title: Subject_AF0330_FollowingSleepExtension_T6

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0330

hyb_protocol: Labelled cRNA (1.65 μg) was hybridized on a Whole Human Genome 4  44K custom oligonucleotide microarray (G2514F, AMADID 026817; Agilent Technologies). Standard manufacturer's instructions for one-colour gene expression hybridization and washing steps were followed. The microarrays were hybridized at 65°C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, pre-warmed Wash Buffer 2 (37C) and acetonitrile according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 sec.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide scanned at 10% and 100% PMT were imported into Agilent Feature Extraction software (Version 10.7.1.1) for image analysis.

data_processing: Individual samples were filtered based on AgilentQC metrics of reproducibility statistics, minimum detection level estimates and feature flags. Samples with a median coefficient of variation of less than 10% in spike ins or non-control replicated probes (NCRPs) were retained and quantile-normalised using the R Bioconductor package limma. NCRPs along with their corresponding flags were averaged. Probes with more than 5 flagged samples within a subject in more than half of the total number of subjects were excluded. In addition, for time-series analyses, series with 2 consecutive or more than 2 missing time points were excluded.

label_protocol: cRNA was synthesized and fluorescently labelled with Cy3-CTP from 100 ng of total RNA using Agilent's Low Input Quick Amp Labeling Kit.

growth_protocol: Blood samples were collected via an indwelling venous cannula sited in the forearm for minimum discomfort and restriction of movement. Cannulae were kept patent by the use of sterile saline. Each sample tube was coded for subject and sample collection time (participant code/sample type/sequential number)

extract_protocol: Total RNA was isolated using a PAXgene Blood RNA Kit and a QiaCube robot (Qiagen, Hilden, Germany). The RNA was quantified and the A260/280 nm and A260/230 nm ratios were determined using a NanoDrop ND1000 spectrophotometer (Wilmington, DE). RNA quality was assessed using the Bioanalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: 2.5 ml of blood is drawn into the PAXGene tube at each sampling point. The tube is inverted 10 times to mix. The tube is then stored at room temperature for 4 hours in upright position. The tube is transferred to -50°C and placed lying down (never in upright position as this may cause the tube to crack) for storage at the university of Surrey Clinical Research Centre. The tube is transferred on ice to University of Surrey Faculty of Health and Medical Sciences for storage/processing

value: Blood

tag: sleep protocol

value: Sleep Extension

tag: time sample taken

tag: circadian phase


title: Liver_control diet_32week_rep3

status: Public on Feb 08 2017

type: RNA

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

description: gene expression data from liver from maternal chromium restriction

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Genespring v12.5 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: control diet, 32 week

label_protocol: biotin

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (mirVanaTM, ABI).

tag: tissue

value: Liver

tag: age

value: 32 week


title: Decidua basalis from control pregnancy 1

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

country: USA

institute: UCSF

hyb_protocol: Sample processing and hybridization were done according to protocols that were devised by the UCSF Gladstone (NHLBI) Genomics Core Facility.

scan_protocol: GeneChips were scanned using a GeneArray Scanner

data_processing: Gene level expression data quality was confirmed, normalized (RMA) and summarized (Affymetrix Expression Console Software). Significant differential expression was determined by statistical analysis of false discovery rate (ANOVA p < 0.05) and absolute linear fold change >2 (Affymetrix Transcriptome Analysis Console Software).

organism: Homo sapiens

source_name: decidua basalis

label_protocol: Samples were prepared using the Ambion Whole-Transcript (WT) Expression kit, used in conjunction with the Affymetrix GeneChip  WT Terminal Labeling and Controls Reagent kit

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plus Micro

treatment_protocol: We used laser microdissection to isolate the decidua basalis and parietalis from sPE and nPTB samples (n=4/ group). Biopsies of the placenta/decidua basalis and smooth chorion/decidua parietalis were washed repeatedly in cold PBS to remove blood contaminants then placed in cryomolds containing OCT, frozen over a dry ice/ethanol slurry, and stored at -80C. The blocks were sectioned at 20 microns by using a Leica CM3050 cryostat. The sections were mounted on UV treated PEN-membrane slides, and stored under dry ice prior to laser capture microdissection later that day. Immediately prior to the procedure, sections were immersed in cold PBS until the OCT dissolved (~1 min), dipped in 0.1% toluidine blue for 30 s, washed in cold PBS, dehydrated (30 s/treatment) in a graded ethanol series (75%, 75%, 95%, 100%), then rapidly dried with compressed nitrogen. All solutions were made with nuclease-free water. Decidua basalis and parietalis were laser microdissected (Leica LMD 7000) and collected directly into RLT Plus (Qiagen RNeasy Plus Micro kit). Total RNA was isolated according to the manufacturer’s protocol and concentrations were measured photometrically (NanoDrop 2000c). RNA integrity was determined via microfluidic phoresis (Agilent Bioanalyzer 2100). The samples were stored at -80C.

value: preterm birth control


title: Subject_AF0330_FollowingSleepExtension_T10

description: Blood taken at timepoint 10 following Sleep Extension for Subject AF0330

tag: genotype


title: Decidua parietalis from preeclampsia pregnancy 4

source_name: decidua parietalis

value: preeclampsia


title: Decidua basalis from preeclampsia pregnancy 1


title: Decidua parietalis from preeclampsia pregnancy 2


title: Decidua parietalis from control pregnancy 3


title: Subject_AF0330_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0330


title: Subject_AF0330_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0330

value: Sleep Restriction


title: Subject_AF0330_FollowingSleepRestriction_T1

description: Blood taken at timepoint 1 following Sleep Restriction for Subject AF0330


title: Subject_AF0250_FollowingSleepExtension_T10

description: Blood taken at timepoint 10 following Sleep Extension for Subject AF0250


title: Subject_AF0330_FollowingSleepRestriction_T7

description: Blood taken at timepoint 7 following Sleep Restriction for Subject AF0330


title: Staphylococcus aureus LAC vehicle rep 2

status: Public on Feb 09 2017

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description:
LAC vehicle
Gene expression data from_Staphylococcus aureus LAC vehicle rep 2

hyb_protocol: Samples were hybridized onto custom Affymetrix GeneChip containing Sa according to manufacturer's recommendations

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

data_processing: The data were analyzed with EC 1.1 using Affymetrix default analysis

organism: Staphylococcus aureus

source_name: Staphylococcus aureus LAC vehicle rep 2

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: frozen stocks were cultured in trypticase soy broth (TSB) (Becton Dickinson)

extract_protocol: For mRNA analysis, RNA was extracted using RNeasy spin columns (Qiagen) followed by DNAse treatment.

treatment_protocol: presence or absence of savirin (5 μg ml-1)

value: LAC

tag: treatment

value: vehicle


title: Subject_AF0250_FollowingSleepExtension_T6

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0250


title: Subject_AF0244_FollowingSleepRestriction_T1

description: Blood taken at timepoint 1 following Sleep Restriction for Subject AF0244


title: Subject_AF0220_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0220


title: Subject_AF0244_FollowingSleepExtension_T10

description: Blood taken at timepoint 10 following Sleep Extension for Subject AF0244


title: Subject_AF0250_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0250


title: Subject_AF0250_FollowingSleepRestriction_T6

description: Blood taken at timepoint 6 following Sleep Restriction for Subject AF0250


title: Subject_AF0250_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0250


title: Subject_AF0244_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0244


title: Subject_AF0220_FollowingSleepExtension_T10

description: Blood taken at timepoint 10 following Sleep Extension for Subject AF0220


title: Subject_AF0244_FollowingSleepRestriction_T6

description: Blood taken at timepoint 6 following Sleep Restriction for Subject AF0244


title: Subject_AF0193_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0193


title: Subject_AF0244_FollowingSleepExtension_T6

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0244


title: Subject_AF0180_FollowingSleepExtension_T6

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0180


title: Subject_AF0193_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0193


title: Subject_AF0180_FollowingSleepRestriction_T6

description: Blood taken at timepoint 6 following Sleep Restriction for Subject AF0180


title: Subject_AF0250_FollowingSleepRestriction_T1

description: Blood taken at timepoint 1 following Sleep Restriction for Subject AF0250


title: Subject_AF0062_FollowingSleepExtension_T6

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0062


title: Subject_AF0193_FollowingSleepRestriction_T6

description: Blood taken at timepoint 6 following Sleep Restriction for Subject AF0193


title: Subject_AF0180_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0180


title: Subject_AF0035_FollowingSleepRestriction_T6

description: Blood taken at timepoint 6 following Sleep Restriction for Subject AF0035


title: Subject_AF0244_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0244


title: Subject_AF0062_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0062


title: Subject_AF0035_FollowingSleepExtension_T6

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0035


title: Subject_AF0062_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0062


title: Subject_AF0180_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0180


title: Subject_AF0062_FollowingSleepExtension_T10

description: Blood taken at timepoint 10 following Sleep Extension for Subject AF0062


title: Subject_AF0220_FollowingSleepExtension_T6

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0220


title: Subject_AF0035_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0035


title: Subject_AF0035_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0035


title: Subject_AF0032_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0032


title: Subject_AF0032_FollowingSleepRestriction_T1

description: Blood taken at timepoint 1 following Sleep Restriction for Subject AF0032


title: Subject_AF0032_FollowingSleepExtension_T10

description: Blood taken at timepoint 10 following Sleep Extension for Subject AF0032


title: Subject_AF0035_FollowingSleepExtension_T10

description: Blood taken at timepoint 10 following Sleep Extension for Subject AF0035


title: Subject_AF0031_FollowingSleepRestriction_T10

description: Blood taken at timepoint 10 following Sleep Restriction for Subject AF0031


title: Subject_AF0031_FollowingSleepRestriction_T1

description: Blood taken at timepoint 1 following Sleep Restriction for Subject AF0031


title: BloodAtTimepoint1,followingSleepOutOfPhaseWithMelatoninForSubjectBB0214

description: Blood taken at timepoint 1 ,following sleep out of phase with melatonin, for Subject BB0214

tag: sampletype

value: out of phase

tag: time sampletaken


title: Subject_AF0032_FollowingSleepExtension_T6

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0032


title: Subject_AF0032_FollowingSleepRestriction_T6

description: Blood taken at timepoint 6 following Sleep Restriction for Subject AF0032


title: Subject_AF0031_FollowingSleepRestriction_T7

description: Blood taken at timepoint 7 following Sleep Restriction for Subject AF0031


title: Subject_AF0031_FollowingSleepExtension_T6

description: Blood taken at timepoint 6 following Sleep Extension for Subject AF0031


title: BloodAtTimepoint4,followingSleepOutOfPhaseWithMelatoninForSubjectBB0081

description: Blood taken at timepoint 4 ,following sleep out of phase with melatonin, for Subject BB0081


title: Subject_AF0031_FollowingSleepExtension_T10

description: Blood taken at timepoint 10 following Sleep Extension for Subject AF0031


title: BloodAtTimepoint3,followingSleepOutOfPhaseWithMelatoninForSubjectBB0214

description: Blood taken at timepoint 3 ,following sleep out of phase with melatonin, for Subject BB0214


title: BloodAtTimepoint7,followingSleepInPhaseWithMelatoninForSubjectBB0214

description: Blood taken at timepoint 7 ,following sleep in phase with melatonin, for Subject BB0214

value: in phase


title: BloodAtTimepoint4,followingSleepOutOfPhaseWithMelatoninForSubjectBB0214

description: Blood taken at timepoint 4 ,following sleep out of phase with melatonin, for Subject BB0214


title: Subject_AF0031_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0031


title: BloodAtTimepoint5,followingSleepInPhaseWithMelatoninForSubjectBB0081

description: Blood taken at timepoint 5 ,following sleep in phase with melatonin, for Subject BB0081


title: HTCE_4C

type: genomic

city: Torrance

first: luo

last: lu

address: 1124 W. Carson Street

department: molecular medicine

institute: LA BioMed

description: 4C assay

hyb_protocol: The labeled DNA probes were precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Further processing steps:
Filter out peaks with FDR >: 0.05
Map peaks to overlapping features upto bp upstream: 5000
Map peaks to overlapping features upto bp downstream: 1000
For each peak report: All pairs of peaks overlapping/nearby features
Further processed data file: 2011-09-23_09-01_513913_ratio_peaks.gff

molecule: genomic DNA

source_name: 4C target genomic DNA library from HTCE cell

label_protocol: For NimbleGen arrays, DNAs prepared from 4C assay and input were directly labeled by Klenow (New England Biolabs) random priming with Cy3 and Cy5 nonamers, respectively per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: (HTCE) cells were cultured in defined keratinocyte-SFM medium containing 90 μM calcium in a humidified incubator at 37 °C with 5% CO2.

extract_protocol: DNA-protein complexes were cross-linked in 1% formaldehyde at room temperature (RT) for 10 minutes, purified and digested with HindIII to separate the non-cross-linked DNAs from the cross-linked ones. These digested fragments were ligated intramolecular in the presence of T4 DNA ligase at 16 °C for overnight.  The process to reverse cross-link was performed in a high temperature treatment for 10 min. These ligated DNA fragments were further cleaved with a frequent cutter DpnI, and were subsequently re-ligated to form small DNA circles. The pool of these circular fragments became the 4C product library and small captured fragments in the library were amplified by inverse PCR using bait-specific primers facing outward. These PCR products were used for characterization of target genes on an array listed.

treatment_protocol: 4C target enrichment

tag: cell line

value: HTCE

source_name: Input DNA from HTCE cell

treatment_protocol: control


title: BloodAtTimepoint5,followingSleepInPhaseWithMelatoninForSubjectBB0214

description: Blood taken at timepoint 5 ,following sleep in phase with melatonin, for Subject BB0214


title: BloodAtTimepoint6,followingSleepInPhaseWithMelatoninForSubjectBB0065

description: Blood taken at timepoint 6 ,following sleep in phase with melatonin, for Subject BB0065


title: BloodAtTimepoint1,followingSleepOutOfPhaseWithMelatoninForSubjectBB0081

description: Blood taken at timepoint 1 ,following sleep out of phase with melatonin, for Subject BB0081


title: BloodAtTimepoint6,followingSleepInPhaseWithMelatoninForSubjectBB0214

description: Blood taken at timepoint 6 ,following sleep in phase with melatonin, for Subject BB0214


title: BloodAtTimepoint4,followingSleepOutOfPhaseWithMelatoninForSubjectBB0065

description: Blood taken at timepoint 4 ,following sleep out of phase with melatonin, for Subject BB0065


title: BloodAtTimepoint1,followingSleepOutOfPhaseWithMelatoninForSubjectBB0065

description: Blood taken at timepoint 1 ,following sleep out of phase with melatonin, for Subject BB0065


title: BloodAtTimepoint3,followingSleepOutOfPhaseWithMelatoninForSubjectBB0081

description: Blood taken at timepoint 3 ,following sleep out of phase with melatonin, for Subject BB0081


title: BloodAtTimepoint7,followingSleepInPhaseWithMelatoninForSubjectBB0065

description: Blood taken at timepoint 7 ,following sleep in phase with melatonin, for Subject BB0065


title: BloodAtTimepoint7,followingSleepInPhaseWithMelatoninForSubjectBB0081

description: Blood taken at timepoint 7 ,following sleep in phase with melatonin, for Subject BB0081


title: BloodAtTimepoint3,followingSleepOutOfPhaseWithMelatoninForSubjectBB0065

description: Blood taken at timepoint 3 ,following sleep out of phase with melatonin, for Subject BB0065


title: BloodAtTimepoint4,followingSleepOutOfPhaseWithMelatoninForSubjectBB0008

description: Blood taken at timepoint 4 ,following sleep out of phase with melatonin, for Subject BB0008


title: BloodAtTimepoint5,followingSleepInPhaseWithMelatoninForSubjectBB0065

description: Blood taken at timepoint 5 ,following sleep in phase with melatonin, for Subject BB0065


title: BloodAtTimepoint7,followingSleepInPhaseWithMelatoninForSubjectBB0008

description: Blood taken at timepoint 7 ,following sleep in phase with melatonin, for Subject BB0008


title: BloodAtTimepoint1,followingSleepOutOfPhaseWithMelatoninForSubjectBB0008

description: Blood taken at timepoint 1 ,following sleep out of phase with melatonin, for Subject BB0008


title: BloodAtTimepoint6,followingSleepInPhaseWithMelatoninForSubjectBB0008

description: Blood taken at timepoint 6 ,following sleep in phase with melatonin, for Subject BB0008


title: BloodAtTimepoint3,followingSleepOutOfPhaseWithMelatoninForSubjectBB0008

description: Blood taken at timepoint 3 ,following sleep out of phase with melatonin, for Subject BB0008


title: BloodAtTimepoint5,followingSleepInPhaseWithMelatoninForSubjectBB0008

description: Blood taken at timepoint 5 ,following sleep in phase with melatonin, for Subject BB0008


title: TMD8 AZD1480 Treated - 24 hours - mAdbID:112352

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 112352

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: TMD8 AZD1480 Treated - 24 hours

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted with TRIzol (Invitrogen) and subsequently cleaned-up with RNeasy mini columns (Qiagen).

treatment_protocol:
Treatment type: compound
Agent: AZD1480
Treatment dose: 2 uM
Treatment time: 24 hours

tag: cell type

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: TMD8 DMSO Treated

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: compound
Agent: DMSO (Dimethyl sulfoxide)
In-vitro treatment: Cells were treated with DMSO.


title: MLN on HBL1 6h

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

description: date of measurement: 1/11/2010

hyb_protocol: Hybridization was performed according Agilent Technologies protocol.

scan_protocol: Scanned on an Agilent Technologies Scanner.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization. An additional strong spot filter was applied to exclude any noise artefacts from probes with low brightness.

source_name: DLBCL cell line HBL1 - IKKbeta inhbibitor MLN120b treatment, 6 hours

label_protocol: Cy3 and Cy5 labeling was performed according Agilent Technologies protocol (Two-Color Microarray-Based Gene Expression Analysis - Low Input Quick Amp Labeling v.6.5)

growth_protocol: Cell lines were maintained in RPMI medium with 10%FBS at 37°C with 5% CO2.

extract_protocol: RNA was isolated using standard methods.

treatment_protocol: Cell lines were treated with the indicated inhibitors.

source_name: DLBCL cell line HBL1 - DMSO treatment, 6 hours


title: MLN on HBL1 12h

description: date of measurement: 1/11/2010

source_name: DLBCL cell line HBL1 - IKKbeta inhbibitor MLN120b treatment, 12 hours

source_name: DLBCL cell line HBL1 - DMSO treatment, 12 hours


title: PI3K on HBL1 48h

description: date of measurement: 2/1/2010

source_name: DLBCL cell line HBL1 - PI3K inhbibitor 15e treatment, 48 hours

source_name: DLBCL cell line HBL1 - DMSO treatment, 48 hours


title: PI3K on HBL1 12h

description: date of measurement: 2/1/2010

source_name: DLBCL cell line HBL1 - PI3K inhbibitor 15e treatment, 12 hours


title: shVGLL4 relicate 2

city: Shanghai

first: Shi

last: Jiao

address: 320 Yue Yang Road

institute: Shanghai Institutes of Biological Sciences

description:
Gene expression of HCT 116 cells after transfection with shVGLL4
S2@251485081567_S01_GE1_107_Sep09_1_4

hyb_protocol: Each slide was hybridized with 1.65 ug Cy3-labeled cRNA using Gene Expression Hybridization kit (Agilent) in Hybridization Oven (Agilent), according to the manufacturer's instructions. After 17 h hybridization, slides were washed in staining dishes (Thermo Shandon) with Gene Expression Wash Buffer Kit (Agilent), following the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) with default setting, Dye channel: Green, Scan resolution 5 um, PMT 100%, 10%, 16 bit.

data_processing:
Data were extracted with Feature Extraction Software 10.7 (Agilent).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent).

label_protocol: The total RNA was labeled by Low input Quick Amp Labeling kit, one-Color (Agilent). Labeled cRNA were purified by Rneasy mini kit (QIAGEN).

growth_protocol: HCT116 cell were culture in DMEM medium supplemented with 10%  fetal bovine serums at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: The total RNA was extracted using Trizol Reagent (Life technologies) following the manufacturer's instructions and checked for a RIN mumber to inspet RNA integrity b an Agilent Bioanalyzer 2100 (Agilent). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN) and RNase-Free DNase Set (QIAGEN).

treatment_protocol: HCT116 cell were then tranfected with VGLL4 or shVGLL4 for 48 h.

tag: gender

value: male

value: colorectal cancer cell line

tag: transfected with


title: MLN on HBL1 24h

description: date of measurement: 1/11/2010

source_name: DLBCL cell line HBL1 - IKKbeta inhbibitor MLN120b treatment, 24 hours

source_name: DLBCL cell line HBL1 - DMSO treatment, 24 hours


title: shVGLL4 relicate 1

description:
Gene expression of HCT 116 cells after transfection with shVGLL4
S1@251485081567_S01_GE1_107_Sep09_1_3


title: TMD8 AZD1480 Treated - 6 hours - mAdbID:112351

description: mAdb experiment ID: 112351

source_name: TMD8 AZD1480 Treated - 6 hours

treatment_protocol:
Treatment type: compound
Agent: AZD1480
Treatment dose: 2 uM
Treatment time: 6 hours


title: EV relicate 1

description:
Gene expression of HCT 116 cells after transfection with empty vector
EV1@251485081647_S01_GE1_107_Sep09_1_1

value: empty vector


title: Scr relicate 1

description:
Gene expression of HCT 116 cells after transfection with scamble
N1@251485081567_S01_GE1_107_Sep09_1_1

value: scamble


title: MLN on HBL1 48h

description: date of measurement: 1/11/2010

source_name: DLBCL cell line HBL1 - IKKbeta inhbibitor MLN120b treatment, 48 hours


title: EV relicate 2

description:
Gene expression of HCT 116 cells after transfection with empty vector
EV2@251485081647_S01_GE1_107_Sep09_1_2


title: PI3K on TMD8 12h

description: date of measurement: 9/29/2010

source_name: DLBCL cell line TMD8 - PI3K inhbibitor 15e treatment, 12 hours

source_name: DLBCL cell line TMD8 - DMSO treatment, 12 hours


title: PI3K on TMD8 24h

description: date of measurement: 9/29/2010

source_name: DLBCL cell line TMD8 - PI3K inhbibitor 15e treatment, 24 hours

source_name: DLBCL cell line TMD8 - DMSO treatment, 24 hours


title: TMD8 AZD1480 Treated - 3 hours - mAdbID:112350

description: mAdb experiment ID: 112350

source_name: TMD8 AZD1480 Treated - 3 hours

treatment_protocol:
Treatment type: compound
Agent: AZD1480
Treatment dose: 2 uM
Treatment time: 3 hours


title: PI3K on HBL1 24h

description: date of measurement: 2/1/2010

source_name: DLBCL cell line HBL1 - PI3K inhbibitor 15e treatment, 24 hours


title: VGLL4 relicate 2

description:
Gene expression of HCT 116 cells after transfection with VGLL4
V2@251485081647_S01_GE1_107_Sep09_1_4


title: PI3K on TMD8 36h

description: date of measurement: 9/29/2010

source_name: DLBCL cell line TMD8 - PI3K inhbibitor 15e treatment, 36 hours

source_name: DLBCL cell line TMD8 - DMSO treatment, 36 hours


title: VGLL4 relicate 1

description:
Gene expression of HCT 116 cells after transfection with VGLL4
V1@251485081647_S01_GE1_107_Sep09_1_3


title: PI3K on TMD8 48h

description: date of measurement: 9/29/2010

source_name: DLBCL cell line TMD8 - PI3K inhbibitor 15e treatment, 48 hours

source_name: DLBCL cell line TMD8 - DMSO treatment, 48 hours


title: TMD8 AZD1480 Treated - 1 hour - mAdbID:112349

description: mAdb experiment ID: 112349

source_name: TMD8 AZD1480 Treated - 1 hour

treatment_protocol:
Treatment type: compound
Agent: AZD1480
Treatment dose: 2 uM
Treatment time: 1 hour

source_name: TMD8 DMSO Treated


title: Scr relicate 2

description:
Gene expression of HCT 116 cells after transfection with scamble
N2@251485081567_S01_GE1_107_Sep09_1_2


title: Root tip (3 cm), ngr mutant, biological rep 3

city: Ardmore

first: Rujin

last: Chen

state: OK

address: 2510 Sam Noble Pkw

department: Plant Biology Division

institute: The Samuel Roberts Noble Foundation, Inc.

description: Gene expression data from root tips

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Medicago Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Genechip Gcanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization.

organism: Medicago truncatula

source_name: Medicago ngr mutant root tip

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

growth_protocol: Medicago truncatula wild type and ngr mutant seedlings were grown in half strength MS media in an aeroponic system, under 16 hr light 8 hr dark photoperiod.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified with Qiagen Min Elute Kit.

treatment_protocol: 3 cm-long root tips were excised and stored immediated in liquid nitrogen.

value: Root tip ( 3 cm)

value: ngr

value: five days after stratification


title: Root tip (3 cm), ngr mutant, biological rep 2

description: Gene expression data from root tips


title: Root tip (3 cm), wild type, biological rep 3

description: Gene expression data from root tips

source_name: Medicago wild type root tip

value: Jemalong A17


title: Root tip (3 cm), wild type, biological rep 1

description: Gene expression data from root tips


title: PI3K on HBL1 36h

description: date of measurement: 2/1/2010

source_name: DLBCL cell line HBL1 - PI3K inhbibitor 15e treatment, 36 hours

source_name: DLBCL cell line HBL1 - DMSO treatment, 36 hours


title: Lungs at T24h, B6, 12.5 Gy, Biological rep 1

city: Baltimore

first: Yuji

address: 660 W. Redwood Street

institute: University of Maryland

description: Gene expression data from lung tissue following sham or whole thoraxirradiation.

hyb_protocol: Hybridization targets were prepared with MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, Tx) from total RNA, hybridzed to Affymetrix Mouse Genome 430 2.0 gene chips in Affymetrix GeneChips hybridization overn 645, washed in Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Mouse arrays were scanned using the Affymetrix GeneChip Scanner 7G (Affymetrix, Santa Clara, CA) according to standard Affymetrix GeneChip Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara, CA).

data_processing: Data processing was performed using the Affymetrix Expression Console version 1.1 (Affymetrix, Santa Clara, CA).

label: Biotin

source_name: Lung tissue after 12.5 Gy irradiation

label_protocol: Labeling protocol was performed using MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, Tx) from total RNA.

growth_protocol: Female CBA/J, C57L/J, and C57BL/6J mice (10-12 weeks of age at time of irradiation), Jackson Labs, Bar Harbor, ME

extract_protocol: RNA isolation was performed using the Qiagen Rneasy kit (Qiagen, Valencia, CA) according to the manufacturer's protocol with slight modifications.RNA quality was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only RNA with an RNA Integrity Number (RIN) above 9.0 was used. Samples were not pooled.

treatment_protocol: Animals were exposed to whole thorax lung irradiation with shielding of the head, abdomen, and forelimbs, at a dose of 0, 12.5 or 15 Gy of 320 kVp X-rays (Precision X-ray, Inc., North Branford, CT, HVL = 1 mm Cu, dose rate = 67cGy/min). Animals were euthanized by sodium pentobarbital overdose in accordance with an approved IACUC protocol at 24 hours postexposure.

tag: strain

tag: lung radiation dose

tag: pathology

value: Pulmonary Fibrosis, mild Pneumonitis


title: Lungs at T24h, C57, 15 Gy, Biological rep 1

source_name: Lung tissue after 15 Gy irradiation

value: 15 Gy

value: Mixed-Pneumonitis/Pulmonary Fibrosis


title: Lungs at T24h, CBA,, 15 Gy, Biological rep 2

value: C2 CBA

value: Pneumonitis Only


title: Lungs at T24h, CBA, 0 Gy, Biological rep 1

source_name: Lung tissue after 0 Gy irradiation

value: C3 CBA

value: 0 Gy


title: Lungs at T24h, B6, 0 Gy, Biological rep 2


title: Lungs at T24h, B6, 15 Gy, Biological rep 1


title: Subject_AF0032_FollowingSleepExtension_T1

description: Blood taken at timepoint 1 following Sleep Extension for Subject AF0032

value: Blood

tag: sleep protocol

value: Sleep Extension


title: Lungs at T24h, CBA, 15 Gy, Biological rep 1


title: Lungs at T24h, B6, 12.5 Gy, Biological rep 2


title: Lungs at T24h, CBA, 12.5 Gy, Biological rep 2


title: Lungs at T24h, B6, 12.5 Gy, Biological rep 3


title: Lungs at T24h, C57, 15 Gy, Biological rep 2


title: Lungs at T24h, CBA, 0 Gy, Biological rep 2


title: Lungs at T24h, B6, 0 Gy, Biological rep 3


title: Lungs at T24h, B6, 15 Gy, Biological rep 3


title: Lungs at T24h, B6, 0 Gy, Biological rep 1


title: Lungs at T24h, CBA, 12.5 Gy, Biological rep 1


title: Lungs at T24h, C57, 15 Gy, Biological rep 3


title: Lungs at T24h, CBA, 15 Gy, Biological rep 3

value: C1 CBA


title: Lungs at T24h, C57, 12.5 Gy, Biological rep 3


title: Root tip (3 cm), ngr mutant, biological rep 1

description: Gene expression data from root tips


title: Lungs at T24h, CBA, 12.5 Gy, Biological rep 3


title: Lungs at T24h, CBA, 0 Gy, Biological rep 3


title: Lungs at T24h, C57, 0 Gy, Biological rep 2


title: Root tip (3 cm), wild type, biological rep 2

description: Gene expression data from root tips


title: Lungs at T24h, B6, 15 Gy, Biological rep 2


title: Lungs at T24h, C57, 12.5 Gy, Biological rep 2


title: Lungs at T24h, C57, 0 Gy, Biological rep 3


title: Lungs at T24h, C57, 0 Gy, Biological rep 1


title: Lungs at T24h, C57, 12.5 Gy, Biological rep 1


title: N135

type: SRA

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description: normal colon tissue was isolated from a patient with colorectal adenocarcinoma

library_source: genomic

data_processing:
GAII Illumina paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to hg18 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*Xma/(c*Xma+Sma)), where c=2.342 was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), MethReads (observed number of reads corresponding to methylated CpG, Xma), UnmethReads (observed number of reads corresponding to unmethylated CpG, Sma), RawMethylation (unadjusted methylation value), AdjMethylation (methylation value adjusted based on the spiked in standards).

source_name: proximal colon

extract_protocol:
phenol-chloroform
Five micrograms of genomic DNA spiked with 500 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

treatment_protocol: untreated tissue

tag: tissue of origin

value: colon

tag: disease

value: normal tissue

value: male


title: N110


title: Patient 76_Tumor-rich core

city: Pittsburgh

first: Rekha

last: Gyanchandani

address: 204 Craft Avenue

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh

description: 141 genes from 5 GEPs (Oncotype Dx, MammaPrint, PAM50, EndoPredict, and BCI) were measured in 181 samples from 71 breast cancers using NanoString nCounter analysis.

scan_protocol: See manufacturer's website http://www.nanostring.com for protocol. Digital Analyzer was set to scan at 1155 FOV (fields of view).

data_processing: See manufacturer's website http://www.nanostring.com for protocol. Raw intensities were normalized to the geometric mean of the positive controls and housekeeping genes using the R NanoStringNorm package.

label: biotin-labeled capture probe and a fluorescent barcode-labeled reporter probe

source_name: Primary breast cancer

extract_protocol: For the tumor section, the whole section was scraped (without macrodissection), and the paraffin shavings were used to isolate RNA. Additionally, 1-3 cores from each sample were also used for RNA isolation.  RNA was isolated using RNeasy® FFPE Kit (Qiagen, Valencia, CA) and quantified using UV spectroscopy (Nanodrop Technologies, Wilmington, DE).

tag: histology

value: Infiltrating ductal carcinoma

tag: fixative

value: Formalin-fixed paraffin embedded tissue


title: Patient 76_Section

hyb_protocol: See manufacturer's website http://www.nanostring.com for protocol.


title: Patient 77_High Ki67 core

label_protocol: See manufacturer's website http://www.nanostring.com for protocol.


title: Patient 77_Tumor-rich core


title: wild type KDM5A, biological replicate 1

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

description: gene expression data

hyb_protocol: Fragmented and labeled  DNA target was hybridizated to Affymetrix M430 2.0 chips using the GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: The probe array was scanned using an Affymetrix® GeneChip® Scanner 3000.

data_processing: Raw profiling data were normalized with affy::RMA.

source_name: Immortalized KDM5A-/- MEFs with re-introduction of wild-type KDM5A

label_protocol: Fragmented single-stranded DNA was labeled by TdT using the GeneChip® WT Terminal Labeling Kit.

growth_protocol: Subconfluent mouse embryonic fibroblasts were grown in DMEM with 10% fetal bovine serum at 37 C.

extract_protocol: Extraction of total RNA was performed by RNeasy mini kit with on-column DNase digestion (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were havested by trypsinization, quenched with growth medium, and washed with PBS

tag: background strain

value: mixed

value: mouse embryonic fibroblasts


title: Empty vector (EV), biological replicate 2

description: gene expression data

source_name: Immortalized KDM5A-/- MEFs with empty vector (EV)


title: Empty vector (EV), biological replicate 1

description: gene expression data


title: mutant KDM5A, biological replicate 1

description: gene expression data

source_name: Immortalized KDM5A-/- MEFs with re-introduction of  KDM5A-H483A mutant.


title: wild type KDM5A, biological replicate 2

description: gene expression data


title: Patient 75_Section


title: Patient 75_Tumor-rich core


title: Patient 77_Section


title: Patient 74_Section


title: Patient 73_Section

value: Infiltrating ductal mixed w/ other types of carcinoma


title: Patient 74_High Ki67 core


title: Patient 74_Tumor-rich core


title: Patient 73_Tumor-rich core


title: mutant KDM5A, biological replicate 2

description: gene expression data


title: Patient 73_High Ki67 core


title: Patient 72_Section

value: Infiltrating lobular mixed w/ other types of carcinoma


title: Patient 71_Section


title: Patient 69_Section


title: naphtalene+bleomycin 3

city: Fukuoka

first: Toyoshi

last: Yanagihara

state: Fukuoka

address: Maidashi, Higashi-ku

department: Immunobiology and neuroscience

country: Japan

institute: Medical institute of bioregulation, Kyushu University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: naphtalene+bleomycin 3

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen)  according to the manufacturer's instructions.

tag: tissue

value: lung


title: Patient 71_Tumor-rich core


title: bleomycin2


title: naphtalene+bleomycin 1

source_name: naphtalene+bleomycin 1


title: Patient 72_Tumor-rich core


title: Patient 70_Tumor-rich core


title: Patient 70_Section


title: bleomycin3


title: naphtalene2


title: control2


title: Patient 69_Tumor-rich core


title: bleomycin1


title: control3


title: naphtalene1


title: naphtalene3


title: control1


title: Patient 67_Section


title: Patient 72_Low PR core


title: Patient 66_Tumor-rich core


title: Patient 68_Section


title: naphtalene+bleomycin 2

source_name: naphtalene+bleomycin 2


title: Patient 69_High Ki67 core


title: Patient 68_Tumor-rich core


title: Patient 67_Tumor-rich core


title: Patient 69_Low PR core


title: Patient 65_Section

value: Lobular carcinoma


title: Patient 63_Low PR core


title: Patient 62_Section


title: Patient 65_Tumor-rich core


title: Patient 62_Low PR core


title: Patient 62_Tumor-rich core


title: Patient 64_Tumor-rich core


title: Patient 61_Tumor-rich core

value: Infiltrating ductal and lobular carcinoma


title: Patient 63_Section


title: Patient 64_Section


title: Patient 61_Section


title: Patient 62_High Ki67 core


title: Patient 66_Section


title: Patient 59_Tumor-rich core


title: Patient 59_Section


title: Patient 60_Tumor-rich core


title: Patient 60_Section


title: Patient 58_Tumor-rich core


title: Patient 58_Section


title: Patient 57_Section


title: Patient 65_High Ki67 core


title: Patient 56_Tumor-rich core


title: Patient 58_High Ki67 core


title: Patient 55_Section


title: Patient 56_Low PR core


title: Patient 54_Tumor-rich core


title: Patient 53_Section


title: Patient 52_Section


title: Patient 53_Tumor-rich core


title: Patient 55_Tumor-rich core


title: Patient 51_Section


title: Patient 55_High Ki67 core


title: Patient 50_Low PR core


title: Patient 50_Tumor-rich core


title: Patient 58_Low PR core


title: Patient 57_Tumor-rich core


title: Patient 49_Section


title: Patient 50_Section


title: Patient 52_Tumor-rich core


title: Patient 56_Section


title: Patient 47_Section


title: Patient 48_High Ki67 core


title: Patient 48_Tumor-rich core


title: Patient 47_Tumor-rich core


title: Patient 54_Section


title: Patient 45_Tumor-rich core


title: Patient 45_Section


title: Patient 45_Low PR core


title: Patient 51_Tumor-rich core


title: Patient 49_Tumor-rich core


title: Patient 47_High Ki67 core


title: Patient 44_Section


title: Patient 44_Tumor-rich core


title: Patient 42_Section


title: Patient 43_Low PR core


title: Patient 40_Section


title: Patient 42_Tumor-rich core


title: Patient 41_Tumor-rich core


title: Patient 48_Section


title: Patient 41_Section


title: Patient 43_Tumor-rich core


title: Patient 40_High Ki67 core


title: Patient 39_Tumor-rich core


title: Patient 40_Tumor-rich core


title: Patient 39_Section


title: Patient 39_Low PR core


title: Patient 43_Section


title: Patient 39_High Ki67 core


title: Patient 38_Section


title: Patient 38_Tumor-rich core


title: Patient 37_Section


title: Patient 38_High Ki67 core


title: Patient 37_Tumor-rich core


title: Patient 37_Low PR core


title: Patient 33_Tumor-rich core


title: Control r5

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

hyb_protocol: 5.5 ug labeled and fragmented cDNA were hybridized onto GeneChip®MTA_1.0

scan_protocol: Chips were washed in a FS 450 fluidics station and then scanned on GeneChip® Scanner 3000 7G following Affymetrix recommendations

data_processing: Data was normalized using RMA as implemented in Partek and later analyzed using BRB-Array tools

source_name: Young control mice that were single-housed in a cage without a running wheel. These young mice have normal hearing

label_protocol: 100 ng total RNA was labeled using GeneChip® WT PLUS Reagent Kit (WT PLUS Kit) from Affymetrix following manufacturer's instructions

extract_protocol: Inner ear tissues were frozen in liquid nitrogen and then ground into a powder in a 1.5 ml tube using a tissue homogenizer (Kimble-Chase, Vineland, NJ). Total RNA from the powdered tissue was isolated using the NucleoSpin RNA II kit

value: CBA/CaJ

value: cochlea

tag: developmental age

value: 6 months


title: Patient 33_High Ki67 core


title: Control r2


title: RW r5

source_name: Young control mice that were single-housed in a cage with a running wheel. These young mice have normal hearing


title: Patient 35_Tumor-rich core


title: Patient 32_Section


title: Control r1


title: Patient 31_Section


title: Patient 34_Section


title: Patient 32_Tumor-rich core


title: Control r4


title: Control r3


title: Patient 31_High Ki67 core


title: RW r1


title: RW r3


title: Patient 30_Section


title: RW r2


title: Patient 35_Section


title: Patient 30_Tumor-rich core


title: Patient 33_Section


title: Patient 30_High Ki67 core


title: Patient 34_Tumor-rich core


title: Patient 29_Section


title: RW r4


title: Patient 31_Tumor-rich core


title: Patient 28_Section


title: Patient 27_Section


title: Patient 28_Tumor-rich core


title: Patient 29_High Ki67 core


title: Patient 27_High Ki67 core


title: Patient 27_Tumor-rich core


title: Patient 26_Tumor-rich core


title: Patient 25_Section


title: Cortex_29 - control

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

hyb_protocol: 50 ng total RNA was processed by using a GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA) and hybridised to Affymetrix Rat Gene 1.0 ST gene chips.

scan_protocol: Chips were stained and washed with an Affymetrix GeneChip Fluidics Station 450, and scanned in an Affymetrix GeneChip 7G Plus scanner. All procedures were done according to the manufacturer's instructions.

data_processing:
Cel files were imported with RMA background correction, quantile normalization, log base 2 transformation, and median polish, using PArtek Genomcis Suite v 6.5 (www.Partek.com). Batch effect removal was applied using ANOVA for the factor Scan date. Gene summary and quantification was performed on the basis of the mean of the expression values of the exons per  gene.
probe group file: RaEx-1_0-st-v1.r2.pgf
meta-probeset file: RaEx-1_0-stv1.r2.dt1.rn4.full.mps

organism: Rattus norvegicus

source_name: control

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Male Wistar rats were separated in two groups: The control group received a standard rodent diet (Specialty Foods, Perth, Australia) and tap water ad libitum for 6 months.  The experimental group was fed 60 mM lithium/kg dry food for 6 months. Water was available ad libitum. All rats given lithium were supplied with a salt block to maintain sodium balance and prevent lithium intoxication.    At 6 months, the animals were sacrificed by decapitation and their kidneys removed.

extract_protocol: Total RNA from the kidneys was isolated with TrizolR (Invitrogen, Life Technologies, USA), followed by cleaning in Norgen Total RNA columns (Norgen Biotek Corp., Canada). RNA was quantified using a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and its (purity and) quality determined on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: The two kidneys from each animal were cut in half longitudinally; one half was put in 10% neutral buffered formalin for histology, and the other 3 halves were snap frozen in liquid nitrogen and stored at -80°C until further use.

value: renal cortex

value: Wistar


title: Cortex_18 - treated

source_name: treated (diet containing lithium (40 mmol/kg food for 7 days, followed by 60mmol/kg food for the rest of the experimental period. Total 6 months treatment)


title: Cortex_19 - treated


title: Cortex_30 - control


title: Cortex_21 - treated


title: Cortex_17 - treated


title: Cortex_15 - control


title: Patient 29_Tumor-rich core


title: Patient 25_Tumor-rich core


title: Cortex_22 - treated


title: Patient 24_Tumor-rich core


title: Patient 24_Section


title: Cortex_01 - control


title: Patient 63_Tumor-rich core


title: Cortex_06 - treated


title: Cortex_16 - control


title: Patient 26_Section


title: Cortex_13 - control


title: Patient 23_Section


title: Patient 23_Tumor-rich core


title: Patient 22_Tumor-rich core


title: Medulla_30 - control

value: renal medulla


title: Patient 22_Section


title: Patient 22_High Ki67 core


title: Patient 21_Tumor-rich core


title: Patient 21_Section


title: Patient 20_Section


title: Patient 20_Tumor-rich core


title: Medulla_22 - treated


title: Medulla_21 - treated


title: Patient 19_Section


title: Medulla_29 - control


title: Medulla_18 - treated


title: Medulla_16 - control


title: Medulla_19 - treated


title: Medulla_15 - control


title: Medulla_01 - control


title: Medulla_13 - control


title: Patient 19_Tumor-rich core


title: Medulla_06 - treated


title: Patient 19_High Ki67 core


title: PHYBpro vs phyB-9 Rc 4 day grown #4

city: Daejeon

first: Giltsu

last: Choi

address: 335 Gwahangno

department: Biological Sciences

country: South Korea

institute: KAIST

hyb_protocol: Each 850ng of cyanine 3-labeled and cyanine 5-labeled cRNA target were mixed and the fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent Arabidopsis (V4) GE 4X 44K Microarray. The arrays hybridized at 65oC for 17 h using Agilent Hybridization oven(Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner (Agilent Technology, USA)

data_processing: Background correction was performed using the normexp method in LIMMA and intensity data were normalized using LOWESS method

organism: Arabidopsis thaliana

source_name: Whole seedling of phyB-9 grown under continuous red condition for 4 days

label_protocol: Total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions Briefly, each 25ng total RNA was and T7 promoter primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 10min. The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours. Amplified and labeled cRNA was purified on RNase mini column (Qiagen) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Seeds were stratified for 3 days in dark and germination was induced in white light for 6 hours. After germination induction, seeds were subjected to continuous red light condition (11.4 μmol·m−2·s−1) for 4 days before harvested.

extract_protocol: Total RNA was extracted using the Spectrum plant total RNA kit (Sigma, St. Louis, MO, USA) according to the manufacturer’s protocol.

tag: developmental stage

value: Seedling

source_name: Whole seedling of PHYBpro:PHYBGFP/phyB-9 grown under continuous red condition for 4 days


title: Medulla_17 - treated

value: male


title: KDM3A knockdown using shRNA 2, biological rep 1

city: Aurora

first: Paul

last: Jedlicka

state: CO

department: Pathology, MS-8104

institute: University of Colorado Denver Anschutz Medical Campus

description:
A673_sh2_rep1
Gene expression data from A673 cells, with KDM3A knockdown via shRNA

hyb_protocol: Standard Affymetrix procedure.

scan_protocol: Standard Affymetrix procedure.

data_processing: Data were background corrected and normalized using RMA

source_name: A673 cells_ KDM3A knockdown using shRNA

label_protocol: 250 ng of total RNA was processed using the Whole Transcript Expression kit (Ambion) and Whole Transcript Terminal Labeling kit (Affymetrix).

growth_protocol: Cells were grown in DMEM with 10% Fetal bovine serum, 1% Pen/Strep, 10mM Hepes, 1X MEM non-essential amino acids, and 1mM Sodium Pyruvate.

extract_protocol: Total RNA was harvested using Trizol according to the manufacturer’s protocol

treatment_protocol: Cells were stably transduced with scrambled shRNA control, KDM3A knockdown shRNA sequence 1 or KDM3A knockdown shRNA sequence 2, and were harvested at 70-80% confluence

tag: cell line

tag: shRNA


title: PHYBpro vs phyB-9 Rc 4 day grown #3


title: PHYBpro vs phyB-9 Rc 4 day grown #1


title: KDM3A knockdown using shRNA 2, biological rep 3

description:
A673_sh2_rep3
Gene expression data from A673 cells, with KDM3A knockdown via shRNA


title: Patient 18_Tumor-rich core

value: Infiltrating ductal carcinoma


title: Patient 18_High Ki67 core

value: Formalin-fixed paraffin embedded tissue


title: Patient 18_Section


title: Tertiary trisomy 2, rep2

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

description: Gene expression data from tertiary trisomy 2

hyb_protocol: Hybridization, and detection followed the manufacturer's instructions (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS; Version1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Tertiary trisomy 2, 26-d-old, rosette leaves

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

growth_protocol: The plants were cultivated in growth chambers under long-day conditions (16 h-light/8 h-dark) at 22°C with light intensity 100-150 μE m-2 s-1.

extract_protocol: The total RNA from multiple plants (Combined from 21 to 35 plants) were extracted using RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: No additional treatment before sample collection. The rosette leaves of the 26-d-old plants were collected.

tag: karyotype

value: Tertiary trisomy 2

value: rosette leaves

tag: genetic background


title: Patient 16_Section

value: Infiltrating ductal mixed w/ other types of carcinoma


title: Trisomy 2, rep2

description: Gene expression data from trisomy 2

source_name: Trisomy 2, 26-d-old, rosette leaves

value: Trisomy 2


title: Trisomy 2, rep1

description: Gene expression data from trisomy 2


title: KDM3A knockdown using shRNA 2, biological rep 2

description:
A673_sh2_rep2
Gene expression data from A673 cells, with KDM3A knockdown via shRNA


title: KDM3A knockdown using shRNA 1, biological rep 2

description:
A673_sh1_rep2
Gene expression data from A673 cells, with KDM3A knockdown via shRNA


title: KDM3A knockdown using shRNA 1, biological rep 3

description:
A673_sh1_rep3
Gene expression data from A673 cells, with KDM3A knockdown via shRNA


title: ML1pro vs phyB-9 Rc 4 day grown #4

source_name: Whole seedling of ML1pro:PHYBGFP/phyB-9 grown under continuous red condition for 4 days


title: ML1pro vs phyB-9 Rc 4 day grown #3


title: PHYBpro vs phyB-9 Rc 4 day grown #2


title: Tertiary trisomy 2, rep1


title: KDM3A knockdown using shRNA 1, biological rep 1

description:
A673_sh1_rep1
Gene expression data from A673 cells, with KDM3A knockdown via shRNA


title: Patient 16_Tumor-rich core

source_name: Primary breast cancer


title: scrambled control shRNA, biological rep 3

description:
A673_scram_rep3
Gene expression data from A673 cells, no KDM3A knockdown

source_name: A673 cells_no KDM3A knockdown

value: scram


title: scrambled control shRNA, biological rep 2

description:
A673_scram_rep2
Gene expression data from A673 cells, no KDM3A knockdown


title: Wild type, rep1

description: Gene expression data from wild type

source_name: Wild type, 26-d-old, rosette leaves

value: Wild type


title: scrambled control shRNA, biological rep 1

description:
A673_scram_rep1
Gene expression data from A673 cells, no KDM3A knockdown


title: ML1pro vs phyB-9 Rc 4 day grown #1


title: ML1pro vs phyB-9 Rc 4 day grown #2


title: Al response in  AvSAMS1 expressing transformant_#2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

description: exp2_Al treated sample vs untreated sample in AvSAMS1 expressing transformant

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) containing fragmented Cydye-labeled cRNA labeled were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially by Wash Buffer 1 (6× SSPE, 0.005% N-lauroylsarcosine) and Wash Buffer 2 (0.06× SSPE, 0.005% N-lauroylsarcosine) for 1 min at room temperture.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1 ).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization. Further analysis were performed by GeneSpring GX12.5.

source_name: AvSAMS1 expressing transformant, untreated

label_protocol: Total RNA samples (200 ng) from untreated and treated shoots were used to prepare Cy3- or Cy5-labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer's instructions

growth_protocol: Seeds (ecotype Columbia-0 and AvSAMS1 expressing transformant) were grown in soil at 25ºC under long day conditions (16 h light/8 h dark) for approximately 3 weeks.

extract_protocol: Total RNA extracted using Agilent Plant RNA isolation Mini Kit (Agilent Technologies) following manufacturer's instructions

treatment_protocol: Whole plants of Arabidopsis seedlings (approximately 3 weeks old) were treated with 300 mM aluminum chloride solution (adjusted at pH4.2) for 2 d.

tag: age

tag: ecotype

tag: genotype

value: AvSAMS1 expressing TF

tag: treatment

value: non-treatment

tag: time after treatment

value: 2 d

value: Whole plant

source_name: AvSAMS1 expressing transformant, treated

value: 300 mM Al treatment for 2 d


title: Patient 15_Section


title: Wild type, rep2

description: Gene expression data from wild type


title: Patient 15_Tumor-rich core


title: Patient 15_High Ki67 core


title: Patient 14_Section


title: Patient 14_Tumor-rich core


title: Patient 13_Section

value: Infiltrating ductal and lobular carcinoma


title: Patient 13_Tumor-rich core


title: Al response in  AvSAMS1 expressing transformant_#1

description: exp1_Al treated sample vs untreated sample in AvSAMS1 expressing transformant

value: 0 d


title: Tenascin C BT025, rep1

city: Calgary

first: Voon

middle: Wee

last: Yong

state: Alberta

address: 3330 Hospital drive NW

department: Clinical Neurosciences

country: Canada

institute: University of Calgary

description:
Tenascin C 1
Gene expression data from 6h of tenascin C treatment

hyb_protocol: Following fragmentation, hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array at 45 °C for 16 h.

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 7G System.

data_processing: Array data files were generated with GeneChip Command Console Software (AGCC) and statistical significant analysis was carried out on software of GeneSpring (Agilent Technologies). The fold change between treatment and control was based on the P < 0.05 from unpaired t test (Asymptotic and Benjamini Hochberg FDR).

source_name: BT025 human BTICs, tenascin C

label_protocol: 100 μg of RNA of each sample with a RIN higher than 9 was labeled with the 3' _IVT Express Kit (Ambion).

extract_protocol: RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer's protocol. Total RNA was purified with the RNeasy Plus Micro Kit (Qiagen) to remove genomic DNA. The RNA quality of integrity number (RIN) was measured with an Agilent RNA 6000 NanoChip on 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: BTIC cells (BT025 cells) were untreated or treated with tenascin C (TNC) for 6h.

tag: cell type

value: brain tumor initiating cells (BTICs)

value: tenascin C


title: Patient 12_Section

value: Infiltrating ductal carcinoma


title: Control BT025, rep1

description:
Control 1
Gene expression data from 6h of untreated sample.

source_name: BT025 human BTICs, untreated

value: untreated


title: Tenascin C BT025, rep2

description:
Tenascin C 2
Gene expression data from 6h of tenascin C treatment


title: Control BT025, rep2

description:
Control 2
Gene expression data from 6h of untreated sample.


title: Control BT025, rep3

description:
Control 3
Gene expression data from 6h of untreated sample.


title: Al response in Columbia-0 line_#2

description: exp2_Al treated sample vs untreated sample in Columbia-0 line

source_name: Columbia-0, untreated

value: wild type

source_name: Columbia-0, treated


title: Tenascin C BT025, rep3

description:
Tenascin C 3
Gene expression data from 6h of tenascin C treatment


title: Patient 12_Tumor-rich core

description: 141 genes from 5 GEPs (Oncotype Dx, MammaPrint, PAM50, EndoPredict, and BCI) were measured in 181 samples from 71 breast cancers using NanoString nCounter analysis.

value: Formalin-fixed paraffin embedded tissue


title: Patient 12_High Ki67 core


title: Al response in Columbia-0 line_#1

description: exp1_Al treated sample vs untreated sample in Columbia-0 line


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, GTMMN microRNA 2

city: Durham

first: Nicolas

last: Christoforou

state: NC

address: 136 Hudson Hall, Box 90281

department: Biomedical Engineering

institute: Duke University

description:
GTMMN microRNA 2
Cells overexpressing GATA4, TBX5, MEF2C, MYOCD, NKX2-5 and transfected with miR-1 and miR-133.

hyb_protocol: Hybridized to GeneChip® Human Genome U133A 2.0 arrays in Affymetrix GeneChip® hybridization oven 645 and washed in Affymetrix GeneChip® Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara, CA). This work was performed at the Duke University microarray core facility.

scan_protocol: Scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara, CA). This work was performed at the Duke University microarray core facility.

data_processing: CEL files were imported into Partek Genomics Suite. Data was adjusted and condensed using RMA normalization. Significance, FDR Step up (Benjamini & Hochberg, 1995) is used as default <0.05.

source_name: HDFs induced to transdifferentiate, cardiac TF overexpression and microRNA transfection, 2 wks

label_protocol: Total RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA) and NanoDrop 8000 spectrophotometer (Thermo Scientific / NanoDrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX) from total RNA according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara, CA). This work was performed at the Duke University microarray core facility.

extract_protocol: Total RNA was collected from cells undergoing transdifferentiation (RNeasy Mini, Qiagen, 74104) 2 weeks following initiation of the process.

treatment_protocol: Human dermal fibroblasts (HDFs) were induced to transdifferentiate for 2 weeks. Group 1: Cardiac TF and microRNA, Group 2: Cardiac TF only, Group 3: Control (M2rtTA only). Conversion occurred using transdifferentiation medium supplemented with JAK1 inhibitor and sodium butyrate.

value: human dermal fibroblasts (HDFs) induced to transdifferentiate

value: GATA4, TBX5, MEF2C, MYOCD, and NKX2-5 overexpression, and miR-1 and miR-133 transfection

tag: time point

value: 2 weeks post initiation


title: Fulv sensitive MCF7 replicate6

city: Odense C

first: Daniel

last: Elias

address: J. B. Winsløwsvej 25

department: Cancer and Inflammation Research

country: Denmark

institute: University of Southern Denmark

description: MCF7 breast cancer cell line sensitive to fulvestrant

hyb_protocol: Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174  Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000175

scan_protocol: Affymetrix Gene ChIP Scanner 3000 Dx. Standard Affymetrix Cel file scan protocol.

data_processing: Microarray data were normalized and processed by Partek® Genomics Suite using RMA normalization methods

source_name: fulvestrant sensitive MCF7 subline

label_protocol: dMicroarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174  Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP0000017

growth_protocol: The human breast cancer cell line MCF-7 was originally obtained from The Breast Cancer Task Force Cell Culture Bank, Mason Research Institute (Edinburgh, UK). The MCF-7 cells were gradually adapted to grow in low serum concentration and the fulvestrant-sensitive subline MCF-7/S0.5 was used to establish the four fulvestrant resistant cell lines: MCF-7/ICI164R1 (ICI164R6), MCF-7/ICI182R1 (ICI182R1) and MCF-7/ICI182R6 (ICI182R6) and MCF- by long-term treatment with 10-7Mfulvestrant. Cells were kept within 10 passages throughout the experiments to reduce variability between experimental results.

extract_protocol: Total RNA was extracted by lysing cells in Trizol and total RNA was precipitated using 75% ethanol.

treatment_protocol: FulvR cells were treated with 10^-7M fulvestrant prior to RNA extraction

tag: cell line source

tag: cell subline

value: ER+ breast cancer cell line

tag: subline cell type

value: fulvestrant sensitive


title: Fulv sensitive MCF7 replicate3


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, GTMMN 3

description:
GTMMN 3
Cells overexpressing GATA4, TBX5, MEF2C, MYOCD, NKX2-5.

source_name: HDFs induced to transdifferentiate, cardiac TF overexpression, 2 wks

value: GATA4, TBX5, MEF2C, MYOCD, and NKX2-5 overexpression


title: Patient 10_Section

tag: histology

tag: fixative


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, GTMMN microRNA 3

description:
GTMMN microRNA 3
Cells overexpressing GATA4, TBX5, MEF2C, MYOCD, NKX2-5 and transfected with miR-1 and miR-133.


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, GTMMN microRNA 1

description:
GTMMN microRNA 1
Cells overexpressing GATA4, TBX5, MEF2C, MYOCD, NKX2-5 and transfected with miR-1 and miR-133.


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, GTMMN 2

description:
GTMMN 2
Cells overexpressing GATA4, TBX5, MEF2C, MYOCD, NKX2-5.


title: Fulv sensitive MCF7 replicate5


title: Patient 9_Section


title: Fulv sensitive MCF7 replicate4


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, GTMMN 1

description:
GTMMN 1
Cells overexpressing GATA4, TBX5, MEF2C, MYOCD, NKX2-5.


title: Fulv sensitive MCF7 replicate2


title: Patient 9_High Ki67 core


title: ICI182R6e

description: MCF7 breast cancer cell lines resistant to fulvestrant

source_name: fulvestrant resistant MCF7 subline ICI182R6

value: fulvestrant resistant


title: Patient 8_Section


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, Control 2

description:
Control 2
Control cells (M2rtTA only).

source_name: HDFs induced to transdifferentiate, control, 2 wks

value: control (M2rtTA only)


title: Fulv sensitive MCF7 replicate1

description: MCF7 breast cancer cell lines sensitive to fulvestrant


title: Patient 8_Tumor-rich core


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, Control 3

description:
Control 3
Control cells (M2rtTA only).


title: ExVivoBlood_fasting 16

city: Suita

first: Norikazu

last: Maeda

state: Osaka

department: Graduate School of Medicine

institute: Osaka University

description: Gene expression before breakfast in human blood

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 whole human genome 4 × 44 K oligo-DNA microarray (Agilent Technologies, Santa Clara, CA). After hybridization, arrays were washed consecutively by using Gene Expression Wash Pack (#5188-5327, Agilent Technologies, Santa Clara, CA).

scan_protocol: Fluorescence images of the hybridized arrays were generated using the Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: The feature intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1. The raw microarray intensities were processed by the percentile shift method (75th percentile) with GeneSpring GX 13.0 (Agilent Technologies) so as to normalize the range of expression intensities for inter-microarray. Genes whose expressions were available in more than 50% of hybridizations were included for further analyses. The normalized data were exported from the GeneSpring GX software.

source_name: Peripheral blood, fasting, VFA xxx

label_protocol: 100 ng of total RNA was converted to cDNA, amplified, and labeled with Cy3-labeled CTP using the Quick Amp Labeling kit (#5190-0442, Agilent Technologies, Santa Clara, CA) according to manufacturer's protocol.

extract_protocol: For total RNA isolation, blood sample was collected into PaxGene Blood RNA tubes (PreAnalytiX/QIAGEN Inc., Valensia, CA) before breakfast.

tag: tissue

value: whole blood

tag: gender

value: male

tag: vfa (cm2)

tag: sfa (cm2)


title: Cells undergoing transdifferentiation 2 weeks post initiation of the process, Control 1

description:
Control 1
Control cells (M2rtTA only).


title: ICI182R6d


title: ExVivoBlood_fasting 17


title: ICI182R1e

source_name: fulvestrant resistant MCF7 subline ICI182R1


title: ICI182R6c


title: ExVivoBlood_fasting 15


title: ICI182R6a


title: Patient 9_Tumor-rich core


title: Patient 8_High Ki67 core


title: ExVivoBlood_fasting 13

value: female


title: ExVivoBlood_fasting 14


title: ICI182R1d


title: Patient 7_Section


title: Laminin α1 HT29 cells 3

city: Strasbourg

first: Olivier

last: Lefebvre

address: 3 Avenue Molière

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were generated using the Affymetrix AGCC v3.1 software and analyzed with Affymaetrix Expression Console v1.1 using Affymetrix default analysis settings and global scaling as normalization method (RMA).

source_name: Laminin α1 expression

label_protocol: Cy3 cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 7 days

extract_protocol: Tri Reagent of total RNA was performed according to the manufacturer's instructions.

tag: cell line

tag: expression construct

value: Laminin α1 expression


title: ExVivoBlood_fasting 12

tag: age


title: ExVivoBlood_fasting 10


title: ICI182R1c


title: ExVivoBlood_fasting 11


title: Laminin α1 HT29 cells 2


title: ICI182R1b


title: Patient 7_Tumor-rich core

source_name: Primary breast cancer


title: Patient 6_Section


title: Patient 5_Section

value: Tubular adenocarcinoma


title: Patient 6_Tumor-rich core

value: Infiltrating ductal carcinoma


title: ICI182R1a


title: ExVivoBlood_fasting 8


title: Laminin α1 HT29 cells 1


title: Control HT29 cells 1

source_name: control

value: Control


title: ExVivoBlood_fasting 9


title: Patient 5_Tumor-rich core


title: ICI164R1d

source_name: fulvestrant resistant MCF7 subline ICI164R1


title: Control HT29 cell 2


title: ICI164R1e


title: ExVivoBlood_fasting 6


title: Control HT29 cell 3


title: ExVivoBlood_fasting 4


title: ExVivoBlood_fasting 5


title: ExVivoBlood_fasting 7


title: ExVivoBlood_fasting 3


title: Patient 5_High Ki67 core


title: ICI164R1b


title: ICI164R1c


title: Patient 3_Section


title: Patient 5_Low PR core


title: Patient 10_Tumor-rich core


title: Patient 3_Tumor-rich core


title: Patient 2_Section


title: pre-therapy, biological rep3

city: Houston

first: Hao

last: Zhao

state: TX

address: 7455 Fannin St

institute: The University of Texas MD Anderson Cancer Center

description: Gene expression data from pre-therapy prostate cancer tissue

hyb_protocol: The samples were hybridyzed using the GeneChip Hybridization Control Kit according to the manufacture's instructions.

scan_protocol: The GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The data were processed using the aroma.affymetrix bioconductor package

source_name: prostate cancer tissue before treatment

label_protocol: The extracted RNA was labeled using the GeneChip WT Terminal Labeling Kit according to the manufacture's instructions.

extract_protocol: The  samples were collectef for total RNA isolation using the Qiagen miRNeasy Mini Kit according to the manufacture's instructions.

treatment_protocol: The post-therapy were treated with leuprolide acetate plus ipilimumab

value: prostate cancer


title: post-therapy, biological rep5

description: Gene expression data from post-therapy treated prostate cancer tissue

source_name: prostate cancer tissue after leuprolide acetate plus Ipilimuman treatment


title: Patient 3_Low PR core

value: Formalin-fixed paraffin embedded tissue


title: post-therapy, biological rep6


title: ICI164R1a


title: ICI164R4e

source_name: fulvestrant resistant MCF7 subline ICI164R4


title: pol32[L2]_2

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Slides were hybridized to custom Agilent tiling arrays and washed as per Agilent recommendations

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer's protocol

data_processing:
Raw data (*.txt) was LOESS normalized using the Ringo package in R (*.bed.txt)
The *bed.txt contains normalized log2 ratio (Cy5/Cy3) representing test/reference

organism: Drosophila melanogaster

source_name: stage 13 egg chambers

label_protocol: DNA was labeled by random priming and purified with an Amicon Ultra 30K column (Millipore)

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media.

extract_protocol: Egg chambers were resupended in ChIP lysis buffer  (50mM HEPES/KOH pH 7.5, 140mM NaCl, 1mm EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate), dounced and sonicated in a Bioruptor 300 (Diagenode). Standard phenol/chloroform extraction followed by isopropanol precipitation was used to isolate total genomic DNA.

treatment_protocol: Ovaries were hand dissected from females fattened for 2 days on wet yeast in Grace’s media. Stage 13 egg chambers were isolated and transferred to Grace’s media on ice until 100 egg chambers were collected. Egg chambers were stored at -80ᵒC until all egg chambers from each genotype were collected.

tag: strain

tag: developmental stage

value: stage 13 egg chambers

source_name: Oregon R  0-2 hour embryonic diploid DNA

extract_protocol: Embryos were resupended in 1% SDS in TE, dounced and sonicated in a Bioruptor 300 (Diagenode). Standard phenol/chloroform extraction followed by isopropanol precipitation was used to isolate total genomic DNA.

value: Oregon R

value: 0-2 hour embryos


title: ExVivoBlood_fasting 1


title: ExVivoBlood_fasting 2


title: Patient 2_Tumor-rich core

extract_protocol: For the tumor section, the whole section was scraped (without macrodissection), and the paraffin shavings were used to isolate RNA. Additionally, 1-3 cores from each sample were also used for RNA isolation.  RNA was isolated using RNeasy® FFPE Kit (Qiagen, Valencia, CA) and quantified using UV spectroscopy (Nanodrop Technologies, Wilmington, DE).


title: ICI164R4c

value: ER+ breast cancer cell line


title: pol32[L2]_1


title: pol32[L2]_3


title: post-therapy, biological rep3

description: Gene expression data from post-therapy prostate cancer tissue


title: pre-therapy, biological rep2

description: Gene expression data from pre-therapy  prostate cancer tissue


title: post-therapy, biological rep4

description: Gene expression data from post-therapy  prostate cancer tissue


title: pif1[167]_3


title: pif1[167]_1


title: ICI164R4b


title: ICI182R6b


title: post-trerapy, biological rep2


title: UA 2

city: Tangshan

first: Yuntao

last: Zhou

state: Hebei

address: Wenhua Road, No.27

department: Clinical Laboratory Center

institute: Tangshan Gongren Hospital

description: miRNAs in pooled plasma

hyb_protocol: The Hy3-labeled samples were hybridized on the miRCURY LNA Array (v.16.0) (Exiqon) by following manufacturer’s instructions. Briefly, the total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Nimblegen Systems). Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 4 00 rpm/min. The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon).

scan_protocol: Arrays were scanned and digitized using the Axon GenePix 4000B microarray scanner. Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: GenePix pro V6.0 software were used to extract all features of the data from the scanned images. Raw data were normalized using variance stabilizing normalization (VSN) method in limma package in R from the Bioconductor project.

source_name: Plasma from patients with unstable angina pectoris

label_protocol: Total RNA (1 μg) of each sample was labeled with Hy3 dye using the miRCURY Array Power Labeling Kit (Cat #208032-A, Exiqon) according to the manufacturer’s guideline for miRNA labelling. Briefly,1 μg of each sample was 3'-end-labeled with Hy3 fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was extracted from pooled plasma sample using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: 2 mL peripheral venous fasting blood was drawn into EDTA-K2 anticoagulant tube and were processed within 1 hour by two-step centrifugation to remove blood cells and the cellular debris. Plasma samples were obtained by centrifugation at 3000 rpm for 10 min to remove cellular components of blood specimen. The plasma samples were centrifugated at 12000 rpm for 10 min to remove cellular debris. The plasma was transfered to RNase/DNase-free tubes and stored at -80°C.

tag: disease state

value: unstable angina pectoris

value: pooled plasma sample


title: UA 4

description: miRNAs in pooled plasma


title: pif1[167]_2


title: UA 6

description: miRNAs in pooled plasma


title: UA 5

description: miRNAs in pooled plasma


title: pre-trerapy, biological rep1


title: UA 1

description: miRNAs in pooled plasma


title: post-therapy, biological rep1


title: ICI164R4a

tag: cell type

value: fulvestrant resistant


title: ICI164R4d


title: spnA[093],spnB[BU]_2


title: spnA[093],spnB[BU]_1


title: UA 3

description: miRNAs in pooled plasma


title: lig4[169];mus308[null]_2


title: lig4[169];mus308[null]_1


title: mus308[null]_2


title: mus308[null]_1


title: Control 1

description: miRNAs in pooled plasma

source_name: Plasma from healthy subjects

value: healthy


title: Control 2

description: miRNAs in pooled plasma


title: Control 3

description: miRNAs in pooled plasma


title: Control 6

description: miRNAs in pooled plasma


title: Control 7

description: miRNAs in pooled plasma


title: Control 5

description: miRNAs in pooled plasma


title: Control 4

description: miRNAs in pooled plasma


title: Patient 4 257015610720_S01_ALK-pos-1

status: Public on Feb 07 2017

city: Beijing

first: Xiao-Qing

last: Liu

address: 8 Dongda Road

department: Department of Lung Cancer

institute: Affiliated Hospital of Academy of Military Medical Sciences

description: Gene expression in human plasma

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 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary lung cancer

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.

growth_protocol: Not applicable

extract_protocol: Total RNA containing miRNAs was isolated from 200μl plasma with the QIAzol Lysis Reagent (QIAGEN) and purified with the miRNeasy Serum/Plasma Kit (QIAGEN) according to the manufacturer′s instructions.

treatment_protocol: All the participants enrolled had 7ml peripheral venous blood samples collected in the fasting state at morning. Plasma was separated within 30 minutes since the sample collection with the centrifugation at 4,500×g for 10 minutes at 4 ℃ and then stored immediately at -80℃ for further measurements.

tag: plasma

value: primary lung cancer

value: 59 years

value: Male

tag: smoking history

value: Yes

value: Adenocarcinoma

tag: clinical stage

value: IV

tag: alk mutational status

value: ALK positive


title: Patient 5 257015610720_S01_ALK-pos-2

description: Gene expression in human plasma

value: 37 years

value: No

tag: histology


title: Patient 6 257015610721_S01_ALK-pos-3

description: Gene expression in human plasma

value: 43 years

value: Female


title: Patient 2 257015610720_S01_ALK-neg-2

description: Gene expression in human plasma

value: ALK negative


title: Patient 8 257015610721_S01_HS-2

description: Gene expression in human plasma

source_name: healthy donor

value: healthy donor

value: 62 years

value: Not applicable


title: hESC_Ctrl 0.1%BSA_0pM_48h_n4

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and Partek genomics suite version 6.6 (Partek Inc.St.Louis,USA). QC passed CEL files were further analyzed using Partek genomics suite version 6.6. All CEL files

source_name: human embryonic stem cells

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of

growth_protocol: According to Pallocca et al. :Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration. Arch Toxicol (2016) 90:159–180

extract_protocol: Total RNA from 2 days differentiated hESCs in the presence and absence of benchmark concentration (BMC) of toxicants has  been isolated with  Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

treatment_protocol: Human embryonic stem cells (hESC)-derived neural crest cells (NCC) have been treated for 48 hours with non-cytotoxic concentration of different toxicants (Arsenic trioxide, VPA,TSA, Geldanamycin, Triadimefon, PBDE-99, Interferon beta), known to inhibit NCC migration in vitro. Total RNA has been isolated after 48 h treatment and Affymetrix microarray analysis has been performed (for more informations see Pallocca et al. .Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration. Arch Toxicol (2016) 90:159–180)

value: female

value: human embryonic stem cells

tag: cell state

value: differentiated


title: Patient 9 257015610721_S01_HS-3

description: Gene expression in human plasma

value: 64 years


title: Patient 1 257015610720_S01_ALK-neg-1

description: Gene expression in human plasma

value: primary lung cancer

value: 41 years

value: Male


title: hESC_Ctrl DMSO_0nM_48h_n4

tag: tissue


title: Patient 3 257015610720_S01_ALK-neg-3

description: Gene expression in human plasma

value: 52 years

tag: gender

value: Yes

value: Adenocarcinoma

value: IIIB


title: hESC_Arsenic trioxide_1uM_48h_n4


title: Patient 7 257015610721_S01_HS-1

description: Gene expression in human plasma

value: 63 years


title: hESC_Ctrl medium_0nM_48h_n4


title: hESC_TSA_10nM_48h_n5


title: hESC_TSA_10nM_48h_n4


title: hESC_PBDE99_15uM_48h_n5


title: hESC_Ctrl 0.1%BSA_0pM_48h_n5


title: hESC_Ctrl arsenic_0uM_48h_n5


title: hESC_Ctrl arsenic_0uM_48h_n4


title: hESC_Ctrl medium_0nM_48h_n5


title: hESC_VPA_250uM_48h_n5


title: hESC_VPA_250uM_48h_n4


title: hESC_Triadimefon_100uM_48h_n5


title: hESC_PBDE99_15uM_48h_n4


title: hESC_Triadimefon_100uM_48h_n4


title: hESC_Arsenic trioxide_1uM_48h_n5


title: hESC_Ctrl DMSO_0nM_48h_n5


title: hESC_Ctrl arsenic_0uM_48h_n3


title: hESC_Arsenic trioxide_1uM_48h_n3


title: hESC_Arsenic trioxide_1uM_48h_n1


title: hESC_Ctrl medium_0nM_48h_n2


title: hESC_Cyproconazole_10uM_48h_n4


title: hESC_Cyproconazole_10uM_48h_n5


title: hESC_Ctrl DMSO_0nM_48h_n1


title: hESC_Ctrl arsenic_0uM_48h_n2


title: hESC_VPA_250uM_48h_n2


title: hESC_TSA_10nM_48h_n1


title: hESC_Arsenic trioxide_1uM_48h_n2


title: hESC_TSA_10nM_48h_n2


title: hESC_VPA_250uM_48h_n3


title: hESC_Ctrl DMSO_0nM_48h_n3


title: hESC_TSA_10nM_48h_n3


title: hESC_Triadimefon_100uM_48h_n2


title: hESC_Ctrl DMSO_0nM_48h_n2


title: hESC_PBDE99_15uM_48h_n3


title: hESC_Ctrl medium_0nM_48h_n3


title: hESC_Triadimefon_100uM_48h_n1


title: hESC_Ctrl medium_0nM_48h_n1


title: hESC_Cyproconazole_10uM_48h_n3


title: hESC_PBDE99_15uM_48h_n1


title: hESC_PBDE99_15uM_48h_n2


title: hESC_IFNbeta_500pM_48h_n5


title: hESC_IFNbeta_500pM_48h_n4


title: hESC_Triadimefon_100uM_48h_n3


title: hESC_Cyproconazole_10uM_48h_n2


title: hESC_VPA_250uM_48h_n1


title: hESC_Geldanamycin_16nM_48h_n5


title: hESC_Ctrl 0.1%BSA_0pM_48h_n2


title: hESC_Geldanamycin_16nM_48h_n4


title: hESC_Cyproconazole_10uM_48h_n1


title: hESC_Ctrl 0.1%BSA_0pM_48h_n3


title: hESC_IFNbeta_500pM_48h_n1


title: hESC_IFNbeta_500pM_48h_n2


title: hESC_IFNbeta_500pM_48h_n3