title: Epithelial cells Cal51 cocultured with fibroblast Wi38 replicate-2


title: Circadian_40h

status: Public on Nov 21 2013

type: RNA

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

description: Identification of circadian-regulated genes

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: standard Agilent Feature Extraction software protocol

molecule: total RNA

organism: Saccharum hybrid cultivar (mixed)

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

extract_protocol: Trizol followed by DNase treatment and RNA cleanup using QIAGEN kit

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 40: collected at 40 h; experiment in: 14/07/2008

tag: tissue

value: leaves

tag: variety

tag: collect

tag: time

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; pool; experiment in: 14/07/2008

value: control pool


title: Circadian_52h

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 52: collected at 52 h; experiment in: 14/07/2008


title: Patient N30 Sample

type: other

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

country: USA

institute: Michigan State University

description: controls included for normalization

data_processing:
The arrays were scanned to obtain signal location, intensity quantification and identification information using GenePix Pro 6.1. For each array inter-array normalization was performed via the ProCAT algorithm (sliding window of length 15). The arrays were then quantile normalized and a comparison of intensities of probes was carried out using ANOVA in Mathematica 9.0.  The Negative Control was used to eliminate signals not related to plasma response.
Samples:  GenePix Pro intensities, normalized by ProCat Algorithm, and Quantile Normalized in Mathematica 9.  Control: GenePix Pro intensities, normalized by ProCAT Algorithm Mathematica 9

label: Alexa Fluor 555

molecule: other

organism: Homo sapiens

source_name: Plasma

treatment_protocol: Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array for the autoantibodyome profiling. The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software. All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

tag: mds class

value: N

tag: Sex

value: M

tag: age

tag: % blast

tag: iPSs

tag: disease state

value: healthy


title: Circadian_48h

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 48: collected at 48 h; experiment in: 14/07/2008


title: Patient N31 Sample

description: controls included for normalization

hyb_protocol: All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

scan_protocol: The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software.

extract_protocol: Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array


title: Circadian_64hsw

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 64: collected at 64 h; experiment in: 14/07/2008


title: Patient N28 Sample

description: controls included for normalization

label_protocol: All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)


title: Circadian_60h

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 60: collected at 60 h; experiment in: 14/07/2008


title: Patient N27 Sample

description: controls included for normalization


title: Epithelial cells Cal51 cocultured with fibroblast Wi38 replicate-1

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

description: human cells cell cultured- tumors cell lines, human fibroblast strains

hyb_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.

data_processing: We used R package aroma.affymetrix to analyze raw data. Chip type is HuGene-1_0-st-v1, and we used HuGene-1_0-st-v1.r3 as annotation CDF. After RMA background correction and quantile normalization we got probe-level intensity values as shown in the data matrix. We ran quality assessment to check data (not shown). In the further analysis we averaged intensity values for genes with multiple probes, then took log2 tranformed values for each gene.

label: biotin

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol. The optional on-column DNA digestion was performed, using the RNase-free DNase Set (Qiagen).

tag: cell


title: Circadian_32hsw

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 32: collected at 32 h; experiment in: 14/07/2008


title: Circadian_28h

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 28: collected at 28 h; experiment in: 14/07/2008


title: Circadian_40hsw

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 40: collected at 40 h; experiment in: 14/07/2008


title: Circadian_52hsw

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 52: collected at 52 h; experiment in: 14/07/2008


title: Circadian_36h

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 36: collected at 36 h; experiment in: 14/07/2008


title: 30AC5

city: Yangling

first: Wang

last: Huayan

state: Shaanxi

address: No.3 Taicheng Road

department: College of Veterinary Medicine

country: China

institute: Northwest A&F University

description: Gene expression data from porcine iPS

hyb_protocol: The RNA was labeled with IVT Labeling Kit, Affymetrix.

scan_protocol: Hybridized arrays were scanned using GeneChip Scanner 3000, Affymetrix

data_processing: We imported datasets from GEO into GeneSpring GX 11.0 using a guided workflow step to identify interested targets that were both statistically and biologically meaningful. Because pig arrays are poorly annotated, the Affymetrix Pig Annotation Revision 5 (http://www4.ncsu.edu/~stsai2/annotation/) was used for the annotation information of pig probes. Probe sets with gene-level normalized intensities greater than log (base-2.0) of 5.0 in a minimum of one sample were excluded from ANOVA. The data were then filtered based on their flag values P (present) and A (absent) to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values. ANOVA incorporating the Benjamini–Hochberg FDR multiple testing correction, with a significance level of p-value < 0.05 to be performed get the differentially expressed genes between different groups.

organism: Sus scrofa

source_name: porcine iPS

label_protocol: Synthesis of cDNA, in vitro transcription and biotin labeling cRNA, and hybridization to the Affymetrix GeneChip Pig Genome Array were performed according to Affymetrix protocols.

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 15% FBS at 38.5°C, 5% CO2 for 72 hours. The piPS cells were maintained on mitotically inactive mouse embryonic fibroblasts (MEFs) feeder layers derived from ICR mice, and passaged using 1 mg/ml Collagenase type IV (Invitrogen) and 0.05% Trypsin (Invitrogen) every 2 to 3 days.

extract_protocol: RNeasy Mini Kit (QIAGEN) extracted total RNAs from pig iPS cell lines.

tag: cell type

value: iPS

tag: marker expression and plasticity

value: SSEA1+, pluripotent cell


title: Patient N29 Sample

description: controls included for normalization


title: Circadian_68h

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 68: collected at 68 h; experiment in: 14/07/2008


title: Patient N26 Sample

description: controls included for normalization


title: iPF4-2

description: Gene expression data from porcine iPS

value: SSEA3, SSEA4 +, pluripotent cell


title: Patient N25 Sample

description: controls included for normalization


title: Patient N23 Sample

description: controls included for normalization


title: iPSCs-w

description: Gene expression data from porcine iPS


title: Patient N22 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast CCD1112Sk replicate-3

scan_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.


title: Patient N21 Sample

description: controls included for normalization


title: Patient N24 Sample

description: controls included for normalization


title: PS24

description: Gene expression data from porcine iPS

value: SSEA1,SSEA3, SSEA4 +, pluripotent cell


title: PAFSC

description: Gene expression data from porcine amniotic fluid stem cell

source_name: porcine amniotic fluid stem cell

value: amniotic fluid stem cell

value: somatic cell


title: Patient N20 Sample

description: controls included for normalization


title: PEF

description: Gene expression data from porcine embryo fiboblast

source_name: porcine embryo fiboblast

value: embryo fiboblast


title: Patient N19 Sample

description: controls included for normalization


title: wild type (VRK1+/+) rep4

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

description: Biological replicate 4 of 4

hyb_protocol: Standard Agilent procedures.

scan_protocol: Scanned on Agilent Scanner G2505B US45103124 using one color settings, and images were quantified using Agilent Feature Extraction Software v. 9.5.3.1

data_processing: Agilent Feature Extraction Software v. 9.5.3.1 with protocol GE1-v1_95  was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: whole testicular cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was labelled from 0.5 ug total RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by purification with RNeasy Mini Kit (Qiagen) and quantification by Nano Drop 100 spectrophotometer.

extract_protocol: Total RNA was prepared from whole testicular cells using the Trizol reagent (Invitrogen) following the manufacturer's instructions.

tag: gender

value: male

value: testis

tag: genotype


title: mutant (VRK1-/-) rep1

description: Biological replicate 1 of 4


title: wild type (VRK1+/+) rep1

description: Biological replicate 1 of 4


title: wild type (VRK1+/+) rep2

description: Biological replicate 2 of 4


title: Epithelial cells MDAMB231 cocultured with fibroblast CCD1112Sk replicate-1

label_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.


title: Patient N18 Sample

description: controls included for normalization


title: mutant (VRK1-/-) rep3

description: Biological replicate 3 of 4


title: Epithelial cells MDAMB231 cocultured with fibroblast CCD1112Sk replicate-2


title: forebrain_wildtype_5

city: Grand Forks

first: Jacob

middle: Thomas

last: Cain

state: ND

address: 10 Cornell St Stop 9019

department: Biology

institute: University of North Dakota

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip 430.2 arrays (Affymetrix; catalog no. 901230). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G.

data_processing:
Raw .CEL DATA was first analyzed using Affymetrix Expression Console.  Mas5 was used to generate Presence/Absence calls, while PLIER normalized values were used for subsequent analysis.  Since the data was generated in several technical batches, the data was normalized using the R-Script ComBat.R using the following model (Age, Batch, Genotype).  The batch normailized date was then analyzed using a Bayesian-modeled ANOVA using the freeware software BAMarray.  The E9.5 wildtype sampes were used as a baseline, and the program was run on its highest stringency setting. (Note the PLIER and MAS5 values presented in this Matrix table, are not Batch Normalized.  The Log2 Batch normalized values and the group Z-scores will be provided in the metadata.)
PLIER Values, Mas5 detection (A,P,M), Mas5 p-values, Batch Normalized Log2 Values, Group Z scores, Group Significance UP(1)/Down(-1)/Not significant (0)

label_protocol: Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the 3' IVT Express kit (Affymetrix), according to the manufacturer's instructions.

extract_protocol: Extraction of total RNA was performed  PicoPure RNA isolation kit (Applied Biosystems), according to the manufacturer's instructions. RNA purity was checked by OD260/280 readings and RNA integrity was checked using Agilent Bioanalyzer capillary electrophoresis profiles.

treatment_protocol: Embryonic timed pregnancies were collected at E9.5 and the forebrains were microdissected.  The Vegf isoform mice express only the isoforms indicated in their designation.

tag: genetic background

value: wildtype

value: forebrain

tag: technical batch


title: forebrain_Vegf120188_1

growth_protocol: Embryonic timed pregnancies were collected at E9.5 and the forebrains were microdissected

tag: tissue


title: forebrain_wildtype_6


title: forebrain_Vegf120188_3


title: forebrain_Vegf120188_2


title: Patient N17 Sample

description: controls included for normalization


title: forebrain_Vegf188_2


title: Patient N16 Sample

description: controls included for normalization


title: forebrain_Vegf188_3


title: forebrain_Vegf188_1


title: forebrain_Vegf188_4


title: Patient N15 Sample

description: controls included for normalization


title: Epithelial cells Cal51 cocultured with fibroblast CCD1112Sk replicate-3


title: Epithelial cells Cal51 cocultured with fibroblast CCD1112Sk replicate-2


title: Patient N12 Sample

description: controls included for normalization


title: Epithelial cells Cal51 cocultured with fibroblast CCD1112Sk replicate-1


title: Patient N11 Sample

description: controls included for normalization


title: NH2009121402

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: antigen specific murine CD8 T cells (P14 T cells) after exposure in vivo to dendritic cells (DC)

hyb_protocol: We followed the NuGEN FL-Ovation cDNA Biotin Module V2 (p11) and used the Affymetrix Hybe/Wash/Stain (cat # 900720) for washing and staining. We used Fludics Station 450.

scan_protocol: GeneChip Scanner 3000 7G. We used AGCC (Affymetrix Gene Command Console) for the software. Affymetrix 430_2 microarrays (Affymetrix, Santa Clara, CA).

data_processing: Quality control (QC) tests based on the ArrayQualityMetrics 2.4.3 R package under R version 2.10.1 identified four outlier samples:  3 control samples harvested at 24 h ( NH2009120718, NH2009120719, NH2009120727), and   one low dose (1uM) cognate peptide pulsed sample harvested at 12 h (NH2009120737).   The four outlier samples  were  removed from the  data.   The expression data for the remaining 35 samples which passed the QC tests  were  RMA processed. Metadata and raw data for the 4 removed (outlier) Samples are provided as supplementary files at the foot of the Series record.

label_protocol: Nugen FL-Ovation cDNA Biotin Module V2 (cat. #4200-12).

extract_protocol: Total RNA was isolated from TriZol using the Agencourt RNAdvance Tissue Kit (Beckman Coulter, Brea CA), and was amplified using the WT-Ovation Pico RNA Amplification and Labeling System (NuGEN, San Carlos, CA).

tag: strain

tag: time [hours]

tag: dose cognate kavynfatc peptide [um]

tag: qc test

value: passed


title: NH2009121438

source_name: antigen specific murine CD8 T cells (P14 T cells)


title: NH2009121434


title: NH2009121430


title: Patient N13 Sample

description: controls included for normalization

tag: mds class

tag: Sex


title: NH2009121429


title: NH2009121431


title: NH2009121436


title: NH2009121435


title: Patient N10 Sample

description: controls included for normalization

tag: age

tag: % blast


title: NH2009121428


title: Patient N09 Sample

description: controls included for normalization

tag: iPSs

tag: disease state


title: mutant (VRK1-/-) rep4

description: Biological replicate 4 of 4


title: NH2009121432


title: NH2009121401


title: NH2009121439


title: NH2009121433


title: Patient N14 Sample

description: controls included for normalization


title: NH2009121425


title: Patient N08 Sample

description: controls included for normalization


title: NH2009121426


title: NH2009121424


title: NH2009121423


title: Patient N07 Sample

description: controls included for normalization


title: n2a-paupar_knockdown-R2

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

hyb_protocol: Fragmented ssDNA was then labelled and hybridized to the Affymetrix GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Chips were processed on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Chips were scanned on an Affymetrix Scanner 3000.

data_processing: Affymetrix CEL files were analysed using the Limma, oligo, and genefilter R Bioconductor packages. Arrays were RMA background corrected, quantile normalised and summary expression values calculated for Refseq and full length mRNAs. Before differential expression analysis, genes changing upon Paupar knockdown were filtered to remove genes showing little variation in expression (variance cut off of 0.5).

source_name: N2A_Paupar knockdown construct

label_protocol: 200 ng RNA was used to generate labelled sense single stranded DNA (ssDNA) for hybridization with the Ambion WT Expression Kit, the Affymetrix WT Terminal Labelling and Controls Kit and the Affymetrix Hybridization, Wash, and Stain Kit as described by the manufacturer.  Sense ssDNA was fragmented and the distribution of fragment lengths was measured on a BioAnalyzer.

growth_protocol: N2A mouse neuroblastoma cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated using the Qiagen Mini RNeasy kit following the manufacturer’s instructions and RNA integrity assessed on a BioAnalyzer (Agilent Technologies).

treatment_protocol: Approximately 2x10^5 cells were plated per well in a 6 well plate. 16-24 hrs later cells were transfected with 1.5 ug shRNA expression construct using FuGENE 6 (Promega) according to the manufacturer’s instructions. Total RNA was extracted from the cells 2.5 days later.

tag: cell line

value: neuro 2A (N2A)

tag: cell type

value: neuroblastoma

tag: transiently transfected with

value: Paupar knockdown construct


title: Patient N06 Sample

description: controls included for normalization

value: N

value: M


title: n2a-paupar_knockdown-R3


title: Hyphal cells transferred to 37°C versus hyphal control

city: University of Melbourne

first: Alex

last: Andrianopoulos

state: Victoria

address: Royal Parade

department: Department of Genetics

country: Australia

institute: University of Melbourne

description: 3 Biological replicates pooled

hyb_protocol: Unincorporated dyes were removed using QIAquick PCR Purification Kit (QIAGEN). Samples were heated at 100°C for 2 min in hybridization buffer. Samples labelled with Cy3 and Cy5 were then competitively hybridized on microarray slides prehybridized with prehybridization buffer. Hybridizations were performed at 42°C for 16-20 hr. Slides were washed four times in wash buffer containing decreasing concentrations of SSC and SDS. Dye swap was performed for every pairwise comparison.

scan_protocol: Slides were scanned on either a GenePix 4000B or 4100A scanner (Axon Instruments) and images analysed with GenePix Pro 6.1 and Acuity 4.0.

data_processing: Statistical analysis was performed using the limma software package (Smyth 2005, In 'Bioinformatics and Computational Biology Solutions using R and Bioconductor', pp397-420). Intensities were background corrected by the “normexp” method with offset equal to 16 to stabilize the log-ratios of low intensity probes (Ritche et al. 2007 Bioinformatics 23:2700-7).

label: Cy3, Cy5

organism: Talaromyces marneffei

source_name: Hyphal cells transferred to 37°C

label_protocol: First strand cDNA synthesis was performed using the SuperScript™ Indirect cDNA Labelling system (Invitrogen, Life Technologies) according to the manufacturer’s instructions. Total RNA (50 µg) was employed in each labelling reaction. Cy3 and Cy5 dyes (Amersham) were coupled to the amino-allyl groups in 0.1 M sodium bicarbonate pH 9.0 buffer.

growth_protocol: P. marneffei was grown in liquid Brain-Heart Infusion (BHI) (Oxoid) with shaking for hyphal growth at 25°C (2 days) and yeast growth at 37°C (4 days of growth then 10 ml transferred to fresh medium for an additional 2 days). Auxotrophic supplements were added as required. For temperature switching, hyphal cells were transferred to 37°C for 6 hr after two days of growth at 25°C or yeast cells were moved to 25°C for 6 hr after four days of growth at 37°C.

extract_protocol: Total RNA was prepared using the QIAGEN RNAeasy kit according to the manufacture’s instructions, followed by a LiCl2 precipitation step.

tag: sample type

value: Hyphal cells transferred to 37°C

source_name: Hyphal cells

value: Hyphal cells


title: MEFs_control_Wnt3a treated_40 min_1 rep (S1)

type: protein

city: London

first: Daniel

middle: Peter Sayer

last: Osborn

address: Human Genetics Research Centre

institute: St George's University of London

hyb_protocol: according to manufacturer protocol: http://www.fullmoonbiosystems.com/protocols/AntibodyArrayUserGuide.pdf

data_processing: 1. For each spot on the array, the median spot intensity is extracted from the image. 2. Using the median intensity, determine the average signal of replicate spots for each antibody.The data is labeled as Average Signal of Replicate Spots on the Array. 3. Within each array slide, determine the median value of Average Signal of all antibodies in the array.This value is presented as Median Signal. 4.To determine the Normalized Data (Normalized to Median Signal), take the Average Signal of each antibody and divide it by the Median Signal from Step 3.The results are as labeled as Data Normalized to Median Signal. 5. Using the normalized data, determine the fold change between two samples. Fold change = (sample2 - sample1)/sample1). Phospho/non Phospho ratio: 1. Using the Average Signal of Duplicates Spots on the Array, for each pair of phospho-antibody to non-phospho-antibody, determine the ratio of phospho-protein to non-phospho-protein.  Ratio = (Average Signal of Phospho-Antibody)/(Average Signal of Non-Phospho-Antibody). Fold change = (sample2 - sample1)/sample1

molecule: protein

source_name: MEFs, control, Wnt3a treated, 40 min

growth_protocol: Control and Fto deficient MEFs were grown in DMEM medium supplemented with 10% FBS, 1x non-essential amino acids and 50mM  mercaptoethanol.

extract_protocol: Proteins were extracted by using 1% NP-40 buffer

treatment_protocol: Control and Fto deficient cells were treated with Wnt3a conditioned medium for 40 min

value: mouse embryonic fibroblasts (MEFs)

tag: phenotype

value: Fto wild type


title: Yeast cells transferred to 25°C versus yeast control

description: 3 Biological replicates pooled

source_name: Yeast cells tranferred to 25°C

value: Yeast cells tranferred to 25°C

source_name: Yeast cells

value: Yeast cells


title: MEFs_Fto deficient_Wnt3a treated_40 min_1 rep (S2)

scan_protocol: according to manufacturer protocol: http://www.fullmoonbiosystems.com/protocols/AntibodyArrayUserGuide.pdf

source_name: MEFs, Fto deficient, Wnt3a treated, 40 min

value: Fto deficient


title: NH2009121421


title: Patient N04 Sample

description: controls included for normalization

value: healthy


title: NH2009121422


title: Patient N03 Sample

description: controls included for normalization


title: NH2009121420


title: Patient N02 Sample

description: controls included for normalization


title: n2a-paupar_control-R2

source_name: N2A_non-targeting vector

value: non-targeting control vector


title: n2a-paupar_control-R3


title: NH2009121415


title: n2a-paupar_knockdown-R1


title: n2a-paupar_control-R1


title: wer mutant, biological rep3

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description:
m-WER_S7
Analysis conducted at the University of Michigan

hyb_protocol: The cRNA was fragmented in the presence of heat and Mg2+, followed by hybridization to the Affymetrix ATH1 Arabidopsis genechip for 16 hr at 45C.  The arrays were then washed and stained using the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: The data were preprocessed in R using RMA with custom CDF files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp).

organism: Arabidopsis thaliana

source_name: root epidermal cells from wer mutant

label_protocol: Biotin-labeled cRNA was synthesized according to the standard Affymetrix protocol from poly(A) RNA present in the total RNA prep.

growth_protocol: Seedlings were grown for 5 days in continuous light at 23C on vertically-oriented dishes containing MS media + 1% sucrose.

extract_protocol: WER::GFP-expressing cells were collected by FACS.  Total RNA was extracted from GFP-positive cells using the Rneasy kit (Qiagen, Inc).

treatment_protocol: Root were cut approximately 2 mm from the tip, including the entire developmental region.

tag: genotype/variation

value: wer-1 WER::GFP

value: root epidermal cells


title: NH2009121417

value: passed


title: n2a-pax6_knockdown-R3

data_processing: Affymetrix CEL files were analysed using the Limma, oligo, and genefilter R Bioconductor packages. Arrays were RMA background corrected, quantile normalised and summary expression values calculated for Refseq and full length mRNAs. Before differential expression analysis, genes changing upon Pax6 knockdown were filtered to remove genes genes with consistently low expression.

source_name: N2A_Pax6 knockdown construct

treatment_protocol: Approximately 2x10^5 cells were plated per well in a 6 well plate. 16-24 hrs later cells were transfected with 1.5 ug shRNA expression construct using FuGENE 6 (Promega) according to the manufacturer’s instructions. Total RNA was extracted from the cells 3 days later.

value: neuro 2A (N2A)

value: pax6 knockdown construct


title: mutant (VRK1-/-) rep2

description: Biological replicate 2 of 4

tag: gender

value: male

tag: tissue

value: testis

tag: genotype


title: wer mutant, biological rep2

description:
m-WER_90
Analysis conducted at the University of Michigan


title: Patient N01 Sample

description: controls included for normalization

value: N

value: M


title: NH2009121416

tag: strain

tag: time [hours]

tag: dose cognate kavynfatc peptide [um]


title: Patient N05 Sample

description: controls included for normalization

tag: mds class

tag: Sex


title: NH2009121413

tag: qc test


title: n2a-pax6_knockdown-R2

value: neuroblastoma


title: ttg2 mutant, biological rep3

description:
m-TTG2_123
Analysis conducted at the University of Michigan

source_name: root epidermal cells from ttg2 mutant

value: ttg2-1 WER::GFP


title: NH2009121412


title: wild type (VRK1+/+) rep3

description: Biological replicate 3 of 4


title: n2a-pax6_knockdown-R1


title: wer mutant, biological rep1

description:
m-WER_1
Analysis conducted at the University of Michigan


title: n2a-pax6_control-R3


title: n2a-pax6_control-R2


title: n2a-pax6_control-R1


title: NH2009121410


title: NH2009121411


title: ttg2 mutant, biological rep1

description:
m-TTG2_102
Analysis conducted at the University of Michigan


title: ttg2 mutant, biological rep2

description:
m-TTG2_114
Analysis conducted at the University of Michigan


title: try mutant, biological rep3

description:
m-TRY_121
Analysis conducted at the University of Michigan

source_name: root epidermal cells from try mutant

value: try-82 WER::GFP


title: NH2009121407


title: NH2009121408


title: NH2009121409


title: try mutant, biological rep1

description:
m-TRY_88
Analysis conducted at the University of Michigan


title: myb23 mutant, biological rep3

description:
m-MYB23_120
Analysis conducted at the University of Michigan

source_name: root epidermal cells from myb23 mutant

value: myb23-1 WER::GFP


title: try mutant, biological rep2

description:
m-TRY_95
Analysis conducted at the University of Michigan


title: aP2-XBP1_transgenic_rep1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: epididymal adipose tissue, aP2-XBP1 transgenic mouse, replicate 1

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.18.1).

label_protocol: The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.

growth_protocol: Transgenic mice overespressing XBP1 in adipose tissue were were generated on a C57Bl/6J background. Age-matched wild-type C57Bl/6J mice were used as control mice. Mice were housed under standard conditions with a 12-hour light-dark cycle and were fed a standard mouse chow diet with free access to water. Experiments were performed in 17-week old animals.

extract_protocol: Total RNA was prepared from adipose tissue using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Male wild type C57BL/6 mice and aP2-XBP1 transgenic mice were grown until the age of 17 weeks while being fed chow (Harlan Teklad #2914). Animals were then killed and epididymal white adipose tissue was removed. Total RNA was isolated and subjected to gene expression profiling.

tag: background strain

value: aP2-XBP1 transgenic

tag: age

value: 17 weeks

value: epididymal adipose tissue


title: myb23 mutant, biological rep2

description:
m-MYB23_94
Analysis conducted at the University of Michigan


title: NH2009121406


title: aP2-XBP1_transgenic_rep3

description: epididymal adipose tissue, aP2-XBP1 transgenic mouse, replicate 3


title: WAT_WT_rep4

description: epididymal adipose tissue, wild type mouse, replicate 4

value: wild type


title: aP2-XBP1_transgenic_rep2

description: epididymal adipose tissue, aP2-XBP1 transgenic mouse, replicate 2


title: WAT_WT_rep3

description: epididymal adipose tissue, wild type mouse, replicate 3


title: PNET 28

type: genomic

city: Montrea

first: Simon

last: Papillon-Cavanagh

state: Quebec

address: 740 Dr Penfield

department: Human Genetics

country: Canada

institute: McGill University

description:
pnet tumour sample
8784241116_R04C02

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: We removed probes with missing values, binding multiple genomic regions, binding targets with known sequence variants (1000 Genomes Project, SNPs with a minor allele frequency ≥ 2/120), or being located on the X or Y chromosomes. The final set contains 309,015 probes

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PNET sample

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: Primitive neuroectodermal tumor (PNET)

tag: disease state

value: PNET


title: NH2009121405

description: antigen specific murine CD8 T cells (P14 T cells) after exposure in vivo to dendritic cells (DC)

value: passed


title: NH2009121403


title: gl3 mutant, biological rep3

description:
m-GL3_58
Analysis conducted at the University of Michigan

source_name: root epidermal cells from gl3 mutant

value: gl3-1 WER::GFP

value: root epidermal cells


title: myb23 mutant, biological rep1

description:
m-MYB23_87
Analysis conducted at the University of Michigan


title: PNET 27

description:
pnet tumour sample
8784241116_R05C01


title: Donor 4 - Passage 8 - mAdbID:113692

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 113692

hyb_protocol: Agilent Hybridization Protocol Solution: 2x GEx Hybridization Buffer HI-RPM Blocking agent: 10x Blocking Agent Wash procedure: The hybridization gaskets were dissembled in GE Wash Buffer 1, washed in GE Wash Buffer 1 for 1 min at room temperature, and then washed in GE Wash Buffer 2 for 1 min at 37 C. Qty. of labeled target: 750 ng Time: 16 hours Other: 825 ng of amplified cRNA were pooled, fragmented and then hybridized on 4x44K microarrays (Agilent) for 17 hours at 65 C.

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505B US45103062

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Analyzed using BRBArrayTools developed by the Biometric Research Branch, National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html ). Spots with signal intensity less than 20 in both channels were filtered out. If the signal intensity was less than 20 in one channel only, it was set to 20 in computing the log-ratio value. Global median normalization was performed on the filtered data by subtracting out the median log-ratio for each array.
FeatureExtractor_Version: 9.5.1.1
Protocol_Name: GE2-v5_95_Feb07 (Read Only)

source_name: Stratagene Universal Human Reference RNA

label_protocol:
Cy3 Labeling Protocol
Label amount: 500 ng
Other: Human tissue RNA (Agilent, Santa Clara, CA) was amplified and labeled with Cy3-CTP using Agilent Quick Amp Labeling kit (Agilent, Santa Clara, CA).

extract_protocol:
Agilent RNA Extraction
Other: not available

tag: other

value: Composed of total RNA from nine human tissues or cell lines:placental tissue, adult liver tissue, adult brain tissue, adult heart tissue, adult breast tissue, adult colon tissue, adult testis tissue, fetal brain tissue, testis cell line.

source_name: Donor 4 - O9FC44

label_protocol:
Cy5 Labeling Protocol
Label amount: 500 ng
Other: Total RNA (0.5 μg) was amplified and labeled with Cy5-CTP using Quick Amp Labeling kit (Agilent, Santa Clara, CA).

extract_protocol:
Qiagen miRNeasy Mini Kit Protocol
Other: The total RNA was extracted using columns in Qiagen miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using Nano Drop 2000 (Thermo Scientific, Wilmington, DE) with A260/A280 ratios > 2.0 after dilution in DEPC water.

treatment_protocol: In-vitro treatment: Marrow was collected from the posterior iliac crest of 7 healthy donors. A total of 1.5 to 4.5 mL of marrow was collected in Bone Marrow Prep Syringes (Pharmacy Department, NIH, Bethesda, MD) and then washed with Hank's Balanced Salt Solution (Lonza, Walkersville, MD) (HBSS). A single cell suspension was made with BMSC culture media (BMSC CM) [alpha MEM with 2 mM glutamine (Lonza), supplemented with 20% lot-selected FBS (Hyclone, Thermo Fischer Scientific, Waltham, MA) and 10 ug/ml Gentamicin] and plated at a density of 2 x 10(5)/cm(2) in T-75 flasks (Culture flasks, canted neck, polystyrene, Corning Life Sciences, Corning NY) and were incubated at 37 C in 5% CO2. Non adherent cells were removed after 24 hours and the media was changed. Thereafter, the media was changed every three days until the colonies reach 70-80% confluence and were harvested, which generally was on day 13 of culture. The primary BMSCs were washed with 10mL HBSS twice and incubated with 5mL recombinant human trypsin (TrypLE Express, Invitrogen, Life Technologies, Grand Island, NY) for 10 minutes; and then neutralized with 5mL of BMSC CM, rinsed with 5ml HBSS and centrifuged at 406 x g for 10 minutes. The cell number was counted and viability was assessed by Trypan Blue exclusion method. The cells harvested at this stage were designated as Passage 1, and serial passage numbers were designated thereafter. After passage 1, the BMSCs were seeded in T-75 flasks at a density of 3000 cells per cm2 and incubated 37 C in 5% CO2 until the cells reach 70-80% confluence, during which time the culture medium was changed every three days. The cells were harvested as described above. The number of BMSCs at every passage was manually counted using a C-Chip Disposable Hemacytometers (Incyto, Chonhung, Korea) and viability was assessed by the Trypan Blue exclusion method. The Population Doubling for each passage was calculated using the below equation: N=[log10(NH)-log10(N1)]/log10(2) where N = population doublings, N(H) = cell harvest number, and N(I) = plating cell number. Cumulative population doublings (PD) were calculated in relation to the cell numbers at the first passage. Population doubling time (PDT) was calculated by the below equation on each passage, PDT= time of culture (hrs)/N, where N = population doubling.

value: Bone Marrow

tag: cell type

value: Bone Marrow Stromal Cell (BMSC)

tag: individual


title: PNET 26

description:
pnet tumour sample
8784241104_R01C02


title: gl3 mutant, biological rep2

description:
m-GL3_17
Analysis conducted at the University of Michigan


title: gl3 mutant, biological rep1

description:
m-GL3_8
Analysis conducted at the University of Michigan


title: PNET 25

description:
pnet tumour sample
8784241104_R03C01


title: Donor 4 - Passage 4 - mAdbID:113691

description: mAdb experiment ID: 113691


title: WAT_WT_rep2

description: epididymal adipose tissue, wild type mouse, replicate 2

value: male


title: WAT_WT_rep1

description: epididymal adipose tissue, wild type mouse, replicate 1


title: NH2009121404

source_name: antigen specific murine CD8 T cells (P14 T cells)


title: Adrenocortical Carcinoma, ACC-MPI2 [Agilent]

city: Tempe

first: Kimberly

middle: J.

last: Bussey

state: AZ

address: 1001 S. McAllister Ave.

institute: Arizona State University

hyb_protocol: Labeled RNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol

scan_protocol: The arrays were scanned using Agilent Technologies Scanner G2505B US23502420.

data_processing: Data was extracted from the TIFF files using Agilent FE 8.1.  The data quality was assessed using the arrayQuality package in Bioconductor.  The packages marray and limma (Bioconductor) were used for the purpose of further normalizing the data. Controls were removed from the Agilent dataset. The function backgroundCorrect from the package marray was used for minimum background subtraction. This data was then normalized within arrays using the median values across the probes. It was then normalized across arrays using quantile normalization.

source_name: tumor, flash-frozen

label_protocol: RNA was reverse transcribed, amplified and labeled with a fluorescent nucleotide (Cy5 for tumors and Cy3 for normal adrenals) using the Low Input RNA Linear Lableing kit (Agilent) according to manufacturer's protocol.

extract_protocol:
Tumor samples from patients with adrenocortical carcinoma were flash-frozen and maintaned at -80 degrees C until chipped for RNA extraction
100 mg of tumor was chipped from flash frozen samples.  The tissue was homogenized by sonication using the Covaris S-2 tissue processor in the presence of the RLT buffer from the Qiagen Rneasy kit.  RNA was extracted with Trizol/chloroform and the aqueous phase purified using the RNeasy kit.

value: adrenocortical carcinoma

tag: extent of disease

value: Unknown

tag: tumor grade

tag: functional

value: F

tag: survival in years

source_name: Pooled Total RNA from whole normal adrenal gland

extract_protocol: 100 mg of whole adrenal gland was chipped from flash frozen samples.  The tissue was homogenized by sonication using the Covaris S-2 tissue processor in the presence of the RLT buffer from the Qiagen Rneasy kit.  RNA was extracted with Trizol/chloroform and the aqueous phase purified using the RNeasy kit.

value: whole adrenal gland


title: Adrenocortical Carcinoma, ACC-7 [Agilent]

tag: tissue

value: Localized

value: Cushings

tag: gender

value: M


title: PNET 23

description:
pnet tumour sample
8784225140_R06C02


title: Donor 3 - Passage 8 - mAdbID:113690

description: mAdb experiment ID: 113690

source_name: Donor 3 - 09FC43


title: Adrenocortical Carcinoma, ACC-MPI1 [Agilent]


title: PNET 21

description:
pnet tumour sample
8784225140_R01C01


title: PNET 20

description:
pnet tumour sample
8667045134_R04C02


title: Donor 7 - Passage 10 - mAdbID:113689

description: mAdb experiment ID: 113689


title: egl3 mutant, biological rep2

description:
m-EGL3_78
Analysis conducted at the University of Michigan

source_name: root epidermal cells from egl3 mutant

tag: genotype/variation

value: egl3-1 WER::GFP


title: Adrenocortical Carcinoma, ACC-28 [Agilent]


title: PNET 19

description:
pnet tumour sample
8667045134_R05C01

value: Primitive neuroectodermal tumor (PNET)


title: NH2009121414

tag: strain

tag: time [hours]

tag: dose cognate kavynfatc peptide [um]


title: PNET 24

description:
pnet tumour sample
8784241018_R02C02

value: PNET


title: cpc ttg2 mutant, biological rep2

description:
m-CPCTTG2_150
Analysis conducted at the University of Michigan

source_name: root epidermal cells from cpc ttg2 mutant

value: cpc-1 ttg2-1 WER::GFP


title: Adrenocortical Carcinoma, ACC-23 [Agilent]


title: cpc ttg2 mutant, biological rep3

description:
m-CPCTTG2_151
Analysis conducted at the University of Michigan


title: PNET 22

description:
pnet tumour sample
8784225140_R05C02


title: Adrenocortical Carcinoma, ACC-27 [Agilent]


title: Donor 7 - Passage 9 - mAdbID:113688

description: mAdb experiment ID: 113688


title: Donor 7 - Passage 8 - mAdbID:113687

description: mAdb experiment ID: 113687


title: egl3 mutant, biological rep3

description:
m-EGL3_92
Analysis conducted at the University of Michigan


title: egl3 mutant, biological rep1

description:
m-EGL3_5
Analysis conducted at the University of Michigan


title: Donor 7 - Passage 6 - mAdbID:113685

description: mAdb experiment ID: 113685


title: cpc ttg2 mutant, biological rep1

description:
m-CPCTTG2_147
Analysis conducted at the University of Michigan


title: Donor 7 - Passage 7 - mAdbID:113686

description: mAdb experiment ID: 113686


title: PNET 18

description:
pnet tumour sample
8667045060_R06C02


title: Adrenocortical Carcinoma, ACC-22 [Agilent]


title: Adrenocortical Carcinoma, ACC-11 [Agilent]

value: aldosterone


title: PNET 17

description:
pnet tumour sample
8667045060_R04C01


title: cpc mutant, biological rep3

description:
m-CPC_S6
Analysis conducted at the University of Michigan

source_name: root epidermal cells from cpc mutant

value: cpc-1 WER::GFP

value: root epidermal cells


title: PNET 16

description:
pnet tumour sample
8667045060_R02C01


title: cpc mutant, biological rep2

description:
m-CPC_97
Analysis conducted at the University of Michigan


title: Donor 7 - Passage 5 - mAdbID:113684

description: mAdb experiment ID: 113684

value: Composed of total RNA from nine human tissues or cell lines:placental tissue, adult liver tissue, adult brain tissue, adult heart tissue, adult breast tissue, adult colon tissue, adult testis tissue, fetal brain tissue, testis cell line.

value: Bone Marrow


title: Adrenocortical Carcinoma, ACC-9 [Agilent]


title: cpc mutant, biological rep1

description:
m-CPC_3
Analysis conducted at the University of Michigan


title: Adrenocortical Carcinoma, ACC-26 [Agilent]

value: Regional


title: Tibia_Load_5

city: amsterdam

first: Nathalie

last: Bravenboer

address: de Boelelaan 1117

department: Clinical Chemistry

institute: VU Medical Center

description: LOAD 5

hyb_protocol: The hybridization protocol was adapted from Snijders and colleagues [21] with minor modifications. Pre-hybridization was performed in a hybridization mixture containing 60 µg yeast tRNA (ribonucleic acid transfer, Sigma), 12 µg polyA (Amersham Biosciences) and 24 µg human Cot 1 DNA (Invitrogen) and 30 µg salmon sperm DNA (Invitrogen) in a total volume of 29.2 µl per array. After precipitation the pellet was dissolved in mastermix (50% formamide, 2xSSC, 9.4% dextran sulphate) and 0.2% SDS in a total volume of 130.2 µl per array. Pre-hybridization was maintained for 45 min at 37°C in the Hybridization Station (GenetacTM hybridization station or HybArray12 (Perkin Elmer)). The pre-hybridization mix was gently removed and slides were dried by centrifugation at 200 g for 3 min. The probe-hybridization mixture contained 16.0 µl Cy3 and 16.0 µl Cy5 labeled samples and 26.2 µl hybridization mixture (60 µg yeast tRNA, 12 µg polyA and 24 µg human Cot 1 DNA). After precipitation the pellet was dissolved in mastermix and 0.2% SDS in a total volume of 130.2 µl per array. Probe mix was denaturated at 70ºC for 15 min and incubated at 37ºC for 60 min. Hybridization was initiated and maintained for 16 h at 30ºC in the hybridization station, while the hybridization mixture was agitating. After hybridization, excess hybridization mixture was automatically rinsed off with 50% formamide, 2xSSC, pH 7.0 at 35ºC and followed by a wash step with PN buffer (0.1 M sodium phosphate, 0.1% Igepal CA630, pH 8) at 25ºC. Excess salt was removed by subsequently rinsing in 0.2xSSC, 0.1xSSC and 0.01xSSC at 25ºC. Slides were dried by centrifugation at 200 g for 3 min.

scan_protocol: After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. Array images were processed with BlueFuse version 3.0 for microarrays (BlueGnome, Cambridge, UK).

data_processing: Automatically flagged genes (spots with a confidence value < 0.11) and manually flagged genes (dirty spots and spots with a confidence value between 0.11 0.15 with a low intensity or bad morphology) were excluded from further analysis. The duplicates of the Cy3 and Cy5 intensities were not averaged, but were treated as separate spots in the analysis. The log2 values of the Cy5 to Cy3 ratios were normalized in an intensity dependent fashion (lowess). Genes with more than one missing value across arrays were excluded from the statistical analysis. Differentially expressed genes were identified by fitting a separate linear model to the expression data for each gene using the language R (http://www.r-project.org). Duplicate spots for each gene, printed on each array, were taken into account [Smyth GK, Michaud J, Scott HS (2005), Bioinformatics. 21:2067-2075]. Differential expression was analyzed using moderated t statistics based on empirical Bayes estimation [Smyth GK, Michaud J, Scott HS (2005), Bioinformatics. 21:2067-2075] and P-values were adjusted according to the linear step-up method of Benjamini and Hochberg to reflect the false discovery rate [Benjamini Y, Hochberg Y (1995), Journal of the Royal Statistical Society Series B-Methodological 57:289-300; Reiner A, Yekutieli D, Benjamini Y (2003), Bioinformatics. 19:368-375]. Genes with a false discovery rate <20% were considered to reflect statistical significance. Estimated relative differential expression for LOAD (i.e., relative to its contra lateral control) was compared to the estimated relative differential expression for SHAM (i.e. relative to its contra lateral control). Thus, aspects of the experimental intervention bending and squeezing were compared with squeezing resulting in the net effect of bending.

organism: Rattus norvegicus

source_name: Control

label_protocol: RNA from five rats of each group was used for microarray analysis cDNA probes were generated from 15 µg total RNA with an oligo-dT ((dT)20 VN) primer (Isogen, Maarssen, The Netherlands) and SuperScript™ II Reverse Transcriptase (Invitrogen), with incorporation of aminoallyl-dUTP (Ambion). Probes were indirectly labeled with Fluorolink Cy3 or Cy5 mono-functional dyes according to a dye-swap design. The dye-swap design was used to avoid a possible bias caused by the molecular structure of Cy3 and Cy5. The treated tibia (LOAD or SHAM) was hybridized together with its own contra lateral control tibia creating unique intra-rat hybridization.

extract_protocol: The diaphysis of the tibia from experiment A was pulverized in presence of Trizol (Invitrogen) using the Freezer mill 6750 (Spex Certiprep, Metuchen, NY, USA) subsequently followed by a Trizol extraction, a chloroform/isoamylalcohol extraction, and a second Trizol extraction according to the manufacturer’s instructions. The RNA pellet was dissolved in RNase-free water and stored at  80ºC prior to use.

tag: strain background

value: Wistar

value: left tibia

tag: sample group

value: Contralateral control

source_name: Load

value: right tibia

value: LOAD (300 cycles (2 Hz) using a peak magnitude of 60 N)


title: Donor 7 - Passage 2 - mAdbID:113681

description: mAdb experiment ID: 113681

value: Bone Marrow Stromal Cell (BMSC)


title: Tibia_Sham_5

description: SHAM 5

source_name: Sham

value: SHAM


title: Adrenocortical Carcinoma, ACC-MPI3 [Agilent]

value: adrenocortical carcinoma

value: Metastatic

value: Unknown

value: F

tag: age

value: whole adrenal gland


title: PNET 13

description:
pnet tumour sample
6929689154_R06C01

value: Primitive neuroectodermal tumor (PNET)

tag: disease state

value: PNET


title: Adrenocortical Carcinoma, ACC-21 [Agilent]

value: Localized

value: Cushings


title: Adrenocortical Carcinoma, ACC-17 [Agilent]


title: Donor 7 - Passage 3 - mAdbID:113682

description: mAdb experiment ID: 113682

tag: other

value: Composed of total RNA from nine human tissues or cell lines:placental tissue, adult liver tissue, adult brain tissue, adult heart tissue, adult breast tissue, adult colon tissue, adult testis tissue, fetal brain tissue, testis cell line.

value: Bone Marrow


title: Tibia_Sham_4

description: SHAM 4

value: Wistar

value: left tibia


title: PNET 14

description:
pnet tumour sample
6929689164_R02C01


title: Donor 1 - Passage 10 - mAdbID:113678

description: mAdb experiment ID: 113678

source_name: Donor 1 - 09FC20

tag: cell type


title: Donor 1 - Passage 9 - mAdbID:113677

description: mAdb experiment ID: 113677

tag: individual


title: Adrenocortical Carcinoma, ACC-12 [Agilent]

tag: extent of disease

value: M


title: Donor 1 - Passage 8 - mAdbID:113676

description: mAdb experiment ID: 113676


title: Donor 7 - Passage 4 - mAdbID:113683

description: mAdb experiment ID: 113683


title: PNET 11

description:
pnet tumour sample
6929689068_R06C01


title: PNET 10

description:
pnet tumour sample
6969568075_R02C02


title: Tibia_Load_4

description: LOAD 4

value: right tibia

value: LOAD (300 cycles (2 Hz) using a peak magnitude of 60 N)

value: Contralateral control


title: Tibia_Sham_3

description: SHAM 3

value: SHAM


title: PNET 12

description:
pnet tumour sample
6929689145_R03C01


title: Adrenocortical Carcinoma, ACC-10 [Agilent]

value: adrenocortical carcinoma

tag: tumor grade


title: Tibia_Load_2

description: LOAD 2


title: Tibia_Load_3

description: LOAD 3


title: Tibia_Sham_2

description: SHAM 2


title: Tibia_Sham_1

description: SHAM 1


title: PNET 9

description:
pnet tumour sample
6969568075_R05C01


title: Donor 1 - Passage 7 - mAdbID:113675

description: mAdb experiment ID: 113675

value: Bone Marrow Stromal Cell (BMSC)


title: Tibia_Load_1

description: LOAD 1


title: Donor 1 - Passage 5 - mAdbID:113673

description: mAdb experiment ID: 113673


title: Donor 1 - Passage 6 - mAdbID:113674

description: mAdb experiment ID: 113674


title: Donor 1 - Passage 4 - mAdbID:113672

description: mAdb experiment ID: 113672


title: PNET 15

description:
pnet tumour sample
6929689164_R05C02


title: Donor 6 - Passage 4 - mAdbID:113668

description: mAdb experiment ID: 113668

source_name: Donor 6 - 09FC49


title: Adrenocortical Carcinoma, ACC-150 [Affymetrix]

description: liver metastasis matching ACC-149

hyb_protocol: Labeled cRNA was fragmented and hybridized to Affymetrix U133 Plus 2 human genome arrays following the manufacture’s protocol.

scan_protocol: Scanning and washing was completed on the Fluidic Stations FS450 and the GeneChip® Scanner 3000 with Workstation.

data_processing: All processing was done in GenePattern. Data was normalized by gcRMA with quantile normalization and background subtraction after using the ExpressionFileCreator. Data was then floored at 5.5 using PreprocessDataset. The data was subsequently filtered to remove 1) probes with more than 35 floored values and/or 2) probes where all values from one batch were floored while values from the other batch were not. Further batch effects were minimized using ComBat with the parametric option. Data was then floored at 2. Differentially expressed genes were determined using a T-test with multiple comparison correction as implemented by Comparative Marker Selection in Gene Pattern. Genes with the corrected p-value < 0.005 and the FDR < 0.075 were selected for further study. For comparing high to low grade or primary to recurrence, the FDR cut-off was increased to < 0.13. Survival analysis was conducted using Prism 6 (GraphPad) to generate Kaplan-Meier curves that were compared by log-rank.

label_protocol: Purified total RNA was amplified and reverse transcribed utilizing the MessageAmp II Biotin Enhanced Kit (Ambion, Inc). Biotin-labeled cRNA was synthesized according to standard protocol, followed by purification through provided cRNA Filter Cartridges.

growth_protocol: Tumor samples were flash-frozen and maintaned at -80 degrees C until chipped for RNA extraction

extract_protocol: 100 mg of tumor was chipped from flash frozen samples. For the ACC4-28, MPI1-3 and normal adrenal tissue, the tissue was homogenized by sonication using the Covaris S-2 tissue processor in the presence of the RLT buffer from the Qiagen Rneasy kit. RNA was extracted with Trizol/chloroform and the aqueous phase purified using the RNeasy kit. ACC30-150 were sent as chipped samples to Clinical Reference Laboratory (Lenexa, KS) for RNA extraction and array processing.

tag: Stage

value: Unknown

tag: functional

tag: age in years

tag: survival status

tag: tumor size in cm

tag: tumor weight in grams

value: unknown

tag: batch


title: Donor 6 - Passage 5 - mAdbID:113669

description: mAdb experiment ID: 113669

tag: tissue


title: Donor 5 - Passage 6 - mAdbID:113667

description: mAdb experiment ID: 113667

source_name: Donor 5 - 09FC45


title: Adrenocortical Carcinoma, ACC-140 [Affymetrix]

tag: gender

tag: survival in years

value: alive


title: PNET 8

description:
pnet tumour sample
6969568071_R05C02

source_name: PNET sample

value: Primitive neuroectodermal tumor (PNET)

value: PNET


title: Donor 1 - Passage 3 - mAdbID:113671

description: mAdb experiment ID: 113671


title: Donor 5 - Passage 5 - mAdbID:113666

description: mAdb experiment ID: 113666


title: Adrenocortical Carcinoma, ACC-136 [Affymetrix]

value: Recurrence

value: dead


title: Donor 4 - Passage 5 - mAdbID:113664

description: mAdb experiment ID: 113664

value: Composed of total RNA from nine human tissues or cell lines:placental tissue, adult liver tissue, adult brain tissue, adult heart tissue, adult breast tissue, adult colon tissue, adult testis tissue, fetal brain tissue, testis cell line.

value: Bone Marrow


title: Adrenocortical Carcinoma, ACC-134 [Affymetrix]

value: aldosterone

value: F


title: PNET 6

description:
pnet tumour sample
6969568068_R05C01


title: PNET 4

description:
pnet tumour sample
6969568067_R02C01


title: Donor 1 - Passage 2 - mAdbID:113670

description: mAdb experiment ID: 113670


title: Donor 3 - Passage 5 - mAdbID:113661

description: mAdb experiment ID: 113661


title: Adrenocortical Carcinoma, ACC-132 [Affymetrix]


title: PNET 5

description:
pnet tumour sample
6969568067_R01C02


title: PNET 3

description:
pnet tumour sample
6969568042_R03C02


title: Donor 3 - Passage 4 - mAdbID:113660

description: mAdb experiment ID: 113660


title: PNET 7

description:
pnet tumour sample
6969568068_R04C02


title: Adrenocortical Carcinoma, ACC-123 [Affymetrix]


title: PED CTRL 13

description:
normal brain sample
8784241116_R01C01

source_name: pediatric control brain

value: pediatric brain

value: normal (control)


title: Adrenocortical Carcinoma, ACC-118 [Affymetrix]

value: M


title: Donor 2 - Passage 9 - mAdbID:113659

description: mAdb experiment ID: 113659

source_name: Stratagene Universal Human Reference RNA

source_name: Donor 2 - 09FC37

value: Bone Marrow Stromal Cells (BMSC)


title: Adrenocortical Carcinoma, ACC-129 [Affymetrix]

value: Cortisol, aldosterone, testosterone


title: Adrenocortical Carcinoma, ACC-117 [Affymetrix]


title: Donor 2 - Passage 5 - mAdbID:113658

description: mAdb experiment ID: 113658


title: PED CTRL 9

description:
normal brain sample
8784241018_R01C02


title: PED CTRL 10

description:
normal brain sample
8784241018_R06C02


title: Donor 2 - Passage 4 - mAdbID:113657

description: mAdb experiment ID: 113657


title: PNET 1

description:
pnet tumour sample
6969568009_R02C01


title: Adrenocortical Carcinoma, ACC-115 [Affymetrix]

value: Aldosterone


title: PNET 2

description:
pnet tumour sample
6969568042_R06C01


title: Donor 7 - Passage 11 - mAdbID:113650

description: mAdb experiment ID: 113650

value: Bone Marrow Stromal Cell (BMSC)


title: PED CTRL 6

description:
normal brain sample
8784225140_R03C01


title: PED CTRL 7

description:
normal brain sample
8784225140_R04C02


title: PED CTRL 11

description:
normal brain sample
8784241104_R03C02


title: PED CTRL 12

description:
normal brain sample
8784241104_R05C02


title: Adrenocortical Carcinoma, ACC-149 [Affymetrix]

value: Unknown

value: unknown


title: PED CTRL 14

description:
normal brain sample
8784241116_R04C01


title: PED CTRL 8

description:
normal brain sample
8784241018_R05C01


title: Adrenocortical Carcinoma, ACC-114 [Affymetrix]


title: Adrenocortical Carcinoma, ACC-85 [Affymetrix]


title: Adrenocortical Carcinoma, ACC-84 [Affymetrix]

value: Virulizing


title: Adrenocortical Carcinoma, ACC-61 [Affymetrix]


title: Adrenocortical Carcinoma, ACC-59 [Affymetrix]


title: Adrenocortical Carcinoma, ACC-112 [Affymetrix]


title: Donor 4 - Passage 10 - mAdbID:107990

description: mAdb experiment ID: 107990

source_name: Donor 4 - O9FC44


title: Donor 5 - Passage 3 - mAdbID:107995

description: mAdb experiment ID: 107995


title: Donor 4 - Passage 9 - mAdbID:107991

description: mAdb experiment ID: 107991


title: Donor 5 - Passage 9 - mAdbID:107992

description: mAdb experiment ID: 107992


title: Donor 5 - Passage 7 - mAdbID:107994

description: mAdb experiment ID: 107994


title: Adrenocortical Carcinoma, ACC-51 [Affymetrix]

source_name: tumor, flash-frozen


title: Donor 5 - Passage 8 - mAdbID:107993

description: mAdb experiment ID: 107993


title: Donor 4 - Passage 11 - mAdbID:107989

description: mAdb experiment ID: 107989


title: PED CTRL 4

description:
normal brain sample
8667045134_R02C02


title: PED CTRL 1

description:
normal brain sample
8667045060_R01C01


title: PED CTRL 3

description:
normal brain sample
8667045134_R04C01


title: PED CTRL 5

description:
normal brain sample
8784225140_R02C01


title: Donor 5 - Passage 2 - mAdbID:107988

description: mAdb experiment ID: 107988


title: PED CTRL 2

description:
normal brain sample
8667045060_R05C02


title: FETAL CTRL 9

description:
normal brain sample
8221916038_R01C02

source_name: fetal control brain

value: fetal brain


title: Adrenocortical Carcinoma, ACC-47 [Affymetrix]

value: Recurrence


title: Adrenocortical Carcinoma, ACC-48 [Affymetrix]


title: Donor 3 - Passage 10 - mAdbID:107987

description: mAdb experiment ID: 107987

source_name: Donor 3 - 09FC43


title: Adrenocortical Carcinoma, ACC-45 [Affymetrix]


title: Donor 3 - Passage 11 - mAdbID:107986

description: mAdb experiment ID: 107986


title: Donor 4 - Passage 2 - mAdbID:107985

description: mAdb experiment ID: 107985


title: Adrenocortical Carcinoma, ACC-35 [Affymetrix]


title: Donor 4 - Passage 3 - mAdbID:107984

description: mAdb experiment ID: 107984


title: Donor 2 - Pasage 12 - mAdbID:107983

description: mAdb experiment ID: 107983


title: Adrenocortical Carcinoma, ACC-31 [Affymetrix]

value: dead


title: FETAL CTRL 8

description:
normal brain sample
8221916011_R04C01


title: Adrenocortical Carcinoma, ACC-30 [Affymetrix]

value: Cushings


title: Donor 3 - Passage 2 - mAdbID:107982

description: mAdb experiment ID: 107982

value: Composed of total RNA from nine human tissues or cell lines:placental tissue, adult liver tissue, adult brain tissue, adult heart tissue, adult breast tissue, adult colon tissue, adult testis tissue, fetal brain tissue, testis cell line.

value: Bone Marrow


title: FETAL CTRL 6

description:
normal brain sample
8221916011_R02C01


title: FETAL CTRL 7

description:
normal brain sample
8221916011_R03C01


title: Adrenocortical Carcinoma, ACC-MPI1 [Affymetrix]

extract_protocol:
Tumor samples were flash-frozen and maintaned at -80 degrees C until chipped for RNA extraction
100 mg of tumor was chipped from flash frozen samples. The tissue was homogenized by sonication using the Covaris S-2 tissue processor in the presence of the RLT buffer from the Qiagen Rneasy kit. RNA was extracted with Trizol/chloroform and the aqueous phase purified using the RNeasy kit.

value: alive


title: FETAL CTRL 3

description:
normal brain sample
7970376148_R03C02


title: Adrenocortical Carcinoma, ACC-32 [Affymetrix]

value: F


title: Adrenocortical Carcinoma, ACC-MPI2 [Affymetrix]


title: Adrenocortical Carcinoma, ACC-4 [Affymetrix]


title: FETAL CTRL 4

description:
normal brain sample
7970376151_R05C01

value: normal (control)


title: Donor 2 - Passage 2 - mAdbID:107979

description: mAdb experiment ID: 107979


title: Adrenocortical Carcinoma, ACC-28 [Affymetrix]


title: FETAL CTRL 5

description:
normal brain sample
8221916011_R01C01


title: Donor 3 - Passage 9 - mAdbID:107980

description: mAdb experiment ID: 107980


title: Adrenocortical Carcinoma, ACC-27 [Affymetrix]

value: M


title: Donor 2 - Passage 10 - mAdbID:107977

description: mAdb experiment ID: 107977

value: Bone Marrow Stromal Cells (BMSC)


title: Adrenocortical Carcinoma, ACC-23 [Affymetrix]


title: Donor 3 - Passage 3 - mAdbID:107981

description: mAdb experiment ID: 107981


title: Adrenocortical Carcinoma, ACC-22 [Affymetrix]


title: FETAL CTRL 1

description:
normal brain sample
7973219008_R05C01


title: FETAL CTRL 2

description:
normal brain sample
7970376148_R01C01


title: Donor 6 - Passage 6 - mAdbID:107957

description: mAdb experiment ID: 107957


title: Donor 2 - Passage 11 - mAdbID:107976

description: mAdb experiment ID: 107976


title: Donor 6 - Passage 2 - mAdbID:107958

description: mAdb experiment ID: 107958


title: Adrenocortical Carcinoma, ACC-11 [Affymetrix]

value: aldosterone


title: Donor 6 - Passage 8 - mAdbID:107955

description: mAdb experiment ID: 107955


title: Adrenocortical Carcinoma, ACC-21 [Affymetrix]


title: Adrenocortical Carcinoma, ACC-26 [Affymetrix]


title: ETMR 8

description:
etmr tumour sample
6969568007_R01C02

source_name: ETMR sample

value: Embryonal tumor with multilayered rosettes (ETMR)

value: ETMR


title: ETMR cell line amp

description:
etmr tumour sample
9296930148_R02C01

source_name: ETMR cell line


title: Adrenocortical Carcinoma, ACC-MPI3 [Affymetrix]

value: Unknown


title: ETMR 10

description:
etmr tumour sample
9296931124_R04C02


title: ETMR xeno

description:
etmr tumour sample
9296930138_R06C01

source_name: ETMR xenograph


title: Adrenocortical Carcinoma, ACC-9 [Affymetrix]


title: Anaerobic glucose-limited IMZ383 chemostat-2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description:
IMZ383 2
S. cerevisiae anaerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

hyb_protocol: Hybridization and washing of Affymetrix chips were done according to manufacturer's instructions. For each strain analysed, microarrays were run on three independent cultures.

scan_protocol: Scanning of Affymetrix chips was done according to manufacturer's instructions.

data_processing: Processing of expression data (normalization, expression cut-off, etc.) was performed as described previously (Boer et al., J Biol Chem., 278:3265-74). The Significance Analysis of Microarrays (SAM, version 3.0) (Tusher et al., Proc Natl Acad Sci U S A., 98:5116-21) add-in to Microsoft Excel was used for comparison of replicate array experiments using a minimal fold change of two and false discovery rate of 1%. Overrepresentation of functional categories in sets of differentially expressed genes was analysed according to (Knijnenburg et al., BMC Genomics., 8:25).

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Glucose-limited chemostat culture -0.1H-1, IMZ383, anaerobic

label_protocol: Processing of total RNA was performed according to Affymetrix's instructions. RNA target preparation for microarray expression analysis was carried out according to the GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, USA) using 200 ng of total RNA for both pure and mixed cultures. The protocol was carried out with minor modifications, i.e. the Affymetrix polyA RNA controls were excluded from the aRNA amplification protocol and the IVT reactions were incubated for 16 h at 40°C. The quality of total RNA, cDNA, cRNA, and fragmented aRNA was checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

growth_protocol: Controlled batch and chemostat cultivation was carried out at 30°C in 2-L laboratory bioreactors (Applikon, Schiedam, The Netherlands) with working volumes of 1 L. Synthetic medium (Verduyn et al., Yeast, 8:501-17) supplemented with 7.5 g L-1 or 20 g L-1 glucose was used in aerobic and anaerobic cultures, respectively. In anaerobic bioreactor batch cultures, the medium contained 25 g L-1 glucose. Culture pH was maintained at 5.0 by automatic addition of 2 M KOH. In aerobic cultures, antifoam Pluronic PE 6100 (BASF, Ludwigshafen, Germany) was used. The antifoam was autoclaved (110 °C) separately from the other medium ingredients and added as a 15% (w/v) stock solution to give a final concentration of 0.15 g L-1. Aerobic bioreactors were sparged with 500 mL min-1 air and stirred at 800 rpm to ensure fully aerobic conditions. Anaerobic bioreactors were stirred at 800 rpm and sparged with 500 mL min-1 nitrogen (< 10 ppm oxygen). To minimize diffusion of oxygen, the bioreactors were equipped with Nonprene tubing and Viton O-rings and medium reservoirs were continuously flushed with nitrogen. Anaerobic growth media were supplemented with the anaerobic growth factors ergosterol (10 mg L-1) and Tween 80 (420 mg L-1). In anaerobic cultures, antifoam C Emulsion (Sigma-Aldrich) was autoclaved separately (120 °C) as 20 % (w/v) solution and added to a final concentration of 0.2 g L-1.

extract_protocol: Total RNA extraction was performed as described previously (Piper et al., J Biol Chem. 277:37001-8).

treatment_protocol: Sampling for transcriptome analysis from chemostat cultures was performed as described previously (Piper et al., J Biol Chem. 277:37001-8).

tag: strain

tag: genetic background

value: CEN.PK102-12A (MATa MAL2-8C SUC2 ura3-52 leu2-3,112 his3-Δ1)

tag: genotype/variation

value: MATa MAL2-8C SUC2 ura3-52 leu2-3,112 his3-Δ1 acs2::loxP-HIS3-loxP acs1::loxP-LEU2-loxP pUDE204 (URA3, pflB, pflA Escherichia coli)

tag: carbon source

value: glucose

tag: culture type

value: anaerobic


title: ETMR 5

description:
etmr tumour sample
6929689068_R01C01

tag: disease state


title: Donor 2 - Passage 3 - mAdbID:107978

description: mAdb experiment ID: 107978

tag: other

tag: cell type

tag: individual


title: Donor 6 - Passage 3 - mAdbID:107843

description: mAdb experiment ID: 107843

value: Bone Marrow Stromal Cell (BMSC)


title: Donor 6 - Passage 7 - mAdbID:107956

description: mAdb experiment ID: 107956


title: ETMR 4

description:
etmr tumour sample
6969568068_R01C01


title: ETMR 3

description:
etmr tumour sample
6969568042_R01C02


title: Anaerobic glucose-limited IMZ383 chemostat-3

description:
IMZ383 3
S. cerevisiae anaerobic glucose-limited chemostat with a dilution rate of 0.1h-1.


title: ETMR 6

description:
etmr tumour sample
6929689068_R04C02


title: ETMR 2

description:
etmr tumour sample
6969568009_R04C02


title: Anaerobic glucose-limited CEN.PK113-7D chemostat-1

description:
CEN.PK113-7D 4
S. cerevisiae anaerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

source_name: Glucose-limited chemostat culture -0.1H-1, CEN.PK113-7D, anaerobic

value: CEN.PK113-7D (MATa MAL2-8C SUC2)

value: MATa MAL2-8C SUC2


title: Anaerobic glucose-limited CEN.PK113-7D chemostat-2

description:
CEN.PK113-7D 5
S. cerevisiae anaerobic glucose-limited chemostat with a dilution rate of 0.1h-1.


title: ETMR 1

description:
etmr tumour sample
6969568009_R01C02


title: ETMR 7

description:
etmr tumour sample
6929689145_R05C02


title: ADULT CTRL 9

description:
normal brain sample
7973219007_R01C01

source_name: adult control brain

value: adult brain


title: Anaerobic glucose-limited CEN.PK113-7D chemostat-3

description:
CEN.PK113-7D 6
S. cerevisiae anaerobic glucose-limited chemostat with a dilution rate of 0.1h-1.


title: Adrenocortical Carcinoma, ACC-10 [Affymetrix]

tag: Stage

tag: tumor grade

tag: functional

tag: age in years

value: dead


title: Aerobic glucose-limited IMZ305 chemostat-3

description:
IMZ305 3
S. cerevisiae aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

source_name: Glucose-limited chemostat culture -0.1H-1, IMZ305, aerobic

value: MATa MAL2-8C SUC2 ura3-52 leu2-3,112 his3-Δ1ald2-ald3::loxP-LEU2-loxP ald4::loxP-HIS3-loxP ald5::loxP-KanMX4-loxP ald6::loxP-hphNT1-loxP acs2::loxP-natNT2-loxP acs1::AmdS pUDE151(URA3, eutE E. coli)

value: aerobic


title: Adrenocortical Carcinoma, ACC-5 [Affymetrix]

value: M

tag: survival status

tag: tumor size in cm

tag: tumor weight in grams

tag: batch


title: Adrenocortical Carcinoma, ACC-13 [Affymetrix]

value: Cushings

tag: gender

tag: survival in years


title: Adrenocortical Carcinoma, ACC-12 [Affymetrix]


title: ADULT CTRL 10

description:
normal brain sample
7973219007_R03C02

tag: tissue

value: normal (control)


title: ETMR 9

description:
etmr tumour sample
6929689154_R04C02

value: Embryonal tumor with multilayered rosettes (ETMR)


title: ADULT CTRL 7

description:
normal brain sample
7973219001_R03C02


title: Adrenocortical Carcinoma, ACC-17 [Affymetrix]

value: Recurrence

value: F

value: unknown


title: Adrenocortical Carcinoma, ACC-19 [Affymetrix]


title: Aerobic glucose-limited CEN.PK113-7D chemostat-3

description:
CEN.PK113-7D 3
S. cerevisiae aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

source_name: Glucose-limited chemostat culture -0.1H-1, CEN.PK113-7D, aerobic

tag: strain

tag: genetic background

tag: genotype/variation

tag: carbon source


title: S. kudriavzevii IFO 1802 replicate B, 12ºC fermentation against 28ºC fermentation.

city: Paterna

first: Jordi

last: Tronchoni

address: Avda. Agustín Escardino, 7

country: Spain

institute: CSIC

description: Comparative gene expression of S. kudriavzevii IFO1802 at 12ºC with respect to 28ºC. Replicate B

hyb_protocol: A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight.  (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution

scan_protocol: Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.

data_processing: Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).The individual data sets were normalized to a log2 ratio value of 1. After normalization, data were filtered to remove spots flagged as not found. Genes with a two-fold log2 ratio values were considered to be significantly expressed.

organism: Saccharomyces kudriavzevii

source_name: yeast cells from wine fermentation at 28ºC

label_protocol: 2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA).

growth_protocol: Wine fermentations in Tempranillo must at 12ºC or 28ºC

extract_protocol: RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).

tag: growth phase

value: Beginning of exponential phase

source_name: yeast cells from wine fermentation at 12ºC


title: S. kudriavzevii IFO 1802 replicate A, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. kudriavzevii IFO1802 at 12ºC with respect to 28ºC. Replicate A


title: Aerobic glucose-limited IMZ305 chemostat-1

description:
IMZ305 1
S. cerevisiae aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

value: CEN.PK102-12A (MATa MAL2-8C SUC2 ura3-52 leu2-3,112 his3-Δ1)

value: glucose

tag: culture type


title: ADULT CTRL 5

description:
normal brain sample
f3

tag: disease state


title: Normal adrenal gland, ACC-Norm2 [Affymetrix]

source_name: whole normal adrenal gland

extract_protocol:
normal adrenal gland samples were flash-frozen and maintaned at -80 degrees C until chipped for RNA extraction
100 mg of normal adrenal gland was chipped from flash frozen samples. The tissue was homogenized by sonication using the Covaris S-2 tissue processor in the presence of the RLT buffer from the Qiagen Rneasy kit. RNA was extracted with Trizol/chloroform and the aqueous phase purified using the RNeasy kit.

tag: Stage

tag: tumor grade

value: Unknown


title: Adrenocortical Carcinoma, ACC-8 [Affymetrix]

tag: functional

tag: age in years


title: ADULT CTRL 6

description:
normal brain sample
7973219001_R01C01


title: ADULT CTRL 11

description:
normal brain sample
7973219044_R04C01


title: Aerobic glucose-limited IMZ305 chemostat-2

description:
IMZ305 2
S. cerevisiae aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.


title: Normal adrenal gland, ACC-0523 [Affymetrix]

tag: survival status

tag: tumor size in cm


title: S. kudriavzevii IFO 1802 replicate C, Dye Swap, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. kudriavzevii IFO1802 at 12ºC with respect to 28ºC. Replicate C with Dye Swap.


title: Aerobic glucose-limited CEN.PK113-7D chemostat-1

description:
CEN.PK113-7D 1
S. cerevisiae aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

value: CEN.PK113-7D (MATa MAL2-8C SUC2)


title: Aerobic glucose-limited CEN.PK113-7D chemostat-2

description:
CEN.PK113-7D 2
S. cerevisiae aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

value: MATa MAL2-8C SUC2


title: S. cerevisiae T73 replicate B, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. cerevisiae T73 at 12ºC with respect to 28ºC. Replicate B

value: Lalvin T73


title: S. cerevisiae T73 replicate C, Dye Swap, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. cerevisiae T73 at 12ºC with respect to 28ºC. Replicate C with Dye Swap.


title: S. cerevisiae T73 replicate A, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. cerevisiae T73 at 12ºC with respect to 28ºC. Replicate A


title: Normal adrenal gland, ACC-Norm1 [Affymetrix]

tag: tumor weight in grams

tag: batch


title: Hdac6 KD,replicate A

status: Public on Nov 20 2013

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

institute: A*STAR

description: gene expression in indicated KD

hyb_protocol: Fifty picomoles of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 125 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4X44K Whole Mouse Genome Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner (G2565CA)  immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107 and Grid: 026655_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. We used the quantile normalization in R (bioconductor) to obtain the value in the Sample data tables.

source_name: embryonic stem cells, KD replicate A

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 5 ug of total RNA using Low Input Quick Amp Labeling Kit protocol (Agilent) with minor modifications. Briefly, cRNA was amplified by in vitro transcription with amino-allyl UTP (3:2 ratio for amino-ally UTP: UTP) overnight at 37°C. Then, cRNA was purified using Zymo RNA purification columns (Zymo, Irvine, CA) and labelled with Cy3 (GE healthcare) at RT for 60 minutes in the dark. The fluorescence intensity of Cy3 was determined by NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.

extract_protocol: Trizol, followed by Zymo RNA columns.

treatment_protocol: In one 10 cm2 dish, 1X10^6 cells were infected with 30 ul of concentrated lentivirus. After 12-15 hours, the media was replaced and cells were cultured until 72 hours post-infection.

tag: development stage

tag: treatment

value: Lentiviral-based shRNA was used for Hdac6 knock down


title: Tip60 KD,replicate A

description: gene expression in indicated KD

value: Lentiviral-based shRNA was used for Tip60 knock down


title: ADULT CTRL 8

description:
normal brain sample
7973219005_R05C01

tag: tissue

value: adult brain


title: Normal adrenal gland, ACC-0520 [Affymetrix]

tag: gender

tag: survival in years


title: 300mM 3NP at 3d

city: Tokyo

first: Masato

last: Fujioka

address: 35 Shinanomachi Shinjuku

department: Otorhinolaryngology

country: Japan

institute: Keio University School of Med

description: Gene expression data from upper basal trun of cochlear lateral wall 3 day after 300mM of 3NP treatment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Expression Array using Affymetrix genechip hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Molecular Dynamicfs GenePix4000A Lucida Module1(Amersham parmacia biotech Ludica base).

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.

source_name: Upper basal trun of cochlear lateral wall 3 day after 300mM of 3NP treatment

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: Female Sprague-Dawley rats weighing between 180 g and 210 g (8–10 weeks old) were purchased and bread in a SPF graded clean room.

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

treatment_protocol: After general anesthesia with pentobarbital (30–40 mg/kg, i.p.) and the local administration of lidocaine (1%), an incision was made posterior to the left pinna near the external meatus. The left otic bulla was opened and the round window niche was infused with 3-NP (500 mM or 300 mM) dissolved in saline (pH adjusted to 7.4 with NaOH). Infusion with saline alone was used as a control. Following treatment, and before the wound was closed, a small piece of gelatin was placed onto the niche to keep the solution in place and to allow for head movement after the animals awoke. The right cochlea was surgically destroyed to avoid cross-hearing during the recording of auditory brain-stem responses. The second turn of the lateral wall (excluding the stria vascularis) was harvested under the dissection microscope.

value: cochlear lateral wall

tag: time

value: 3 d

tag: model

value: acute mitochondrial dysfunction model in the cochlea

tag: strain

value: Sprague-Dawley


title: Tip60Hdac6 KD,replicate B

description: gene expression in indicated KD

source_name: embryonic stem cells, KD replicate B

value: Lentiviral-based shRNA was used for Tip60 & Hdac6 knock down


title: Tip60Hdac6 KD,replicate A

description: gene expression in indicated KD


title: 300mM 3NP at  1d

description: Gene expression data from upper basal trun of cochlear lateral wall 1 day after 300mM of 3NP treatment

source_name: Upper basal trun of cochlear lateral wall 1 day after 300mM of 3NP treatment

value: 1 d


title: Anaerobic glucose-limited IMZ383 chemostat-1

description:
IMZ383 1
S. cerevisiae anaerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

tag: genetic background

tag: genotype/variation

value: MATa MAL2-8C SUC2 ura3-52 leu2-3,112 his3-Δ1 acs2::loxP-HIS3-loxP acs1::loxP-LEU2-loxP pUDE204 (URA3, pflB, pflA Escherichia coli)

tag: carbon source

tag: culture type

value: anaerobic


title: ADULT CTRL 4

description:
normal brain sample
f2

tag: disease state

value: normal (control)


title: ADULT CTRL 3

description:
normal brain sample
f1


title: TRAIL R1 siRNA R1si_40h_3

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: miRNA expression profiles from cell culture

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using AGCC (Affymetrix default settings) and normalized using RMA

source_name: Panc1 cells, treated with TRAIL R1 siRNA for 40h

growth_protocol: Cells were cultured as previously described (Trauzold et al., 2001). For transient transfections DharmaFECT1 transfection reagent (Thermo Scientific, Dharmacon Epsom, UK; Panc1, MDA-MB-231, HCT116 cells) or NeoFX (Ambion, Applied Biosystems, Germany; Panc89 cells) were used. The in vitro differentiation assay of A818-6 cells was performed as described (Lehnert et al., 2001).

extract_protocol: RNA extracted using miRVana (Ambion) according to the manufacturers guidelines

treatment_protocol: Panc1 cells were treated for 40h with siRNA (On-Targetplus® smart pool siRNA; Dharmacon) against TRAIL-R2 or with control siRNA in experimental setups with 5 biological replicates per group.

value: TRAIL R1 siRNA

tag: cell line


title: Tip60 KD,replicate B

description: gene expression in indicated KD


title: TRAIL R1 siRNA R1si_40h_4

label_protocol: according to the manufacturers guidelines (Affymetrix)


title: saline at 1d

description: Gene expression data from upper basal trun of cochlear lateral wall 1 day after saline treatment

source_name: Upper basal trun of cochlear lateral wall 1 day after saline treatment

value: saline


title: Hdac6 KD,replicate B

description: gene expression in indicated KD


title: ADULT CTRL 1

description:
normal brain sample
a1


title: EGFP KD,replicate B

description: gene expression in indicated KD

value: control


title: EGFP KD,replicate A

description: gene expression in indicated KD


title: TRAIL R1 siRNA R1si_40h_1


title: TRAIL R1 siRNA R1si_40h_5


title: TRAIL R1 siRNA R1si_40h_2


title: TRAIL R2 siRNA R2si_40h_4

source_name: Panc1 cells, treated with TRAIL R2 siRNA for 40h

value: TRAIL R2 siRNA


title: TRAIL R2 siRNA R2si_40h_2


title: control siRNA Ksi_40h_4

source_name: Panc1 cells, treated with control siRNA for 40h

value: control siRNA


title: control siRNA Ksi_40h_3


title: control siRNA Ksi_40h_1


title: control siRNA Ksi_40h_2


title: TRAIL R2 siRNA R2si_40h_3


title: ADULT CTRL 2

description:
normal brain sample
a2


title: control siRNA Ksi_40h_5


title: saline at 3d

description: Gene expression data from upper basal trun of cochlear lateral wall 3 day after saline treatment

source_name: Upper basal trun of cochlear lateral wall 3 day after saline treatment


title: CO-160

city: Seville

first: Purificacion

last: Estevez-Garcia

state: Seville

address: Manuel Siurot avenue

department: Molecular Oncology

institute: Institute of Biomedicine

description: test

data_processing: Relative quantification of gene expression was determined using the comparative cycle threshold method (2(-ddCt)) as previously described Ref : Livak, K. J., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408. .

label: FAM

source_name: colorectal cell fraction

label_protocol: FAM.

extract_protocol: All colorectal tissue samples were maintained at -80ºC until RNA extraction and grinded under liquid nitrogen. Homogenization was achieved using QIAshredder homogenizers and total RNA was extracted using RNeasy Mini kit (both kits from Qiagen Inc; Valencia, CA, USA).

tag: response to chemotherapy

value: CONTROL

value: colorectal tissue


title: PGK-212

description: test


title: PGK-204

description: test


title: PGK-210

description: test


title: PGK-202

description: test


title: PGK-220

description: test


title: PGK-208

description: test


title: PGK-198

description: test


title: CO-163

description: test


title: CO-142

description: test


title: CO-162

description: test


title: PGK-216

description: test


title: CO-140

description: test


title: CO-138

description: test


title: CO-150

description: test


title: CO-131 (PGK-258)

description: test


title: CO-145

description: test


title: CO-123 (PGK-241)

description: test


title: CO-127 (PGK-250)

description: test


title: CO-121 (PGK-236)

description: test


title: CO-19.3

description: test


title: CO-18.3

description: test


title: CO-20.3

description: test


title: CO-16.1

description: test


title: CO-14.1

description: test


title: CO-6.1

description: test


title: CO-8.3

description: test


title: CO-175

description: test

value: NON-RESPONDER

value: colorectal cancer tumor


title: CO-5.1

description: test


title: CO-4.1

description: test


title: CO-164

description: test

value: RESPONDER


title: CO-10.3

description: test


title: CO-13.2

description: test


title: CO-165

description: test


title: CO-170

description: test


title: CO-174

description: test


title: CO-22.3

description: test


title: CO-130 (PGK-256)

description: test


title: CO-159

description: test


title: CO-161

description: test


title: PGK-265

description: test


title: PGK-267

description: test


title: PGK-269

description: test


title: CO-158

description: test


title: CO-172

description: test


title: CO-168

description: test


title: TRAIL R2 siRNA R2si_40h_5


title: PGK-263

description: test


title: PGK-261

description: test


title: PGK-257 (CO-203)

description: test


title: PGK-255

description: test


title: PGK-251

description: test


title: PGK-270

description: test


title: PGK-249

description: test


title: PGK-247

description: test


title: PGK-246

description: test


title: PGK-242

description: test


title: PGK-235

description: test


title: PGK-239

description: test


title: PGK-259

description: test


title: PGK-244

description: test


title: MDH2

type: SRA

city: Lausanne

first: Marion

last: LELEU

address: Station 15

country: Switzerland

institute: EPFL

description:
Primer name: MDH2_4C_seq_F2
Sequence: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTCTGATACTGGAGCCCGAGATGA
Primer name: MDH2_4C_seq_R
Sequence: CAAGCAGAAGACGGCATACGACCCAGTTCTGTTAGGCGTTC

library_source: genomic

data_processing:
Reads were normalized to the total number of reads. Smoothed data were obtained by applying a running mean algorithm with 19 fragments per window.As the data from the three replicated viewpoints were strongly correlated,  we used the average of each fragments for these experiments.
We used a domainogram algorithm to detect significantly interacting regions without imposing a fixed window size as suggested in [de Wit et al, Global chromatin domain organization of the Drosophila genome, PLoS Genet. 2008 Mar 28;4(3)]. The positive signals were ranked per chromosome and Bricks (Blocks of Regulators In Chromosomal Kontext) were called based on a FDR threshold of 0.1 for “short-range” interactions, defined as interactions within 2.5 Mb up- and downstream of GBAS and MDH2, the first and last viewpoint, respectively (HSA7 coordinates: 53,532,296-78,116,172; about 25 Mb around the WBSCR). Genomic space outside of these borders was called the “long-range” region. As interactions in this long-range region are more subject to random interactions, we used a more stringent FDR threshold of 0.001. To determine differentially interacting regions between the WBS and Ctrl cells, we first computed the log2 ratio of WBS over Ctrl of the smoothed profile corrected data and selected ratio Bricks (as described above) that were specific to either WBS or Ctrl.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files: The 2 "smoothed" files correspond to smoothed data for 2 conditions (WT and WBS), while file "ratios_selectedBricks.bedGraph" is a list of significantly interacting regions obtained as described above.

source_name: EBV transformed mononuclear cells from peripheral blood

growth_protocol: Lymphoblastoid cell lines were grown in RPMI1640 medium supplemented with 10% FCS and 1% PS

extract_protocol:
50 million exponentially growing cells were harvested and crosslinked with 1% formaldehyde, lysed and cut with the restriction enzyme BglII. After ligation and reversal of the crosslinks, the DNA was purified to obtain the 3C library. This 3C library was further digested with NlaIII and circularized to obtain a 4C library. The inverse PCR primers to make the 4C-seq templates were designed to contain the Illumina adaptor tails, as well as the bait-specific sequences for each of the six loci we interrogated. 4C libraries were multiplexed (three samples per mulitplex), libraries were prepared according to Illumina's instructions for ChIP-seq but without size selection and sequenced on Illumina GAIIxl (76-mer single end tags)
Instrument model: Illumina GAIIxl
library_strategy: 4C-seq

tag: cell type

value: Lymphoblastoid cells

tag: control lymphoblastoid cell line id

tag: wbs lymphoblastoid cell line id

tag: interrogated locus


title: POR

description:
Primer name: POR_4C_seq_F
Sequence: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGTCTCTTCCCCTCCCTACCAC
Primer name: POR_4C_seq_R
Sequence: CAAGCAGAAGACGGCATACGATACGTAAGGAACGCGTCCAA

value: POR


title: Breast control PTB shRNA, PTBP1 knockdown, Dox treated, biological rep4

city: Tucson

first: Vincent

last: Gardeux

address: 1657 East Helen Street, PO Box 210240

department: Medicine

institute: University of Arizona

description: Gene expression data

hyb_protocol: Hybridization were performed following Affymetrix protocols

scan_protocol: standard Affymetrix protocol

data_processing: The raw data were normalized according to the Robust Multiple-array Average (RMA) technique using Affymetrix Power Tools (APT).

source_name: Breast cancer cell line MDA-MB231

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

growth_protocol: Cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine in a humid environment at 37°C, with 5% CO2.

extract_protocol: For each of the cell lines, MDA-MB231 and A2780, total RNAs were extracted from four biological replicates of PTBP1-depleted cells, PTBP1-KD (4× PTBP1/+DOX) and eight biological replicates control cells (4× PTBP1/-DOX and 4× LUCshRNA/+DOX) by Direct-zol RNA kit (Zymo Research, Irvine, CA) . All paired samples consist of PTBP1-depleted cells (PTBP1-KD) and matched control cells. Qualities of RNA were assessed based on the RNA quality indicator (RQI ≥ 8) using Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA).

treatment_protocol: In order to analyze the effect of PTBP1 depletion, two consecutive viral transductions were performed in both MDA-MB231 and A2780 cell lines. Cells were plated on 24-well plate (10-20×104 cells/well), maintained in culture for 16 hours, and then medium containing LV-tTR/KRAB-Red lentiviral particles was added. Following 16 h of incubation, cells were transduced a second time by LV-THM/PTBshRNA or LV-THM/LUCshRNA lentiviral particles. Clones expressing both red and green fluorescent protein (dsRED and GFP respectively) were selected and expanded. Following 16 h of incubation, cells were washed and split in two subcultures, one without doxycycline (PTBP1/-DOX; Control , express PTBP1 WT) and the other with Doxycycline (DOX) at a final concentration of 1 μg/ml (PTBP1/+DOX; PTBP1-KD). Doxycycline was prepared according to the manufacturer’s recommendations (Sigma-Aldrich, St. Louis, MO). Five days later, cells were analyzed by fluorescence microscopy, and PTBP1 gene expression was assessed using PCR and Western Blotting (data not shown). The cells that were transduced by LV-LUCshRNA express PTBP1 regardless of the presence of DOX (LUCshRNA/+DOX). Constructs and lentivirus preparation were performed as previously described

tag: tissue

value: Epithelial, breast adenorcinoma

value: Breast cancer cell line MDA-MB231

tag: age

value: derived from breast adenocarcinoma of female 51 years adult

tag: treatment