wildtype


title: sen1Δ-2

source_name: rRNA depleted RNA of sen1Δ


title: Red1-Flag-TEV-protein A(FTP) -1


title: mtl1-17-2

description: Tagged strain with flag in C-terminal

source_name: rRNA depleted RNA of mtl1-17

source_name: rRNA depleted RNA of mtl1-flag


title: Red5-Flag-TEV-protein A(FTP) -1


title: sen1Δ-1


title: mmi1Δ mei4-P572

source_name: rRNA depleted RNA of mmi1Δ

value: mmi1Δ mei4-P572

source_name: rRNA depleted RNA of mei4-P572 strain


title: iss10Δ-1

source_name: rRNA depleted RNA of iss10Δ


title: iss10Δ-2


title: cid14Δ-1

source_name: rRNA depleted RNA of cid14Δ


title: Mtl1-Flag-TEV-protein A(FTP) -2


title: gray-00298: s0301-scan

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

description: Array Type: HA20

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Cancer

tag: chemotherapy treatment

value: no

tag: p53 positive (ihc)

value: yes

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

value: Caucasian

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

value: breast cancer

tag: hormonal therapy

tag: estrogen receptor status

value: positive

tag: biosource type

tag: progesterone receptor status

value: negative

tag: alive at endpoint

value: dead

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment

source_name: normal female genomic DNA

value: female


title: mtl1-17-1

description: Tagged strain with flag in C-terminal

tag: genotype/variation

tag: strain


title: pab2Δ-1

source_name: rRNA depleted RNA of pab2Δ


title: red1Δ-1

source_name: rRNA depleted RNA of red1Δ


title: gray-00298: s0226-scan

description: Array Type: HA20

scan_protocol: See mage-tab files linked to series entry for additional details

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

value: mammary gland

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

value: alive

tag: gender


title: gray-00298: s0205-scan

description: Array Type: HA20

data_processing: See mage-tab files linked to series entry for additional details

value: Asian

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)


title: gray-00298: s0204-scan

description: Array Type: HA20

label_protocol: See mage-tab files linked to series entry for additional details

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: recurrence

tag: radiation treatment


title: cid14Δ-2

tag: genotype/variation

tag: strain


title: gray-00298: s0200-scan

description: Array Type: HA20

extract_protocol: See mage-tab files linked to series entry for additional details

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: gender


title: gray-00298: s0201-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)


title: gray-00298: s0210-scan

description: Array Type: HA114

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0189-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: gender


title: gray-00298: s0191-scan

description: Array Type: HA114

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)


title: pab2Δ-2

tag: genotype/variation

tag: strain


title: rrp6Δ-2

source_name: rRNA depleted RNA of rrp6Δ


title: SEES2 at passage 45

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: Genomic DNA extracted from cells was genotyped using HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit (Illumina).

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip array was scanned using the iScan (Illumina)

data_processing: Data were processed using GenomeStudio V2011.1

label: C-Bio and A-DNP

source_name: human embryonic stem cells

label_protocol: Illumina's standard protocol

growth_protocol: The SEES lines were routinely cultured onto a feeder layer of freshly plated gamma-irradiated MEFs in the human ES cell culture media. The media consisted of KnockoutTM-Dulbecco’s modified Eagle’s medium supplemented with 20% KnockoutTM-Serum Replacement, 2 mM Glutamax-I, 0.1 mM non-essential amino acids, 50 U/ml penicillin-50 μg/ml streptomycin (Pen-Strep), 0.055 mM beta-mercaptoethanol, and recombinant human full-length bFGF.

extract_protocol: Genomic DNA extracted from cells using QIAamp DNA Mini Kit (Qiagen).

tag: cell line

tag: passage


title: gray-00298: s0181-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: SEES2 at passage 25


title: gray-00298: s0190-scan

description: Array Type: HA114

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: s0176-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status


title: gray-00298: s0175-scan

description: Array Type: HA20

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0188-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: s0170-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status


title: gray-00298: s0183-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0168-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: s0177-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status


title: rrp6Δ-1

tag: genotype/variation

tag: strain


title: gray-00298: s0163-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: s0162-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: gray-00298: s0158-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

value: African American

tag: dead of disease

tag: tumor grading

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00298: s0229-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: gray-00298: s0151-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: gender


title: SEES2 at passage 10

tag: cell line

tag: passage


title: SEES1 at passage 60


title: gray-00298: s0146-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00298: s0138-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: recurrence

tag: radiation treatment


title: SEES3 at passage 25

tag: cell line

tag: passage


title: gray-00298: s0136-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0133-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0141-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: recurrence

tag: radiation treatment


title: gray-00298: s0116-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: tumor size (mm)

tag: gender


title: gray-00298: s0119-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: SEES1 at passage 4

tag: cell line

tag: passage


title: gray-00298: s0110-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: recurrence

tag: radiation treatment


title: gray-00298: s0109-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0124-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0107-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0129-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: SEES2 at passage 4

tag: cell line

tag: passage


title: SEES3 at passage 4


title: gray-00298: s0115-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0104-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: recurrence

tag: radiation treatment


title: SEES1 at passage 10

tag: cell line

tag: passage


title: SEES1 at passage 25


title: gray-00298: s0103-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: tumor size (mm)

tag: gender


title: SEES3 at passage 10


title: gray-00298: s0106-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: red1Δ-2

tag: genotype/variation

tag: strain


title: gray-00298: s0101-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: recurrence

tag: radiation treatment


title: gray-00298: s0096-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0100-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0098-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0094-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0090-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0088-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: recurrence

tag: radiation treatment


title: d25 cardiomyocytes miR-208a-Bim-switch

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

description: miR-208a-Bim-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day25 for mRNA

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: MYH6-EIP4 day25 cardiomyocytes (miR-208a-Bim-switch transfection day1)

label_protocol: Manufature's protocol

growth_protocol: For hPSCs, Primate ESC medium (ReproCELL) supplemented with 4 ng/ml bFGF at 37 ºC in a humidified incubator with 5% CO2. For cardiomyocytes, StemPro-34 supplemented with 2 mM L-glutamine, 4x10-4 M monothioglycerol (MTG), 50 mg/ml ascorbic acid (AA), 150 mg/ml transferrin, 0.5% penicillin/streptomycin, bFGF (10 ng/ml, final 5 ng/ml), activin A (12 ng/ml, final 6 ng/ml) and BMP4 (18 ng/ml, final 10 ng/ml)

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: hiPSCs were differentiated to cardiac lineage cells using ActivinA and BMP4.

tag: cell type


title: d21 cardiomyocytes without transfection

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day21 for mRNA

source_name: MYH6-EIP4 day21 cardiomyocytes (without transfection day1)


title: gray-00298: s0087-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: d19 cardiomyocytes miR-208a-Bim-switch

description: miR-208a-Bim-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day19 for mRNA

source_name: MYH6-EIP4 day19 cardiomyocytes (miR-208a-Bim-switch transfection day1)


title: d22 VCAM1+ sorted cells

description: VCAM1+ sorted cells differentiated from 201B7 on day 22 for mRNA

source_name: 201B7 derived d22 VCAM1+ sorted cells

value: 201B7 derived cells (cardiomyocytes)


title: d19 cardiomyocytes without transfection

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day19 for mRNA

source_name: MYH6-EIP4 day19 cardiomyocytes (without transfection day1)


title: gray-00298: s0086-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: age at diagnosis

tag: recurrence time


title: d21 cardiomyocytes miR-208a-Bim-switch

description: miR-208a-Bim-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day21 for mRNA

source_name: MYH6-EIP4 day21 cardiomyocytes (miR-208a-Bim-switch transfection day1)

tag: cell type


title: d25 cardiomyocytes without transfection

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day25 for mRNA

source_name: MYH6-EIP4 day25 cardiomyocytes (without transfection day1)


title: d25 cardiomyocytes without transfection-2

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day25 ex2 for mRNA

source_name: MYH6-EIP4 day25 cardiomyocytes (without transfection day7) ex2


description: VCAM1+ negative fraction sorted cells differentiated from 201B7 on day 22 for mRNA

source_name: 201B7 derived d22 VCAM1+ negative fraction sorted cells

value: 201B7 derived cells


title: gray-00298: s0084-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0154-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: hiPSCs (201B7)

description: Human induced pluripotent stem cell line (201B7) for mRNA

source_name: Human induced pluripotent stem cell line (201B7 P18)

tag: cell type

value: Undifferentiated human induced pluripotent stem cells


description: miR-208a-BFP negative fraction sorted cells differentiated from 201B7 on day 22 for mRNA

source_name: 201B7 derived d22 miR-208a negative fraction sorted cells


title: d25 cardiomyocytes miR-switch-2

description: miR-1-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day25 ex2 for mRNA

source_name: MYH6-EIP4 day25 cardiomyocytes (miR-1-switch transfection day7) ex2


title: d25 cardiomyocytes without transfection-1

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day25 ex1 for mRNA

source_name: MYH6-EIP4 day25 cardiomyocytes (without transfection day7) ex1


title: d22 SIRPA+LIN- sorted cells

description: SIRPA+LIN- sorted cells differentiated from 201B7 on day 22 for mRNA

source_name: 201B7 derived d22 SIRPA+LIN- sorted cells


title: d25 cardiomyocytes miR-switch-1

description: miR-1-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day25 ex1 for mRNA

source_name: MYH6-EIP4 day25 cardiomyocytes (miR-1-switch transfection day7) ex1


description: SIRPA+LIN- negative fraction sorted cells differentiated from 201B7 on day 22 for mRNA

source_name: 201B7 derived d22 SIRPA+LIN- negative fraction sorted cells


title: d25 cardiomyocytes without transfection-3

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day25 ex3 for mRNA

source_name: MYH6-EIP4 day25 cardiomyocytes (without transfection day7) ex3


title: d22 miR-208a sorted cells

description: miR-208a-BFP sorted cells differentiated from 201B7 on day 22 for mRNA

source_name: 201B7 derived d22 miR-208a sorted cells


title: gray-00298: s0080-scan

description: Array Type: HA114

source_name: Cancer

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

source_name: normal female genomic DNA


title: d19 cardiomyocytes without transfection-1

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day19 ex1 for mRNA

source_name: MYH6-EIP4 day19 cardiomyocytes (without transfection day1) ex1


title: gray-00298: s0077-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: d19 cardiomyocytes without transfection-2

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day19 ex2 for mRNA

source_name: MYH6-EIP4 day19 cardiomyocytes (without transfection day1) ex2

tag: cell type


title: d25 cardiomyocytes miR-switch-3

description: miR-1-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day25 ex3 for mRNA

source_name: MYH6-EIP4 day25 cardiomyocytes (miR-1-switch transfection day7) ex3


title: d19 cardiomyocytes without transfection-3

description: nontransfected Cardiomyocytes differentiated from MYH6-EIP4 on day19 ex3 for mRNA

source_name: MYH6-EIP4 day19 cardiomyocytes (without transfection day1) ex3


title: d19 cardiomyocytes miR-switch-1

description: miR-1-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day19 ex1 for mRNA

source_name: MYH6-EIP4 day19 cardiomyocytes (miR-1-switch transfection day1) ex1


title: gray-00298: s0071-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: disease state

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: d19 cardiomyocytes miR-switch-2

description: miR-1-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day19 ex2 for mRNA

source_name: MYH6-EIP4 day19 cardiomyocytes (miR-1-switch transfection day1) ex2


title: d18 cardiomyocytes-1

description: Cardiomyocytes differentiated from MYH6-EIP4 on day18 ex1 for mRNA

source_name: MYH6-EIP4 day18 cardiomyocytes (before transfection) ex1


title: d19 cardiomyocytes miR-switch-3

description: miR-1-switch transfected Cardiomyocytes differentiated from MYH6-EIP4 on day19 ex3 for mRNA

source_name: MYH6-EIP4 day19 cardiomyocytes (miR-1-switch transfection day1) ex3


title: d18 cardiomyocytes-2

description: Cardiomyocytes differentiated from MYH6-EIP4 on day18 ex2 for mRNA

source_name: MYH6-EIP4 day18 cardiomyocytes (before transfection) ex2


title: gray-00298: s0067-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: hiPSC3

description: Human induced pluripotent stem cell line 3 for mRNA

source_name: Human induced pluripotent stem cell line 1 (MYH6-EIP4 P29)

tag: cell type


title: gray-00248: b0420

description: No Processed Data

source_name: mammary gland

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: disease state

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0063-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: d18 cardiomyocytes-3

description: Cardiomyocytes differentiated from MYH6-EIP4 on day18 ex3 for mRNA

source_name: MYH6-EIP4 day18 cardiomyocytes (before transfection) ex3

tag: cell type


title: gray-00298: s0059-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0060-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0053-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00248: b0337

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0054-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: hiPSC2

description: Human induced pluripotent stem cell line 2 for mRNA

source_name: Human induced pluripotent stem cell line 1 (MYH6-EIP4 P20)

tag: cell type


title: gray-00298: s0050-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00248: b0357

description: No Processed Data

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0049-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0046-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0040-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor grading

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0047-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: hiPSC1

description: Human induced pluripotent stem cell line 1 for mRNA

source_name: Human induced pluripotent stem cell line 1 (MYH6-EIP4 P17)

tag: cell type


title: gray-00298: s0039-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0037-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0048-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0035-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0026-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0031-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0019-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0021-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0025-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0032-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0004-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0042-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0566-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0018-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00248: b0335

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0006-scan

description: Array Type: HA114

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0013-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0551-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00248: b0447

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: followup time

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0515-scan

description: Array Type: HA20

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: ethnicity

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: b0521-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0530-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0502-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: b0512-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0499-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0494-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: b0447-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00248: b0299

description: No Processed Data

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0468-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: s0029-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00248: b0372

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: followup time

tag: ethnicity

value: Other

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0434-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: b0428-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0427-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0421-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: b0420-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0414-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0404-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00248: s0226

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0371-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0383-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: b0382-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0374-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0387-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00248: b0296

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0365-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0370-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: b0357-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0433-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0341-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time

tag: gender


title: gray-00298: b0358-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0359-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00248: b0414

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0344-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: dead of disease

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment

tag: gender


title: gray-00298: b0339-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: organism part

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)


title: gray-00298: b0340-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: family history

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00248: b0346

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: organism part

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0338-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: followup time

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: b0394-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0337-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0348-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: b0372-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00248: b0317

description: No Processed Data

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: followup time

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0334-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: b0346-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0229-onco

description: Array Type: G950

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0301-onco

description: Array Type: G950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: b0318-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0226-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: followup time

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0305-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0205-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0326-scan

description: Array Type: HA20

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: s0204-onco

description: Array Type: E950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: b0299-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: b0297-scan

description: Array Type: HA114

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: followup time

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0317-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: s0200-onco

description: Array Type: F950

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: gray-00298: s0201-onco

description: Array Type: E950

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: followup time

tag: tumor grading

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: gray-00298: b0336-scan

description: Array Type: HA20

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: family history

tag: ethnicity

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: tumor size (mm)

tag: gender


title: gray-00298: b0296-scan

description: Array Type: HA114

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: dead of disease

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: age at diagnosis

tag: recurrence time


title: FT1

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

description: total RNA

hyb_protocol: Standard Affymetix protocol.

scan_protocol: Standard Affymetix protocol.

data_processing: Raw data were normalized globally and processed with Microarray Suite, version 5.0 (Affymetrix) and Data Mining Tool (Affymetrix) software.

source_name: Isolated and in vitro cultured placental trophoblasts

label_protocol: cDNA was labeled with the RNA Transcript Labeling Kit from Enzo diagnostics

growth_protocol: Prior to microarray analysis 800,000 trophoblasts w in flasks (25 cm²) using DMEM Medium with 5% FCS, or 800,000 placental endothelial cells were seeded in flasks (75 cm²) using EBM medium with 5% FCS. Cells were cultured for 48 h at 21% O2/5% CO2 environment at 37°C.

extract_protocol:
RNA isolation with TRI REAGENT according to manufacturer
cDNA was synthesized with SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen)

tag: tissue

value: placenta

tag: cell type

value: cytotrophoblasts


title: EC3

description: total RNA

source_name: Isolated and in vitro cultured placental endothelial cells

value: endothelial cells


title: FT3

description: total RNA