title: H441 transfected with ETS2-specific siRNA 2

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description:
Time of RNA isolation after siRNA transfection  is 48 hours
Gene expression of H441 cells transfected with siRNA against the ETS2 gene- biological replicate 2

hyb_protocol: 2.5 ug of fragmented and labeled cDNA, was generated using the Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, were hybridized onto Human Gene 1.0 ST arrays according to the manufacturer’s instructions (Affymetrix). Hybridization cocktails containing samples, control oligonucleotide and eukaryotic hybridization controls in addition to hybridization mixes, DMSO and nuclease-free water were heat denatured at 99oC for 5 minutes, cooled to 45oC for 5 minutes, and finally centrifuged at maximum speed for 1 minute.   After injecting 80 uL of the hybridization cocktails, arrays were incubated for 17 hours in a hybridization oven set to a temperature of 45oC with 60 rpm rotation.   Arrays were washed, stained and processed using Affymetrix GeneChip Fluidics Station 450 systems

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G for subsequent generation of raw data (*CEL files)

data_processing: Raw expression data were normalized and summarized using the Robust Multichip Analysis (RMA) method along with log2 transformation using the integrated BRB-Array Tools software developed by Dr. Richard Simon and the BRB-Array Tools development team.

source_name: H441 lung cancer cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Affymetrix).

growth_protocol: H441 cells were cultured with DMEM/F12 in a humidified incubator with 5CO2

extract_protocol: Total RNA was isolated 48 hours following transfection using the RNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with control or ETS2-specific siRNA (siRNA from Dharmacon) using Lipofectamine RNAiMAX reagent from Life Technologies according to the manufacturer's instructions.

value: siRNA against ETS2


title: H441 transfected with ETS2-specific siRNA 3

status: Public on Nov 01 2013

type: RNA

country: USA

description:
Time of RNA isolation after siRNA transfection  is 48 hours
Gene expression of H441 cells transfected with siRNA against the ETS2 gene- biological replicate 3

label: Biotin

molecule: total RNA

organism: Homo sapiens

tag: treatment

tag: cell line


title: Adult, fadrozole, 30ug, day 2, replicate 8

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters to obtain signal intensities.

organism: Pimephales promelas

source_name: Ovary tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 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: Fish used in this study were reproductively mature female FHM (5-6 months of age) obtained from an onsite culture facility at the US EPA Mid-Continent Ecology Division (Duluth, MN). All procedures involving animals were reviewed and approved by the Animal Care and Use Committee in accordance with Animal Welfare Act and Interagency Research Animal Committee guidelines.

extract_protocol: Qiagen Rneasy

treatment_protocol: Exposures were conducted in 20L glass aquaria containing 10 L ultraviolet light-treated, membrane filtered, Lake Superior water containing 0 or 3, or 30 μg/L FAD. Treatments were delivered via water at a continuous flow of approximately 45 mL/min without the use of carrier solvents.

tag: tissue

value: ovary

value: fadrozole, 30ug, day 2


title: H441 transfected with ETS2-specific siRNA 1

description:
Time of RNA isolation after siRNA transfection  is 48 hours
Gene expression of H441 cells transfected with siRNA against the ETS2 gene- biological replicate 1


title: 4 µg/L of AgNO3, replicate 4 [Liver tissue]

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file 036574_D_F_20110917.xml to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by quantile normalizaton and baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA to test for significant differential expression of microarray targets.

source_name: Liver tissue

growth_protocol: FHM were obtained from Aquatic Biosystems (Fort Collins, CO), held in aerated dechlorinated tap water and fed three times daily with Zeigler® AquaTox Feed Gardners, PA, USA).

treatment_protocol: Fish were exposed in triplicate, five females per replicate, at 4 µg/L of silver nitrate (AgNO3) or 70 µg/L of PVP-AgNPs (Luna Innovations, Blackburn, VA) for 96 hours at 24°C ± 1 with a 90% water change at 48 hours.

tag: agent

value: silver nitrate (AgNO3)


title: 4 µg/L of AgNO3, replicate 3 [Liver tissue]


title: H441 transfected with scrambled siRNA 3

description:
Time of RNA isolation after siRNA transfection  is 48 hours
Gene expression of H441 cells transfected with control siRNA-biological replicate 3

value: control scrambled siRNA


title: 4 µg/L of AgNO3, replicate 2 [Liver tissue]


title: H441 transfected with scrambled siRNA 2

description:
Time of RNA isolation after siRNA transfection  is 48 hours
Gene expression of H441 cells transfected with control siRNA-biological replicate 2


title: Adult, fadrozole, 30ug, day 2, replicate 6


title: Adult, fadrozole, 30ug, day 2, replicate 7


title: H441 transfected with scrambled siRNA 1

description:
Time of RNA isolation after siRNA transfection  is 48 hours
Gene expression of H441 cells transfected with control siRNA-biological replicate 1


title: 4 µg/L of AgNO3, replicate 1 [Liver tissue]


title: Adult, fadrozole, 30ug, day 2, replicate 5


title: Adult, fadrozole, 30ug, day 2, replicate 4


title: Adult, fadrozole, 30ug, day 2, replicate 3


title: control, replicate 4 [Liver tissue]

value: control sample


title: Adult, fadrozole, 3ug, day 2, replicate 7

value: fadrozole, 3ug, day 2


title: 70 µg/L of PVP-AgNPs, replicate 4 [Brain tissue]

source_name: Brain tissue

value: polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs)


title: 70 µg/L of PVP-AgNPs, replicate 2 [Brain tissue]


title: 70 µg/L of PVP-AgNPs, replicate 3 [Brain tissue]


title: Adult, fadrozole, 30ug, day 2, replicate 2


title: Adult, fadrozole, 30ug, day 2, replicate 1


title: Adult, fadrozole, 3ug, day 2, replicate 8


title: Adult, fadrozole, 3ug, day 2, replicate 6


title: control, replicate 6 [Brain tissue]


title: Adult, fadrozole, 3ug, day 2, replicate 4


title: Adult, fadrozole, 3ug, day 2, replicate 5


title: 70 µg/L of PVP-AgNPs, replicate 5 [Brain tissue]


title: control, replicate 5 [Brain tissue]


title: 70 µg/L of PVP-AgNPs, replicate 1 [Brain tissue]


title: control, replicate 4 [Brain tissue]


title: Adult, fadrozole, 3ug, day 2, replicate 3


title: Adult, fadrozole, 3ug, day 2, replicate 2


title: MDA-MB-231 GF200 005

type: protein

city: Guangzhou

first: Shicheng

last: Su

address: 107 Yanjiang West Road

country: China

institute: Sun-Yat-Sen Memorial Hospital

hyb_protocol: Human Cytokine Antibody Arrays V kit (Raybiotech) was used according to the manufacturer’s instructions. Briefly, the arrays were blocked, incubated with 100 μL of CM overnight, incubated with biotin-conjugated antibodies (1/250) for 2 hours and with HRP-linked secondary antibody (1/1000) overnight. The membranes were incubated with chemiluminescent substrate and exposed to x-ray film for 15 minutes before development.

scan_protocol: Quantitative array analysis was performed using Array Vision Evaluation 8.0 (GE Healthcare Life Science)

data_processing: To obtain relative expression, signal intensity was subtracted for negative controls and normalized to internal positive. The intensities of signals can be quantified by densitometry.

label: biotin

molecule: protein

source_name: conditioned media from MDA-MB-231 cells

label_protocol: Samples were labeled according to the manufacturer’s instructions.

growth_protocol: MDA-MB-23 and MCF-7 breast cancer cells were obtained from American Type Culture Collection (ATCC) and grown according to standard protocols.

extract_protocol: Afterward, cells were washed in PBS and grown in adherent condition with cytokine/serum-free media which were harvested 24 hours later. The conditioned media was centrifuged at 4 。C for 20 min and the cell-free supernatant was collected.

treatment_protocol: MCF7 were treated with 5 ng/mL TGF-β , 10 ng/mL TNF-α(PeproTech, Rocky Hill, NJ) in 10%FBS DMEM for 2 weeks or given prolonged mammosphere culture for 5 weeks as previously described (Guttilla et al., 2012).

tag: cell type

value: breast cancer


title: Adult, water, day 2, replicate 8

value: water, day 2


title: control, replicate 3 [Brain tissue]


title: Adult, water, day 2, replicate 7


title: control, replicate 2 [Brain tissue]


title: 4 µg/L of AgNO3, replicate 5 [Brain tissue]


title: 4 µg/L of AgNO3, replicate 3 [Brain tissue]


title: control, replicate 1 [Brain tissue]


title: Adult, water, day 2, replicate 6


title: TNF-α-MCF7 GF200 003

source_name: conditioned media from MCF7 cells treated with TNF-α


title: TGF-β-MCF7 GF200 002

source_name: conditioned media from MCF7 cells treated with TGF-β


title: MCF7M GF200 004

source_name: conditioned media from MCF7 by prolonged mammosphere culture


title: Adult, water, day 2, replicate 5


title: 4 µg/L of AgNO3, replicate 2 [Brain tissue]


title: MCF7 GF200 001

source_name: conditioned media from MCF7 cells


title: 4 µg/L of AgNO3, replicate 1 [Brain tissue]


title: Infect-6h vs Control-6h

city: XI'AN

first: Li

last: Dengyun

address: Xinong Raod 22

institute: NWSUAF

description: No treated tissues

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

organism: Sus scrofa

source_name: lung

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada), following the manufacturer's recommended protocol.

treatment_protocol: PAM cells were isolated from 60d old healthy piglets and  inoculated with HuN4,a strain of highly pathogenic porcine reproductive and respitory syndrome  virus (HP-PRRSV) and were collected at 6h post-inoculation (pi).

tag: age

value: PAM

tag: infection

value: PRRSV strain HuN4

value: control


title: 4 µg/L of AgNO3, replicate 4 [Brain tissue]


title: Adult, fadrozole, 3ug, day 2, replicate 1


title: Adult, fadrozole, 30ug, day 1, replicate 7

value: fadrozole, 30ug, day 1


title: Adult, water, day 2, replicate 3


title: Adult, water, day 2, replicate 1


title: Adult, fadrozole, 30ug, day 1, replicate 5


title: Adult, water, day 2, replicate 4


title: Adult, water, day 2, replicate 2


title: Adult, fadrozole, 30ug, day 1, replicate 6


title: Adult, fadrozole, 30ug, day 1, replicate 4


title: Adult, fadrozole, 30ug, day 1, replicate 3


title: Adult, fadrozole, 3ug, day 1, replicate 8

value: fadrozole, 3ug, day 1


title: Adult, fadrozole, 3ug, day 1, replicate 7


title: Lung tissue: healthy uninfected macaque biological rep 3

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from healthy macaque lung tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus macaque 3' IVT arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneSpring software, version 9

organism: Macaca mulatta

source_name: Healthy uninfected macaque lung tissue

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

extract_protocol: RNA was extracted with the Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: One SIV infected macaque (30378) was administered antiretroviral therapy beginning at 6 weeks post-infection, and two SIV infected macaques (33162 and 34540) were administered antiretroviral therapy beginning at 10 weeks post-infection

value: lung mucosa

value: 4-6 years


title: Lung tissue: healthy uninfected macaque biological rep 1


title: Lung tissue: SIV infected, untreated macaque biological rep 5

description: Gene expression data from SIV infected, untreated macaque lung tissue


title: Lung tissue: SIV infected, untreated macaque biological rep 4

source_name: SIV infected, untreated macaque lung tissue


title: Adult, fadrozole, 3ug, day 1, replicate 6


title: Lung tissue: SIV infected, untreated macaque biological rep 2


title: Adult, fadrozole, 3ug, day 1, replicate 3


title: Adult, fadrozole, 30ug, day 1, replicate 2


title: Lung tissue: SIV infected, antiretroviral therapy treated macaque biological rep 2

description: Gene expression data from SIV infected, antiretroviral therapy treated macaque lung tissue


title: Lung tissue: healthy uninfected macaque biological rep 2


title: Lung tissue: SIV infected, untreated macaque biological rep 1


title: Lung tissue: SIV infected, antiretroviral therapy treated macaque biological rep 3

source_name: SIV infected, antiretroviral therapy treated macaque lung tissue


title: Lung tissue: SIV infected, untreated macaque biological rep 3


title: Adult, fadrozole, 30ug, day 1, replicate 1


title: Adult, fadrozole, 3ug, day 1, replicate 2


title: Primary Hippocampla Neurons-2_NanoString

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

description: MG400 custom Nanostring codesets

data_processing: Data was proccessed using nSolver, normalized to Positive controls, Housekeeping genes and negative controls

label: NanoString oligonucleotide tag

organism: Mus musculus

source_name: Primary Hippocampla Neurons-2

extract_protocol: Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol

tag: strain

value: Hippocampus

value: Primary Neuron


title: Adult, fadrozole, 3ug, day 1, replicate 1

value: ovary


title: Primary Hippocampla Neurons-1_NanoString

description: MG400 custom Nanostring codesets

hyb_protocol: according to the manufacturer’s protocol

source_name: Primary Hippocampla Neurons-1


title: Adult, fadrozole, 3ug, day 1, replicate 5


title: Adult, water, day 1, replicate 5

value: water, day 1


title: Adult, water, day 1, replicate 4


title: Primary Cortical Neurons-2_NanoString

description: MG400 custom Nanostring codesets

scan_protocol: according to the manufacturer’s protocol

source_name: Primary Cortical Neurons-2

value: Cortex


title: Adult, water, day 1, replicate 3


title: Primary Cortical Neurons-1_NanoString

description: MG400 custom Nanostring codesets

source_name: Primary Cortical Neurons-1

label_protocol: according to the manufacturer’s protocol


title: Jejunum tissue: healthy uninfected macaque biological rep 2

description: Gene expression data from healthy macaque jejunum tissue

source_name: Healthy uninfected macaque jejunum tissue

value: jejunal mucosa


title: Adult, fadrozole, 3ug, day 1, replicate 4

source_name: Ovary tissue


title: Jejunum tissue: SIV infected, untreated macaque biological rep 4

description: Gene expression data from SIV infected, untreated macaque jejunum tissue


title: Jejunum tissue: healthy uninfected macaque biological rep 1


title: Adult Oligodendrocytes-1_NanoString

description: MG400 custom Nanostring codesets

source_name: Adult Oligodendrocytes-1

value: adult Oligodendrocytes


title: Lung tissue: SIV infected, antiretroviral therapy treated macaque biological rep 1


title: Adult Oligodendrocytes-2_NanoString

description: MG400 custom Nanostring codesets

source_name: Adult Oligodendrocytes-2


title: Jejunum tissue: SIV infected, untreated macaque biological rep 1

source_name: SIV infected, untreated macaque jejunum tissue


title: Jejunum tissue: SIV infected, untreated macaque biological rep 5


title: Adult, water, day 1, replicate 2


title: Jejunum tissue: SIV infected, antiretroviral therapy treated macaque biological rep 1

description: Gene expression data from SIV infected, antiretroviral therapy treated macaque jejunum tissue


title: Jejunum tissue: SIV infected, antiretroviral therapy treated macaque biological rep 3

source_name: SIV infected, antiretroviral therapy treated macaque jejunum tissue


title: Adult, water, day 1, replicate 1


title: Jejunum tissue: healthy uninfected macaque biological rep 3


title: Jejunum tissue: SIV infected, untreated macaque biological rep 3


title: Adult Astrocytes-2_NanoString

description: MG400 custom Nanostring codesets

source_name: Adult Astrocytes-2

value: adult Astrocytes


title: Jejunum tissue: SIV infected, antiretroviral therapy treated macaque biological rep 2


title: Colon tissue: healthy uninfected macaque biological rep 3

description: Gene expression data from healthy macaque colon tissue

source_name: Healthy uninfected macaque colon tissue

value: colonic mucosa


title: Colon tissue: healthy uninfected macaque biological rep 1


title: Adult Astrocytes-1_NanoString

description: MG400 custom Nanostring codesets

source_name: Adult Astrocytes-1


title: Colon tissue: healthy uninfected macaque biological rep 2


title: Microglia-2_NanoString

description: MG400 custom Nanostring codesets

value: microglia


title: microglia (Cortex)_NanoString

description: MG400 custom Nanostring codesets

source_name: microglia (Cortex)


title: microglia (Spinal cord)_NanoString

description: MG400 custom Nanostring codesets

source_name: microglia (Spinal cord)

value: Spinal cord


title: microglia (Hippocampus)_NanoString

description: MG400 custom Nanostring codesets

source_name: microglia (Hippocampus)


title: Adult microglia (Brain)_NanoString

description: MG400 custom Nanostring codesets

source_name: Adult microglia (Brain)

value: Brain

value: adult microglia


title: microglia (Cerebellum)_NanoString

description: MG400 custom Nanostring codesets

source_name: microglia (Cerebellum)

value: Cerebellum


title: Microglia-1_NanoString

description: MG400 custom Nanostring codesets


title: microglia (Olfactory bulb)_NanoString

description: MG400 custom Nanostring codesets

source_name: microglia (Olfactory bulb)

value: Olfactory bulb


title: Colon tissue: SIV infected, untreated macaque biological rep 4

description: Gene expression data from SIV infected, untreated macaque colon tissue


title: Me6 (TA01)

city: Beijing

first: Jing

last: Zhang

address: 27 Taiping Road

institute: Beijing Institute of Transfusion Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with IlluminaGUI/R (v.2011.1).

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

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

treatment_protocol: Cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and with or without small molecule Me6TREN for 24 h

value: Jurkat

value: T cell lymphoblast-like

tag: treated with

value: Me6TREN for 24hr


title: TCPS_4 14d

city: Gaithersburg

first: Carl

last: Simon

state: MD

address: 100 Bureau Drive

department: Biomaterials Group

institute: NIST

description:
178334.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements

data_processing: Data analysis was performed using the BRB-Array Tools version 4.1.0 (Biometric Research Branch, National Cancer Institute). For each sample subset considered, all arrays were referenced to the median array calculated from the arrays present. 24 arrays were normalized in a 6 sample comparison (four replicates per sample condition for a total of 24 arrays) with a unique median calculation. 16 arrays were normalized in a 4 sample comparison. Three sets of 2 sample comparisons were normalized. For each sample subset, 1) replicate spots on array were averaged, 2) intensity values thresholded 3) exclude genes where less than 10% of arrays have a 2.0 fold change from median 4) multiple probes were reduced by selecting the maximally expressed probe. These gene subsets were independently used as inputs in Significance Analysis of Microarrays and was performed within BRB ArrayTools.

source_name: 29 year old female donor

label_protocol: mRNA is converted to cRNA including a biotin label. Subsequent labelingoccurs with a streptavidin-Cy3 conjugate

growth_protocol: Primary human bone marrow stromal cells (hBMSCs, also known as mesenchymal stem cells, Tulane Center for Gene Therapy) were cultured at 37 C with 5 % by volume CO2 in a-minimum essential medium (Invitrogen) supplemented with 16.5 % by volume fetal bovine serum (Atlanta Biologicals) and 4 mmole/L L-glutamine. To wet scaffolds fully with culture medium, medium was added to specimens in wells and plates were placed under vacuum for 1 min. The vacuum was released and reapplied two more times. For seeding scaffolds, hBMSCs (80 % confluent) were dissociated with 0.25 % mass fraction trypsin [containing 1 mmole/L ethylenediaminetetraactate (EDTA)] and re-suspended in medium. Passage 5 cells were used for all microarray experiments.

extract_protocol: Total RNA from hBMSCs in 3D scaffolds and on 2D films was collected by homogenization of the cell lysate using the QIAshredder followed by purification using the RNeasy Minikit (Qiagen).  Four replicates were performed for all treatments wherein a replicate was prepared by pooling cell lysates from 4 samples (expect for PCL_FFF scaffolds where 8 samples were pooled).  Genome-wide transcriptions of hBMSCs were measured by high-throughput screening using the Illumina Human HT-12 v4 Expression BeadChips with 47231 probes for 25130 RefSeq annotated genes (NCBI/NIH) through a contract with Gene Logic (Gaithersburg, MD). RNA collected at Day 14 only was used for the current study.

treatment_protocol: Medium was removed from scaffolds and 10,000 hBMSCs in 0.5 mL of medium was added to each well for 48-well plates (PCL_NF, PCL_SC, PDLLA_NF, PDLLA_SC, TCPS) or 5,000 hBMSCs in 0.2 mL of medium for 96-well plates (PCL_FFF). Medium was changed twice per week and cells cultured for 4 time points (1 d, 7 d, 21 d, 50 d) as indicated in the figures. In some experiments, cells were cultured in medium containing osteogenic supplements (OS): dexamethasone (10 nmole/L), b-glycerophosphate (20 mmol/L) and ascorbic acid (0.05 mmol/L). Those samples are TCPS_OS.

value: primary human bone marrow stromal cells

tag: gender

value: female


title: Colon tissue: SIV infected, untreated macaque biological rep 1

source_name: SIV infected, untreated macaque colon tissue

value: 4-6 years


title: Colon tissue: SIV infected, untreated macaque biological rep 2


title: Colon tissue: SIV infected, antiretroviral therapy treated macaque biological rep 2

description: Gene expression data from SIV infected, antiretroviral therapy treated macaque colon tissue


title: TCPS_2 14d

description:
178332.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Colon tissue: SIV infected, untreated macaque biological rep 3


title: Con

description: Con

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum

value: PBS for 24hr (control)


title: Prostate Cancer LNCaP Spheres 4

city: Gold Coast

middle: Peter

last: Stapelberg

state: Queensland

address: Parklands Drive

country: Australia

institute: Griffith University

description: Spheres replicate 4

data_processing: BeadStudio was used to extract the raw expression data. Pre-processing of microarray data was then done using the R software package Linear Models for Microarray Data (LIMMA). NormExp was used for normalisation of the raw data.

source_name: Prostate Cancer LNCaP Spheres

value: LNCaP

value: prostate adenocarcinoma

tag: culture type

value: spheroid

tag: culture age

value: 5 day


title: Prostate Cancer LNCaP Spheres 3

description: Spheres replicate 3


title: TCPS_1 14d

description:
178331.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Lung macrophages_NanoString

description: MG400 custom Nanostring codesets

source_name: Lung macrophages

value: Lung

value: macrophage


title: TCPS_3 14d

description:
178333.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Colon tissue: SIV infected, antiretroviral therapy treated macaque biological rep 3

source_name: SIV infected, antiretroviral therapy treated macaque colon tissue

value: colonic mucosa


title: PDLLA_BNF_4 14d

description:
178322.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_OS_4 14d

description:
178330.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Colon tissue: SIV infected, antiretroviral therapy treated macaque biological rep 1


title: Prostate Cancer LNCaP Spheres 1

description: Spheres replicate 1


title: TCPS_OS_2 14d

description:
178328.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_OS_3 14d

description:
178329.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_OS_1 14d

description:
178327.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_BNF_3 14d

description:
178321.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: microglia (Eyes)_NanoString

description: MG400 custom Nanostring codesets

source_name: microglia (Eyes)

value: Eye

value: microglia


title: Prostate Cancer LNCaP Adherent cells 4

description: Adherent replicate 4

source_name: Prostate Cancer LNCaP Adherent cells

value: adherent


title: Prostate Cancer LNCaP Spheres 2

description: Spheres replicate 2


title: Kidney macrophages_NanoString

description: MG400 custom Nanostring codesets

source_name: Kidney macrophages

value: Kidney


title: Liver macrophages_NanoString

description: MG400 custom Nanostring codesets

source_name: Liver macrophages

value: Liver


title: Muscle macrophages_NanoString

description: MG400 custom Nanostring codesets

source_name: Muscle macrophages

value: Muscle


title: Ly6G neutrophils (PBMCs)_NanoString

description: MG400 custom Nanostring codesets

source_name: Ly6G neutrophils (PBMCs)

value: Ly6G neutrophils (PBMCs)


title: PCL_BNF_1 14d

description:
178311.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements

value: primary human bone marrow stromal cells

value: female


title: PCL_BNF_3 14d

description:
178313.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SC_4 14d

description:
178306.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Gut macrophages_NanoString

description: MG400 custom Nanostring codesets

source_name: Gut macrophages

value: Gut


title: PDLLA_BNF_2 14d

description:
178320.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_BNF_1 14d

description:
178319.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_SC_1 14d

description:
178307.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Spleen red pulp macrophages_NanoString

description: MG400 custom Nanostring codesets

source_name: Spleen red pulp macrophages

value: Spleen


title: Prostate Cancer LNCaP Adherent cells 2

description: Adherent replicate 2

value: LNCaP

value: prostate adenocarcinoma


title: Mesothelioma IstMes2 Spheres 5

description: Spheres replicate 5

source_name: Mesothelioma IstMes2 Spheres

value: mesothelioma

value: spheroid

value: 5 day


title: PDLLA_SC_3 14d

description:
178309.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Prostate Cancer LNCaP Adherent cells 3

description: Adherent replicate 3


title: PDLLA_SC_4 14d

description:
178310.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Mesothelioma IstMes2 Spheres 4

description: Spheres replicate 4


title: Heart macrophages_NanoString

description: MG400 custom Nanostring codesets

source_name: Heart macrophages

value: Heart

value: macrophage


title: PCL_BNF_4 14d

description:
178314.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Prostate Cancer LNCaP Adherent cells 1

description: Adherent replicate 1


title: Mesothelioma IstMes2 Spheres 2

description: Spheres replicate 2


title: PDLLA_BNF_4 Day 1

description:
178286.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements

data_processing: Data analysis was performed using the BRB-Array Tools version 4.1.0 (Biometric Research Branch, National Cancer Institute). The average of the four replicates of TCPS_1d was used as an in silico reference array for median normalization of all of the individual array data. The “significance analysis of microarrays” (SAM) approach (Tusher et. al. PNAS 2001), with a false discovery rate of 0.05, was chosen to test for significantly changed genes within the osteogenic controls (4 replicates each of TCPS_1d, TCPS_14d, TCPS_OS_1d and TCPS_OS_14d).

extract_protocol: Total RNA from hBMSCs in 3D scaffolds and on 2D surfaces at 1 d and 14 d was collected by homogenization of the cell lysate using the QIAshredder followed by purification using the RNeasy Minikit (Qiagen).  Four replicates were performed for all treatments wherein a replicate was prepared by pooling cell lysates from 4 samples (expect for PCL_FFF scaffolds where 8 samples were pooled).  Genome-wide transcriptions of hBMSCs were measured by high-throughput screening using the Illumina Human HT-12 v4 Expression BeadChips with 47231 probes for 25130 RefSeq annotated genes (NCBI/NIH) through a contract with Gene Logic (Gaithersburg, MD).

treatment_protocol: Medium was removed from scaffolds and 10,000 hBMSCs in 0.5 mL of medium was added to each well for 48-well plates (PCL_SL, PCL_GF, PCL_GFPS, PCL_BNF, PCL_SNF, PCL_SC, PDLLA_BNF, PDLLA_SC, TCPS) or 5,000 hBMSCs in 0.2 mL of medium for 96-well plates (PCL_FFF). Medium was changed twice per week and cells cultured for 4 time points (1 d, 7 d, 21 d, 50 d) as indicated in the figures. In some experiments, cells were cultured in medium containing osteogenic supplements (OS): dexamethasone (10 nmole/L), b-glycerophosphate (20 mmol/L) and ascorbic acid (0.05 mmol/L).


title: PCL_SC_1 14d

description:
178303.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_SC_2 14d

description:
178308.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_4 Day 14

description:
178334.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Dendritic cells (spleen)_NanoString

description: MG400 custom Nanostring codesets

source_name: Dendritic cells (spleen)

value: dendritic cells


title: PCL_BNF_2 14d

description:
178312.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SC_3 14d

description:
178305.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Mesothelioma IstMes2 Spheres 3

description: Spheres replicate 3


title: Splenic Ly6CLow monocytes_NanoString

description: MG400 custom Nanostring codesets

source_name: Splenic Ly6CLow monocytes

value: Ly6CLow monocytes


title: Mesothelioma IstMes2 Spheres 1

description: Spheres replicate 1


title: CD11bLy6C- macrophages_NanoString

description: MG400 custom Nanostring codesets

source_name: CD11bLy6C- macrophages

value: CD11bLy6C- macrophages


title: Splenic Ly6CHi monocytes_NanoString

description: MG400 custom Nanostring codesets

source_name: Splenic Ly6CHi monocytes

value: Ly6CHi monocytes


title: NK cells (spleen) NK1.1_NanoString

description: MG400 custom Nanostring codesets

source_name: NK cells (spleen) NK1.1

value: NK cells NK1.1


title: Bone marrow Ly6CHi monocytes_NanoString

description: MG400 custom Nanostring codesets

source_name: Bone marrow Ly6CHi monocytes

value: Bone marrow


title: Bone marrow Ly6C low monocytes_NanoString

description: MG400 custom Nanostring codesets

source_name: Bone marrow Ly6C low monocytes

value: Ly6C low monocytes


title: TCPS+OS_4 Day 1

description:
178294.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements

source_name: 29 year old female donor

value: primary human bone marrow stromal cells

value: female


title: T reg (Foxp3 spleen) CD4_NanoString

description: MG400 custom Nanostring codesets

source_name: T reg (Foxp3 spleen) CD4

value: Spleen (Foxp3)

value: T reg CD4


title: PCL_GF_4 Day 14

description:
178302.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_FFF_3 Day 14

description:
178325.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Mesothelioma IstMes2 Adherent cells 1

description: Adherent replicate 1

source_name: Mesothelioma IstMes2 Adherent cells

value: adherent


title: PCL_SC_4 Day 1

description:
178270.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SNF_3 Day 14

description:
178317.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_FFF_4 Day 14

description:
178326.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SNF_4 Day 14

description:
178318.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_SC_3 Day 14

description:
178309.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_2 Day 14

description:
178332.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_BNF_4 Day 1

description:
178278.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Mesothelioma IstMes2 Adherent cells 3

description: Adherent replicate 3

value: mesothelioma


title: TCPS_3 Day 14

description:
178333.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Mesothelioma IstMes2 Adherent cells 4

description: Adherent replicate 4


title: Mesothelioma IstMes2 Adherent cells 5

description: Adherent replicate 5


title: Breast Cancer MCF-7 Spheres 5

description: Spheres replicate 5

source_name: Breast Cancer MCF-7 Spheres

value: breast adenocarcinoma

value: spheroid


title: B cells (spleen) B220_NanoString

description: MG400 custom Nanostring codesets

source_name: B cells (spleen) B220

value: Spleen

value: B cells B220


title: PCL_GF_3 Day 14

description:
178301.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_SC_4 Day 14

description:
178310.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Mesothelioma IstMes2 Adherent cells 2

description: Adherent replicate 2

value: 5 day


title: PCL_SNF_2 Day 14

description:
178316.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: T cells (spleen) CD3_CD4_NanoString

description: MG400 custom Nanostring codesets

source_name: T cells (spleen) CD3_CD4

value: T cells CD3/CD4


title: TCPS+OS_3 Day 1

description:
178293.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_BNF_3 Day 1

description:
178285.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_FFF_2 Day 14

description:
178324.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Breast Cancer MCF-7 Spheres 4

description: Spheres replicate 4


title: Breast Cancer MCF-7 Spheres 3

description: Spheres replicate 3


title: Breast Cancer MCF-7 Spheres 2

description: Spheres replicate 2


title: PDLLA_SC_2 Day 14

description:
178308.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_BNF_3 Day 1

description:
178277.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Breast Cancer MCF-7 Adherent cells 5

description: Adherent replicate 5

source_name: Breast Cancer MCF-7 Adherent cells


title: Breast Cancer MCF-7 Spheres 1

description: Spheres replicate 1


title: A81_XYpYm_XYmYp

city: Bloomington

first: Colin

middle: D

last: Meiklejohn

state: IN

address: Jordan Hall, 1001 E. 3rd St.

department: Biology Department

institute: Indiana University

hyb_protocol: Hybridization was done using the 3DNA Array50 kit following the manufacturer's protocols

scan_protocol: Slides were scanned in an Axon 4000B scanner and microarray images were processed with GenePix v6.0

data_processing: Spots were filtered using the following quality control criteria: 70% of the foreground pixels within a spot were required to have a signal intensity higher than two standard deviations above the median background signal intensity in at least one of the two channels (Cy3 or Cy5); the median foreground signal intensity was required to be at least three times as great as the median background signal intensity in at least one of the two channels; a spot must have more than 30 foreground pixels.  Spot-wise log2 ratios were normalized over overall spot signal intensity by loess smoothing using a span of 0.3.  To account for spatial variation in signal across arrays, spot-wise log2 ratios were subsequently normalized by a second loess smoothing over the physical location of the spots on the slide, using a span of 0.002, which corresponds to an effective neighborhood of ~ 250 spots.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole adult flies

label_protocol: At least 20μg total RNA was used as a template for cDNA synthesis and incorporation of fluorescent dyes was done using the 3DNA Array50 kit following the manufacturer’s protocols

growth_protocol: Flies were reared on standard media at 25C on a 12:12 light:dark cycle.  Culture density was controlled by allowing parental genotypes to mate and lay eggs in mating cages, and then transferring 50 3-day old larvae to media vials, where they developed until eclosion.

extract_protocol: RNA was extracted from frozen flies using TRIzol and chloroform

treatment_protocol: Adults were collected as virgins and the sexes were aged separately for 2-3 days before flash-freezing in liquid nitrogen and storage at -80C at the same time of day

tag: Sex

value: male

tag: sex-chromosome parent-of-origin

value: XYpYm

value: XYmYp


title: PCL_GF_2 Day 14

description:
178300.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A60_XYpYm_XYmYp


title: PCL_BNF_2 Day 1

description:
178276.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Breast Cancer MCF-7 Adherent cells 4

description: Adherent replicate 4


title: PCL_SC_3 Day 1

description:
178269.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS+OS_2 Day 1

description:
178292.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Breast Cancer MCF-7 Adherent cells 3

description: Adherent replicate 3


title: A265_XYpYm_XYmYp


title: PDLLA_BNF_2 Day 1

description:
178284.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A59_XYmYp_XYpYm


title: Breast Cancer MCF-7 Adherent cells 2

description: Adherent replicate 2


title: A268_XYpXm_XYmXp

value: XYpXm

value: XYmXp


title: A264_XYmYp_XYpYm


title: A269_XYpXm_XYmXp


title: PDLLA_SC_1 Day 14

description:
178307.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements

value: primary human bone marrow stromal cells


title: A70_XYpXm_XYmXp

value: female


title: PCL_SC_2 14d

description:
178304.AVG_Signal
SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SC_2 Day 1

description:
178268.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: Breast Cancer MCF-7 Adherent cells 1

description: Adherent replicate 1


title: TCPS+OS_1 Day 1

description:
178291.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A67_XYmXp_XYpXm


title: PCL_GF_1 Day 14

description:
178299.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_1 Day 14

description:
178331.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SC_1 Day 1

description:
178267.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SNF_1 Day 14

description:
178315.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: IMR32 CHAF1A knock down day 10, biological rep3

first: Eveline

last: Barbieri

state: Texas

address: 1102 Bates Street

department: Department of Pediatrics

institute: Baylor College of Medicine

description: Gene expression data from cells 10 days after ShRNA induction, rep3

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

scan_protocol: GeneChips were scanned using the Affymetrix GCS 300 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

source_name: IMR32 neuroblastoma cells

label_protocol: Biotinylated cRNA were prepared  from 200 ng total RNA according to the standard Affymetrix RT-IVT protocol for the Affymetrix 3' IVT Express cDNA/cRNA Synthesis and Labeling Kit.

growth_protocol: IMR32 cells were grown in RPMI 10% FBS

extract_protocol: Total RNA was isolated using RNAeasy kit (Quiagen) from IMR32 cells

treatment_protocol: To knock down CHAF1A, expression a TRIPZ lentiviral inducible shRNAmir with Tet-inducible promoter was used (Open Biosystems). To repress CHAF1A expression, doxycycline was added at a final concentration of 1ug ml-1.

tag: inducible shrna

value: inducible CHAF1A ShRNA day 10


title: PDLLA_SC_4 Day 1

description:
178274.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_BNF_4 Day 14

description:
178322.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_BNF_1 Day 1

description:
178275.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_BNF_1 Day 1

description:
178283.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: IMR32 CHAF1A knock down day 10, biological rep2

description: Gene expression data from cells 10 days after ShRNA induction, rep2


title: TCPS+OS_4 Day 14

description:
178330.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A273_XpYm_XmYp

value: XpYm

value: XmYp


title: PCL_BNF_4 Day 14

description:
178314.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A267_XYmXp_XYpXm


title: PCL_FFF_1 Day 14

description:
178323.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_4 Day 1

description:
178298.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_GF_4 Day 1

description:
178266.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SNF_4 Day 1

description:
178282.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A64_XYmXp_XYpXm


title: A66_XYpXm_XYmXp


title: TCPS+OS_3 Day 14

description:
178329.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A266_XYmXp_XYpXm


title: PCL_FFF_4 Day 1

description:
178290.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: SSA_late log phase_expression2

city: Richmond

first: Xiuchun

last: Ge

state: VA

address: 521 North 11th Street

institute: Virginia Commonwealth University

description: Overnight cultures of S. sanguinis cells were diluted 100-fold in brain heart fusion broth and grown at 37 oC under microaerobic condition. The cultures at late log growth phase were collected and used for microarray analysis. RNA from samples was isolated by RNeasy mini kit. Spotted microarray slides were obtained from the Pathogen Functional Genomics Resource Center at JCVI. Each sample was divided into two parts and labeled by Cy5 and Cy3 dyes respectively for microarray. The microarray was hybridized with Cy3- and Cy5-labeled cDNA for 16 h at 42 °C according to the manufacturer’s protocol. Hybridized microarray was scanned using GenePix 4200A Scanner.

hyb_protocol: After prehybridization, spotted microarray was hybridized with Cy3- and Cy5-labeled cDNA for 16 h at 42 °C according to the protocol for hybridization of labeled DNA and cDNA probes at The J. Craig Venter Institute

scan_protocol: Hybridized microarray was scanned using GenePix 4200A Scanner (Axon Instruments).

data_processing:
The microarray data were analyzed using the programs TIGR Spotfinder and Midas to obtain the ratio of one dye to another dye for relative gene expression. The log ratio of Cy5 to Cy3 from the same sample will be zero if there is no bias between Cy3 and Cy5 labeling.  Our data showed there was no significant difference between both labeling, suggesting little bias. The ratio data also indicated the gene was expressed because there was no ratio for the poor expressed genes showing dye intensity not above background after analysis.
Additionally, the ratio of dye intensity to background in a microarray slide obtained after Spotfinder analysis represented absolute expression. DETAILS: After Spotfinder analysis, the data will show the each spot dye intensity and the background intensity around the spot. We calculated the ratio of Cy3 dye intensity to its background and the ratio of Cy5 dye intensity to its background in each spot. There were 4 repeats for each gene in every microarray. We got the geometric means of the Cy3/background and the geometric means of the cy5/background from 4 repeats, respectively. Then, both of them were averaged and the results were used as absolute expression of the gene.

organism: Streptococcus sanguinis

source_name: Streptococcus sanguinis gene expression at late log growth phase [ref]

label_protocol: Aminoallyl-labeled cDNA was labeled by Cy3 as described in the manual for microbial RNA aminoallyl labeling for microarrays at The J. Craig Venter Institute.

growth_protocol: Overnight cultures of S. sanguinis cells were diluted 100-fold in brain heart fusion broth and grown at 37 °C under microaerobic condition

extract_protocol: Total RNA from late log phase samples was isolated by RNeasy mini kit (Qiagen, Valencia, CA).

treatment_protocol: S. sanguinis cells were grown to late log phase in brain heart fusion broth at 37 °C under microaerobic condition

source_name: Streptococcus sanguinis gene expression at late log growth phase [test]

label_protocol: Aminoallyl-labeled cDNA was labeled by Cy5 as described in the manual for microbial RNA aminoallyl labeling for microarrays at The J. Craig Venter Institute.


title: SSA_late log phase_expression3


title: PCL_SC_4 Day 14

description:
178306.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: IMR32 CHAF1A knock down day 10, biological rep1

description: Gene expression data from cells 10 days after ShRNA induction, rep1


title: SSA_late log phase_expression1


title: PCL_BNF_3 Day 14

description:
178313.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A272_XpYm_XmYp


title: IMR32 CHAF1A knock down day 5, biological rep1

description: Gene expression data from cells 5 days after ShRNA induction, rep1

value: inducible CHAF1A ShRNA day 5


title: IMR32 ctrl, biological rep3

description: Gene expression data from uninduced cells, rep3

value: uninduced


title: PDLLA_BNF_3 Day 14

description:
178321.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A270_XmYp_XpYm


title: IMR32 CHAF1A knock down day 5, biological rep3

description: Gene expression data from cells 5 days after ShRNA induction, rep3


title: TCPS+OS_2 Day 14

description:
178328.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_BNF_2 Day 14

description:
178320.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: IMR32 CHAF1A knock down day 5, biological rep2

description: Gene expression data from cells 5 days after ShRNA induction, rep2


title: PCL_BNF_2 Day 14

description:
178312.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_3 Day 1

description:
178297.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: IMR32 ctrl, biological rep2

description: Gene expression data from uninduced cells, rep2


title: PCL_FFF_3 Day 1

description:
178289.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A74_XpYm_XmYp


title: A271_XmYp_XpYm


title: PCL_SNF_3 Day 1

description:
178281.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A73_XmYp_XpYm


title: PCL_GF_3 Day 1

description:
178265.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_2 Day 1

description:
178296.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: IMR32 ctrl, biological rep1

description: Gene expression data from uninduced cells, rep1


title: A72_XpYm_XmYp


title: PCL_SC_2 Day 14

description:
178304.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PDLLA_SC_3 Day 1

description:
178273.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SNF_2 Day 1

description:
178280.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_FFF_2 Day 1

description:
178288.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_SC_1 Day 14

description:
178303.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: polysomal RNA, UL38-induced NHDFs, 48 hr post-induction rep2

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description: Polysomal RNA converted to cRNA

hyb_protocol: labeled and fragmented cRNA hybridized to HG_U133_Plus 2.0 Affymetrix GeneChips using standard techniques recommended by the manufacturer. Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station FS 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring GX11 program. No further adjustments were made to the data in the table.

source_name: NHDFs, UL38 induced 48 hr post-induction

label_protocol: Labeled target cRNA population was generated with the Affymetrix 3’-IVT Express kit from 100 ng polysomal or total RNA. The cRNA was fragmented and biotin labeled according to manufacturer's instructions.

growth_protocol: Normal human dermal fibroblasts (NHDFs) and NHDFs ransduced with a lentivirus expressing doxycyclin (dox)-inducible HCMV UL38 were grown in DMEM + fetal bovine serum.

extract_protocol: Total RNA was isolated and used unfractionated or cell free extracts were first fractionated on 15-50% linear sucrose gradients and RNA isolated from pooled polysomal fractions

treatment_protocol: NHDFs were mock-infected or infected with HCMV. NHDFs containing a dox-inducible UL38 were treated +/- dox

tag: sample type

value: polysomal RNA

value: Normal fibroblasts

value: UL38 induced


title: polysomal RNA, UL38-induced NHDFs, 48 hr post-induction rep1

description: Polysomal RNA converted to cRNA


title: PDLLA_SC_2 Day 1

description:
178272.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: A71_XmYp_XpYm


title: polysomal RNA, uninduced NHDFs rep1

description: polysomal RNA converted to cRNA

source_name: NHDFs, uninduced


title: PCL_SNF_1 Day 1

description:
178279.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: extracted total RNA, UL38-induced, 48 hr post-induction rep2

description: Total RNA converted to cRNA

value: extracted total RNA


title: Brg1 vs Wild Type

city: Bradford

first: Michael Y

last: Fessing

address: Richmond Road

country: United Kingdom

institute: University of Bradford

description: Brg1(i)ep-/- mice were obtained by breeding K14-CreERT2/Brg1L2/L2 mice with Brg1L2/L2 mice and administaring tamoxifen to pregnant females from E10.5 onwards as described in (Indra et al., 2005, Development 132: 4533-4544

hyb_protocol: Tecan HS Pro Hybridization (Agilent Technologies Inc.)

scan_protocol: Scanned on an Agilent G2565AA scanner.

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

source_name: Wild Type, Mouse Epidermis

label_protocol: Quick Amp Labeling Kit, Two-Color (Agilent Technologies Inc.)

extract_protocol: Total RNA was isolated from  laser capture microdisected epidermis of the wild type and conditionally knocked out mice at E16.5 eratinocytes  and processed for two-round amplification using RiboAmp RNA Amplification Kit (Molecular Devices, USA) as described in (Sharov et al., 2006, Proc. Natl. Acad. Sci. USA 103:18166-18171)

value: Epidermis

value: Embryonic Day E16.5

source_name: Brg1 EP -/- , Mouse Epidermis

value: Embryonic Day 16.5


title: polysomal RNA, uninduced NHDFs rep2

description: polysomal RNA converted to cRNA


title: TCPS+OS_1 Day 14

description:
178327.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_FFF_1 Day 1

description:
178287.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: extracted total RNA, uninduced NHDFs rep2

description: Total RNA converted to cRNA


title: PDLLA_SC_1 Day 1

description:
178271.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_GF_2 Day 1

description:
178264.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: TCPS_1 Day 1

description:
178295.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: extracted total RNA, UL38-induced, 48 hr post-induction rep1

description: Total RNA converted to cRNA


title: PCL_BNF_1 Day 14

description:
178311.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: HDAC4 overexpression 4

city: Daejeon

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

country: South Korea

institute: Konyang university

description: replicate HDAC4 overexpression

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. The normalized data were derived from filtering (Detection p value 0.05), log transformation and quantile normalization of non-normalization data. We identified only 21140 genes after normalization.

extract_protocol: RNA was extracted with Nucleospin RNAII kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: variation

value: HDAC4 overexpression


title: PDLLA_BNF_1 Day 14

description:
178319.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: PCL_GF_1 Day 1

description:
178263.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements


title: extracted total RNA ,uninduced NHDFs rep1

description: Total RNA converted to cRNA

tag: treatment


title: polysomal RNA, HCMV-infected NHDFs, 48 hr post-infection rep2

description: Polysomal RNA converted to cRNA

value: HCMV infected


title: HDAC4 overexpression 3

description: replicate HDAC4 overexpression

tag: cell line


title: polysomal RNA, HCMV-infected NHDFs, 48 hr post-infection rep1

description: Polysomal RNA converted to cRNA


title: HDAC4 overexpression 2

description: replicate HDAC4 overexpression


title: TH-S whitefly_female adult_rep3

first: Nina

last: Yang

state: Beijing

address: 12 Zhongguancun Nandajie, Haidian District

institute: Chinese Academy of Agricultural Sciences

description: gene expression at female adult stage in TH-S strain

hyb_protocol: 875ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 10×Blocking Agent and 25×Fragmentation Buffer follow manuscript instruction,  On completion of the fragmentation reaction,55ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent whitefly Oligo Microarrays (G2545A) 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: Slide were scanned immediately after washing on the Agilent eArray Scanner (G2565BA) using one color setting for 8*15k array slides, scan region 71 x 21.6 mm, scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and 10%, respectively).

data_processing: The raw data files which contain Processed Signal were processed using the limma package (v.3.15.4) developed within the Bioconductor project (v.2.12) in the R (v. 2.15.1) statistical programming environment. After log2 transformation, the data normalized using quantile method. The data were filtered to 1) keep features within the dynamic range of the scanner and 2) retain features of good quality. For each set of replicated probes, a unique probe value obtained by computing the median of the intensities of the probes belonging to the replicated probe set.

organism: Bemisia tabaci

source_name: TH-S whitefly_female adult

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2ug using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions,followed by QIAGEN RNeasy mini kit purification (QIAGEN, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The B-biotype B. tabaci susceptible strain (TH-S) and resistant strain to thiamethoxam (TH-R) were maintained on cabbage under the same conditions. The TH-S strain was cultured without exposure to any chemical insecticides. While the TH-R strain exhibited >70-fold resistance to thiamethoxam compared to the TH-S.

extract_protocol: Total RNA was isolated from TH-S and TH-R whitefly samples using Trizol (Invitrogen) according to the manufacturer’s protocol. RNA quantity and quality confirmed using Nanodrop ND1000. Total RNA purified by QIAGEN RNeasy ® Kit following by the RNeasy Mini protocol.

treatment_protocol: Thiamethoxam susceptible (TH-S) and resistant (TH-R) B. tabaci strain were maintained on cabbage (Brassica oleracea L., cv. Jingfeng 1) under the same conditions. The TH-S strain was cultured without exposure to any chemical insecticides. While the TH-R strain had been exposed to thiamethoxam for more than 60 generations, and exhibited >70-fold resistance to thiamethoxam in comparision to the TH-S strain

tag: strain phenotype

value: thiamethoxam-susceptible (TH-S)

tag: development stage

value: one-day-old unmated adult females


title: HDAC4 overexpression 1

description: replicate HDAC4 overexpression


title: M5_GFP-

city: Paris

first: Antonio

middle: Angelo

last: Freitas

address: 25 Rue du Dr. Roux

department: Lymphocyte Population Biology Unit

institute: Institut Pasteur

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Conventional CD4+ T lymphocytes

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: RNA was isolated using the RNeasy Mini® (Qiagen). For the subseqent amplification of the RNA the SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: Mice were untreated before extraction.

value: female

value: Tg IL-2-GFP

tag: organs

value: Spleen/Lymph nodes

tag: developmental stage

value: adult

tag: population

value: GFP-


title: PCL_SC_3 Day 14

description:
178305.AVG_Signal
GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements

source_name: 29 year old female donor

tag: cell type

value: primary human bone marrow stromal cells


title: TH-S whitefly_female adult_rep2


title: M4_GFP-

tag: strain


title: M2_GFP-

tag: gender


title: control transfected pcDNA 2

description: replicate control

value: control transfected


title: polysomal RNA, uninfected NHDFs rep2

description: polysomal RNA converted to cRNA

source_name: HCMV-infected NHDFs, 48 hr post-infection

value: polysomal RNA

value: Normal fibroblasts

value: Mock infected


title: control transfected pcDNA 3

description: replicate control


title: control transfected pcDNA 4

description: replicate control


title: M5_GFP+

value: GFP+


title: TH-S whitefly_nymph_rep3

description: gene expression at nymph stage in TH-S strain

source_name: TH-S whitefly_nymph

value: the fourth nymphs


title: M4_GFP+


title: M3_GFP-


title: polysomal RNA, uninfected NHDFs rep1

description: polysomal RNA converted to cRNA


title: TH-S whitefly_nymph_rep2


title: TH-S whitefly_female adult_rep1


title: control transfected pcDNA 1

description: replicate control


title: M1_GFP-


title: extracted total RNA, HCMV-infected NHDFs, 48 hr post-infection rep2

description: Total RNA converted to cRNA

value: extracted total RNA


title: TH-S whitefly_nymph_rep1


title: Donor C 2hr  IL-1RA+B-glucan

city: Frederick

first: Marco

last: Cardone

address: 1050 Boyles Street

department: CIP

institute: NCI/NIH

description: Gene expression analysis of mono-DCs 12h after treatment with beta-glucan and IL1RA

hyb_protocol: cRNA was fragmented to uniform size and hybridized to Agilent Whole Genome 4x44K arrays. Arrays were hybridized at 65°C for 17 h in a rotating incubator, and washed afterwards at 37°C for 1 min.

scan_protocol: Slides were washed and scanned on an Agilent G2565 Microarray Scanner at 5 micron resolution

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) and Partek Genomics Suite 6.6

source_name: Mono-DC, 12h, beta-glucan and IL1RA treated

label_protocol: First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: Human monocyte-derived DC were obtained by a 6/7-d cultures of freshly isolated monocytes in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum plus recombinant human IL-4 (10 ng/ml) and GM-CSF (50 ng/ml). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using the Rneasy Mini Kit (QIAGEN) and residual genomic DNA was digested twice. RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was assessed with an Agilent Bioanalyzer.

treatment_protocol: Human DC derived from monocytes from three different healthy volunteers were left untreated or stimulated for 4 and 12 h with beta-glucan, in absence or presence of IL-1RA, in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: monocyte-derived Dendritic cells

tag: subject

value: donor C

value: beta-glucan and IL1RA treated

tag: time


title: M3_GFP+


title: Donor C 4hr  IL-1RA+B-glucan

description: Gene expression analysis of mono-DCs 4h after treatment with beta-glucan and IL1RA

source_name: Mono-DC, 4h, beta-glucan and IL1RA treated


title: TH-S whitefly_egg_rep3

description: gene expression at egg stage in TH-S strain

source_name: TH-S whitefly_egg

value: thiamethoxam-susceptible (TH-S)

value: egg


title: TH-S whitefly_egg_rep2


title: extracted total RNA, uninfected NHDFs (normal human dermal fibroblasts) rep1

description: Total RNA converted to cRNA

source_name: mock-infected NHDFs


title: extracted total RNA, uninfected NHDFs (normal human dermal fibroblasts) rep2

description: Total RNA converted to cRNA


title: extracted total RNA, HCMV-infected NHDFs, 48 hr post-infection rep1

description: Total RNA converted to cRNA

value: HCMV infected


title: M2_GFP+

value: female

value: Tg IL-2-GFP

value: Spleen/Lymph nodes


title: M1_GFP+

value: adult


title: Donor C Untr

description: Gene expression analysis of untreated mono-DCs

source_name: Mono-DC, Untreated

value: Untreated


title: TH-R whitefly_nymph_rep3

description: gene expression at nymph stage in TH-R strain

source_name: TH-R whitefly_nymph

value: thiamethoxam-resistant (TH-R)


title: MSC-IPS EB d14 34+38-45- biological rep1

city: Seattle

first: Sergei

last: Doulatov

state: WA

address: 1795 NE Pacific Street

institute: University of Washington

description: Gene expression from MSCIPS embryoid bodies

hyb_protocol: Hybridization cocktails were prepared by combining the fragmented, biotin-labeled cDNA with hybridization cocktail (Affymetrix Hybridization, Wash, and Stain Kit)

scan_protocol: The stained arrays were scanned at 532 nm using an Affymetrix GeneChip Scanner 3000.

data_processing: Microarray signal intensities were RMA-summarized and quantile normalized and corrected for batch effects using ComBat batch correction

source_name: MSCIPS embryoid bodies

label_protocol: The cDNAs were fragmented and labeled using a Nugen Encore Biotin Module.

growth_protocol: Human embryonic stem cells (CHB6) and induced-pluripotent stem cells (MSC-IPS) were differentiated into d14 embryoid body hematopoietic progenitors. CD34+CD45+ EB progenitors were sorted and transduced with transcription factors ERG, HOXA9 and RORA (3 factors) or ERG, HOXA9, RORA, SOX4, and MYB (5 factors). Transduced cells were cultured for 7-14 days and plated into hematopoietic colonies.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples (up to 50 ng) were processed using a Nugen PICO WTA System V2 kit

treatment_protocol: Samples were thawed, stained with anti-CD34, CD38, CD45, CD90 fluorescent antibodies as indicated in the sample title, and isolated by flow cytometric sorting. Between 10,000 and 50,000 cells were sorted for each sample.

tag: tissue type

value: Embryonic progenitors


title: MSC-IPS EB d14 34+38-45- biological rep2


title: TH-S whitefly_egg_rep1


title: Donor C 12hr  B-glucan

description: Gene expression analysis of mono-DCs 12h after treatment with beta-glucan

source_name: Mono-DC, 12h, beta-glucan treated

value: beta-glucan treated


title: TH-R whitefly_female adult_rep1

description: gene expression at female adult stage in TH-R strain

source_name: TH-R whitefly_female adult

value: one-day-old unmated adult females


title: TH-R whitefly_female adult_rep3


title: CHB6 EARSM 34+38- biological rep1

description: Gene expression from 5 Factor-induced CHB6 ESC

source_name: Factor-induced CHB6 ESC

value: Embryonic progenitors re-specified with transcription factors


title: TH-R whitefly_female adult_rep2


title: CHB6 EARSM 34+38- biological rep2


title: Donor C 4hr B-glucan

description: Gene expression analysis of mono-DCs 4h after treatment with beta-glucan

source_name: Mono-DC, 4h, beta-glucan treated


title: TH-R whitefly_nymph_rep2

value: the fourth nymphs


title: Donor B 12hr  B-glucan

value: monocyte-derived Dendritic cells

value: donor B


title: MSC-IPS EB d14 34+38-45+ biological rep1


title: Donor B 4hr  B-glucan


title: Donor B 12hr  IL-1RA+B-glucan

value: beta-glucan and IL1RA treated


title: MSC-IPS EB d14 34+38-45+ biological rep2


title: Donor B 4hr  IL-1RA+B-glucan


title: Fetal liver 34+38-90+ cultured 24h biological rep3

description: Gene expression from Primary human fetal liver

source_name: Cultured fetal liver

value: Fetal liver stem and progenitors


title: CL-Day 12 of Pregnant-Ewe 569

city: Fort Collins

first: Thomas

last: Hansen

state: CO

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

description: 569 Bovine Gene Array 9-30-10_(Bovine)

hyb_protocol: The resulting cDNA was hybridized oversight to Bovine 1.0 ST Affymetrix arrays. Following hybridization the arrays were washed, stained.

scan_protocol: Scanning was done using an Affymetrix GeneChip system including a 450 fluidics station and high-density GCS 3000 7G scanner.

data_processing:
The array was normalized using RMA algorithm via Affymetrix expression console software.
The data in the matrix table contains the log2 transformed RMA normalized signal from all twelve samples.

organism: Ovis aries

source_name: Corpus Luteum Day 14 Pregnant

label_protocol: 200 ng of total RNA was reversed transcribed and converted to cDNA using the GeneChip WT terminal labeling kit (Affymetrix, Santa Clara CA).

growth_protocol: Pregnancy status was achieved by breeding ewes to fertile ram and monitoring cycle for correct day. Non pregnant ewes were not bred and heat checked with a vasectomized ram to ensure proper day of cycle

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

treatment_protocol: CLs were harvested and snap frozen in liquid nitrogen

tag: tissue

value: Corpus luteum

tag: Sex


title: Donor A 12hr  IL-1RA+B-glucan

value: donor A


title: CL-Day 12 of Pregnant-Ewe 564

description: 564 Bovine Gene Array 9-30-10_(Bovine)

source_name: Corpus Luteum Day 14 Non pregnant

value: female


title: CL-Day 12 of Pregnant-Ewe 570

description: 570 Bovine Gene Array 9-30-10_(Bovine)


title: Fetal liver 34+38-90+ cultured 24h biological rep2


title: TH-R whitefly_nymph_rep1


title: Donor B Untr


title: TH-R white_egg_rep3

description: gene expression at egg stage in TH-R strain

source_name: TH-R white_egg

value: egg


title: Fetal liver 34+38-90+ cultured 24h biological rep1


title: Donor A Untr


title: Fetal liver 34+38+ progenitors biological rep2

source_name: Primary human fetal liver


title: MSC-IPS EAR 34+38-90+ biological rep2

description: Gene expression from 3 Factor-induced MSC-IPS

source_name: Factor-induced MSC-IPS


title: TH-R white_egg_rep2


title: CL-Day 12 of Pregnant-Ewe 502

description: 502 Bovine Genome Array 10-19-10_(Bovine)


title: Fetal liver 34+38-90+ HSC biological rep3


title: CL-Day 12 of Pregnant-Ewe 546

description: 546 Bovine Genome Array 10-19-10_(Bovine)

source_name: Corpus Luteum Day 12 Pregnant


title: MSC-IPS EAR 34+38-90+ biological rep1


title: TH-R white_egg_rep1


title: Fetal liver 34+38-90+ HSC biological rep1


title: CL-Day 12 of Pregnant-Ewe 504

description: 504 Bovine Genome Array 10-19-10_(Bovine)

source_name: Corpus Luteum Day 12 Non pregnant


title: CL-Day 12 of Pregnant-Ewe 537

description: 537 Bovine Genome Array 10-19-10_(Bovine)


title: Donor A 4h  B-glucan


title: Fetal liver 34+38+ progenitors biological rep1


title: CL-Day 12 of Pregnant-Ewe 369

description: 369 Bovine Genome Array 10-19-10_(Bovine)


title: CHB6 EB d14 34+38-45+ biological rep3

description: Gene expression from CHB6 embryoid bodies

source_name: CHB6 embryoid bodies


title: CL-Day 12 of Pregnant-Ewe 518

description: 518 Bovine Genome Array 10-19-10_(Bovine)


title: CL-Day 12 of Pregnant-Ewe 535

description: 535 Bovine Genome Array 10-19-10_(Bovine)


title: Donor A 12hr  B-glucan


title: CL-Day 12 of Pregnant-Ewe 554

description: 554 Bovine Gene Array 9-30-10_(Bovine)


title: Donor A 4hr  IL-1RA+B-glucan

description: Gene expression analysis of mono-DCs 4h after treatment with beta-glucan and IL1RA

source_name: Mono-DC, 4h, beta-glucan and IL1RA treated


title: Fetal liver 34+38-90+ HSC biological rep2


title: CHB6 EB d14 34+38-45+ biological rep2


title: CL-Day 12 of Pregnant-Ewe 512

description: 512 Bovine Genome Array 10-19-10_(Bovine)


title: Pi pool a

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from skeletal muscle of adult pig breed (Pi).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

source_name: Musculus longissimus dorsi tissue from adult pig taken at slaughter

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: Pietrain

value: skeletal muscle


title: Cord blood 34+38+ progenitors biological rep2

description: Gene expression from Primary human cord blood

source_name: Primary human cord blood

value: Neonatal stem and progenitors


title: Cord blood 34+38+ progenitors biological rep1


title: Pi 91 pool a

description: Gene expression data from skeletal muscle of peripubertal pigs breed (Pi).

source_name: Musculus longissimus dorsi tissue from embryo taken at slaughter, pregnancy day 91

value: 91 dpc


title: Cord blood 34+38+ progenitors biological rep3


title: Pi 91 pool c


title: Pi 63 pool c

source_name: Musculus longissimus dorsi tissue from embryo taken at slaughter, pregnancy day 63

value: 63 dpc


title: Tumor 67

type: genomic

city: Bethesda

first: Atsushi

last: Terunuma

address: 37 Convent Drive, 37/3050

department: Dermatology Branch

institute: National Cancer Institute

hyb_protocol: Standard Infinium HD Methylation Assay protocol

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

data_processing: GenomeStudio software v2010.3, Methylation module v1.8.5

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human Breast Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from fresh frozen primary breast tumours following the Qiagen DNeasy Blood and Tissue Kit protocol.  Briefly, tissues were pre-treated with Proteinase K  at 55C over-night, then lysed, bound to the column, washed, and eluted.  DNA was quantified using the nanodrop spectrophotomer.

tag: race

value: European-American

tag: age

value: Tumor

tag: estrogen receptor status

value: Positive

tag: triple negative or basal-like subtype

value: No

tag: Stage

value: IIA

tag: tumor grade

tag: node status

tag: survival (months)

tag: survival event

value: Alive

tag: death due to cancer

tag: neoadjuvant therapy

tag: hormone-therapy

value: Yes

tag: chemotherapy


title: Cord blood 34+38-90+ HSC biological rep2

tag: tissue type


title: Pi 63 pool b

tag: developmental stage

tag: tissue


title: Pi 63 pool a

tag: breed


title: CHB6 EAR 3-factor 34+38- biological rep3

description: Gene expression from 3 Factor-induced CHB6 ESC

source_name: Factor-induced CHB6 ESC

value: Embryonic progenitors re-specified with transcription factors


title: Tumor 28

tag: race

value: African-American

value: IIB


title: Cord blood 34+38-90+ HSC biological rep1


title: Tumor 31

value: Negative


title: Tumor 29

tag: age


title: Tumor 30

tag: estrogen receptor status


title: Tumor 25

tag: triple negative or basal-like subtype

value: IIIA

value: Dead


title: Tumor 65

tag: Stage

value: I


title: Cord blood 34+38-90+ HSC biological rep3

value: Neonatal stem and progenitors


title: Pi pool b

value: Pietrain

value: adult

value: skeletal muscle


title: Pi 35 K pool c

source_name: Musculus longissimus dorsi tissue from embryo taken at slaughter, pregnancy day 35

value: 35 dpc


title: Normal 24

source_name: Human Breast

value: Non-tumor


title: CHB6 EB d14 34+38-45+ biological rep1

value: Embryonic progenitors


title: Tumor 24

value: Tumor

tag: tumor grade

value: No


title: Tumor 66

value: European-American

value: Positive

value: IIA

tag: node status

value: Alive

value: Yes


title: primary breast cancer, sample 55

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol on Affymetrix scanner 3000.

data_processing: Cel files were processed using the affy and frma R packages, available at www.bioconductor.org, using median polish as summarizing method in the fRMA.

source_name: Snap frozen primary breast tumor

label_protocol: Standard Affymetrix protocol.

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer's procedure.

value: primary breast tumor

tag: tn status

value: triple-negative


title: DL pool c

description: Gene expression data from skeletal muscle of adult pig breed (DL).

value: German landrace


title: Pi 35 K pool a


title: Tumor 26

value: African-American

value: Negative

tag: survival (months)

tag: survival event


title: CHB6 EAR 3-factor 34+38- biological rep2

value: Embryonic progenitors re-specified with transcription factors


title: primary breast cancer, sample 73


title: Tumor 63

value: IIB

tag: death due to cancer

tag: neoadjuvant therapy


title: Tumor 32

value: Dead

tag: hormone-therapy

tag: chemotherapy


title: Pi 35 K pool b

value: Pietrain

tag: developmental stage

value: 35 dpc

value: skeletal muscle


title: primary breast cancer, sample 14

tag: tissue


title: DL pool a

tag: breed

value: adult


title: DL pool b


title: DL 91 pool c

description: Gene expression data from skeletal muscle of peripubertal pigs breed (DL).

value: 91 dpc


title: Tumor 64

tag: race

value: European-American

tag: tissue type

value: Tumor

value: No

value: I


title: primary breast cancer, sample 99

value: primary breast tumor


title: CHB6 EAR 34+38- biological rep1


title: Tumor 62

tag: age

tag: estrogen receptor status

value: IIIA

value: Alive

value: Yes


title: Tumor 61

value: Positive

tag: triple negative or basal-like subtype

tag: Stage


title: Pi pool c


title: primary breast cancer, sample 70

value: triple-negative


title: Tumor 73

value: Negative

value: IIIB


title: primary breast cancer, sample 31


title: Tumor 60

value: IIA

tag: tumor grade

tag: node status


title: Pi 91 pool b

value: Pietrain


title: DL 91 pool a

value: German landrace

value: skeletal muscle


title: DL 63 pool c

value: 63 dpc


title: Tumor 23

value: African-American

tag: survival (months)


title: Tumor 27

value: Tumor

tag: survival event


title: DL 35 K pool c

value: 35 dpc


title: primary breast cancer, sample 80

tag: tn status


title: DL 91 pool b

value: 91 dpc


title: Tumor 58

value: European-American

value: No

tag: death due to cancer

tag: neoadjuvant therapy


title: primary breast cancer, sample 44

value: primary breast tumor


title: DL 35 K pool b


title: Normal 57

value: Non-tumor


title: DL 35 K pool a


title: primary breast cancer, sample 47


title: Normal 22


title: primary breast cancer, sample 15


title: primary breast cancer, sample 93


title: primary breast cancer, sample 8


title: primary breast cancer, sample 22


title: primary breast cancer, sample 108


title: K14-caSmad1 vs Wild Type Replicate 1

first: Natalia

middle: V.

last: Botchkareva

description: Biological replicate 1 of 2

source_name: Wild Type, Primary Epidermal Keratinocytes

extract_protocol:
K14-caSmad1 transgenic mice is overexpressing a constitutively active form of Smad1 transcription factor
Total RNA was isolated from primary epidermal keratinocytes of wild type and transgenic mice using RNeasy mini kit (Qiagen, UK), and processed for one-round amplification using RiboAmp RNA Amplification Kit (Molecular Devices, USA)

value: Epidermis

value: Day 20 after birth

tag: strain

value: FVB/NJ

source_name: K14-caSmad1, Primary Epidermal Keratinocytes


title: MPI-754_tonsils

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

hyb_protocol: Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter

scan_protocol: After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260)

source_name: tonsils

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation

extract_protocol: Tonsillar tissue samples were used as whole tissue RNA extracts of healthy individuals. RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

tag: type

value: tonsils

tag: tumor


title: K14-caSmad1 vs Wild Type Replicate 2

description: Biological replicate 2 of 2

tag: tissue


title: MPI-752_tonsils


title: MPI-753_tonsils


title: primary breast cancer, sample 120

value: triple-negative