title: Gut HF ZT0 FT 0714F-02_ZT0 HF1 DI


title: N2, control RNAi (dev), replicate 3

status: Public on Jun 04 2016

type: RNA

city: Berkeley

first: Michael

last: Shapira

state: CA

address: 3060 Valley Life Sciences Bldg room 5163

department: Integrative Biology

country: USA

institute: UC Berkeley

description: poly T cDNA

hyb_protocol: Hybridizations were done at 43C overnight (16-  > 20hrs) in formamide-based buffer using the Genisphere Array350 labeling system in   chambers humidified with 4X SSC buffer

scan_protocol: Scanned on a GenePix 4000B scanner, Images quantified using Genepix Pro 6

data_processing: Median intensity values were used, Signal to Noise (background checking) threshold of 2, LOWESS normalized, cross-file cutoff of 0.7 using MIDAS software

molecule: total RNA

organism: Caenorhabditis elegans

source_name: N2 fed control RNAi during development

label_protocol: Samples labeled using the Genisphere Array 350 labeling system

growth_protocol: Animals grown at 25oC

extract_protocol: Total RNA extracted using Trizol (Invitrogen)

treatment_protocol: Animals fed control  or vhp-1 RNAi during development (egg to L4) or adulthood (L4-D2)

tag: strain

tag: age at time of rnai

value: egg

source_name: Mixed stage C.elegans fed E.coli strain OP50


title: brain-gbm-1

city: New Haven

first: Yong

last: Zhu

state: Connecticut

address: 60 College St

institute: Yale School of Public Health

hyb_protocol: After stopping the labeling procedure, the Cy3-labeled samples were hybridized on the Arraystar Human piRNA Array. Hybridization was performed at 65°C for 17 hours in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After being washed in an ozone-free environment, the slides were fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, piRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

organism: Homo sapiens

source_name: Pooled total RNA from seven GBM FFPE brain specimens

label_protocol: Sample labeling was performed using a RNA ligase method. Briefly, One microgram of each sample was 3'-end-labeled with Cy3 fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Cy3), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Formalin-fixed paraffin-embedded (FFPE) GBM (n=7) and normal brain specimens (n=7; n=6 collected at autopsy for non-cancer causes of death, n=1 collected during temporal lobectomy for epilepsy therapy), matched by age, race, and gender, were purchased from the Cooperative Human Tissue Network. Subjects providing tumor specimens had not undergone radio- or chemotherapy at the time of resection. RNA was isolated from sections corresponding to approximately 8-10 mg of tissue from each specimen using the AllPrep DNA/RNA FFPE Kit (QIAGEN).

tag: sample type

value: GBM FFPE brain specime

tag: tissue

value: glioblastoma multiforme (GBM) tissue


title: brain-gbm-2


title: Sc_pretreatDON24ppm_DON24ppm_OD1_rep1

status: Public on Jun 03 2016

city: Tulln

first: Christoph

last: Schüller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology, UFT-Campus Tulln

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

description: Pre-treatment with 24ppm DON. Gene expression after re-incoluation into 24ppm DON, harvested at OD600 of 1, biological replicate 1

hyb_protocol: The labelled Samples were hybridized to the Microarray slides, according to the standard protocol of the manufacturer.

scan_protocol: The slides were scanned with an Agilent Technologies Scanner G2505C, according to the standard protocol (GE1_107_Sep09) using grid 016322_D_F_20120509 as supplied by the manufacturer. Information from probe features was extracted from microarray scan images using the Agilent Feature Extraction software v10.7.3.

data_processing: The raw intensities were imported into Bioconductor and processed with the limma package. Quality Controls were performed using the arrayQualityMetrics package. Data was background corrected using the normexp method of limma, with an offset of 32 to stabilize low intensity variances. Normalization between arrays was performed using the quantile method and duplicate features were averaged together. Manufacturer control features were removed for further analysis.

organism: Saccharomyces cerevisiae

source_name: S.c. strain BY4741 pdr5Δ::NAT

label_protocol: RNA quality was checked on RNA 6000 Nano chips using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Agilent's Low Input Quick Amp Labeling Kit, one-color (Kat. No.: 5190-2305) was used to generate fluorescent cRNA. The amplified cyanine 3-labeled cRNA samples were then purified using Promega's SV Total RNA Isolation System. and hybridized to Agilent Yeast (V2) Gene Expression Microarrays 8x15K. Microarray slides were washed and scanned with an Agilent Scanner, according to the standard protocol of the manufacturer.

growth_protocol: Yeast cells were pre-grown in liquid YPD medium over night. After dilution to OD 0.1 in fresh YPD grown to OD 0.5 were Deoxynivalenol (DON) was added to final concentration of 0, 12ppm or 24 ppm  and were harvested after reaching an OD600 of 1.0 or 1.5. Sustained DON treatment was done over night with a pre-treatment  with 24ppm and re-inoculated at a starting OD600 of 0.1 into liquid YPD  containing 24 ppm  and harvested when the culture reached OD 1.

extract_protocol: Cells were harvested at the reference points and treatment endpoints washed and frozen. Extracts were made with bead beating with the phenol chloroform method. RNA was precipitated with ethanol, and dissolved in RNAse free water.

treatment_protocol: Yeast cells were pre-treated with 0 or 24ppm DON (characteristics: 24ppm DON pre-treatment) and after re-inoculation again treated with 0, 12 or 24ppm DON (characteristics: DON treatment) until an OD of 1.0 or 1.5 was reached (characteristics: OD600).

tag: 24ppm don pre-treatment

value: Yes

tag: don treatment


title: brain-normal-2

source_name: Pooled total RNA from seven normal FFPE brain specimens

value: normal FFPE brain specimens

value: normal brain


title: brain-normal-1


title: Sc_pretreatDON24ppm_DON24ppm_OD1_rep2

description: Pre-treatment with 24ppm DON. Gene expression after re-incoluation into 24ppm DON, harvested at OD600 of 1, biological replicate 2


title: Sc_pretreatDON24ppm_DON24ppm_OD1_rep3

description: Pre-treatment with 24ppm DON. Gene expression after re-incoluation into 24ppm DON, harvested at OD600 of 1, biological replicate 3


title: Sc_DON24ppm_OD1_rep1

description: Gene expression after 24ppm DON treatment, harvested at OD600 of 1, biological replicate 1

value: No


title: Sc_DON24ppm_OD1.5_rep1

description: Gene expression after 24ppm DON treatment, harvested at OD600 of 1.5, biological replicate 1


title: Sc_DON12ppm_OD1.5_rep3

description: Gene expression after 12ppm DON treatment, harvested at OD600 of 1.5, biological replicate 3


title: Sc_DON0ppm_OD1.5_rep2

description: Gene expression after 0ppm DON treatment, harvested at OD600 of 1.5, biological replicate 2


title: Sc_DON0ppm_OD1_rep2

description: Gene expression after 0ppm DON treatment, harvested at OD600 of 1, biological replicate 2


title: Sc_DON12ppm_OD1_rep2

description: Gene expression after 12ppm DON treatment, harvested at OD600 of 1, biological replicate 2


title: N2, control RNAi (dev), replicate 2

description: poly T cDNA


title: N2, control RNAi (dev), replicate 1

description: poly T cDNA


title: Sc_pretreatDON24ppm_DON0ppm_OD1_rep3

description: Pre-treatment with 24ppm DON. Gene expression after re-incoluation into 0ppm DON, harvested at OD600 of 1, biological replicate 3


title: Sc_DON0ppm_OD1_rep1

description: Gene expression after 0ppm DON treatment, harvested at OD600 of 1, biological replicate 1


title: Sc_DON0ppm_OD1.5_rep1

description: Gene expression after 0ppm DON treatment, harvested at OD600 of 1.5, biological replicate 1


title: Sc_pretreatDON24ppm_DON0ppm_OD1_rep2

description: Pre-treatment with 24ppm DON. Gene expression after re-incoluation into 0ppm DON, harvested at OD600 of 1, biological replicate 2


title: Sc_DON12ppm_OD1_rep1

description: Gene expression after 12ppm DON treatment, harvested at OD600 of 1, biological replicate 1


title: Sc_DON24ppm_OD1_rep2

description: Gene expression after 24ppm DON treatment, harvested at OD600 of 1, biological replicate 2


title: Sc_pretreatDON24ppm_DON0ppm_OD1_rep1

description: Pre-treatment with 24ppm DON. Gene expression after re-incoluation into 0ppm DON, harvested at OD600 of 1, biological replicate 1


title: Sc_DON12ppm_OD1_rep3

description: Gene expression after 12ppm DON treatment, harvested at OD600 of 1, biological replicate 3


title: Sc_DON24ppm_OD1.5_rep3

description: Gene expression after 24ppm DON treatment, harvested at OD600 of 1.5, biological replicate 3


title: Sc_DON12ppm_OD1.5_rep1

description: Gene expression after 12ppm DON treatment, harvested at OD600 of 1.5, biological replicate 1


title: Sc_DON12ppm_OD1.5_rep2

description: Gene expression after 12ppm DON treatment, harvested at OD600 of 1.5, biological replicate 2


title: Sc_DON24ppm_OD1.5_rep2

description: Gene expression after 24ppm DON treatment, harvested at OD600 of 1.5, biological replicate 2


title: Mammarygl_I3CBPA250_rep4

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

description: Gene expression array of mammary gland in post-natal day 21

hyb_protocol: 1.65 ug of labeled cRNA was hybridized to microarray slides (Whole rat genome-4X44K oligo microarrays-G4112F, Agilent Technologies) at 65°C for 17 hours. Slides were then washed and scanned following Agilent’s recommendations.

scan_protocol: The hybridization signals were captured using the GenePix 4000B scanner (Molecular Devices, LLC, Sunnyvale, CA USA).

data_processing:
The scanned images were analyzed with Feature Extraction Software v9.5.3.1 using the default protocol to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Intensity values represent: after normexp background correction, quantile normalization and filtering of probes without EntrezID and intensity signal close to the background signal

organism: Rattus norvegicus

source_name: Mammary gland, BPA250+indole-treated, replicate 4

label_protocol: 150 ng of total RNA were hybridized onto whole rat genome 4x44K oligo microarrays (G4131F, Agilent Technologies) using one color (Cy3) Low input Quick Amp labeling kit (Agilent Technologies, Inc. Life Sciences and Chemical Analysis Group, Santa Clara, CA, USA), according to manufacturer instructions. Briefly, total RNA plus spike-in controls were reverse transcribed into double stranded cDNA. The primers used for this reaction contained consecutive thymine bases attached to a T7 promoter that paired at the 5’ end of the first strand of cDNAs. Next, the T7 polymerase was added along with nucleotides labeled with fluorescent cyanine-3 (Cy3) dye, which amplified the anti-sense complementary RNAs (cRNA).

extract_protocol: Total RNA was extracted from the abdominal left mammary gland using the miRNeasy kit (QIAGEN Inc. USA Valencia, CA - USA) according to the manufacturer’s instructions. The extracted RNA was stored at -80°C. RNA was quantified in a spectrophotometer NanoVue (GE Healthcare UK Limited, UK) and the integrity was evaluated using the equipment Agilent 2100 Bioanalyzer (Agilent Technologies, Inc. Life Sciences and Chemical Analysis Group, Santa Clara, CA, USA) under standard conditions.

value: Sprague-Dawley

tag: treatment (pregnant rat)

tag: gender (offspring)

value: Female

tag: tissue (offspring)

value: Mammary gland

tag: age (offspring)

value: post-natal day 21


title: Sc_DON24ppm_OD1_rep3

description: Gene expression after 24ppm DON treatment, harvested at OD600 of 1, biological replicate 3


title: Mammarygl_I3CBPA250_rep5

source_name: Mammary gland, BPA250+indole-treated, replicate 5


title: Mammarygl_I3CBPA250_rep3

source_name: Mammary gland, BPA250+indole-treated, replicate 3


title: Mammarygl_I3CBPA25_rep4

source_name: Mammary gland, BPA25+indole-treated, replicate 4


title: Mammarygl_I3CBPA250_rep2

source_name: Mammary gland, BPA250+indole-treated, replicate 2


title: HaCaT_miR-21-3p-mimic_3

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

hyb_protocol: Affymetrix mouse gene 1.0ST arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 2.3μg of fragmented target, at 45°C for 16 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: RMA algorithm was applied to data, using Affymetrix Expression Console software.

label: biotin

source_name: keratinocytes HaCaT, miR-21-3p mimic transfection

label_protocol: For each sample, 100ng of total RNA were amplified using the Ambion® WT Expression Kit (4411973, life technologies) kit. 5.5μg of the cDNA was fragmented and labeled with GeneChip® WT Terminal Labeling kit (901525, Affymetrix).

growth_protocol: Human immortalized keratinocytes HaCaT (Cell Line Service; Germany) cells were maintained in DMEM growth medium (Gibco) supplemented with 4500 mg/l glucose, 10% fetal bovine serum, 100 units/ml of penicillin G and 100 μg/ml of streptomycin. Cells were grown in a 5% CO2 atmosphere at 37 °C.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen).

treatment_protocol: miR-21-3p mimic (Miridian, Thermo Scientific Dharmacon) or cel-miR-67-3p used as a control (Miridian, Thermo Scientific Dharmacon) were transfected to the cells at a concentration of 50 nM using the Lipofectamine RNAi max (Invitrogen). Cells were harvested 24h after transfection for gene expression analysis.

tag: cell line

value: HaCaT

tag: transfection


title: Mammarygl_I3CBPA250_rep1

source_name: Mammary gland, BPA250+indole-treated, replicate 1


title: Sc_DON0ppm_OD1_rep3

description: Gene expression after 0ppm DON treatment, harvested at OD600 of 1, biological replicate 3


title: HaCaT_ctl_3

source_name: keratinocytes HaCaT, control transfection

value: control


title: HaCaT_miR-21-3p-mimic_2


title: HaCaT_ctl_2


title: HaCaT_ctl_1


title: Mammarygl_GenBPA250_rep5

source_name: Mammary gland, BPA250+genistein-treated, replicate 5


title: Mammarygl_I3CBPA25_rep5

source_name: Mammary gland, BPA25+indole-treated, replicate 5


title: Mammarygl_GenBPA250_rep4

source_name: Mammary gland, BPA250+genistein-treated, replicate 4


title: HaCaT_miR-21-3p-mimic_1


title: skin_12weeks_WT_3_mRNA

data_processing: Background subtraction, quantile normalization and probeset summarization were performed with the Affymetrix Power Tools command line tool, using the RMA method.

organism: Mus musculus

source_name: dorsal skin, 12 weeks UV irradiated, WT(Ppard+/+)

label_protocol: For each sample, 100ng of total RNA were amplified using the Affymetrix Whole-Transcript (WT) Sense Taget Labeling protocol. 5.5μg of the cDNA was fragmented and labeled with GeneChip® WT Terminal Labeling kit (901525, Affymetrix).

growth_protocol: Mice in standard colony, with water and food ad libitum

extract_protocol: Total RNA containing the small RNA fraction was isolated using TRIzol reagent (Invitrogen).

treatment_protocol: Irradiated mice: 70mJ/cm2 of UVB three times a week

tag: background strain

value: skin

tag: uv irradiation

tag: genotype

value: WT(Ppard+/+)


title: skin_12weeks_WT_4_mRNA


title: skin_12weeks_KO_4_mRNA

source_name: dorsal skin, 12 weeks UV irradiated, KO(Ppard-/-)

value: KO(Ppard-/-)


title: skin_12weeks_WT_1_mRNA


title: Mammarygl_I3CBPA25_rep2

source_name: Mammary gland, BPA25+indole-treated, replicate 2


title: Mammarygl_I3CBPA25_rep3

source_name: Mammary gland, BPA25+indole-treated, replicate 3


title: Mammarygl_I3CBPA25_rep1

source_name: Mammary gland, BPA25+indole-treated, replicate 1


title: skin_12weeks_KO_2_mRNA


title: skin_12weeks_KO_3_mRNA


title: skin_12weeks_KO_1_mRNA


title: skin_12weeks_WT_2_mRNA


title: Mammarygl_GenBPA250_rep3

source_name: Mammary gland, BPA250+genistein-treated, replicate 3


title: skin_noUv_WT_1_mRNA

source_name: dorsal skin, not irradiated, WT(Ppard+/+)


title: skin_noUv_KO_4_mRNA

source_name: dorsal skin, not irradiated, KO(Ppard-/-)


title: Mammarygl_GenBPA25_rep5

source_name: Mammary gland, BPA25+genistein-treated, replicate 5


title: Mammarygl_GenBPA25_rep2

source_name: Mammary gland, BPA25+genistein-treated, replicate 2


title: Mammarygl_GenBPA25_rep4

source_name: Mammary gland, BPA25+genistein-treated, replicate 4


title: skin_noUv_KO_3_mRNA


title: Mammarygl_GenBPA25_rep1

source_name: Mammary gland, BPA25+genistein-treated, replicate 1


title: skin_noUv_KO_2_mRNA


title: Mammarygl_BPA250_rep4

source_name: Mammary gland, BPA250-treated, replicate 4


title: skin_noUv_WT_4_mRNA


title: Mammarygl_BPA250_rep5

source_name: Mammary gland, BPA250-treated, replicate 5


title: skin_noUv_WT_2_mRNA


title: skin_noUv_KO_1_mRNA


title: Mammarygl_GenBPA250_rep1

source_name: Mammary gland, BPA250+genistein-treated, replicate 1


title: Mammarygl_BPA250_rep3

source_name: Mammary gland, BPA250-treated, replicate 3


title: Mammarygl_BPA25_rep5

source_name: Mammary gland, BPA25-treated, replicate 5


title: Mammarygl_BPA250_rep2

source_name: Mammary gland, BPA250-treated, replicate 2


title: Mammarygl_GenBPA250_rep2

source_name: Mammary gland, BPA250+genistein-treated, replicate 2


title: skin_noUv_WT_3_mRNA


title: skin_noUv_KO_4_miRNA

hyb_protocol: The labeled RNA was hybridized to Agilent mouse miRNA microarrays for 20 hours at 55°C with rotation.

scan_protocol: The arrays were scanned with an Agilent Technologies Scanner G2505B with high dynamic range settings as specified by the manufacturer.

data_processing: Agilent Feature Extraction Software (version 9.5.3.1) was used to extract the data and quantile normalization was applied to the Total Gene Signal intensity values

label_protocol: Each sample was prepared according to the Agilent’s miRNA Microarray System protocol. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH, Otelfingen, Switzerland), denatured with dimethyl sulfoxide and labeled with pCp-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH, Otelfingen, Switzerland).


title: skin_noUv_WT_4_miRNA


title: skin_noUv_WT_3_miRNA


title: skin_noUv_WT_2_miRNA


title: skin_12weeks_KO_4_miRNA

source_name: dorsal skin, 12 weeks UV irradiated, KO(Ppard-/-)


title: skin_noUv_KO_2_miRNA


title: skin_noUv_KO_3_miRNA


title: Mammarygl_BPA25_rep1

source_name: Mammary gland, BPA25-treated, replicate 1


title: skin_noUv_KO_1_miRNA


title: Mammarygl_BPA25_rep3

source_name: Mammary gland, BPA25-treated, replicate 3


title: skin_12weeks_KO_3_miRNA


title: RWPE1_ODC3

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description: ODC1 overexpression

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomStudio and futher filtered in R

source_name: Prostate epithelial cells

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

growth_protocol: Cells were grown in DMEM medium with 20% FBS, 1% NEAA and 1% Pen/Strep

extract_protocol: Total RNA was extracted using the QIAGEN RNAeasy Mini kit (Valencia, CA USA). RNA quality was assessed using Bioanalyzer 2100 (Agilent Technologies)

tag: genotype/variation

value: ODC1 overexpression


title: Mammarygl_negcontrol_rep3

source_name: Mammary gland, negative control, replicate 3

value: negative control


title: RWPE1_ODC2

description: ODC1 overexpression


title: Mammarygl_negcontrol_rep4

source_name: Mammary gland, negative control, replicate 4


title: skin_noUv_WT_1_miRNA

source_name: dorsal skin, not irradiated, WT(Ppard+/+)


title: RWPE1_P2

description: control


title: RWPE1_ODC1

description: ODC1 overexpression


title: Mammarygl_BPA25_rep2

source_name: Mammary gland, BPA25-treated, replicate 2


title: Mammarygl_BPA250_rep1

source_name: Mammary gland, BPA250-treated, replicate 1


title: RWPE1_P3

description: control


title: Mammarygl_negcontrol_rep2

source_name: Mammary gland, negative control, replicate 2


title: RWPE1_P1

description: control


title: Mammarygl_negcontrol_rep1

source_name: Mammary gland, negative control, replicate 1


title: skin_12weeks_KO_2_miRNA


title: Mammarygl_BPA25_rep4

source_name: Mammary gland, BPA25-treated, replicate 4


title: skin_12weeks_KO_1_miRNA


title: skin_12weeks_WT_4_miRNA

source_name: dorsal skin, 12 weeks UV irradiated, WT(Ppard+/+)


title: skin_12weeks_WT_2_miRNA


title: skin_12weeks_WT_3_miRNA


title: skin_12weeks_WT_1_miRNA


title: Mammarygl_negcontrol_rep5

source_name: Mammary gland, negative control, replicate 5


title: cKO-Ctcf testes, mouse 4

city: Stockholm

first: Abrahan

last: Hernández-Hernández

address: Berzeliuz väg 35

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Affymetrix WT Array Hybridization Protocol was used for preparation of hybridization cocktail and hybridization of final Targets

scan_protocol: Scanning of arrays were done in Affymetrix Gene Chip scanner 7G

data_processing:
Raw data was pre-processed in Affymetrix Expression Console (v. 1.4.1) using RMA. Gene level differential expression was analyzed with the Transcriptome Analysis Console 3.0 (Affimetrix).
MTA-1_0.Probeset Annotations
MTA-1_0.na35.mm10.transcript.cvs
RMA signal estimates from Expression Console Software 1.4.1 (#%affymetrix-algorithm-param-apt-opt-analysis-name=rma-gene-full). Gene Level Differential Expression Analysis from Transcriptome Analysis Console, Algorithm Options: One-way between-Subject ANOVA (unpaired). Fold change (linear) < -2 or fold change (linera) > 2. ANOVA p-value (condition pair) < 0.05

source_name: cKO-Ctcf testes

label_protocol: 150ng total RNA was used as input. 5.2 ug of fragmentedand  labelled ss-cDNA was hybridized to each  MTA 1.0 array.  Affymetrix WT Plus Labeling protocol was used

extract_protocol: RNA was extracted and purified with the RNeasy kit (QIAGEN)

treatment_protocol: Tunica albuginea of wild-type and Ctcf-cKO testes was removed and seminiferous tubules were transported to the lab bench in RNA stabilization reagent RNAlater (QIAGEN)

value: cKO-Ctcf

value: Testes

tag: tissue region

value: seminiferous tubules


title: cKO-Ctcf testes, mouse 3


title: 439551_A04_CRT_1_2010-10-05_532

city: Edmonton

first: Marek

last: Michalak

state: Alberta

address: 87 Avenue

department: Biochemistry

country: Canada

institute: University of Alberta

description: This sample is of calreticulin transgenic mouse C57BL/6. It is the first of three calreticulin transgenic biological replicates used in this experiment

hyb_protocol: Hybridization to mouse MM9 Expression Array (12 x 135K, NimbleGen) was carried out at 42oC for 20 h in an HX12 Mixer (Roche), to acquire uniform signal and high sensitivity with minimal sample volume across the array surface

scan_protocol: Arrays were scanned using NimbleGen MS 200 software, and the data were extracted using NimbleScan software

data_processing: Array normalization was performed using the quantile normalization method of Bolstad et al (Bolstad, Irizarry et al., 2003). n-fold change ratios for a particular gene in calreticulin transgenic and control heart were calculated using the RMA-processed expression values (RMA calls)

source_name: Mouse C57BL/6 calreticulin transgenic

label_protocol: Purified cDNA was mixed with Cy3 primer and dNTP/Klenow fragment (50 U/ul) (NimbleGen one color labelling kit), and incubated for 2 h at 37oC with a heated lid

growth_protocol: Wild type and transgenic mice were grown in standard animal facility with 12 hour light/dark cycle, and 8-10 weeks-old-male-mice were used in this study

extract_protocol: Total RNA was isolated from wild type and transgenic heart homogenates using TRIzol reagent (Invitrogen), and a double strand cDNA library was constructed from 300 ng of purified RNA using a library synthesis kit (Sigma)

treatment_protocol: Oral administration of tamoxifen to wild type and calreticulin transgenic mice to 8-10 weeks-old-mice for 3 weeks was conducted to induce calreticulin expresssion in the heart

value: calreticulin transgenic

tag: disease state

value: Dilated cardiomyopathy

tag: gender

value: male

tag: age

value: 8-10 weeks


title: 439551_A06_CRT_3_2010-10-05_532

description: This sample is of calreticulin transgenic mouse C57BL/6. It is the third of three calreticulin transgenic biological replicates used in this experiment


title: wild-type testes, mouse 2

source_name: wild-type testes

value: wild-type

tag: tissue


title: cKO-Ctcf testes, mouse 2


title: cKO-Ctcf testes, mouse 1


title: 439551_A02_Sham_2_2010-10-05_532

description: This sample is of wild-type mouse C57BL/6. It is the second of three wild-type biological replicates used in this experiment

source_name: Mouse C57BL/6 wild type

value: wildtype

value: Normal


title: wild-type testes, mouse 1


title: 439551_A03_Sham_3_2010-10-05_532

description: This sample is of wild-type mouse C57BL/6. It is the third of three wild-type biological replicates used in this experiment


title: wild-type testes, mouse 3


title: 439551_A01_Sham_1_2010-10-05_532

description: This sample is of wild-type mouse C57BL/6. It is the first of three wild-type biological replicates used in this experiment


title: DF(KA)-derived iPSC, clone #11

city: Sinjuku-ku, Tokyo

first: Koki

last: Fujimori

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 °C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were 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 500. Normalized data matrices available on the series record contain MAS 5.0 signal. Normalizations were performed on sample subsets.

source_name: DF(KA)-derived iPSC

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

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

tag: donor id

value: KA

tag: cell type

value: induced pluripotent stem cells (iPSC)

tag: iPSc source

value: Dermal fibroblast (DF)

tag: reprogramming method

value: retrovirus


title: Dermal fibroblast from donor, KA

description: DF(KA)

source_name: Dermal fibroblast from donor


title: DF(KA)-derived iPSC, clone #3

value: episomal vectors


title: 439551_A05_CRT_2_2010-10-05_532

description: This sample is of calreticulin transgenic mouse C57BL/6. It is the second of three calreticulin transgenic biological replicates used in this experiment


title: T-cell(KA)-derived iPSC, clone #4

source_name: T-cell(KA)-derived iPSC

value: T-cell

value: sendai virus


title: T-cell(KA)-derived iPSC, clone #9


title: SLEpatient with lupus nephritis-15 [SLE+LN15]

type: genomic

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: replicate 15

data_processing: Expression values were extracted, filtered and normalized using  an R package (RnBeads). The normalized methylation data were analyzed by SAM (significance analysis of microarrays, Stanford University)

molecule: genomic DNA

source_name: peripheral blood mononuclear cell

label_protocol: Genomic DNA (1μg) was bisulfite converted using EZ DNA Methylation kit (Zymo Research Corp, Orange, CA. Cat. No. D5004), and utilizing a cyclic denaturation step during the conversion reaction. 4ul of bisulfite-converted DNA were used for hybridization on Infinium HumanMethylation 450 BeadChip.

extract_protocol: Genomic DNA was isolation from whole blood cells using genomic DNA extraction kits (Life Technologies, Gaithersburg, MD).

value: blood

tag: Sex

value: Female


title: SLEpatient with lupus nephritis-13 [SLE+LN13]

description: replicate 13


title: SLEpatient with lupus nephritis-14 [SLE+LN14]

description: replicate 14


title: Mammarygl_GenBPA25_rep3

source_name: Mammary gland, BPA25+genistein-treated, replicate 3

tag: strain

value: Sprague-Dawley

tag: treatment (pregnant rat)

tag: gender (offspring)

tag: tissue (offspring)

value: Mammary gland

tag: age (offspring)

value: post-natal day 21


title: SLEpatient with lupus nephritis-10 [SLE+LN10]

description: replicate 10


title: SLEpatient with lupus nephritis-11 [SLE+LN11]

description: replicate 11

value: Male


title: SLEpatient with lupus nephritis-08 [SLE+LN08]

description: replicate 8


title: SLEpatient with lupus nephritis-09 [SLE+LN09]

description: replicate 9


title: LCL(KA)-derived iPSC, clone #36

source_name: LCL(KA)-derived iPSC

value: lymphoblastoid cell line (LCL)


title: LCL(KA)-derived iPSC, clone #29


title: LCL(PB)-derived iPSC, clone #1

source_name: LCL(PB)-derived iPSC

value: PB


title: LCL(PB)-derived iPSC, clone #7


title: HB-236 PDX

city: Badalona

first: Carolina

last: Armengol

state: Barcelona

address: C/ Canyet, Camí de les Escoles, s/n

country: Spain

institute: Health Siences Research Institute Germans Trias i Pujol

hyb_protocol: Sample was hybridized to Affymetrix® Genome-Wide Human SNP Array 6.0 using a GeneChip Hybridization Oven 640 and posteriorly washed and stained using the Fluidics Station 450

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing:
CEL files, generated by AGCC Viewer. CYCHP, generated by Chromosome Analysis Suite (all provided by Affymetrix)
Raw data and normalized data with netaffx version na 33.1.  CYCHP provide data for copy number and LOH analysis.
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.16.0
program-name = apt-copynumber-cyto.exe
program-version = 1.16.0
program-company = Affymetrix

label: Biotin

source_name: HB-236 PDX

label_protocol: 500ng starting genomic DNA were processed using the Affymetrix® Cytogenetics Copy Number Assay User Guide (P/N 702607 Rev. 2)

extract_protocol: MagMax DNA Multi-Sample kit (Thermo Fisher Scientific)

tag: patient/sample source id

tag: sample type

value: PLC-PDXs (Pediatric Liver Cancer-Patient Derived Xenografts)

tag: host strain

value: Athymic Nude-Foxn1nu (ENVIGO-Harlan Laboratories, Gannat, France)


title: HB-252 patient

source_name: HB-252 patient

value: Primary Tumor

value: F

tag: age (months)

tag: pretext stage


title: T-cell from donor, KA

description: T-cell(KA)

source_name: T-cell from donor

value: KA


title: HB-239 PDX

source_name: HB-239 PDX


title: HB-244-RED-239 patient

source_name: HB-244-RED-239 patient

value: Recurrence Tumor


title: HB-252 PDX

source_name: HB-252 PDX


title: SLEpatient with lupus nephritis-07 [SLE+LN07]

description: replicate 7

tag: age


title: SLEpatient with lupus nephritis-12 [SLE+LN12]

description: replicate 12

tag: tissue


title: Lymphoblastoid B-cell line from donor, KA

description: LCL(KA)

source_name: Lymphoblastoid B-cell line from donor

tag: donor id


title: Lymphoblastoid B-cell line from donor, PB

description: LCL(PB)

tag: cell type


title: HB-239 patient

source_name: HB-239 patient

tag: gender

value: M


title: HB-233 PDX

source_name: HB-233 PDX


title: patient 44

city: Nottingham

first: Hernan

middle: Pablo

last: Fainberg

address: Derby Rd

department: Division of Child Health, Obstetrics & Gynaecology

country: United Kingdom

institute: The University of Nottingham

description: Gene expression data from EAT age group 2 to 7 years old

hyb_protocol: 10 μg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Detection used a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The raw image files (.DAT files) were analyzed using Affymetrix GeneChip Operating Software to generate .CEL files.Normalization and network analysis was performed, unless otherwise stated, using free and open source packages, from the R project (http://cran.r-project.org/). The open source Bioconductor community (http://www.bioconductor.org/), provides specific resources for microarray analysis including the Human Genome U133A plus 2 arrays (Affymetrix). We used the function “gcrma” embedded in the “affy” package for pre-processing data stages, including background correction, normalization and probe match verification.

label: Biotin labeling

source_name: EAT Child

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

growth_protocol: A sample of EAT (approximately 5 grams) will be collected during the dissection of the epicardium as a part of the standard process undertaken during cardiac surgery.

extract_protocol: 100-1000 mg of EAT biopsies were dissected for analysis into 2ml of TRI® reagent (Sigma Chemical Co. Poole, UK). Total RNA was extracted using RNeasy Plus® kit (Qiagen, West Sussex, UK) according to the manufacturer’s instructions.

treatment_protocol: No extra procedure will be done in order to obtain the sample and the time of surgery will not be prolonged due to sample collection. Half of this tissue will be placed in a collection tube containing 20mls of RNAlater® (Applied Biosystems, Warrington, U.K.)

value: epicardial adipose tissue

tag: developmental stage

value: child


title: HB-236 patient

source_name: HB-236 patient


title: patient 46


title: patient 43


title: SLEpatient with lupus nephritis-04 [SLE+LN04]

description: replicate 4

value: blood

tag: Sex


title: HB-244-RED-239 PDX


title: TT-001 patient

source_name: TT-001 patient


title: SLEpatient with lupus nephritis-03 [SLE+LN03]

description: replicate 3

value: Female


title: patient 42


title: SLEpatient with lupus nephritis-06 [SLE+LN06]

description: replicate 6


title: TT-001 PDX

source_name: TT-001 PDX


title: patient 41


title: patient 40


title: patient 39

description: Gene expression data from EAT age group 6 to 24 days old

source_name: EAT  Neonatal

value: neonatal


title: HB-233 patient

source_name: HB-233 patient


title: patient 38


title: patient 45


title: patient 37


title: SLEpatient with lupus nephritis-02 [SLE+LN02]

description: replicate 2

source_name: peripheral blood mononuclear cell


title: SLEpatient with lupus nephritis-01 [SLE+LN01]

description: replicate 1


title: HB-238-RED-231 PDX


title: patient 35


title: patient 34


title: patient 32


title: HB-232 patient

source_name: HB-232 patient


title: patient 33


title: SLE patient-15 [SLE15]

description: replicate 15


title: SLE patient-11 [SLE11]

description: replicate 11


title: SLE patient-12 [SLE12]

description: replicate 12


title: SLE patient-07 [SLE07]

description: replicate 7


title: patient 31


title: SLE patient-13 [SLE13]

description: replicate 13


title: patient 30


title: patient 29


title: patient 28

description: Gene expression data from EAT age group 40 days to 1 year old

source_name: EAT  infant

value: infant


title: SLE patient-06 [SLE06]

description: replicate 6


title: SLE patient-09 [SLE09]

description: replicate 9


title: SLE patient-02 [SLE02]

description: replicate 2


title: patient 25


title: SLE patient-08 [SLE08]

description: replicate 8


title: SLE patient-05 [SLE05]

description: replicate 5


title: SLE patient-04 [SLE04]

description: replicate 4


title: patient 26


title: SLEpatient with lupus nephritis-05 [SLE+LN05]

description: replicate 5


title: patient 27


title: patient 24


title: patient 36


title: patient 23


title: SLE patient-03 [SLE03]

description: replicate 3


title: HB-232 PDX

source_name: HB-232 PDX


title: patient 22


title: patient 21


title: SLE patient-10 [SLE10]

description: replicate 10


title: patient 20


title: patient 18


title: normal control-24 [NC24]

description: replicate 24


title: patient 17


title: SLE patient-01 [SLE01]

description: replicate 1


title: HB-213 PDX

source_name: HB-213 PDX


title: normal control-22 [NC22]

description: replicate 22


title: patient 19


title: normal control-20 [NC20]

description: replicate 20


title: normal control-25 [NC25]

description: replicate 25


title: HB-229 patient

source_name: HB-229 patient


title: patient 15


title: patient 14


title: patient 16


title: normal control-19 [NC19]

description: replicate 19


title: patient 13


title: patient 12


title: normal control-23 [NC23]

description: replicate 23


title: SLE patient-14 [SLE14]

description: replicate 14


title: patient 11


title: normal control-16 [NC16]

description: replicate 16


title: normal control-18 [NC18]

description: replicate 18


title: normal control-21 [NC21]

description: replicate 21


title: patient 10


title: patient 9


title: normal control-15 [NC15]

description: replicate 15


title: patient 7


title: patient 6


title: patient 4


title: patient 5


title: normal control-14 [NC14]

description: replicate 14


title: patient 2


title: patient 3


title: patient 1


title: normal control-13 [NC13]

description: replicate 13


title: normal control-07 [NC07]

description: replicate 7


title: HB-213 patient

source_name: HB-213 patient


title: normal control-10 [NC10]

description: replicate 10


title: normal control-12 [NC12]

description: replicate 12


title: normal control-11 [NC11]

description: replicate 11


title: normal control-09 [NC09]

description: replicate 9


title: normal control-08 [NC08]

description: replicate 8


title: Differentially expressed genes by knocking down of TPD52-1 in EBC-1

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell line

value: lung squamous cell carcinoma

tag: transfection

value: no transfection

source_name: si-TPD52-1 transfected cell line


title: Differentially expressed genes by knocking down of MMP13 in TE-9

value: esophageal cancer

source_name: si-MMP13 transfected cell line


title: Differentially expressed genes by knocking down of TPD52-2 in EBC-1

source_name: si-TPD52-2 transfected cell line


title: Differentially expressed genes by knocking down of ZFP36L2-3 in PANC-1

value: pancreatic cancer

source_name: si-ZFP36L2-3 transfected cell line


title: normal control-06 [NC06]

description: replicate 6


title: normal control-01 [NC01]

description: replicate 1


title: Identification of miR-216b-3p target genes in PANC-1

source_name: miR-216b-3p transfected cell line


title: Differentially expressed genes by knocking down of ZFP36L2-2 in PANC-1

source_name: si-ZFP36L2-2 transfected cell line


title: Identification of miR-150-3p target genes in EBC-1

source_name: miR-150-3p transfected cell line


title: Differentially expressed genes by knocking down of MTDH-3 in EBC-1

source_name: si-MTDH-3 transfected cell line


title: normal control-02 [NC02]

description: replicate 2


title: normal control-03 [NC03]

description: replicate 3


title: Identification of miR-216b-3p target genes in SW1990


title: Identification of miR-150-5p target genes in EBC-1

source_name: miR-150-5p transfected cell line


title: Differentially expressed genes by knocking down of MTDH-1 in EBC-1

source_name: si-MTDH-1 transfected cell line


title: normal control-04 [NC04]

description: replicate 4

source_name: peripheral blood mononuclear cell

value: Male


title: normal control-05 [NC05]

description: replicate 5


title: FNAR-C1, Aldefluor High replicate 3

status: Public on Jun 02 2016

city: Baltimore

first: Richard

middle: J

last: Jones

state: MD

address: 1650 Orleans St.

institute: Johns Hopkins University School of Medicine

hyb_protocol: 0.825 μg of each Cy3-labeled sample was used for hybridization according to manufacturers protocol.

scan_protocol: Microarrays were scanned using an Agilent G2565AA Scanner with Agilent Scan Control 7.0 software.

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

source_name: FNAR-C1, Aldefluor High

label_protocol: Samples were amplified and labeled using the Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Aldefluor low cells were cultured in standard medium containing 10% FBS.  Aldefluor high samples were cultured in KnockOut medium.

extract_protocol: Cells were stained with Aldefluor, then sorted by flow cytometry into RNAprotect.  Total RNA was isolated with the RNeasy Mini Kit with QIAshredder columns.

tag: aldefluor level

value: High


title: Identification of miR-145-3p target genes in SAS

value: SAS

value: tongue squamous cell carcinoma

source_name: miR-145-3p transfected cell line


title: FNAR-C1, Aldefluor High replicate 1


title: FNAR-C1, Aldefluor Low, replicate 2

source_name: FNAR-C1, Aldefluor Low

value: Low


title: FNAR-C1, Aldefluor Low, replicate 1


title: Differentially expressed genes by knocking down of MMP13 in TE-8


title: Identification of miR-145-5p target genes in SAS

source_name: miR-145-5p transfected cell line


title: H207VNp21_rep2

first: Sara

last: Pijuan-Galitó

address: University Park

department: STEM Centre for Biolomolecular Sciences

institute: University of Nottingham

description:
AC2_H207VNp21.1_11R07C01
9721420037; R07C01
data files: NF-0569_160523_PCF_Matrix*txt

hyb_protocol: Hybridization was performed according to the manufacturers (Illumina) protocol: Infinium® HD Assay Super, Automated Protocol, (Inf_HD_Super_Assay_Auto_EUC_11322291_RevC.pdf)

scan_protocol: After allele-specific staining the BeadChips were coated with XC4/ethanol , dried for 1 hour and scanned on the iScan BeadChip reader (Illumina Inc).

data_processing:
Genomic DNA was genotyped using the Infinium assay and the HumanOmniExpressExome-8v1-2_A genotyping BeadChips from Illumina Inc. The signal intensities from scanning  were analyzed and converted to genotypes using the software GenomeStudio 2011.1 from Illumina Inc.
Genotype: AA,AB,BB,or NC (no call)

label: cy3 and cy5

source_name: hPS_16-21 passages_Vitronectin (VN)

label_protocol: Labeling was performed according to the manufacturers (Illumina) protocol: Infinium® HD Assay Super, Automated Protocol, (Inf_HD_Super_Assay_Auto_EUC_11322291_RevC.pdf)

growth_protocol: Four different human pluripotent stem cells from different labs were adapted to E8 medium and Vitronectin-peptide coating (VN) all from Stem Cell Technologies, and following manufacturer's instructions. After 2-5 passages in this commercial protocol, samples were taken for DNA extraction as initial samples (comparizon for late-passage samples).

extract_protocol: Total DNA extraction was performed using the DNA Blood and Tissue Kit (Cat. No. 69504, Qiagen) following manufacturer's instructions.

treatment_protocol: Then the four cell lines were grown for 15-20 passages in E8 medium with VN coating (positive control) and ITI supplementation (query) and the DNA was harvested again.

value: Human embryonic stem cell

tag: passage

value: 16-21 passages

tag: culture method

value: Vitronectin (VN)


title: FNAR-C1, Aldefluor Low, replicate 3


title: Identification of miR-150-5p target genes in FaDu

source_name: mock

value: FaDu

value: hypopharyngeal squamous cell carcinoma


title: K02CITIP17

description:
AC2_K02CITIP17.1_1R03C01
9721846015; R03C01
data files: NF-0569_160523_PCF_Matrix*txt

source_name: hPS_16-21 passages_Inter-alpha inhibitor (ITI)

value: Human induced pluripotent stem cell

value: Inter-alpha inhibitor (ITI)


title: MA9;2abc;CreER_96hr_OHT_rep2

city: Copenhagen

first: Karl

last: Agger

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: Agilent design Id : 028005

hyb_protocol: Samples were hybridized to Agilent SurePrint G3 Mouse GE 8x60K arrays (Agilent G4852A) using Gene Expression Hybridization kit (Agilent #5188-5242) according to manufacturer’s instructions.

scan_protocol: Arrays were scanned according to manufacturers instructions.

data_processing: The raw data was processed in R using the 'limma' package. Raw data was imported using function 'read.maimages' (source=agilent,green.only=TRUE), background corrected using 'backgroundCorrect' (method=normexp,offset=50) and normalized using 'normalizeBetweenArrays' (method=quantile).

label_protocol: Samples were labeled according to manufacturer’s instructions using LowInput QuickAmp Labeling Kit One Color (Agilent #5190-2305) and One-Color RNA Spike-In kit (Agilent #5188-5282).

growth_protocol: Cells were grown in RPMI containing 20% FBS and 10ng/ml IL-3

extract_protocol: RNA was purified using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: To induce knockout cells were grown in the presence of 500nM OHT 4-hydroxytamoxifen.

value: L-GMP transformed with MLL-AF9

tag: genotype

tag: strain background


title: MA9;2abc;CreER_96hr_OHT_rep3

description: Agilent design Id : 028005


title: H207VNp21_rep1

description:
AC2_H207VNp21.1_2R06C01
9684394039; R06C01
data files: NF-0569_160523_PCF_Matrix*txt


title: H207ITIP21

description:
AC2_H207ITIP21.1_2R07C01
9684394039; R07C01
data files: NF-0569_160523_PCF_Matrix*txt


title: HUES1VNP20

description:
AC2_HUES1VNP20
9684394039; R08C01
data files: NF-0569_160523_PCF_Matrix*txt

value: Female


title: H181VNP20

description:
AC2_H181VNP20.1_2R04C01
9684394039; R04C01
data files: NF-0569_160523_PCF_Matrix*txt


title: H181ITIP16

description:
AC2_H181ITIP16.1_2R05C01
9684394039; R05C01
data files: NF-0569_160523_PCF_Matrix*txt


title: HUES1ITIP18

description:
AC2_HUES1ITIP18.1_1R01C01
9721846015; R01C01
data files: NF-0569_160523_PCF_Matrix*txt


title: normal control-17 [NC17]

description: replicate 17

value: blood


title: MA9;2abc;CreER_48hr_OHT_rep1

description: Agilent design Id : 028005


title: K02CVNP19

description:
AC2_K02CVNP19.1_1R02C01
9721846015; R02C01
data files: NF-0569_160523_PCF_Matrix*txt


title: K02Cp17 E8VNp2

description:
AC1_K02Cp17E8VNp2.1_2R08C01
9721420029; R08C01
data files: NC-0513_160520_PCF_Matrix*txt

source_name: hPS_2-5 passages_Vitronectin (VN)

value: 2-5 passages


title: MA9;2abc;CreER_48hr_OHT_rep2

description: Agilent design Id : 028005


title: MA9;2abc;CreER_0hr_OHT_rep3

description: Agilent design Id : 028005


title: MA9;2abc;CreER_0hr_OHT_rep2

description: Agilent design Id : 028005


title: MA9;2abc;CreER_48hr_OHT_rep3

description: Agilent design Id : 028005


title: HUES1p30 E8VNp2

description:
AC1_HUES1p30E8VNp2.1_2R07C01
9721420029; R07C01
data files: NC-0513_160520_PCF_Matrix*txt


title: HB-238-RED-231 patient

source_name: HB-238-RED-231 patient

tag: patient/sample source id

tag: sample type

value: Recurrence Tumor

value: F


title: MA9;2abc;CreER_96hr_OHT_rep1

description: Agilent design Id : 028005


title: MA9;2abc;CreER_0hr_OHT_rep4

description: Agilent design Id : 028005


title: MA9;2abc;CreER_0hr_OHT_rep1

description: Agilent design Id : 028005


title: H181p34 E8VNp4

description:
AC1_H181p34E8VNp4.1_2R05C01
9721420029; R05C01
data files: NC-0513_160520_PCF_Matrix*txt


title: H207p44 E8VNp5_rep2

description:
AC1_H207p44E8VNp5.1_2R06C01
9721420029; R06C01
data files: NC-0513_160520_PCF_Matrix*txt

value: Male


title: patient 8

source_name: EAT  infant

value: epicardial adipose tissue

value: infant


title: HB-229 PDX

source_name: HB-229 PDX

value: PLC-PDXs (Pediatric Liver Cancer-Patient Derived Xenografts)

tag: host strain

value: Athymic Nude-Foxn1nu (ENVIGO-Harlan Laboratories, Gannat, France)


title: H207p44 E8VNp5_rep1

description:
AC1_H207p44E8VNp5.1_1R02C01
9684393135; R02C01
data files: NC-0513_160520_PCF_Matrix*txt

value: Human embryonic stem cell


title: MA9;2abc;CreER_48hr_OHT_rep4

description: Agilent design Id : 028005


title: normal_127

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: total RNA extracted from formalin-fixed paraffin-embedded tissue sections

hyb_protocol: 2.53 µg of cDNA was hybridized at 48 degrees C on Human Gene ST 2.1 arrays

scan_protocol: Arrays were washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: RMA normalization was performed at the gene level using the “target=core” option for the rma function (R package: oligo).

source_name: skin

label_protocol: Biotinylated cDNA was prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2).

growth_protocol: Formalin-fixed, paraffin-embedded blocks of sebaceous hyperplasia (five different individuals) and NN skin (three different individuals) were accessed from the archives of the Department of Pathology at the University of Michigan. Diagnosis was confirmed by review of archival hematoxylin and eosin stained sections by a board-certified dermatopathologist.

extract_protocol: Five 20 micron microtome sections from paraffin-embedded sebaceous hyperplasia samples and normal skin were used to isolate RNA with the E.Z.N.A. FFPE RNA kit (Omega bio-tek) according to manufacturer’s instructions.

treatment_protocol: No treatments were applied to samples.

value: skin

tag: disease state

value: normal skin


title: SH_125

tag: tissue

value: sebaceous hyperplasia


title: normal_126


title: normal_128


title: 8R CA3 total  RNA, rep 1

city: Detroit

first: Donald

middle: James

last: DeGracia

address: 540 E. Canfield

institute: Wayne State University

description:
8hR3T1
gene expression data from  CA3 after 10 min ischemia and 8 hours reperfusion

hyb_protocol: Fragmented, biotin-labeled cDNA was hybridized for 17 hr at 45oC to GeneChip Rat Gene 2.0 ST Arrays

scan_protocol: Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner.

data_processing: Background correction by the PM-CGBG method and probe set signal summarization using the PLIER algorithm was performed in Affymetrix Expression Console. Quantile normalization, filtering, and class comparisons to identify probe sets exhibiting statistically significant differential expression were performed using BRB-ArrayTools

source_name: 8R CA3 total  RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard rat laboratory housing

treatment_protocol: complete normothermic global brain ischemia was induced by 2 vessel carotid artery occlusion and hypovoluemic hypotension to MAP = 45 mm Hg

value: male

tag: strain

value: Long Evans

tag: stress

value: 10 min ischemia and 8 hours reperfusion

value: brain

tag: region

tag: molecule type

value: total RNA


title: SH_121


title: 8R CA3 polysome RNA, rep 4

description:
8hR3P4
polysome-bound transcript data from  CA3 after 10 min ischemia and 8 hours reperfusion

source_name: 8R CA3 polysome RNA

tag: gender

value: polysome RNA


title: 8R CA3 total  RNA, rep 2

description:
8hR3T2
gene expression data from  CA3 after 10 min ischemia and 8 hours reperfusion


title: SH_124


title: 8R CA3 polysome RNA, rep 1

description:
8hR3P1
polysome-bound transcript data from  CA3 after 10 min ischemia and 8 hours reperfusion


title: 8R CA3 polysome RNA, rep 2

description:
8hR3P2
polysome-bound transcript data from  CA3 after 10 min ischemia and 8 hours reperfusion


title: SH_123


title: 8R CA1 polysome RNA, rep 1

description:
8hR1P1
polysome-bound transcript data from  CA1 after 10 min ischemia and 8 hours reperfusion

source_name: 8R CA1 polysome RNA


title: 8R CA1 total  RNA, rep 4

description:
8hR1T4
gene expression data from  CA1 after 10 min ischemia and 8 hours reperfusion

source_name: 8R CA1 total  RNA


title: 8R CA1 total  RNA, rep 3

description:
8hR1T3
gene expression data from  CA1 after 10 min ischemia and 8 hours reperfusion


title: Identification of miR-150-3p target genes in FaDu

tag: cell line

value: FaDu

tag: cell type

value: hypopharyngeal squamous cell carcinoma

value: no transfection

source_name: miR-150-3p transfected cell line


title: Cre+ IFNg LPS 3

middle: Franklin

last: Carson

address: 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Medical School

description: mRNA expression in Cre+ macrophages stimulated with Interferon gamma + LPS for six hours

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse ST 2.1 plates, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515)

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 3.1.1. RMA was used to fit log2 transformed expression values.

source_name: Bone marrow derived macrophages

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Total bone marrow from indicated mice was cultured in L-cell conditioned media (RPMI 1640 with 30% L-cell conditioned supernatant, 20% FCS, Penicillin/Streptomycin) for seven days for macrophage differentiation. Cells were harvested and replated in minimal media (RPMI 1640, 10% FCS, Penicillin/Streptomycin) prior to restimulation.

extract_protocol: Trizol-extracted RNA was further purified/cleaned with Qiagen RNeasy MinElute clean up columns. Purified RNA was then submitted to the University of Michigan DNA Sequencing Core for QC and further processing.

treatment_protocol: Cells were stimulated in vitro with IFNgamma (10 ng/ml), LPS (100 ng/ml) or the combination of IFNgamma+LPS for six hours. Cells were then processed in Trizol reagent for RNA extraction.

tag: genotype/variation

value: Lys2-Cre +/- MLL1 fx/fx


title: Cre+ IFNg 3

description: mRNA expression in Cre+ macrophages stimulated with Interferon gamma for six hours


title: Cre+ IFNg LPS 2


title: 8R CA1 polysome RNA, rep 3

description:
8hR1P4
polysome-bound transcript data from  CA1 after 10 min ischemia and 8 hours reperfusion


title: Cre+ LPS 3

description: mRNA expression in Cre+ macrophages stimulated with LPS for six hours


title: Cre+ LPS 1


title: FNAR-C1, Aldefluor High replicate 2

source_name: FNAR-C1, Aldefluor High

tag: aldefluor level

value: High


title: Cre+ LPS 2


title: Cre+ IFNg 2


title: NIC CA3 total  RNA, rep 1

description:
NIC3T1
gene expression data from control CA3

source_name: NIC CA3 total  RNA

value: control


title: NIC CA1 total  RNA, rep 1

description:
NIC1T1
gene expression data from control CA1

source_name: NIC CA1 total  RNA


title: Cre+ Unstimulated 2

description: Baseline mRNA expression in resting Cre+ macrophages


title: NIC CA1 total  RNA, rep 3

description:
NIC1T3
gene expression data from control CA1


title: NIC CA3 polysome RNA, rep 3

description:
NIC3P3a
polysome-bound transcript data from control CA3

source_name: NIC CA3 polysome RNA


title: NIC CA3 polysome RNA, rep 2

description:
NIC3P2a
polysome-bound transcript data from control CA3


title: Cre+ Unstimulated 1


title: NIC CA1 polysome RNA, rep 3

description:
NIC1P3a
polysome-bound transcript data from control CA1

source_name: NIC CA1 polysome RNA


title: NIC CA3 total  RNA, rep 2

description:
NIC3T2
gene expression data from control CA3


title: Cre- IFNg LPS 2

description: mRNA expression in Cre- macrophages stimulated with Interferon gamma + LPS for six hours

value: Lys2-Cre -/- MLL1 fx/fx


title: Cre+ IFNg LPS 1


title: 8R CA1 total  RNA, rep 1

description:
8hR1T1
gene expression data from  CA1 after 10 min ischemia and 8 hours reperfusion


title: Cre+ IFNg 1


title: Cre- IFNg LPS 3


title: NIC CA1 polysome RNA, rep 1

description:
NIC1P1a
polysome-bound transcript data from control CA1


title: Cre+ Unstimulated 3


title: NIC CA1 polysome RNA, rep 2

description:
NIC1P2a
polysome-bound transcript data from control CA1


title: Cre- IFNg LPS 1


title: NIC CA3 polysome RNA, rep 1

description:
NIC3P1a
polysome-bound transcript data from control CA3


title: 8R CA3 total  RNA, rep 3

description:
8hR3T3
gene expression data from  CA3 after 10 min ischemia and 8 hours reperfusion


title: Cre- LPS 1

description: mRNA expression in Cre- macrophages stimulated with LPS for six hours


title: 8R CA1 total  RNA, rep 2

description:
8hR1T2
gene expression data from  CA1 after 10 min ischemia and 8 hours reperfusion


title: 8R CA3 polysome RNA, rep 3

description:
8hR3P3
polysome-bound transcript data from  CA3 after 10 min ischemia and 8 hours reperfusion


title: 8R CA3 total  RNA, rep 4

description:
8hR3T4
gene expression data from  CA3 after 10 min ischemia and 8 hours reperfusion


title: Cre- LPS 3


title: Cre- IFNg 2

description: mRNA expression in Cre- macrophages stimulated with Interferon gamma for six hours


title: Cre- Unstimulated 3

description: Baseline mRNA expression in resting Cre- macrophages


title: Cre- Unstimulated 1


title: SH_122

description: total RNA extracted from formalin-fixed paraffin-embedded tissue sections


title: Cre- Unstimulated 2


title: 8R CA1 polysome RNA, rep 2

description:
8hR1P3
polysome-bound transcript data from  CA1 after 10 min ischemia and 8 hours reperfusion


title: Cre- IFNg 3


title: Cre- IFNg 1


title: OA-7

city: Nijmegen

first: Marieke

last: de Vries

address: Geert Groteplein 28

department: Rheumatology

country: Netherlands

institute: Radboudumc

hyb_protocol: Hybridization to U133Plus 2.0 was performed according to the Affymetrix Expression Analysis Technical Manual for two-cycle amplification.

scan_protocol: The arrays were scanned using a GeneChip Scanner (Affymetrix)

data_processing: The arrays were analyzed using Affymetrix GeneChip Operating Software version 1.4. Array normalization and expression value calculation were performed using DNA-Chip Analyzer version 1.3. The Invariant Set Normalization method and the model-based method were used for computing expression values.

source_name: synovium

label_protocol: Biotinylated cRNA was generated according to the Affymetrix Expression Analysis Technical Manual for two-cycle amplification.

extract_protocol: Total RNA was isolated from the synovial samples using the Rneasy kit for fibrous tissue according the manufacturer's protocol (Qiagen, Venlo, Netherlands).

value: Osteoarthritis

value: synovium


title: OA-9


title: Transfected-3

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description:
T2.3
Replicate-3

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Transfected, THLE 2 cells

growth_protocol: THLE 2 is an adherent cell line cultured in BEGM, 10%FBS, antibiotic solution containing penecillin and streptomycin supplemented along with 70 ng/ml phosphoethanolamine, 5 ng/ml epidermal growth factor. It was grown under 37°C incubator with 5% Co2.

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 Bioanalyzer.

treatment_protocol: THLE2 cells were treated with optimized FASN siRNA concentration complexed with lipoifectamine using manufacturer's protocol. After 48 hours incubation in  37°C incubator with 5% Co2, the cells were removed and washed with 1xPBS.

value: THLE 2 normal liver cell line

tag: transfection

value: FASN siRNA


title: OA-5


title: Control-1

description:
T1.1
Replicate-1

source_name: Control, THLE 2 cells

value: Control


title: OA-6


title: Cre- LPS 2


title: OA-10


title: Transfected-2

description:
T2.2
Replicate-2


title: OA-8


title: Mouse injected with ncRNAVLP rep 3

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

description: replicate 3

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. Rawdata were log2 transformed and filtered for probes with bad detection p-values in all samples within a comparison. A given probe is kept if detected in 67% of samples within at least one experimental group.

source_name: Dendritic cells

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.

tag: age

value: 6 weeks

tag: cells

value: Dendritic cells

tag: treatment

value: ncRNAVLP


title: Mouse injected with ncRNAVLP rep 4

description: replicate 4


title: Control-3

description:
T1.3
Replicate-3


title: Mouse injected with ncRNAVLP rep 2

description: replicate 2


title: OA-2


title: Mouse injected with ncRNAVLP rep 1

description: replicate 1


title: NIC CA1 total  RNA, rep 2

description:
NIC1T2
gene expression data from control CA1

value: male

value: Long Evans

value: brain

value: total RNA


title: Mouse injected with VLP rep 3

description: replicate 3

value: VLP


title: NIC CA3 total  RNA, rep 3

description:
NIC3T3
gene expression data from control CA3


title: Control Mouse rep 3

description: replicate 3

value: PBS


title: Mouse injected with VLP rep 1

description: replicate 1


title: Transfected-1

description:
T2.1
Replicate-1


title: Control Mouse rep 2

description: replicate 2


title: HC-7

value: Healthy control


title: HC-4


title: Mouse injected with VLP rep 2

description: replicate 2


title: OA-4


title: HC-5


title: Mouse injected with VLP rep 4

description: replicate 4


title: Control Mouse rep 1

description: replicate 1


title: OA-1


title: HC-6


title: merco-00121: R163

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

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

source_name: Prostate

tag: diseasestate

value: Normal

tag: Sex

tag: organismpart

value: Prostate


title: merco-00121: R250

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

value: Prostate Cancer


title: HC-2

tag: disease state

tag: tissue

value: synovium


title: HC-3


title: KO Asynchronous 1

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

hyb_protocol: Fragmented and labelled cDNA from three biological replicates was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

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

data_processing: Mouse Gene 1.0 ST arrays were normalised using rma-sketch implemented in Expression Consol Software 1.2.1

source_name: KO ES_Asynchronous

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (100ng Whole Transcript Labelling Assay, 2008, Affymetrix).

growth_protocol: Both wildtype and Dicer-deficient ES cells were cultured without feeders in a 50:50 ratio of serum+LIF media, and N2B27+2i media (Ying et al., Nature (453) 2008)

extract_protocol: RNA-Bee extraction of RNA was performed according to manufacturers instructions.

treatment_protocol: Populations of wildtype or Dicer-deficient asynchronous and early G1 cells were collected via trypsinisation of culture plates, washing the cells in PBS, and resuspension of the cell pellet in RNA-Bee (Tel-Test).

value: embryonic stem (ES) cells

value: Dicer-deficient


title: merco-00121: R309

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


title: merco-00121: R308

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


title: merco-00121: R255

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


title: merco-00121: R214


title: merco-00121: R165


title: merco-00121: R262


title: OA-3

value: Osteoarthritis


title: merco-00121: R223


title: merco-00121: R258


title: merco-00121: R256


title: WT Asynchronous 3

source_name: WT ES_Asynchronous

value: wild type


title: merco-00121: R208


title: merco-00121: R209


title: merco-00121: R221


title: merco-00121: R254


title: merco-00121: R249


title: WT Asynchronous 2


title: merco-00121: R289


title: merco-00121: R306


title: merco-00121: R143


title: merco-00121: R147


title: 6 DPCP Non Lesional day 3 a

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

source_name: Patient 6, Non Lesional, day 3

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Not Provided

tag: patient

tag: diagnosis

value: Melanoma

value: Diphencyprone (DPCP)

value: Non Lesional

tag: time

value: day 3

tag: sample

value: a


title: 6 DPCP Lesional day 21 a

source_name: Patient 6, Lesional, day 21

value: Lesional

value: day 21


title: 6 DPCP Lesional day 128 b

source_name: Patient 6, Lesional, day 128

value: day 128

value: b


title: WT Asynchronous 1


title: HC-1

value: Healthy control


title: 6 DPCP Lesional day 0 a

source_name: Patient 6, Lesional, day 0

value: day 0


title: 6 DPCP Lesional day 128 a


title: merco-00121: R144

value: Normal

value: male

value: Prostate


title: merco-00121: R226

value: Prostate Cancer


title: merco-00121: R251


title: merco-00121: R225


title: merco-00121: R263


title: merco-00121: R213


title: merco-00121: R207


title: 6 DPCP Lesional day 66 a

source_name: Patient 6, Lesional, day 66

value: day 66


title: 6 DPCP Non Lesional day 0 a

source_name: Patient 6, Non Lesional, day 0


title: merco-00121: R164


title: merco-00121: R292


title: 5 DPCP Lesional day 49 a

source_name: Patient 5, Lesional, day 49

value: day 49


title: merco-00121: R261


title: merco-00121: R287


title: 5 DPCP Non Lesional day 0 a

source_name: Patient 5, Non Lesional, day 0

value: Melanoma


title: merco-00121: R288


title: 5 DPCP Lesional day 0 a

source_name: Patient 5, Lesional, day 0

value: Diphencyprone (DPCP)


title: 5 DPCP Non Lesional day 3 a

source_name: Patient 5, Non Lesional, day 3

value: Non Lesional


title: merco-00121: R153


title: 5 DPCP Lesional day 21 a

source_name: Patient 5, Lesional, day 21


title: merco-00121: R229


title: merco-00121: R245


title: merco-00121: R247


title: merco-00121: R264


title: merco-00121: R219


title: merco-00121: R167


title: merco-00121: R202


title: merco-00121: R215


title: merco-00121: R248


title: 4 DPCP Lesional day 21 a

source_name: Patient 4, Lesional, day 21


title: merco-00121: R149


title: merco-00121: R142


title: merco-00121: R286


title: merco-00121: R227


title: merco-00121: R152


title: merco-00121: R303


title: 4 DPCP Non Lesional day 3 a

source_name: Patient 4, Non Lesional, day 3

value: day 3


title: 4 DPCP Lesional day 0 a

source_name: Patient 4, Lesional, day 0

value: a


title: merco-00121: R301

source_name: Prostate


title: 3 DPCP Non Lesional day 98 a

source_name: Patient 3, Non Lesional, day 98

value: day 98


title: merco-00121: R155


title: 4 DPCP Non Lesional day 0 a

source_name: Patient 4, Non Lesional, day 0


title: merco-00121: R203


title: merco-00121: R145


title: merco-00121: R151


title: merco-00121: R222


title: merco-00121: R310


title: merco-00121: R304


title: 3 DPCP Lesional day 128 a

source_name: Patient 3, Lesional, day 128

value: Lesional


title: merco-00121: R290


title: merco-00121: R146


title: 3 DPCP Non Lesional day 0 a

source_name: Patient 3, Non Lesional, day 0


title: 3 DPCP Non Lesional day 3 a

source_name: Patient 3, Non Lesional, day 3


title: 2 DPCP Lesional day 49 a

source_name: Patient 2, Lesional, day 49


title: KO Asynchronous 2

source_name: KO ES_Asynchronous

value: embryonic stem (ES) cells

value: Dicer-deficient


title: 3 DPCP Lesional day 0 a

source_name: Patient 3, Lesional, day 0


title: 2 DPCP Lesional day 21 a

source_name: Patient 2, Lesional, day 21

value: day 21


title: 2 DPCP Non Lesional day 3 a

source_name: Patient 2, Non Lesional, day 3


title: merco-00121: R305


title: 2 DPCP Non Lesional day 0 a

source_name: Patient 2, Non Lesional, day 0

value: day 0


title: merco-00121: R210

value: Normal


title: merco-00121: R244

value: male


title: Control-2

description:
T1.2
Replicate-2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

source_name: Control, THLE 2 cells

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

tag: cell line

value: THLE 2 normal liver cell line

value: Control


title: 2 DPCP Lesional day 0 a

source_name: Patient 2, Lesional, day 0


title: merco-00121: R243

value: Prostate


title: 1 DPCP Lesional day 21 a

source_name: Patient 1, Lesional, day 21


title: 1 DPCP Lesional day 0 a

source_name: Patient 1, Lesional, day 0


title: merco-00121: R161

value: Prostate Cancer


title: merco-00121: R284


title: merco-00121: R291


title: merco-00121: R162


title: merco-00121: R302


title: merco-00121: R212


title: 4 DPCP Lesional day 66 a

source_name: Patient 4, Lesional, day 66

value: Melanoma

value: day 66


title: merco-00121: R150

source_name: Prostate


title: merco-00121: R204


title: 1 DPCP Non Lesional day 3 a

source_name: Patient 1, Non Lesional, day 3

value: Diphencyprone (DPCP)

value: Non Lesional


title: merco-00121: R154


title: merco-00121: R259


title: merco-00121: R285


title: merco-00121: R228


title: merco-00121: R148


title: merco-00121: R166


title: merco-00121: R260


title: merco-00121: R220


title: merco-00121: R206


title: merco-00121: R252


title: merco-00121: R141


title: merco-00121: R257


title: merco-00121: R201


title: iPSC-NPC

city: Taipei City

first: Hsei-Wei

last: Wang

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang Ming University

description: iPSCs were generated according to Huang HP, Yu CY, Chen HF et al. J Biol Chem. 2010.

hyb_protocol: Not provided

scan_protocol: Chips are stained on Affymetrix GCS3000 scanner (scanner type M10)

data_processing: RNA log expression units were calculated from Affymetrix GeneChip array data using the ‘affy’ package of the Bioconductor suite of software for the R statistical programming language.

source_name: iPSCs from a 20-year-old male donor

label_protocol: cRNA probes were prepared for an array hybridization, and the data analysis was performed as Wang HS, Hung SC, Peng ST et al. Mesenchymal stem cells in the Wharton's jelly of the human,umbilical cord. Stem Cells. 2004;22:1330-1337.

growth_protocol: iPSCs were detached from the feeder cells with dispase (0.5 mg/ml, Invitrogen) and transferred onto Ultra-Low adhesion plates in differentiation medium consisting of Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) for embryoid body (EB) formation. After 6 days in the suspension cultures, the EBs were plated onto gelatin-coated culture dishes to allow for EB attachment. The medium was replaced for neural differentiation with N2 medium consisting of DMEM/F12 medium supplemented with non-essential amino acids, L-glutamine, ITS supplement (Invitrogen), and human basic fibroblast growth factor (bFGF, 10 ng/ml) for 8 weeks prior to use.

extract_protocol: Using the RNeasy Mini Kit (Qiagen), we extracted total cellular RNA from the co-cultured human iPSC-NPCs.

tag: cell type

value: Induced pluripotent stem cell-derived neural progenitor cells


title: merco-00121: R216


title: merco-00121: R246


title: 1 DPCP Non Lesional day 0 a

source_name: Patient 1, Non Lesional, day 0

value: a


title: merco-00121: R205


title: MU3

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

description: SAMPLE 9

hyb_protocol: Affymetrix standard Protocol

scan_protocol: Affymetrix standard Protocol

data_processing: Partek GS (v.6.4), R (v.3.1.1), (Bioconductor), Dchip (2010.01)

source_name: Human Normal muscle derived cells

label_protocol: Affymetrix standard Protocol

growth_protocol: Bone marrow stromal cells were isolated and cultured as previously described PMID: 17956733); Periosteal cells were isolated and cultured as per established methods (PMID: 17613258); Human cord blood MSCs (>36 weeks of gestation) were isolated and cultured as alreadi described (PMID: 20331358). Normal muscle samples (1-30x102 mg) were obtained from 17 human adults patients (aged 25-65 yrs) undergoing orthopedic surgery, from vastus lateralis (1), quadriceps femoris (5), triceps brachii (2), deltoides (4), gluteus maximus (5). Samples were washed with Hank’s balanced salt solution  without Ca2+/Mg2+ (HBSS, Invitrogen Life Technologies Corp., Carlsbad, California) containing 30mM HEPES (Sigma, St. Louis, MO), 100U/ml penicillin, 100μg/ml streptomycin (Invitrogen) for 10 min at room temperature with gentle agitation. Tissue samples were used for explant cultures, or to obtain single cell suspensions. For explant cultures, tissues were manually minced into 1x1 mm fragments, and placed into 100 mm culture dishes containing complete medium [αMEM (Invitrogen) with 20% FBS (Invitrogen), 2 mM L-glutamine, 100U/ml penicillin, 100 μg/ml streptomycin]. Explants were monitored daily for outgrowth of adherent cells and fresh medium was added every 3rd day. At sub-confluence, adherent cells were detached with trypsin and replated for further study, and tissue fragments were discarded. To obtain single cell suspensions, tissue fragments were digested twice with 100 U/ml Clostridium histolyticum type II collagenase (Invitrogen) supplemented with 3mM CaCl2 in Ca2+/Mg2+-free PBS (Invitrogen) for 40 min at 37°C with gentle agitation. The samples were centrifuged at 1000 rpm for 5 min at 4°C, washed with Ca2+/Mg2+-free PBS, resuspended in PBS, passed through 18 gauge needles to break up cell aggregates, and filtered through a 40 μm pore size cell strainer (Becton Dickinson, Bedford, MA) to obtain a single cell suspension. Nucleated cells were counted using a haemocytometer. Cell suspensions were used for to obtain cultures of unfractionated total cells, or for sorting of CD146+ cells, CD146+/CD56+ cells, CD146+/CD34+ cells, or CD146+/ALP+. To obtain non-clonal cultures, cells were seeded at a density of 1.6x103-1.6x105cells/cm2 in 75 cm2 flasks or in 100 mm dishes (Becton Dickinson). For multi-clonal cultures (multi-CFU-F cultures), cells were seeded into 100 mm dishes at a density of 1.6 cells/cm2, and formation of discrete colonies was scored after 14 days. Non-clonal cultures were passaged when subconfluent; multi-clonal cultures were passaged on day 14

extract_protocol: Total cellular RNA was isolated from multiclonal cultures of cell populations using RNeasy RNA isolation kit (Qiagen, Valencia, CA) following manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit) were used to determine the concentration and purity/integrity of RNA samples using an Agilent 2100 bioanalyzer

value: Human Normal muscle derived cells


title: PE3

description: SAMPLE 12

source_name: Human Periosteal cells

value: Human Periosteal cells


title: merco-00121: R241


title: PE1

description: SAMPLE 10


title: MU1

description: SAMPLE 7


title: merco-00121: R307


title: CB3

description: SAMPLE 6

source_name: Human cord blood MSCs

value: Human cord blood MSCs


title: BM1

description: SAMPLE 1

source_name: Human Bone marrow stromal cells

value: Human Bone marrow stromal cells


title: MU2

description: SAMPLE 8


title: TC32: Parental-Rep5

status: Public on Jun 01 2016

type: protein

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

description: RPPA

hyb_protocol: Protein-lysed-spots were probed with 179 validated primary antibodies and detected using a DakoCytomation-catalyzed system with secondary antibodies.

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images. Spots from tiff images were identified and their densities were quantified by MicroVigene. Relative protein levels for each sample were determined by interpolation of each dilution curve from the standard curve (supercurve) of the slide (antibody). Supercurve is constructed from a script in R written by the informatics department. These raw values are given as log2 values.  MicroVigene software program (VigeneTech) was used for automated spot identification, background correction, and individual spot-intensity determination.

data_processing: Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal – log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).  Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Ward’s linkage method as the clustering algorithm to link entities (proteins or genes) and samples.

label: 115 Primary Antibodies

molecule: protein

source_name: Parental Sensitive Ewing Sarcoma

label_protocol: Using a 2470 Arrayer (Aushon BioSystems), sample arrays were were processed, spotted onto nitrocellulose-coated FAST slides.

growth_protocol: Ewing Sarcoma cell lines sensitive or resistant to OSI-906 and NVP-ADW-742 grown in 2D-monolayer cultures were maintained in RPMI 1640 medium (Mediatech) containing 10% (vol/vol) fetal bovine serum (Gemini Bio-Products) and antibiotics (100 IU/ml penicillin and 100 mg/ml streptomycin [Mediatech]) in a humidified incubator at 37°C in a 5% CO2 atmosphere.

extract_protocol: Protein extraction from cell lines was performed by homogenizing an approximate 10 mg of frozen tissue in 500 ul of the lysis buffer containing protease and phosphatase inhibitors using an electric tissue homogenizer (Pro Scientific). Total lysed proteins were quantified using BCA protein assay kit and stored for further analyses for RPPA.

treatment_protocol: TC32 and TC71 ES clones with acquired resistance to OSI-906 or NVP-ADW-742 were generated by maintaining the corresponding parental cell lines with increasing concentrations of the agents (up to 2.3 μM for OSI-906, 1.5 μM for NVP-ADW-742) for 7 months. All parental and acquired drug resistant cell lines were tested twice per year for mycoplasma contamination using the MycoAlert Detection Kit (Lonza Group Ltd.) according to the manufacturer’s protocol and validated using short-tandem repeat fingerprinting with an AmpFLSTR Identifier kit as previously described. Herein, we determine subtle differences in acquired mechanism of resistance by two promising small molecule inhibitors of IGF-1R/IR-α. OSI-906, which inhibits IGF-1R and IR, and NVP-ADW-742, which inhibits only IGF-1R, were evaluated using in vitro assays to decipher the mechanism(s) by which IGF-1R inhibition induces drug resistance in Ewing sarcoma cells.

value: Ewing Sarcoma cell line


title: TC32: Parental-Rep4

description: RPPA


title: TC71: Parental-Rep5

description: RPPA


title: CB2

description: SAMPLE 5


title: BM2

description: SAMPLE 2


title: BM3

description: SAMPLE 3


title: PE2

description: SAMPLE 11


title: Monocytes from a premenopausal low BMD woman (SCOR536_2 PreL.CEL)

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 2001

department: Dept. of Biostatistics and Bioinformatics

institute: Tulane University School of Public Health

hyb_protocol: Preparation of cDNA, hybridization, and scanning of the GeneChip Human Exon 1.0 ST Array was performed according to the manufacturer's protocol for the Exon 1.0 Array (Affymetrix, Santa Clara, CA).

data_processing: we used RMA (robust multiarray average) method to normalize the array signals through the Bioconductor’s Oligo package. After normalization of a certain dataset, we performed differential expression analysis using t test through the Bioconductor’s LIMMA (linear models for microarray data) package

source_name: monocytes

extract_protocol: Total RNA from monocytes was extracted using Qiagen RNeasy Mini kit (Qiagen, Inc., Valencia, CA). We used Agilent Bioanalyzer (Agilent, Santa Clara, CA) to control the RNA quality before each array experiment, where RNA integrity number (RIN) should be no less than 7.0.

treatment_protocol: Monocyte isolation from whole blood was performed with a monocyte-negative isolation kit (Miltenyi Biotec Inc, Auburn, CA) following manufacturer's recommendation.

tag: gender

value: Female

tag: bone mineral density

value: low BMD

tag: state

value: premenopausal

value: monocytes


title: Monocytes from a postmenopausal low BMD woman (SCOR537 PostL.CEL)

scan_protocol: Preparation of cDNA, hybridization, and scanning of the GeneChip Human Exon 1.0 ST Array was performed according to the manufacturer's protocol for the Exon 1.0 Array (Affymetrix, Santa Clara, CA).

value: postmenopausal


title: CB1

description: SAMPLE 4


title: TC32: Parental-OSI906-72hrs

description: RPPA

source_name: TC32 Parental Treated Sensitive Ewing Sarcoma


title: Monocytes from a premenopausal high BMD woman (SCOR535 PreH.CEL)

label_protocol: Preparation of cDNA, hybridization, and scanning of the GeneChip Human Exon 1.0 ST Array was performed according to the manufacturer's protocol for the Exon 1.0 Array (Affymetrix, Santa Clara, CA).

value: high BMD


title: Monocytes from a premenopausal low BMD woman (SCOR533 PreL.CEL)


title: TC71: Parental-OSI906-72hrs

description: RPPA

source_name: TC71 Parental Treated Sensitive Ewing Sarcoma


title: TC71: NVP-ADW-742-Selected-C6

description: RPPA

source_name: Resistant Ewing Sarcoma Cell line to IGF-1R blockade

value: TC71 clone


title: Monocytes from a premenopausal high BMD woman (SCOR528 PreH.CEL)


title: TC32: Parental-NVP-ADW-742-72hrs

description: RPPA


title: TC71: NVP-ADW-742-Selected-C1

description: RPPA


title: TC71: Parental-NVP-ADW-742-72hrs

description: RPPA


title: Monocytes from a postmenopausal high BMD woman (SCOR532 PostH.CEL)


title: TC71: Parental-Rep4

description: RPPA

source_name: TC71: Parental Sensitive Ewing Sarcoma


title: Monocytes from a premenopausal low BMD woman (SCOR525 PreL.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR530_2 PostH.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR527 PreH.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR526 PostL.CEL)


title: Monocytes from a premenopausal low BMD woman (SCOR523 PreL.CEL)


title: Monocytes from a premenopausal low BMD woman (SCOR524 PreL.CEL)


title: TC71: OSI906-Selected-C7

description: RPPA

source_name: Resistant Ewing Sarcoma Cell line to IGF-1R/IR blockade


title: TC71: OSI906-Selected-C6

description: RPPA


title: TC32: OSI906-Selected-C5

description: RPPA

value: TC32 clone


title: Monocytes from a premenopausal low BMD woman (SCOR519_2 PreL.CEL)


title: TC32: OSI906-Selected-C4

description: RPPA


title: TC32: OSI906-Selected-CP

description: RPPA


title: TC32: NVP-ADW-742-Selected-C1

description: RPPA


title: TC71: NVP-ADW-742-Selected-C2

description: RPPA


title: TC32: NVP-ADW-742-Selected-C9

description: RPPA


title: Monocytes from a premenopausal low BMD woman (SCOR522 PreL.CEL)


title: TC32: NVP-ADW-742-Selected-CP

description: RPPA


title: TC71: Parental-Rep3

description: RPPA


title: Monocytes from a postmenopausal high BMD woman (SCOR515_2 PostH.CEL)


title: TC32: Parental-Rep3

description: RPPA

source_name: TC32: Parental Sensitive Ewing Sarcoma


title: TC71: OSI906-Selected-C4

description: RPPA


title: Monocytes from a postmenopausal low BMD woman (SCOR513_2 PostL.CEL)


title: Monocytes from a premenopausal low BMD woman (SCOR506 PreL.CEL)


title: TC71: Parental-Rep2

description: RPPA


title: TC32: Parental-Rep2

description: RPPA


title: Monocytes from a postmenopausal high BMD woman (SCOR505 PostH.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR521 PreH.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR518 PostH.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR507 PostH.CEL)


title: Monocytes from a premenopausal low BMD woman (SCOR520 PreL.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR503_2 PostH.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR511 PreH.CEL)


title: hoxH3

city: Kawasaki

first: Takashi

last: Osanai

state: Kanagawa

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

institute: Meiji University

description: hoxH mutant

hyb_protocol: Labeling cDNAs are spotted onto Agilent microarray, followed by incubation at 60 degree for overnight

scan_protocol: Hybridization signals were measured with a GenePix Personal 4100A array scanner (Axon Instruments) and a software GenePixPro Software. Cy3 signals were scanned with 532 nm laser.

data_processing: Normalization was performed for adjusting total signal intensities of cy3 from a GT sample by Excel (Microsoft). Each signal intensity was divided by total signal intensities.

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis_hoxH mutant

label_protocol: cDNAs were synthesized from total RNA by Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies).

growth_protocol: Cells grown in modified BG-11 liquid mediumam (5 mM NH4Cl as nitrogen sources)

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

treatment_protocol: Cells were collected by centrifugation and stored at -30 degree.

tag: growth condition

value: Cells grown under normal growth conditions

tag: genotype

value: hoxH mutant


title: Monocytes from a postmenopausal high BMD woman (SCOR502_3 PostH.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR DS94 PreH.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR512_2 PostH.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR DS93 PreH.CEL)


title: hoxH2

description: hoxH mutant


title: hoxH1

description: hoxH mutant


title: GT3

description: Glucose-tolerant Synechocystis strain

value: wildtype


title: Monocytes from a premenopausal high BMD woman (SCOR DS90 PreH.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR504_2 PostH.CEL)


title: GT2

description: Glucose-tolerant Synechocystis strain


title: Monocytes from a premenopausal low BMD woman (SCOR DS38 PreL.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR DS166 PostL.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR DS150 PostL.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR DS31 PreH.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR DS115 PreH.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR DS129 PostL.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR DS139 PreH.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR DS49 PostL.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR DS167 PostH.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR DS114 PostH.CEL)


title: Monocytes from a premenopausal high BMD woman (SCOR DS113 PreH.CEL)


title: Monocytes from a postmenopausal high BMD woman (SCOR DS72 PostH.CEL)


title: PancTuRef vs. HD1643

city: Santa Monica

first: Habib

last: Hamidi

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

hyb_protocol: 825 ng each of labeled reference mix (cy3 label) and individual sample (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol

scan_protocol: Slides were read on an Agilent G2505B scanner.  All  experiments were scanned with extended dynamic range enabled.

data_processing:
Agilent Feature Extraction Software (v9.5.1) was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used to determine to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.

source_name: 66 pooled pancreatic tumors

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's protocol.

tag: reference

value: 66 pooled pancreatic tumors

tag: morphology

value: Tumor

tag: pdac

value: Y

tag: rin


title: Monocytes from a premenopausal high BMD woman (SCOR DS05 PreH.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR DS159 PostL.CEL)


title: PancTuRef vs. HD1648


title: PancTuRef vs. HD1682


title: GT1

description: Glucose-tolerant Synechocystis strain


title: PancTuRef vs. HD1697


title: Monocytes from a postmenopausal high BMD woman (SCOR DS04 PostH.CEL)


title: PancTuRef vs. HD1642


title: PancTuRef vs. HD1633

value: N


title: Monocytes from a postmenopausal high BMD woman (SCOR DS03 PostH.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR DS02 PostL.CEL)


title: PancTuRef vs. HD1620


title: Monocytes from a premenopausal high BMD woman (SCOR DS07 PreH.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR 543 PostL.CEL)


title: PancTuRef vs. HD1603


title: Monocytes from a postmenopausal high BMD woman (SCOR DS06 PostH.CEL)


title: Monocytes from a postmenopausal low BMD woman (SCOR 542 PostL.CEL)


title: PancTuRef vs. HD1591


title: Monocytes from a premenopausal low BMD woman (SCOR 541 PreL.CEL)


title: PancTuRef2 vs. 10397A


title: PancTuRef2 vs. 14393A


title: PancTuRef2 vs. BN1750


title: Monocytes from a premenopausal low BMD woman (KCOFS-NF51 PreL.CEL)


title: PancTuRef2 vs. 22025A


title: PancTuRef2 vs. 27071A


title: PancTuRef vs. HD1602


title: Monocytes from a premenopausal low BMD woman (KCOFS-NF53 PreL.CEL)


title: PancTuRef2 vs. 26337A


title: Monocytes from a premenopausal high BMD woman (SCOR 540 PreH.CEL)


title: PancTuRef2 vs. 25547A


title: PancTuRef2 vs. 26856A


title: Monocytes from a postmenopausal low BMD woman (KCOFS-NF50 PostL.CEL)


title: Monocytes from a postmenopausal low BMD woman (KCOFS-NF34 PostL.CEL)


title: PancTuRef2 vs. HD1705


title: Monocytes from a premenopausal high BMD woman (KCOFS-NF47 PreH.CEL)


title: Monocytes from a premenopausal low BMD woman (KCOFS-NF19_2 PreL.CEL)


title: Monocytes from a postmenopausal high BMD woman (KCOFS-NF18 PostH.CEL)


title: Monocytes from a postmenopausal high BMD woman (KCOFS-NF49 PostH.CEL)


title: PancTuRef vs. HD151


title: PancTuRef vs. HD150-1


title: Monocytes from a premenopausal low BMD woman (KCOFS-NF52 PreL.CEL)


title: PancTuRef2 vs. HD1729


title: Monocytes from a postmenopausal high BMD woman (KCOFS-NF08 PostH.CEL)


title: Monocytes from a postmenopausal high BMD woman (KCOFS-NF10 PostH.CEL)


title: PancTuRef vs. HD120-1


title: PancTuRef vs. HD125-1


title: PancTuRef vs. HD148


title: PancTuRef vs. HD112-1


title: Monocytes from a postmenopausal high BMD woman (KCOFS-NF29_2 PostH.CEL)


title: Monocytes from a postmenopausal low BMD woman (DS48 postL.CEL)


title: PancTuRef vs. HD135-1


title: Monocytes from a postmenopausal low BMD woman (DS36 PostL.CEL)


title: PancTuRef vs. HD111-1


title: Monocytes from a postmenopausal high BMD woman (DS22 PostH.CEL)


title: Monocytes from a postmenopausal high BMD woman (DS13 PostH.CEL)


title: PancTuRef vs. HD94-1


title: Monocytes from a postmenopausal high BMD woman (DS96 PostH.CEL)


title: PancTuRef vs. HD1567


title: PancTuRef vs. HD1525


title: PancTuRef vs. 25610A


title: PancTuRef vs. HD78-2


title: Ovarian metastatic tumor tissue, technical rep 1

city: BETHESDA

first: Anna

last: Roschke

address: 37 Center Dr

institute: NCI-NIH

description: Gene expression data from ovarian metastatic tumor tissue

hyb_protocol: Hybridization was performed following Affymetrix GeneChip 3'IVT Express Manual P/N 702646 Rev 6. For washing and staining Affymetrix GenChip Fluidics Station 450/240 User's Guide P/N 08-0092 Rev. G was followed.

scan_protocol: Scanning was done using the Affymetrix GeneChip Scanner 3000

data_processing: The data were  analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Data analysis was also performed using BRB-ArrayTools Version 4.3.0-Beta_3. Genes showing minimal variation across the set of arrays were excluded from the analysis. Genes whose expression differed by at least 1.5 fold from the median in at least 20% of the arrays were retained.

source_name: Metastatic tumor tissue

label_protocol: RNA amplification, fragmentation and labeling were performed following the Affymetrix GeneChip 3'IVT Express Manual P/N 702646 Rev 6

growth_protocol: The OVDM1 cell line was cultured in a medium of equal volumes of MCDB 105 Medium and Medium 199 (both Sigma-Aldrich, St. Louis, MO), heat inactivated FBS, 50 ug/ml of Gentamicin and 100X Antibiotic/Antimycotic (all Invitrogen/Life Technologies) were added to a final concentration of 5%, 50 ug/ml and 1X respecitvely. When close to confluence, cell were subcultured in a split ratio of 1 to 4.

extract_protocol: Total RNA was extracted utilizing the Qiagen miRNeasy MiniKit (Qiagen, Valencia, CA)

value: Metastatic tumor tissue


title: Monocytes from a postmenopausal high BMD woman (DS117 PostH.CEL)


title: PancTuRef vs. HD1575


title: Monocytes from a postmenopausal high BMD woman (DS09 PostH.CEL)


title: PancTuRef vs. HD1569


title: OVDM1 cell line at early passage, technical rep 1

description: Gene expression data from OVDM1 cell line at early passage

source_name: OVDM1 cell line at early passage


title: PancTuRef2 vs. 26741A


title: PancTuRef2 vs. 26181A


title: PancTuRef2 vs. 22722A


title: PancTuRef2 vs. 11045A


title: PancTuRef vs. HD1579


title: OVDM1 cell line at early passage, technical rep 2


title: Ovarian metastatic tumor tissue, technical rep 2


title: OVDM1 cell line at early passage, technical rep 3


title: Ovarian metastatic tumor tissue, technical rep 3


title: PancTuRef2 vs. 22653A


title: OVDM1 cell line at late passage, technical rep 1

description: Gene expression data from OVDM1 cell line at late passage

source_name: OVDM1 cell line at late passage


title: PancTuRef vs. 7230A


title: PancTuRef vs. 22335A


title: OVDM1 cell line at late passage, technical rep 3


title: PancTuRef vs. HD1524


title: PancTuRef vs. BN1654


title: Monocytes from a postmenopausal low BMD woman (SCOR DS74 PostL.CEL)


title: PancTuRef vs. BN1245