title: 1833 expressing HOXA9, biological replicate 1

city: Chicago

first: Miao

institute: University of Chicago

hyb_protocol: Following fragmentation, 5.5 ug cRNA were hybridized on GeneChip Hu-ST1.0 Array using GeneChip Hybridization, Wash and Stain Kit according to manufacturer's protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Using fluidics protocol FS450_0007, and scan with Fluidics Station 450.

data_processing: Hybridization and background correction according to the standard protocols, the quantified signals were normalized using Robust Multi-array Average (RMA), an algorithm performing background adjustment, quantile normalization, and log-transformation using R version 2.11 and related packages from Bioconductor version 2.4 3 for analysis of the normalized data.

source_name: 1834 cells with HOXA9-expression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA Using GeneChip WT terminal Labeling Kit.

growth_protocol: Cells were cultured in complete medium consisting of DMEM supplemented with 10% FBS, 50 U/ml penicillin and 50 μg/ml streptomycin. For Tet1 or HOXA9 inducible cells, Tet System Approved FBS was used instead.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit following the manufacturer’s instructions.

treatment_protocol: HMGA2 depletion were achieved by transducing the cells with HMGA2 shRNA in a pLKO.1 lentiviral vector, and were selected and maintained in 0.5 μg/ml puromycin. The inducible Tet1 or HOXA9 expressing cell line was generated by co-transducing the cells with pLVX-TRE3G-Flag-Tet1 (expressing inducible Tet1) or pLVX-TRE3G-HOXA9 (expressing inducible HOXA9) and pCMV-Tet3G (expressing Tet-On 3G) in the lentiviral vectors (Clontech, Mountain View, CA), and were selected in 0.5 μg/ml puromycin and 500 μg/ml G418.

value: breast cancer cells

tag: genotype/variation

value: expressing induced HOXA9


title: 2D MDCK, biological rep3

status: Public on Jun 03 2013

type: RNA

city: New Haven

first: Erika

middle: Krystal

last: Wells

state: CT

address: 333 Cedar Street SHM B117/119

department: Cellular and Molecular Physiology

country: USA

institute: Yale University

description: Gene expression data from flat sheets of MDCK cells derived from 2D collagen type I culture

hyb_protocol: Fragments of 35-200 bases were hybridized to Affymetrix Canine Genome 2.0 Array at 45oC for 16 hours. Genechips were washed and stained with an Affymetrix fluidics station, stained with streptavidin-phycoerythrin and scanned with an Affymetrix GeneChip Scanner 3000.

scan_protocol: GeneChips were analyzed with Affymetrix GeneChip Operating Software (GCOS).

data_processing: The data were analyzed using Guanine and Cysteine-Robust Multiarray Analysis (GC-RMA).

label: biotin

molecule: total RNA

organism: Canis lupus familiaris

source_name: MDCK cells grown in 2-dimensional collagen culture for 8 days

label_protocol: 5 ug of pooled total RNA was used to obtain biotinylated cRNA following the standard Affymetrix protocol

growth_protocol: MDCK II tet-off cells were grown in DMEM (Invitrogen) supplemented with 10% FBS, 1% penicillin/streptomycin, 1% L-glutamine and G418 (Gibco). Cells were maintained at 37oC with 5% CO2 atmosphere in a humidified incubator.

extract_protocol: Type I collagen gels were digested with 5 mls of a 0.01% collagenase mixture containing RNase OUT in PBS at 4oC for approximately 1 hour on a rotator. Following two low speed (500 rpm) spins and PBS washes 1ml TRIZol reagent was added to each individual sample. Total RNA was isolated following the manufacturer's instructions. Total RNA was purified using the Qiagen RNeasy Kit according to the manufacturer's instructions. Due to limitations in yield, 4 separate RNA samples were pooled for application to each individual array.

treatment_protocol: Fresh media was applied on the initial day of growth (day 0) and subsequently changed on days 3 and 6 of growth.  All cultures were grown until day 8.

tag: final morphology

value: Flat sheet

tag: cell line

value: Madin-Darby Canine Kidney

tag: growth condition


title: 1833 shHMGA2, biological replicate 1

last: Sun

organism: Homo sapiens

source_name: 1833 cells with HMGA2-depletion

tag: cell type

value: expressing HMGA2 shRNA


title: 1833 expressing Tet1, biological replicate 3

source_name: 1834 cells with Tet1-expression

value: expressing induced Tet1


title: 1833 shHMGA2, biological replicate 3


title: 1833 expressing Tet1, biological replicate 2


title: 1833 expressing HOXA9, biological replicate 3


title: 1833 shHMGA2, biological replicate 2


title: 2D MDCK, biological rep1


title: 2D MDCK, biological rep2


title: Primary tumour region 2 P6

status: Public on Jun 04 2013

type: genomic

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

description: clear cell Renal Cell Carinoma, region 2

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
B Allele Frequencies and logRs were obtained using the aroma R package.
B Allele Frequencies: estimated ratio of allele B against allele A;  logR: logarithmic ratio of DNA content against expectations.

molecule: genomic DNA

source_name: kidney

label_protocol: standard Affymetrix protocol

extract_protocol: Fresh frozen

treatment_protocol: Patients P5, P6 and P7 underwent 6 weeks of Everolimus pre-treatment before a week wash-out followed by nephrectomy. All 5 other patients were untreated.

tag: tissue

value: Primary tumour

tag: tissue section

value: region 2

tag: subject

tag: disease state

value: clear cell Renal Cell Carinoma

tag: batch


title: Primary tumour region 1 P6

description: clear cell Renal Cell Carinoma, region 1

value: region 1


title: 1833 control, biological replicate 1

source_name: 1833 cells


title: iF_donor4_clonal1

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute • Transfer 80μl of hyb solution to each array, then tape holes • Hybridize 16 hours at 45° at 60rpm • Fluidics washing is FS450_00007

scan_protocol: according to Affymetrix protocol - Affymetrix Gene ChIP Scanner 3000 7G

data_processing: normalization method: RMA

source_name: iPSC clonal cultivated

label_protocol: Samples were amplified and labelled using the Ambion® WT Expression Kit, combined with the GeneChip® WT Terminal Labeling and Controls Kit according to the manufacturers instructions.

growth_protocol: Cells were grown in hIPS-medium (Knockout-DMEM with 20 % Knockout serum replacement,100 U/ml penicillin/streptomycin, 2 mM l-Glutamin, 0,1 mM ß-Mercaptoethanol (all Gibco) and 10 ng/ml basic fibroblast growth factor (bFGF; PeproTech, NJ, USA))

extract_protocol: In P3 (Negative control) or P10 (Bulk/Clonal Cultures) cells were harvested and RNA was isolated using a NucleoSpin miRNA Kit (Macherey Nagel)

treatment_protocol: Human dermal fibroblasts (HDFs) were isolated from skin samples of patients undergoing surgical interventions after written consent according to the guidelines specifically approved by the Ethics Committee of the RWTH Aachen University (Permit Number 163/07). When reaching Passage 2 or 3, cells were transfected with episomal plasmid mixtures as described by Okita et al. (Nature Methods, 2011, 8, 409-412) using a NEON transfection system. Transfected cells without plasmids were used as negative control. After 21 days, emerged iPS-like colonies were dissociated using collagenase and reseeded as bulk culture on MEFs or single colonies were picked manually and transferred into new culture vessels.

tag: gender

value: male

value: iPSC

tag: cultures

value: clonal


title: iF_donor3_bulk1

source_name: iPSC bulk cultivation

growth_protocol: Cells were grown in hIPS-medium (Knockout-DMEM with 20 % Knockout serum replacement, 100 U/ml penicillin/streptomycin, 2 mM l-Glutamin, 0,1 mM ß-Mercaptoethanol (all Gibco) and 10 ng/ml basic fibroblast growth factor (bFGF; PeproTech, NJ, USA))

value: female

value: bulk


title: iF_donor1_bulk1


title: iF_donor1_clonal1


title: iF_donor3_clonal2


title: F_donor2

source_name: Fibroblasts

value: fibroblasts


title: iF_donor3_bulk3

growth_protocol: Cells were grown in hIPS-medium (Knockout-DMEM with 20 % Knockout serum replacement, 100 U/ml penicillin/streptomycin, 2 mM L-Glutamin, 0,1 mM ß-Mercaptoethanol (all Gibco) and 10 ng/ml basic fibroblast growth factor (bFGF; PeproTech, NJ, USA)


title: 1833 expressing Tet1, biological replicate 1


title: Ph+ ALL_Bcor Fl/Y CRE-3

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: RMA- Partek Genomics suite 6.5

label: Biotin

organism: Mus musculus

source_name: Total RNA from Ph+ ALL

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

tag: strain

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL

value: Bcor fl/Y

tag: transduction

tag: treatment

value: 2 days 4OH-Tamoxifen 0.5 micromolar


title: F_donor1

growth_protocol: Cells were grown in hIPS-medium (Knockout-DMEM with 20 % Knockout serum replacement, 1% penicillin/streptomycin, 2 mM l-Glutamin, 0,1 mM ß-Mercaptoethanol (all Gibco) and 10 ng/ml basic fibroblast growth factor (bFGF; PeproTech, NJ, USA))


title: iF_donor3_bulk2


title: Ph+ ALL_Bcor Fl/Y CRE-2

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)


title: Ph+ ALL_Bcor Fl/Y ERT-3


title: 1833 expressing HOXA9, biological replicate 2

value: breast cancer cells

value: expressing induced HOXA9


title: Primary tumour region 7 P5

description: clear cell Renal Cell Carinoma, region 7

value: region 7


title: Primary tumour region 3 P5

description: clear cell Renal Cell Carinoma, region 3

value: Primary tumour

value: region 3


title: Ph+ ALL_Bcor Fl/Y ERT-1


title: Normal kidney P6

description: normal adult kidney

value: Normal kidney

value: normal


title: Primary tumour region 5 P5

description: clear cell Renal Cell Carinoma, region 6

value: region 5

value: clear cell Renal Cell Carinoma


title: Ph+ ALL_Bcor Fl/Y ERT-2


title: Primary tumour region 6 P5

value: region 6


title: Ph+ ALL_ETV5 WT-3

value: ETV5 WT


title: Ph+ ALL_SPRY1-2 fl/fl ERT-3

value: FvB/N

value: SPRY1/2 fl/fl


title: Ph+ ALL_SPRY1-2 fl/fl ERT-2

value: BCR-ABL1 transformed pre-B cells


title: Ph+ ALL_ETV5 KO-1

value: BCR-ABL1-driven ALL

value: ETV5 KO


title: Ph+ ALL_SPRY1-2 fl/fl CRE-3

value: 2 days 4OH-Tamoxifen 0.5 micromolar


title: iF_donor3_clonal3

value: female

value: iPSC

value: clonal


title: Ph+ ALL_SPRY1-2 fl/fl CRE-2


title: Ph+ ALL_SPRY1-2 fl/fl ERT-1


title: Ph+ ALL_ETV5 KO-3


title: Ph+ ALL_ETV5 KO-2


title: Normal kidney P5

description: normal adult kidney


title: Ph+ ALL_Dusp6 KO-3

value: Dusp6 KO


title: Ph+ ALL_Dusp6 KO-2


title: 1833 control, biological replicate 3

value: breast cancer cells


title: Ph+ ALL_Ptpn6 +/fl_CRE-3

value: Ptpn6 +/fl


title: Ph+ ALL_Ptpn6 +/fl_CRE-2


title: Ph+ ALL_Dusp6 KO-1


title: Ph+ ALL_Dusp6 WT-3

value: Dusp6 WT


title: Ph+ ALL_Ptpn6 +/fl_CRE-1


title: Ph+ ALL_Dusp6 WT-2


title: Ph+ ALL_Dusp6 WT-1


title: Ph+ ALL_Ptpn6 +/fl_ERT-3


title: Ph+ ALL_Ptpn6 +/fl_ERT-2


title: Ph+ ALL_Inpp5d fl/fl_CRE-3

value: Inpp5d fl/fl


title: Ph+ ALL_Inpp5d fl/fl_ERT-2


title: Ph+ ALL_Inpp5d fl/fl_CRE-2


title: Ph+ ALL_Bcor Fl/Y CRE-1

value: Bcor fl/Y


title: Ph+ ALL_Ptpn6 +/fl_ERT-1


title: Ph+ ALL_Inpp5d fl/fl_ERT-3


title: Ph+ ALL_Pten fl/fl_CRE-3

data_processing: RMA-Partek Genomics suite 6.5

value: Pten fl/fl


title: Ph+ ALL_ETV5 WT-1

value: ETV5 WT


title: Ph+ ALL_Pten fl/fl_ERT-3


title: Ph+ ALL_SPRY1-2 fl/fl CRE-1

value: FvB/N


title: Ph+ ALL_Inpp5d fl/fl_CRE-1


title: Immortalized breast epithelium cell line  MCF12A

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

hyb_protocol: The array hybridization followed the standard affymetrix protocols.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files was uploaded into Partek Genomics Suites 6.5 and processed using the mRNA expression pipeline. The data was quantile-normalized, summarized (median polish), and log2-transformed.

label_protocol: One μg of small RNA from each sample was labeled with biotin using the FlashTag Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: Breast cancer cell lines BT474, MDA-MB-468, T47D, ZR-75-1, MCF7, SK-BR3, MDA-MB-231, HS578T, BT549, SUM159 cell line were cultured in DMEM media with 10% fetal bovine serum (FBS). Immortalized breast epithelium cell lines MCF10A and MCF12A were cultured in DMEM/F12 supplemented with 5% horse serum, 20 ng/mL EGF, 10 μg/mL insulin, 100 ng/ml cholera toxin, and 500 ng/ml hydrocortisone.

extract_protocol: Total RNA was extracted using the QiazolTM Lysis reagent (Qiagen, Valencia, CA, USA). Small molecular weight RNA was extracted using the mirVanaTM miRNA Isolation Kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.

value: breast

tag: cell line type

value: Immortalized breast epithelium cells

tag: molecule subtype

value: small RNA


title: Immortalized breast epithelium cell line  MCF10A


title: Breast cancer cell line HS578T

source_name: aggressive breast cancer cell line

value: Aggressive cell line

value: Breast cancer cells


title: Ph+ ALL_ETV5 WT-2

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL

tag: genotype/variation


title: Breast cancer cell line BT549


title: Breast cancer cell line SUM159


title: Ph+ ALL_Pten fl/fl_CRE-2

value: 2 days 4OH-Tamoxifen 0.5 micromolar


title: Breast cancer cell line MDA-MB-231


title: Ph+ ALL_Inpp5d fl/fl_ERT-1


title: Breast cancer cell line SK-BR3

source_name: Less-aggressive breast cancer cell line

value: Less-aggressive cell line


title: Breast cancer cell line MCF7


title: Breast cancer cell line ZR-75-1


title: Ph+ ALL_Pten fl/fl_ERT-1


title: iF_donor3_clonal1

value: female

value: iPSC

value: clonal


title: 1833 control, biological replicate 2

value: breast cancer cells


title: Breast cancer cell line T47D


title: Ph+ ALL_Pten fl/fl_ERT-2


title: Primary tumour region 1 P5

value: Primary tumour

value: region 1

value: clear cell Renal Cell Carinoma


title: Primary tumour region 4 P5

description: clear cell Renal Cell Carinoma, region 4

value: region 4


title: wt RNA pooled from embryonic murine heart tissue

city: Heidelberg

first: Sandra

last: Hoffmann

address: Im Neuenheimer Feld 366

department: Department of Human Molecular Genetics

institute: Institute of Human Genetics

description: Gene expression data from murine widtype right atria E11.5

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, versin 4, from SAS. Gene expression profiling was performed using arrays of MoGene-1_0_st-V1 -type from Affymetrix. A Custom CDF Version 14 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: heart tissue

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

extract_protocol: Tissue was stored at 80°C until RNA preparation. We dissected the right atria of E11.5 hearts that comprise the Shox2 expressing sinus venosus myocardium and venous valves. For total RNA isolation by TRIzol® (Invitrogen), samples from embryonic right atria (E11.5) of the same genotype (wildtype and Shox2-/-) were pooled. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: outbred line

tag: genotype

value: WT


title: ko RNA pooled from embryonic murine heart tissue

description: Gene expression data from murine shox2 knockout right atria E11.5


title: Breast cancer cell line MDA-MB-468

tag: cell line

value: breast


title: Breast cancer cell line BT474

tag: cell type

value: small RNA


title: Pt7_0

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

hyb_protocol: Samples were hybridized to the human Illumina WG 8v2 Sentrix Beadchip Array according to standard Illumina protocol.

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina BeadStudio v.3.0 software was used to export expression levels and detection p-values for each probe of each sample. Arrays were quantile normalized and filtered to remove non-informative probes. A probe was called non-informative if it had expression signals with detection p-value>0.05 in all samples.

source_name: Peripheral Blood Mononuclear Cells (PBMC) from patients treated with romidepsin

label_protocol: Illumina Label Protocol

extract_protocol: RNA purification was carried out at Wistar using TriReagent Molecular Research) as recommended and controlled for quality using the Bioanalyzer. Only samples with 28S/16S ratios >0.75 were used for further studies. A constant amount (500ng) of total RNA was amplified as recommended by Illumina.

tag: time class

tag: sample id


title: Pt6_0


title: Pt6_4


title: Primary tumour region 2 P5

tag: tissue

tag: tissue section

value: region 2

tag: subject


title: Pt4_0


title: FCB-br1 vs FCB - repeat 4 - mAdbID:84878

city: Rockville

first: Sanjay

middle: Arvind

last: Desai

state: Maryland

address: 12735 Twinbrook Parkway

department: Laboratory of Malaria and Vector Research

institute: National Institute of Allergy and Infectious Diseases, NIH

description: mAdb experiment ID: 84878

hyb_protocol: Sample Hybridization Protocol Other: Hybridizations to microarray slides were done in 5× SSC/0.2% SDS/25% formamide with 180 mg/mL salmon sperm DNA at 45C overnight.

scan_protocol: Creator: GenePix Pro 6.0.1.27 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.68;; 3.76 Temperature: 29.71

data_processing:
mAdb Data Processing Protocol (v. 2)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

organism: Plasmodium falciparum

source_name: FCB-br1 - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: cDNA was generated from 30 µg total RNA by priming with a mixture of (dT)12-20 primer and random hexamers before labeling with either dUTP-Cy5 (Amersham Pharmacia Biosciences).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was isolated from tightly synchronized trophozoite-stage cultures (24 h into the parasite's intracellular cycle) with TRIzol (Invitrogen) after treatment with 0.05% saponin to remove excess hemoglobin.

value: FCB-br1 mutant

tag: mutant description

value: A clonal PSAC (plasmodial surface anion channel) mutant generated by in-vitro selection with blasticidin S.

source_name: Wild-type FCB - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: cDNA was generated from 30 µg total RNA by priming with a mixture of (dT)12-20 primer and random hexamers before labeling with either dUTP-Cy3 (Amersham Pharmacia Biosciences).

value: Wild-type FCB


title: Pt4_4


title: FCB vs FCB-br1 - repeat 3 - rev. flour. - mAdbID:83859

description: mAdb experiment ID: 83859

scan_protocol: Creator: GenePix Pro 6.0.1.27 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.69;; 3.73 Temperature: 30.08

source_name: FCB-br1 - Cy3

source_name: Wild-type FCB - Cy5


title: FCB vs FCB-br1 - repeat 1 - rev. fluor. - mAdbID:83857

description: mAdb experiment ID: 83857

scan_protocol: Creator: GenePix Pro 6.0.1.27 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.7;; 3.74 Temperature: 30.51


title: Pt7_24


title: FCB vs FCB-br1 - repeat 7 - rev. fluor. - mAdbID:84881

description: mAdb experiment ID: 84881

scan_protocol: Creator: GenePix Pro 6.0.1.27 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.69;; 3.74 Temperature: 30.29


title: Pt6_24


title: Pt3_24


title: Pt2_24


title: Pt5_0


title: Pt4_24


title: Pt3_4


title: Pt2-4


title: Pt3_0


title: Pt5_24


title: Pt5_4


title: Pt1_4


title: Pt2_0


title: Pt1_24


title: Pt7_4


title: Pt1_0


title: CCL28 expanded HSPCs rep1

city: Lund

first: Shamit

last: Soneji

address: Sölvegatan 19

department: Biomedicinskt Centrum

country: Sweden

institute: Lund University

hyb_protocol: Hybridisation was performed as per Affymetrix protocols

scan_protocol: Scanning was performed as per Affymetrix protocols

data_processing: Data were dChip summarised.

source_name: HSPCs expanded with SCF+CCL28

label_protocol: Samples were biotin labelled using Affymetrix protocols

growth_protocol: HSPCs were cultured in Serum-Free Expansion Medium (StemCell Technologies) supplemented with stem cell factor.

extract_protocol: Cell lysates were processed through QIAshredder columns (Qiagen) and total cellular RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA was amplified using the NuGen FFPE amplification kit (Roche).

treatment_protocol: 1x10^5 sorted CB-derived CD34+ cells were cultured for 18 hours in either SCF alone, or SCF in combination with TPO and CCL28, respectively.

tag: isolation source

value: cord blood

value: hematopoietic stem- and progenitor cells (HSPCs)


title: TPO expanded HSPCs rep3

source_name: HSPCs expanded with SCF+TPO


title: SCF expanded HSPCs rep3

source_name: HSPCs expanded with SCF


title: SCF expanded HSPCs rep1


title: TPO expanded HSPCs rep1


title: CCL28 expanded HSPCs rep2


title: PK-09-27864

city: Boston

first: Otto

last: Metzger

state: MA

address: 450 Brookline ave, Yawkey 1238

institute: Dana Farber Cancer Institut

hyb_protocol: Labeled RNAs were hybridized using the Hybridization, Wash & Stain kit (P/N 900720).

scan_protocol: Hybridized samples were washed, stained and scanned using the Hybridization, Wash & Stain kit (P/N 900720).

data_processing: The data were analyzed using R : RMA backround correction and a quantile normalization against an internal reference dataset were applied.

source_name: primary breast tumor - fresh surgical samples

label_protocol: Extracted RNA was processed using the GeneChip 3' IVT Express kit

extract_protocol: Extraction was performed using the RNeasy mini Kit manufactured by Qiagen (ref: 74104) with a maximum of 30 mg per column

tag: centre

tag: age

tag: comorb

value: minor

tag: menop

tag: hist

value: ductal

tag: grade histo

tag: size (mm)

tag: nodes

tag: er

tag: pr

tag: ggi

tag: gg


title: PK-09-27866

value: premenopausal


title: TPO expanded HSPCs rep2

tag: cell type


title: SCF expanded HSPCs rep2


title: PK-09-27869

value: postmenopausal

value: equivocal


title: CCL28 expanded HSPCs rep3


title: FCB vs FCB-br1 - repeat 2 - rev. fluor. - mAdbID:83858

description: mAdb experiment ID: 83858

scan_protocol: Creator: GenePix Pro 6.0.1.27 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.71;; 3.74 Temperature: 30.63

tag: genotype/variation


title: PK-09-27870

value: average for age

value: lobular


title: PK-09-27530

value: perfect health


title: PK-09-27531


title: PK-09-27865


title: PK-09-27525


title: PK-09-27527

value: major problems


title: PK-09-27523


title: PK-09-27526


title: PK-09-27529


title: PK-09-27518


title: PK-09-27519


title: PK-09-27524


title: FCB vs FCB-br1 - repeat 5 - rev. fluor. - mAdbID:84879

description: mAdb experiment ID: 84879

scan_protocol: Creator: GenePix Pro 6.0.1.27 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.68;; 3.76 Temperature: 29.87


title: PK-09-27501


title: PK-09-27294


title: PK-09-27499


title: PK-09-27492


title: PK-09-27403


title: FCB-br1 vs FCB - repeat 6 - mAdbID:84880

description: mAdb experiment ID: 84880

scan_protocol: Creator: GenePix Pro 6.0.1.27 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.69;; 3.74 Temperature: 30.14


title: PK-09-27397


title: PK-09-27493


title: PK-09-27404


title: PK-09-27400


title: PK-09-27402


title: PK-09-27289


title: PK-09-27514


title: PK-09-27413


title: PK-09-27399


title: PK-09-27396


title: PK-09-27284


title: PK-09-27292


title: PK-09-27288


title: PK-09-27282


title: PK-09-27280


title: PK-09-27286


title: PK-09-27205


title: PK-09-27023


title: PK-09-27207


title: PK-09-27013


title: PK-09-27020


title: PK-09-27019


title: PK-09-26903


title: PK-09-26905


title: PK-09-26901


title: PK-09-27200


title: PK-09-27206


title: PK-09-26907


title: PK-09-26899


title: PK-09-26897


title: PK-09-26902


title: PK-09-26904


title: PK-09-26895


title: PK-09-26876


title: PK-09-26898


title: PK-09-26866


title: PK-09-26874


title: PK-09-26900


title: PK-09-26896


title: PK-09-26865


title: PK-09-26863


title: PK-09-26864


title: PK-09-26861


title: PK-09-26862


title: PK-09-26894


title: PK-09-26875


title: PK-09-26869


title: PK-09-26858


title: PK-09-26859


title: PK-09-26807


title: PK-09-26860


title: PK-09-26809


title: PK-09-26857


title: PK-09-26804


title: PK-09-27283


title: PK-09-26854


title: PK-09-26808


title: Ph+ ALL_Pten fl/fl_CRE-1

tag: strain

value: BCR-ABL1 transformed pre-B cells

tag: disease state

value: BCR-ABL1-driven ALL

value: Pten fl/fl

tag: transduction

tag: treatment

value: 2 days 4OH-Tamoxifen 0.5 micromolar


title: PK-09-26783

tag: centre

tag: age


title: PK-09-26784

tag: comorb

tag: menop


title: PK-09-26805

tag: hist

tag: grade histo


title: PK-09-26779

tag: size (mm)

tag: nodes


title: Lame77 Area4

city: Québec

first: Anne-Laure

last: Nivet

state: Québec

address: 2440 Hochelaga Blvd

country: Canada

institute: Laval University

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Tecan scanning protocol.

data_processing: LOWESS normalized, background subtracted, data obtained from log2 of processed Red signal/processed Green signal. Data processed with Elma Embryogene version V1.6-19 update 2012-07-11

organism: Bos taurus

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: granulosa collected in vivo (ovum pick up)

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: 3 rinses, centrifugation 3000 rpm 4-5 min, snap freeze liquid nitrogen, freezing-80

tag: breed

value: Holstein

value: granulosa cells

tag: time

value: 68 hours

value: 44 hours


title: PK-09-26776

tag: er

tag: pr

tag: ggi

tag: gg


title: PK-09-26785

value: minor


title: PK-09-26743

value: ductal


title: PK-09-26781


title: Lame77 Area1

tag: cell type


title: PK-09-26760


title: Lame77 Area3


title: Lame76 Area4

value: 92 hours


title: Lame76 Area3


title: PK-09-26777

value: postmenopausal


title: PK-09-26747

value: premenopausal


title: PK-09-26740


title: Lame77 Area2


title: PK-09-26739


title: Lame76 Area2


title: PK-09-26744

value: equivocal


title: PK-09-26737


title: PK-09-26738


title: PK-09-27281


title: PK-09-26734


title: Lame74 Area4


title: PK-09-27017


title: PK-09-26731


title: Lame76 Area1


title: Lame74 Area3


title: PK-09-26730


title: PK-09-26729


title: Lame45 Area2

value: 20 hours


title: Lame45 Area3


title: PK-09-26727

value: lobular


title: PK-09-26728

value: perfect health


title: Lame32 Area4


title: PK-09-26726


title: PK-09-26725


title: Lame74 Area2


title: Lame45 Area4


title: PK-09-26722


title: Lame45 Area1


title: Lame32 Area2


title: PK-09-26716

value: average for age


title: Lame32 Area3


title: PK-09-26710

value: major problems


title: Lame31 Area2


title: Lame32 Area1


title: Lame74 Area1


source_name: Immortalized breast epithelium cell line

label_protocol: The total RNA was labeled with affymetrix 3' IVT Express Kit according to manufacturor recommended protocols.

extract_protocol: Total RNA was extracted using the QiazolTM Lysis reagent (Qiagen, Valencia, CA, USA).

tag: cell line

tag: tissue

value: breast

tag: cell line type

value: Immortalized breast epithelium cells


title: PK-09-26724

tag: centre

tag: age


title: Lame31 Area1

value: Holstein


title: PK-09-27287

tag: comorb

tag: menop


title: PK-09-26449

tag: hist

tag: grade histo


title: Lame30 Area4

value: granulosa cells


title: PK-09-26723

tag: size (mm)

tag: nodes


title: Breast cancer cell line SUM159

value: Aggressive cell line

value: Breast cancer cells


title: PK-09-26718


title: Lame31 Area4

tag: breed

tag: time

value: 68 hours


title: Lame30 Area3


title: Breast cancer cell line HS578T


title: Breast cancer cell line BT549


value: Immortalized breast epithelium cell line


title: Breast cancer cell line SK-BR3

value: Less-aggressive cell line


title: Breast cancer cell line MDA-MB-231


title: Lame30 Area1


title: Lame29 Area2

value: 44 hours


title: Lame30 Area2


title: Breast cancer cell line MCF7


title: Lame29 Area1


title: Lame28 Area4


title: Lame29 Area4


title: Breast cancer cell line ZR-75-1


title: Breast cancer cell line T47D


title: Lame28 Area3


title: TMZ vs 6BG

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services Department

institute: Miltenyi Biotec GmbH

description: compare gene expression profile of TMZ vs 6BG

hyb_protocol: The fluorescently labeled samples were hybridized overnight to topic-defined PIQORTM Cell Death Human Sense Microarrays  using the Genetac Hybridization Station (Genomic Solution).

scan_protocol: Image capture and signal quantification of hybridized PIQOR (TM) microarrays were done with the laser scanner ScanArrayTM Lite (PerkinElmer Life Sciences, Boston, USA)  and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQOR (TM) microarrays was done using ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same cDNA was computed. The mean ratios were normalised using the Lowess method. For normalisation only those spots were used for which the fluorescent intensity in one of the two channels was twice the mean background of all unflagged spots. Only genes displaying a net signal intensity 2-fold higher than the mean background were used for further analysis.

source_name: TMZ

label_protocol: 1 µg of the respective T7-amplified RNA was labeled by reverse transcription either with Cy3-dCTPs or Cy5-dCTPsas described elsewhere (PMID: 8800675)

extract_protocol: RNA was isolated using the Nucleospin-II-RNA-Extraction-Kit (Macherey&Nagel)

tag: treatment

value: TMZ

value: primary human myeloid precursor cells


title: 6BG/TMZ vs 6BG

description: compare gene expression profile of 6BG/TMZ vs 6BG

source_name: 6BG and TMZ

value: 6BG and TMZ


title: Lame28 Area1

value: 20 hours


title: 6BG/TMZ vs Control

description: compare gene expression profile of 6BG/TMZ vs Control

source_name: Control

value: untreated


title: HuCCT1_control_rep1

status: Public on Jun 02 2013

city: Yonago-city

first: Kinya

last: Okamoto

state: Tottori

address: 36-1, Nishi-cho

department: Second Dept. Internal Medicine

country: Japan

institute: Tottori University

hyb_protocol: We followed the manufacturer's protocol of the miRCURY LNA(TM) microRNA v.11.0 (Exiqon, Inc).

scan_protocol: We followed the manufacturer's protocol, and used GenePix 4000B (Molecular Devices).

data_processing: We used Array-Pro Analyzer Ver.4.5 (Media Cybernetics, Inc.) for quantification.  We performed quantile normalization and probe summarization by median.

source_name: untreated control, 72 hrs

label_protocol: We used miRCURY LNA(TM) microRNA Power Labeling kit (Exiqon, Inc). And we followed manufacture's protocol.

extract_protocol: We used mirVana miRNA Isolation kit (Life Technologies). And we followed manufacture's protocol.

treatment_protocol: The cell line was cultured in RPMI-1640 medium that contained 10% fetal bovine serum and in humidified conditions at 37 ˚C and 5% CO2. Antibiotics were not added to the culture medium.

value: HuCCT1, human intrahepatic cholangiocarcinoma


title: HuCCT1_GEM_rep1

source_name: Gemcitabine treated, final concentration of Gemcitabine was 1 x 10-4M, incubation time 72 hrs

treatment_protocol: The cell line was cultured in RPMI-1640 medium that contained 10% fetal bovine serum and in humidified conditions at 37 ˚C and 5% CO2. Antibiotics were added to the culture medium.

value: gemcitabine


title: HuH28_GEM_rep1

growth_protocol: The cell line was cultured in RPMI-1640 medium that contained 10% fetal bovine serum and in humidified conditions at 37 ˚C and 5% CO2.

value: HuH28, human intrahepatic cholangiocarcinoma


title: Lame28 Area2


title: HuH28_control_rep1


title: Lama29 Area3


title: ErbB2 tumor TKI.6297.Cy3

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

description: RNA isolated from whole flash frozen mammary tissue/tumor.

hyb_protocol: Following fragmentation, 750ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122A) according to the protocols provided by the manufacturer.

scan_protocol: Array was scanned using Agilent's dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantified using Agilent's Feature Extraction software (Palo Alto, CA).

data_processing: Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and within array normalization was performed using spatial and intensity-dependent loess.

source_name: ErbB2 KI tumor from whole murine mammary gland

label_protocol: 500ng of total RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp aRNA kit, Ambion) according to manufacturer's protocol. Cy5-labeled aRNA was prepared from 10ug aRNA using Cy Post-labeling Reactive Dye Pack (Amersham Biosciences).

extract_protocol: RNeasy Midi Kit (Qiagen)

tag: sample identifier

value: T.6297; Sex:Female; Strain:FVB/N

tag: gender

value: female

tag: genetic background

value: FVB/N

tag: genotype

value: ErbB2 knock-in

source_name: Stratagene universal mouse reference

label_protocol: 500ng of total RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp aRNA kit, Ambion) according to manufacturer's protocol. Cy3-labeled aRNA was prepared from 10ug aRNA using Cy Post-labeling Reactive Dye Pack (Amersham Biosciences).

extract_protocol: No extraction

tag: sample type

value: Stratagene universal mouse reference


title: Lame31 Area3

value: Holstein

tag: cell type

value: granulosa cells

value: 68 hours

value: 92 hours


title: 6BG/TMZ vs TMZ

description: compare gene expression profile of 6BG/TMZ vs TMZ

value: TMZ


title: ErbB2 tumor TKI.1498.Cy3

value: T.1498; Sex:Female; Strain:FVB/N

tag: tissue

value: ErbB2 KI tumor from whole murine mammary gland


title: Breast cancer cell line BT474

source_name: Less-aggressive breast cancer cell line

tag: cell line

value: breast

tag: cell line type

value: Less-aggressive cell line

value: Breast cancer cells


title: ErbB2 tumor TKI.6297.Cy5


title: ErbB2 tumor TKI.1498.Cy5


title: ErbB2 tumor TKI.5901.Cy3

value: T.5901; Sex:Female; Strain:FVB/N


title: H shape_48hr serum starved rep 1

status: Public on Jun 01 2013

city: El Paso

first: Brad

middle: Allen

last: Bryan

state: Texas

address: 5001 El Paso Drive

department: Biomedical Sciences

institute: Texas Tech University Health Sciences Center

description:
HCAEC H-SHAPED- 48 hour serum starved rep 1
Cells were serum starved for 48 hours prior to mRNA collection

hyb_protocol: 750 ng of biotinylated aRNA was then briefly heat-denatured and loaded onto Illumina expression arrays to hybridize overnight.

scan_protocol: Illumina ISCAN.

data_processing: Intensity values were transferred to Agilent GeneSpring GX microarray analysis software and data was filtered based on quality of each call.

source_name: HCAEC_H shape

label_protocol: Total RNA was amplified and biotin-labeled using Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: Human coronary artery endothelial cells were cultured on Collagen Type I coated micropatterned Cytoo plates forcing them to conform to Disc, Crossbow, H, Y, or L shapes.  The cells were also plated on non-restrictive Collagen Type I coated regions on the Cytoo micropattern plate as a control.  Cells were grown in vascular cell basal media (ATCC #PCS-100-030) supplemented with 10 mM L-glutamine, 0.75 units/ml heparin sulfate, 1 ug/ml hydrocortisone, 50 ug/ml ascorbic acid, and pen/strep.

extract_protocol: RNA from 18 independent biological replicates per shape was purified using the Pulink RNA micro kit (Ambion) according to manufacturer's instructions.  Quality control was performed with the Nanodrop and Bioanalyzer.

treatment_protocol: Cells were grown on non-restrictive regions of the Cytoo plate or on 1600 um2 spatially defined micropatterns forcing them to conform to Disc, Crossbow, H, Y, or L shapes.

value: coronary artery endothelial cells (HCAEC)

tag: passages

tag: atcc no.

tag: shape

value: H


title: H shape_48hr serum starved rep 3

description:
HCAEC H-SHAPED- 48 hour serum starved rep 3
Cells were serum starved for 48 hours prior to mRNA collection


title: ErbB2 tumor TKI.5901.Cy5


title: ErbB2 tumor TKI.5710.Cy5

value: T.5710; Sex:Female; Strain:FVB/N


title: L shape_48hr serum starved rep 2

description:
HCAEC L-SHAPED- 48 hour serum starved rep 2
Cells were serum starved for 48 hours prior to mRNA collection

source_name: HCAEC_L shape

value: L


title: ErbB2 tumor TKI.5906.Cy3

value: T.5906; Sex:Female; Strain:FVB/N

value: female

value: FVB/N

value: ErbB2 knock-in


title: Disk shape_48hr serum starved rep 2

description:
HCAEC DISK-SHAPED- 48 hour serum starved rep 2
Cells were serum starved for 48 hours prior to mRNA collection

source_name: HCAEC_Disk shape

value: Disk


title: Crossbow shape_48hr serum starved rep 2

description:
HCAEC CROSSBOW- 48 hour serum starved rep 2
Cells were serum starved for 48 hours prior to mRNA collection

source_name: HCAEC_Crossbow shape

value: Crossbow


title: L shape_48hr serum starved rep 3

description:
HCAEC L-SHAPED- 48 hour serum starved rep 3
Cells were serum starved for 48 hours prior to mRNA collection


title: Crossbow shape_48hr serum starved rep3

description:
HCAEC CROSSBOW- 48 hour serum starved rep 3
Cells were serum starved for 48 hours prior to mRNA collection


title: Nonrestricted control_48hr serum starved rep 2

description:
HCAEC CONTROL- 48 hour serum starved rep 2
Cells were serum starved for 48 hours prior to mRNA collection

source_name: HCAEC_Nonrestricted control

value: Non restricted


title: Disk shape_48hr serum starved rep 3

description:
HCAEC DISK-SHAPED- 48 hour serum starved rep 3
Cells were serum starved for 48 hours prior to mRNA collection


title: Nonrestricted control_48hr serum starved rep3

description:
HCAEC CONTROL- 48 hour serum starved rep 3
Cells were serum starved for 48 hours prior to mRNA collection


title: H shape_48hr serum starved rep 2

description:
HCAEC H-SHAPED- 48 hour serum starved rep 2
Cells were serum starved for 48 hours prior to mRNA collection


title: Nonrestricted control_48hr serum starved rep 1

description:
HCAEC CONTROL- 48 hour serum starved rep 1
Cells were serum starved for 48 hours prior to mRNA collection


title: ErbB2 tumor TKI.5906.Cy5

value: Stratagene universal mouse reference


title: ErbB2 tumor TKI.5710.Cy3

value: ErbB2 KI tumor from whole murine mammary gland


title: Crossbow shape_48hr serum starved rep 1

description:
HCAEC CROSSBOW 48 hour serum starved rep 1
Cells were serum starved for 48 hours prior to mRNA collection


title: L shape rep 1

description: replicate 1

source_name: Human coronary artery endothelial cells; <5 passages; ATCC #PCS-100-020

growth_protocol: Human coronary artery endothelial cells were cultured on Collagen Type I coated micropatterned Cytoo plates forcing them to conform to Disc, Crossbow, H, Y, or L shapes.  The cells were also plated on non-restrictive Collagen Type I coated regions on the Cytoo micropattern plate as a control.  Cells were grown in vascular cell basal media (ATCC #PCS-100-030) supplemented with 0.2% bovine brain extract, 5 ng/ml human epidermal growth factor, 10 mM L-glutamine, 0.75 units/ml heparin sulfate, 1 ug/ml hydrocortisone, 50 ug/ml ascorbic acid, 2% fetal bovine serum, and pen/strep.


title: Crossbow shape rep 2

description: replicate 2


title: HEMEC (rep2)

description: replicate 2

source_name: human infantile hemangioma endothelial cells from proliferating tumor

growth_protocol: Human dermal microvascular endothelial cells and infantile hemangioma endothelial cells were cultured to 70% confluence in T75 flasks in vascular cell basal media (ATCC #PCS-100-030) and supplemented with 0.2% bovine brain extract, 5 ng/ml human epidermal growth factor, 10 mM L-glutamine, 0.75 U/ml heparin sulfate, 1 μg/ml hydrocortisone, 50 μg/ml ascorbic acid, 2% fetal bovine serum and penicillin/streptomycin. For all experiments cell lines were used at <5 passages.

extract_protocol: RNA was purified using the Pulink RNA mini kit (Ambion) according to manufacturer's instructions.  Quality control was performed with the Nanodrop and Bioanalyzer.

treatment_protocol: No treatment

value: HEMEC


title: HDMVEC (rep1)

description: replicate 1

source_name: neonatal human dermal microvascular endothelial cells

value: HDMVEC


title: HEMEC (rep1)

description: replicate 1

value: human infantile hemangioma endothelial cells from proliferating tumor


title: HDMVEC (rep2)

description: replicate 2

value: neonatal human dermal microvascular endothelial cells


title: Disk shape rep 1

description: replicate 1


title: L shape rep 2

description: replicate 2


title: Disk shape_48hr serum starved rep 1

description:
HCAEC DISK-SHAPED- 48 hour serum starved rep 1
Cells were serum starved for 48 hours prior to mRNA collection

value: coronary artery endothelial cells (HCAEC)


title: Y shape_48hr serum starved rep 2

description:
HCAEC Y-SHAPED- 48 hour serum starved rep 2
Cells were serum starved for 48 hours prior to mRNA collection

source_name: HCAEC_Y shape

value: Y


title: L shape_48hr serum starved rep 1

description:
HCAEC L-SHAPED- 48 hour serum starved rep 1
Cells were serum starved for 48 hours prior to mRNA collection


title: Y shape_48hr serum starved rep 1

description:
HCAEC Y-SHAPED- 48 hour serum starved rep 1
Cells were serum starved for 48 hours prior to mRNA collection


title: Control_24h_rep1

city: Turku

first: Tao

last: He

address: Itäinen Pitkäkatu 4C

country: Finland

institute: VTT

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol: 750 ng of biotin-labeled cRNA was hybridized.

scan_protocol: Standard Illumina scanning protocol: The arrays were scanned with the Illumina BeadArray Reader and raw data was produced with GenomeStudio (Illumina).

data_processing: The numerical results were extracted with Bead Studio without any normalization or background subtraction. The data was preprocessed by Bioconductor beadarray and lumi (Du,P. et al. 2008) packages. The data were vst transformed and quantile normalized.

label_protocol: Five hundred ng of purified total RNA was amplified with the Illumina Total Prep RNA Amplification kit  (Ambion, Austin, TX).

growth_protocol: Small cell lung cancer U1690 cells were maintained in RPMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using RNeasy (Qiagen GmbH, Germany) according to the manufacturer’s protocol.

treatment_protocol: U1690 cells were either treated with the vehicle control (DMSO) or with 1µM of doxorubicin for 12 or 24h.

tag: agent

value: control (DMSO)

value: Small cell lung cancer


title: Y shape rep 2

description: replicate 2


title: Nonrestricted control rep 2

description: replicate 2


title: H shape rep 2

description: replicate 2

value: H


title: Crossbow shape rep 1

description: replicate 1


title: H shape rep 1

description: replicate 1


title: Doxorubicin_24h_rep1

description: replicate 1

value: 1µM of doxorubicin


title: Control_24h_rep2

description: replicate 2


title: Y shape rep 1

description: replicate 1


title: Doxorubicin_12h_rep2

description: replicate 2


title: Nonrestricted control rep 1

description: replicate 1


title: Doxorubicin_24h_rep2

description: replicate 2


title: Doxorubicin_12h_rep1

description: replicate 1


title: Control_12h_rep1

description: replicate 1


title: Tissue Luminal B J772 3

city: Singapore

first: Peiyong

last: Guan

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: Replicate 3

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: GenomeStudio

source_name: Patient breast cancer tissue

label_protocol: standard Illumina protocol

growth_protocol: All cell lines were obtained from ATCC (Manassas, VA). MDA-MB-231, BT549, MCF7, T47D, BT474, MB361, MB415,MB436, Hs578T, and MB157 cell lines were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum.  SKBR3 cells were maintained in McCoy's 5A medium. HCC1806 and HCC1937 were maintained in RPMI medium supplemented with 10%FBS. All media were supplemented with 5000U/mL penicillin/streptomycin (Invitrogen). All cells were maintained at 37 °C with 5% CO2.

extract_protocol: standard Illumina protocol

value: Breast cancer tissue Luminal B


title: Breast cancer cell line MDA-MB-468

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

value: breast

value: Less-aggressive cell line

value: Breast cancer cells


title: Tissue Luminal B J772 1

description: Replicate 1


title: Tissue Luminal B J508 1

description: Replicate 1


title: Tissue Luminal B H680 3

description: Replicate 3


title: Tissue Luminal B H680 1

description: Replicate 1


title: Tissue Luminal B J639 1

description: Replicate 1


title: Tissue Luminal B G953 3

description: Replicate 3


title: Tissue Luminal B J639 2

description: Replicate 2


title: Tissue Luminal B J772 2

description: Replicate 2


title: Tissue Luminal B H680 2

description: Replicate 2


title: Tissue Luminal B J639 3

description: Replicate 3


title: Tissue Luminal B J562 2

description: Replicate 2


title: Control_12h_rep2

description: replicate 2


title: Tissue Luminal B J562 1

description: Replicate 1


title: Tissue Luminal B J562 3

description: Replicate 3


title: Tissue Luminal B G953 2

description: Replicate 2


title: Tissue Luminal B J508 2

description: Replicate 2


title: Tissue Luminal B F365 2

description: Replicate 2


title: Tissue Luminal B F365 1

description: Replicate 1


title: Tissue Luminal B D881 3

description: Replicate 3


title: Tissue Luminal B F365 3

description: Replicate 3


title: Tissue Luminal B G953 1

description: Replicate 1


title: Tissue Luminal B E367 1

description: Replicate 1


title: Tissue Luminal B F129 2

description: Replicate 2


title: Tissue Luminal B F129 3

description: Replicate 3


title: Tissue Luminal B F129 1

description: Replicate 1


title: Tissue Luminal B E367 2

description: Replicate 2


title: Tissue Luminal A J899 1

description: Replicate 1

value: Breast cancer tissue Luminal A


title: Tissue Luminal A J880 2

description: Replicate 2


title: Tissue Luminal A K028 1

description: Replicate 1


title: Tissue Luminal A K028 3

description: Replicate 3


title: Tissue Luminal B J508 3

description: Replicate 3


title: Tissue Luminal A J856 3

description: Replicate 3


title: Tissue Luminal A J880 1

description: Replicate 1


title: Tissue Luminal A J728 2

description: Replicate 2


title: Tissue Luminal A J899 2

description: Replicate 2


title: Tissue Luminal B D881 1

description: Replicate 1


title: Tissue Luminal B D881 2

description: Replicate 2


title: Tissue Luminal A J899 3

description: Replicate 3


title: Tissue Luminal B D696 2

description: Replicate 2


title: Tissue Luminal A J856 2

description: Replicate 2


title: Tissue Luminal A J856 1

description: Replicate 1


title: Tissue Luminal A J437 1

description: Replicate 1


title: Tissue Luminal A J728 3

description: Replicate 3


title: Tissue Luminal A J728 1

description: Replicate 1


title: Tissue Luminal A J880 3

description: Replicate 3


title: Tissue Luminal B D696 1

description: Replicate 1


title: Tissue Luminal A J451 3

description: Replicate 3


title: Tissue Luminal A J451 2

description: Replicate 2


title: Tissue Luminal A K028 2

description: Replicate 2


title: Tissue Luminal A J437 2

description: Replicate 2


title: Tissue Luminal A J451 1

description: Replicate 1


title: Tissue Luminal A J437 3

description: Replicate 3


title: Tissue Luminal B D696 3

description: Replicate 3


title: Tissue Luminal A J334 3

description: Replicate 3


title: Disk shape rep 2

description: replicate 2

value: Disk


title: Tissue Luminal A C532 3

description: Replicate 3


title: Tissue Luminal A H616 1

description: Replicate 1


title: Tissue Luminal A C532 1

description: Replicate 1


title: Tissue Luminal A E211 2

description: Replicate 2


title: Tissue Basal-like J506 2

description: Replicate 2

value: Breast cancer tissue Basal-like


title: Tissue Luminal A E211 1

description: Replicate 1


title: Tissue Luminal A C532 2

description: Replicate 2


title: Tissue Basal-like J506 1

description: Replicate 1


title: Tissue Luminal A J334 2

description: Replicate 2


title: Tissue Luminal A J334 1

description: Replicate 1


title: Tissue Basal-like E717 2

description: Replicate 2


title: Tissue Luminal A H616 3

description: Replicate 3


title: Tissue Luminal A H616 2

description: Replicate 2


title: Tissue Basal-like E641 2

description: Replicate 2


title: Tissue Basal-like E717 1

description: Replicate 1


title: Tissue Basal-like G843 3

description: Replicate 3


title: Tissue Basal-like E717 3

description: Replicate 3


title: Tissue Basal-like F907 2

description: Replicate 2


title: Tissue Luminal A E211 3

description: Replicate 3


title: Tissue Basal-like G843 1

description: Replicate 1


title: Tissue Basal-like E641 3

description: Replicate 3


title: Tissue Basal-like E387 2

description: Replicate 2


title: Tissue Basal-like J506 3

description: Replicate 3


title: Tissue Basal-like F907 1

description: Replicate 1


title: Tissue Basal-like F907 3

description: Replicate 3


title: Tissue Basal-like E387 3

description: Replicate 3


title: Tissue Basal-like E641 1

description: Replicate 1


title: Tissue Basal-like G843 2

description: Replicate 2


title: RA SH-SY5Y_day8 culture_rep3

city: Amsterdam

first: Joanna

last: Korecka

address: Meibergdreef 47

department: Neuroregeneration

country: Netherlands

institute: Netherlands Institute for Neuroscience

description:
US12302316_251485034517_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after RA treatment in 8 days of culture
RA.D08.N3

hyb_protocol: Labeled cRNA was hybridized on Agilent 4x44K Whole Human Genome arrays (Agilent Technologies, Part Number G4112F) according to the manufacturer’s protocol. Briefly, 825ng of Cy3-CTP or Cy5-CTP labeled cRNA were fragmented for 30min at 60°C in 1X fragmentation buffer (Agilent Technologies) and loaded onto the array in 1X GEx Hybridization Buffer (Agilent Technologies). Arrays were incubated at 60°C in a rotating hybridization chamber for 17h, after which they were washed in 6xSSPE 0.005% N- Lauroylsarcosine (Sigma-Aldrich) for 5min and in 0.06xSSPE 0.005% N-Lauroylsarcosine for one minute. Finally, slides were washed in acetonitril (Sigma-Aldrich) for 30 seconds and dried in a nitrogen flow.

scan_protocol: Microarrays were scanned in an Agilent DNA Microarray Scanner at 5µm resolution at 10% and 100% PMT settings. Scan images were combined and quantified using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Raw expression data, generated by Feature Extraction software, was imported into the R statistical processing environment using the LIMMA package in Bioconductor (http://www.bioconductor.org). All features for which one or more foreground measurements were flagged as non-uniformity outlier or as saturated outliers were excluded from further analysis. We previously demonstrated that the intensity-based analysis of complex ratio-based designs is more efficient and powerful than the standard ratio-based analysis. We have therefore used an intensity-based analysis for this dataset. The individual signal intensities were extracted from the ratio measurements and 2log transformed intensity measurements were used for further analysis. Normalization between arrays was performed using the quintile algorithm in LIMMA.

source_name: SH-SY5Y cells_RA differentiation_day8

label_protocol: RNA samples were amplified and labeled with either Cy5-CTP or Cy3-CTP using the two-color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with the RNA Micro kit according to the manufacturer’s protocol. Quality control was performed where cRNA quantity and dye integration were determined by NanoDrop measurement and cRNA fragment length was investigated with the Bioanalyzer.

growth_protocol: Human SH-SY5Y neuroblastoma cells were obtained from The European Collection of Cell Culture (ECACC, 94030304, Sigma-Aldrich). Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM)/F-12 without L-glutamine (Invitrogen) supplemented with 0.5% fetal calf serum (FCS), 100U/ml penicillin (Sigma) and 0.1mg/ml streptomycin (Sigma) for 8 days at 37°C in 5% CO2. Cells were grown in 96-well plates coated with 0.1mg/ml poly-L-lysine (PLL, Sigma) and 1mg/ml growth factor reduced Matrigel Matrix without phenol red (BD Biosciences). 10,000 cells per well were plated.

extract_protocol: Cells were harvested for RNA isolation at the time points indicated in Figure 1. Cells were lysed by adding 50µl of Trizol Reagent (Invitrogen) to each well, followed by incubation on ice for 10min. Each time point/treatment condition consisted of 30 wells, divided into three replicates of 10 pooled wells. Phase separation was performed with chloroform and Phase Lock Gel (5 Prime). The final aqueous phase was diluted with an equal volume of 70% ethanol. RNA was isolated using RNeasy Micro columns (Qiagen) according to the manufacturer’s instructions. RNA quantity and purity were determined by NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies) and RNA integrity was determined using the RNA Integrity Number (RIN) measured on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: As we were interested in the effects of retinoic acid on the growth and differentiation of SH-SY5Y cells, as well as in the toxic effects of MPP+, cultured cells were assigned to three treatment groups: culture in medium only (noRA), culture with medium and 1µM all trans-retinoic acid (RA, Sigma), and culture with medium, 1µM RA and 0.01mM MPP+ (RA/MPP(+), Sigma-Aldrich).

tag: culutre day

value: Day 8

tag: differentiation

value: RA

value: differentiation


title: Cell Luminal T47D 1

description: Replicate 1

source_name: Breast cancer cell line (T47D)


title: Cell Luminal MB361 1

description: Replicate 1

source_name: Breast cancer cell line (MB361)


title: RA SH-SY5Y_day8 culture_rep1

description:
US12302316_251485015980_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after RA treatment in 8 days of culture
RA.D08.N1


title: RA SH-SY5Y_day8 culture_rep2

description:
US12302316_251485034455_S01_GE2-v5_95_Feb07_1_1.txt
Gene expression after RA treatment in 8 days of culture
RA.D08.N2


title: Tissue Basal-like E387 1

description: Replicate 1


title: Cell Luminal MB415

description: Replicate 1

source_name: Breast cancer cell line (MB415)


title: Cell Basal MB231 1

description: Replicate 1

source_name: Breast cancer cell line (MB231)


title: Tissue Basal-like E226 2

description: Replicate 2


title: Cell Basal MB436 1

description: Replicate 1

source_name: Breast cancer cell line (MB436)


title: Cell Luminal BT474 1

description: Replicate 1

source_name: Breast cancer cell line (BT474)


title: Cell Basal MB157 1

description: Replicate 1

source_name: Breast cancer cell line (MB157)


title: Tissue Basal-like E226 3

description: Replicate 3


title: DC miR29b replicate 3

city: Oxford

first: Oliver

last: Brain

state: Oxfordshire

address: Headley Way

department: TGU

country: United Kingdom

institute: Nuffield Dept of Medicine

description: Biological replicate 3 of 3

hyb_protocol: For each hybridization, equal amounts of Cyanine 3 labeled cRNA and Cyanine 5 labeled cRNA were mixed, fragmented, and hybridized at 65 °C for 17 hours.  After washing, microarrays were scanned using an Agilent DNA microarray scanner.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C. Images were quantified using Agilent Feature Extraction Software (version A.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and Linear LOWESS normalization.

source_name: Monocyte-derived dendritic cells

label_protocol: 1 µg of total RNA was reversed transcribed to double-strand cDNA using a poly dT-T7 promoter primer. Primer, template RNA and quality-control transcripts of known concentration and quality were first denatured at 65 °C for 10 min and incubated for 2 hours at 40 °C with 5X first strand Buffer, 0.1 M DTT, 10 mM dNTP, MMLV RT, and RNase-out. The MMLV RT enzyme was inactivated at 65 °C for 15 min. cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and CY5 labeled or CY3 labeled-CTP and incubated at 40 °C for 2 hours. Labeled cRNAs were purified using QIAGEN’s RNeasy mini spin columns. After amplification and labeling, cRNA quantity and cyanine incorporation were determined using a nanodrop ND.1000 UV-VIS-Spectrophotometer version 3.2.1(Agilent Technologies, Palo Alto, CA).

extract_protocol: Total RNA was extracted from cell pellets with a miRNeasy Kit (Qiagen)

treatment_protocol: 3 million human MDDCs were nucleofected for 16hrs with miR-29 mimics (either miR-29a PM12499, or miR-29b PM10103 Applied Biosystems, final concentration 50nM), or negative control (AM17110, 50 nM). Cells were subsequently stimulated for 8hrs with MDP and Pam3CSK4 1 μg/ml. 3 biological replicates were used.

tag: age

value: day 5

tag: transfected non-coding rna

value: miR-29b mimic

value: mimic negative control


title: DC miR29a replicate 3

description: Biological replicate 2 of 3


title: Cell Luminal MCF7 1

description: Replicate 1

source_name: Breast cancer cell line (MCF7)


title: Cell Basal HCC1937 1

description: Replicate 1

source_name: Breast cancer cell line (HCC1937)


title: Cell Basal HCC1806 1

description: Replicate 1

source_name: Breast cancer cell line (HCC1806)


title: Tissue Luminal B E367 3

description: Replicate 3


title: RA SH-SY5Y_day5 culture_rep3

description:
US12302316_251485015980_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after RA treatment in 5 days of culture
RA.D05.N3

source_name: SH-SY5Y cells_RA differentiation_day5

value: Day 5

tag: treatment


title: Cell Basal BT549 1

description: Replicate 1

source_name: Breast cancer cell line (BT549)


title: RA SH-SY5Y_day5 culture_rep2

description:
US12302316_251485034519_S01_GE2-v5_95_Feb07_1_1.txt
Gene expression after RA treatment in 5 days of culture
RA.D05.N2


title: RA SH-SY5Y_day5 culture_rep1

description:
US12302316_251485015980_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after RA treatment in 5 days of culture
RA.D05.N1


title: DC miR29a replicate 2

description: Biological replicate 3 of 3

value: miR-29a mimic


title: RA SH-SY5Y_day4 culture_rep3

description:
US12302316_251485015980_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after RA treatment in 4 days of culture
RA.D04.N3

source_name: SH-SY5Y cells_RA differentiation_day4

value: Day 4


title: Cell Basal MB468 1

description: Replicate 1

source_name: Breast cancer cell line (MB468)


title: RA SH-SY5Y_day4 culture_rep1

description:
US12302316_251485015980_S01_GE2-v5_95_Feb07_1_2.txt
Gene expression after RA treatment in 4 days of culture
RA.D04.N1


title: RA SH-SY5Y_day3 culture_rep3

description:
US12302316_251485015980_S01_GE2-v5_95_Feb07_1_2.txt
Gene expression after RA treatment in 3 days of culture
RA.D03.N3

source_name: SH-SY5Y cells_RA differentiation_day3

value: Day 3


title: RA SH-SY5Y_day2 culture_rep1

description:
US12302316_251485034456_S01_GE2-v5_95_Feb07_1_1.txt
Gene expression after RA treatment in 2 days of culture
RA.D02.N1

source_name: SH-SY5Y cells_RA differentiation_day2

value: Day 2


title: RA SH-SY5Y_day1 culture_rep3

description:
US12302316_251485034456_S01_GE2-v5_95_Feb07_1_1.txt
Gene expression after RA treatment in 1 days of culture
RA.D01.N3

source_name: SH-SY5Y cells_RA differentiation_day1

value: Day 1


title: noRA SH-SY5Y_day8 culture_rep2

description:
US12302316_251485034456_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after noRA treatment in 8 days of culture
noRA.D08.N2

source_name: SH-SY5Y cells_no RA differentiation_day8

value: noRA

value: no differentiation


title: noRA SH-SY5Y_day8 culture_rep3

description:
US12302316_251485034515_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after noRA treatment in 8 days of culture
noRA.D08.N3


title: RA SH-SY5Y_day1 culture_rep1

description:
US12302316_251485034516_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after RA treatment in 1 days of culture
RA.D01.N1


title: noRA SH-SY5Y_day8 culture_rep1

description:
US12302316_251485034458_S01_GE2-v5_95_Feb07_1_1.txt
Gene expression after noRA treatment in 8 days of culture
noRA.D08.N1


title: RA SH-SY5Y_day2 culture_rep2

description:
US12302316_251485034519_S01_GE2-v5_95_Feb07_1_1.txt
Gene expression after RA treatment in 2 days of culture
RA.D02.N2


title: noRA SH-SY5Y_day5 culture_rep3

description:
US12302316_251485034458_S01_GE2-v5_95_Feb07_1_1.txt
Gene expression after noRA treatment in 5 days of culture
noRA.D05.N3

source_name: SH-SY5Y cells_no RA differentiation_day5


title: DC miR29b replicate 2

description: Biological replicate 1 of 3


title: noRA SH-SY5Y_day5 culture_rep2

description:
US12302316_251485034519_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after noRA treatment in 5 days of culture
noRA.D05.N2


title: noRA SH-SY5Y_day4 culture_rep2

description:
US12302316_251485034517_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after noRA treatment in 4 days of culture
noRA.D04.N2

source_name: SH-SY5Y cells_no RA differentiation_day4


title: noRA SH-SY5Y_day5 culture_rep1

description:
US12302316_251485034455_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after noRA treatment in 5 days of culture
noRA.D05.N1


title: noRA SH-SY5Y_day4 culture_rep3

description:
US12302316_251485034455_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after noRA treatment in 4 days of culture
noRA.D04.N3


title: noRA SH-SY5Y_day4 culture_rep1

description:
US12302316_251485034458_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after noRA treatment in 4 days of culture
noRA.D04.N1


title: DC miR29b replicate 1

description: Biological replicate 2 of 3


title: noRA SH-SY5Y_day3 culture_rep3

description:
US12302316_251485034458_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after noRA treatment in 3 days of culture
noRA.D03.N3

source_name: SH-SY5Y cells_no RA differentiation_day3


title: noRA SH-SY5Y_day3 culture_rep2

description:
US12302316_251485034456_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after noRA treatment in 3 days of culture
noRA.D03.N2


title: noRA SH-SY5Y_day3 culture_rep1

description:
US12302316_251485034455_S01_GE2-v5_95_Feb07_1_2.txt
Gene expression after noRA treatment in 3 days of culture
noRA.D03.N1


title: noRA SH-SY5Y_day2 culture_rep3

description:
US12302316_251485034455_S01_GE2-v5_95_Feb07_1_2.txt
Gene expression after noRA treatment in 2 days of culture
noRA.D02.N3

source_name: SH-SY5Y cells_noRA differentiation_day2


title: noRA SH-SY5Y_day2 culture_rep2

description:
US12302316_251485034519_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after noRA treatment in 2 days of culture
noRA.D02.N2


title: DC miR29a replicate 1

description: Biological replicate 1 of 3


title: RA SH-SY5Y_day3 culture_rep2

description:
US12302316_251485034455_S01_GE2-v5_95_Feb07_1_1.txt
Gene expression after RA treatment in 3 days of culture
RA.D03.N2


title: RA SH-SY5Y_day3 culture_rep1

description:
US12302316_251485034518_S01_GE2-v5_95_Feb07_1_2.txt
Gene expression after RA treatment in 3 days of culture
RA.D03.N1


title: noRA SH-SY5Y_day1 culture_rep3

description:
US12302316_251485034518_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after noRA treatment in 1 days of culture
noRA.D01.N3

source_name: SH-SY5Y cells_noRA differentiation_day1


title: noRA SH-SY5Y_day2 culture_rep1

description:
US12302316_251485034518_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after noRA treatment in 2 days of culture
noRA.D02.N1


title: noRA SH-SY5Y_day1 culture_rep2

description:
US12302316_251485034517_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after noRA treatment in 1 days of culture
noRA.D01.N2


title: noRA SH-SY5Y_day1 culture_rep1

description:
US12302316_251485034515_S01_GE2-v5_95_Feb07_1_4.txt
Gene expression after noRA treatment in 1 days of culture
noRA.D01.N1


title: RA SH-SY5Y_day4 culture_rep2

description:
US12302316_251485034518_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after RA treatment in 4 days of culture
RA.D04.N2


title: RA SH-SY5Y_day1 culture_rep2

description:
US12302316_251485034518_S01_GE2-v5_95_Feb07_1_3.txt
Gene expression after RA treatment in 1 days of culture
RA.D01.N2


title: CT-2

city: Ribeirão Preto

first: Daniel

middle: Guariz

last: Pinheiro

state: São Paulo

address: Rua Tenente Catão Roxo, 2501

department: Departamento de Genética

country: Brazil

institute: Faculdade de Medicina de Ribeirão Preto (Universidade de São Paulo)

description: All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 90% (% of CD4, determined by flow cytometry).

hyb_protocol: The cRNA was purified on an RNeasy column and 10µg were fragmented and hybridized to microarrays overnight (17h at 65oC and 4 RPM) in SureHyb chambers placed in a rotator oven incubator (Agilent, G2534A, G2530-60029 and G2545A), using the “Gene Expression Hybridization Kit” (Agilent, 5188-5242). After posthybridization washes (“Wash Buffers 1 and 2 Kit”, Agilent, 5188-5327), arrays were dried and analyzed.

scan_protocol: After processing, microarray slides were scanned at 535 nm and 5um/pixel resolution using a GenePix 4000B scanner and the software “GenePix Pro 6.0” (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Images were anlyzed with the sofware Feature Extraction software version 9.5.1 (Agilent, Santa Clara, California - USA). Quality control and array normalization were done at http://www.r-project.org with the Agi4x44PreProcess package available at http://bioconductor.org/. Files were modified to be compatible with the Agi4x44PreProcess packages. Normalization and filtering were done following the Agi4x44Pre- Process instructions.

source_name: CD4+ T-lymphocytes, peripheral blood healthy control

label_protocol: Cy3-labelled cRNA was generated using the “Quick Amp Labeling Kit, one-color” (Agilent, 5190-0442), following the manufacturer’s protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA (“One Color RNA Spike-In Kit”, Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from HTLV-1-infected individuals and healthy controls by centrifugation using Ficoll-Paque PLUS, and CD4+ T-cells were immunomagnetically purified using the positive cell Isolation Kit (Miltenyi Biotec).

extract_protocol: Total RNA was extracted using TRIZOL-LS (Invitrogen) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quality was assessed by agarose gel electrophoresis and quantified using a NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE, USA).

treatment_protocol: Anti-biotin magnetic beads pre-loaded with biotinylated antibodies against human CD4 (Miltenyi Biotec) were used  to isolated specific T cells from PBMCs. The all samples included in this study showed purity more than 90% by cytometry analysis.

value: CD4+ T-lymphocytes

value: peripheral blood

tag: disease status

value: healthy control

tag: gender

value: female


title: HAML-2

source_name: CD4+ T-lymphocytes, peripheral blood HTLV-1 associated myelopathy/tropical spastic paraparesis


title: HACH-2

source_name: CD4+ T-lymphocytes, peripheral blood asymptomatic HTLV-1 carrier

value: asymptomatic HTLV-1 carrier

value: male


title: CT-3


title: CT-4


title: MAS98.12 control day3 mouse No53 Right Side

city: Oslo

first: Eldrid

last: Borgan

address: Ullernchausseen 70

department: Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis v5.5

scan_protocol: Agilent Technologies Microarray Scanner G2505C

data_processing: Data were extracted using Feature Extraction software (Agilent Technologies) version 10.1.1.1. The microarray data were detrended for multiplicative effects and log2 transformed. Data from control probes, probes with inferior quality for more than 20 percent of the arrays (such spots were defined as feature outliers from the FE file), and probes that were flagged as present on less than 20 percent of the arrays were omitted from the analysis. After setting spots flagged as outliers to NA, the average value of duplicate probes was used to represent each unique probe. Missing data were imputed using k-nearest neighbors with default k=1 [25], and data were normalized using quantile normalization. For transcripts (based on GeneName, as provided by Agilent Technologies) represented by multiple different probes, the probe with the highest interquartile range (IQR) was chosen to represent each transcript.

source_name: Breast Cancer Xenograft MAS98.12 control day3

label_protocol: low-RNA input Linear Amplification RNA kit (Agilent Technologies)

growth_protocol: Two orthotopic xenograft models, MAS98.12 and MAS98.06, have been established by directly grafted orthotopic implantation of primary breast cancer tissue in SCID mice and are serially transplanted, as previously described. Locally bred athymic nude mice (NCr-Foxn1nu) were kept under pathogen-free conditions, at constant temperature (21.5 ± 0.5 °C) and humidity (55±5 %), 20 air changes/hr and a 12 hr light/dark cycle. The mice were fed RM3 diet (Scanbur BK, Norway) and distilled tap water ad libitum. The water was supplemented with 4 µg/ml 17-β-estradiol, ensuring growth in the luminal-like xenograft. Animals from the two xenograft models were randomly assigned to different treatment groups after the tumor diameter reached approximately 5 mm.

extract_protocol: Total RNA from all 60 tumor pieces was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.

tag: xenograft model

tag: mouse #

tag: side graft

value: Right Side

value: Control

tag: time (d)

tag: intrinsic subtype

value: Basal

value: Basal breast cancer xenograft tumor

tag: rna extraction date

tag: rna concentration (ng/ul)

tag: rin value

tag: amplification date

tag: hybridization date

tag: donor tissue

value: primary human breast cancer


title: MAS98.12 bevacizumab day3 mouse No26 Right Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumab day3

value: Bevacizumab

tag: tissue

tag: comment bioanalyzer

value: Bioanalyzer:looks good


title: MAS98.12 control day10 mouse No33 Left Side

source_name: Breast Cancer Xenograft MAS98.12 control day10

value: Left Side


title: HACH-1

tag: cell type


title: MAS98.06 control-without Estradiol day3 mouse No26 Right Side

source_name: Breast Cancer Xenograft MAS98.06 control-withoutEstradiol day3

tag: treatment

value: Control without Estradiol

value: Luminal

value: Luminal breast cancer xenograft tumor


title: HACL-2

value: CD4+ T-lymphocytes

tag: disease status


title: HAMH-1

value: peripheral blood

value: HTLV-1 associated myelopathy/tropical spastic paraparesis

tag: gender


title: MAS98.12 control day3 mouse No56 Right Side

tag: xenograft model


title: HACL-1

value: female


title: HAML-1


title: MAS98.06 control-without Estradiol day10 mouse No31 Right Side

source_name: Breast Cancer Xenograft MAS98.06 control-withoutEstradiol day10

tag: mouse #


title: MAS98.12 bevacizumab-doxorubicin day10 mouse No61 Right Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumab-doxorubicin day10

tag: side graft

value: Bevacizumab Doxorubicin


title: MAS98.12 bevacizumab day10 mouse No43 Right Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumab day10

tag: time (d)


title: Tissue Basal-like E226 1

description: Replicate 1

source_name: Patient breast cancer tissue

value: Breast cancer tissue Basal-like


title: CT-1

value: healthy control


title: MAS98.06 bevacizumab-doxorubicin day3 mouse No13 Left Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab-doxorubicin day3

tag: intrinsic subtype


title: MAS98.06 control-without Estradiol day3 mouse No1 Right Side

value: Right Side

tag: rna extraction date


title: MAS98.12 control day3 mouse No60 Right Side

value: Control

value: Basal

tag: rna concentration (ng/ul)


title: MAS98.06 bevacizumab day10 mouse No61 Right Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab day10

tag: rin value

value: primary human breast cancer


title: MAS98.06 control-without Estradiol day10 mouse No4 Right Side

tag: amplification date


title: MAS98.06 bevacizumab-without Estradiol day10 mouse No5 Right Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab-withoutEstradiol day10

value: Bevacizumab without Estradiol

tag: hybridization date


title: HAMH-2


title: Cell Luminal SKBR3 1

description: Replicate 1

source_name: Breast cancer cell line (SKBR3)

tag: cell line


title: MAS98.06 bevacizumab-without Estradiol day10 mouse No5 Left Side

tag: tissue

tag: donor tissue


title: MAS98.06 doxorubicin day3 mouse No51 Right Side

source_name: Breast Cancer Xenograft MAS98.06 doxorubicin day3

value: Doxorubicin


title: MAS98.06 bevacizumab day10 mouse No25 Right Side

value: Bevacizumab


title: MAS98.06 bevacizumab-doxorubicin day3 mouse No66 Left Side

value: Left Side


title: MAS98.06 bevacizumab-without Estradiol day10 mouse No44 Left Side

value: Luminal


title: MAS98.06 bevacizumab day10 mouse No53 Left Side

value: Luminal breast cancer xenograft tumor


title: MAS98.12 bevacizumab-doxorubicin day3 mouse No34 Right Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumab-doxorubicin day3

value: Basal breast cancer xenograft tumor


title: MAS98.12 doxorubicin day3 mouse No41 Right Side

source_name: Breast Cancer Xenograft MAS98.12 doxorubicin day3


title: MAS98.12 bevacizumab-doxorubicin day10 mouse No66 Right Side


title: MAS98.12 control day10 mouse No31 Right Side


title: MAS98.12 bevacizumabdoxorubicin day3 mouse No13 Right Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumabdoxorubicin day3

tag: comment bioanalyzer

value: Bioanalyzer:looks good


title: MAS98.06 control day10 mouse No52 Left Side

source_name: Breast Cancer Xenograft MAS98.06 control day10

tag: treatment


title: E9.5 embryos, Hipk1-/-;Hipk2-/- rep 1

city: San Francisco

first: Yulei

last: Shang

address: 513 Parnassus street

department: Pathology

institute: UCSF

hyb_protocol: Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90 oC for 5 minutes and imme diately chill on ice for 5–30 minutes. Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips. Set the shaker speed to 300 rpm and incubate slides for 18–24 h at 37 oC, maintaining a consistent hybridization time for comparative experiments.

scan_protocol: The arrays were then scanned on a Axon GenePix 4000B Scanner with Genepix Pro 3.0 software, Expression 5 uM for this whole genome arrays

data_processing:
The raw data were re-scaled to account for the differences in individual hybridization intensities.  Analyse quality using Codelink Expression Analysis software version 4.0.
The raw data were normalized with Median-Normalization method.
Total 300 spots for positive control and 320 spots for negative control. Therefore, a total of 620 spots data were already eliminated from the whole 35,587 spot data on the T00342 array.

source_name: E9.5 embryo

label_protocol: 1 ug of total RNA was used as a template for reverse transcriptase with MessageAmpTM II-Biotin enhanced Kit (Ambion)

growth_protocol: E9.5 control, Hipk1-/-, Hipk2-/-, Hipk1-/-;2-/- mouse embryos

extract_protocol: Total RNA was extracted from E9.5 embryos using PicoPureTM RNA Isolation Kit (Arcturus).

treatment_protocol: No treatments

tag: strain

value: C57B6/129svj mixed background

value: whole embryo

tag: genotype/variation


title: MAS98.06 doxorubicin day10 mouse No55 Right Side

source_name: Breast Cancer Xenograft MAS98.06 doxorubicin day10

tag: xenograft model


title: E9.5 embryos, Hipk1-/-;Hipk2-/- rep 2


title: MAS98.06 control day3 mouse No30 Right Side

source_name: Breast Cancer Xenograft MAS98.06 control day3

tag: mouse #


title: MAS98.06 doxorubicin day10 mouse No70 Right Side

tag: side graft


title: MAS98.06 bevacizumab-without Estradiol day3 mouse No3 Right Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab-withoutEstradiol day3

tag: time (d)


title: MAS98.12 doxorubicin day10 mouse No14 Right Side

source_name: Breast Cancer Xenograft MAS98.12 doxorubicin day10

tag: intrinsic subtype


title: Cell Basal HS578T 1

description: Replicate 1

source_name: Breast cancer cell line (HS578T)


title: E9.5 embryos, Hipk2-/- rep 3


title: Phc2 L307R MEF_1

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

hyb_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

scan_protocol: ChIP-v1_10_Apr08, Agilent DNA Microarray Scanner G2505C, Agilent Scan Control (Ver. A.8.4.1)

data_processing: Scanned images were quantified with Agilent Feature Extraction software under standard conditions. Extracted signals were normalized between input and IP using rank consistency filter algorithm.

source_name: embryonic fibroblasts

growth_protocol: MEFs were cultured in Dulbecco’s minimal essential medium containing 10% fetal calf serum and 1% (w/v) penicillin/streptomycin on gelatin-coated dishes at 37˚C and 5% CO2.

extract_protocol: MEFs were subjected to ChIP assay using a Ring1b antibody. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification.

tag: age

value: embryonic day 12.5

tag: passage no.

tag: genotype

tag: sample type

value: input

tag: antibody

value: Ring 1B


title: MAS98.06 bevacizumab-without Estradiol day3 mouse No36 Left Side

tag: rna extraction date

tag: rna concentration (ng/ul)

tag: rin value

tag: amplification date

tag: hybridization date


title: MAS98.06 control day3 mouse No2 Left Side

tag: treatment

tag: tissue

tag: donor tissue


title: E9.5 embryos, Hipk1-/-;Hipk2-/- rep 3

tag: strain

tag: genotype/variation


title: MAS98.06 control-without Estradiol day3 mouse No26 Left Side

source_name: Breast Cancer Xenograft MAS98.06 control-withoutEstradiol day3

tag: xenograft model

tag: mouse #

tag: side graft

value: Control without Estradiol

tag: time (d)


title: E9.5 embryos, Hipk2-/- rep 2


title: wild type MEF_promoter_1

label_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

tag: age

tag: passage no.

tag: genotype

value: wild type


title: MAS98.06 doxorubicin day3 mouse No10 Right Side

value: Right Side

tag: intrinsic subtype

tag: rna extraction date


title: Xe-6%_2

type: mixed

city: Qingdao

first: Lu

last: Lin

state: Shandong

address: 189 Songling RD

country: China

institute: QIBEBT

description: Each oligonucleotide probe had two replicates on a single slide. Additionally, six different concentrations (11, 22, 45, 90, 180 and 360 ng/ul) of genomic DNA were spotted (eight duplicates for each of the six concentrations on a single slide) as positive controls.

hyb_protocol: The Cy3 labeled genomic DNA was used as a common reference to co-hybridize the Cy5 labeled RNA samples on each slide. Hybridization was carried out using a TECAN HS4800 Pro Hybridization Station (Tecan, NC) by following the manufacturer’s instructions. This system automatically performs hybridization, washing and drying of arrays.

scan_protocol: slides were scanned using a ProScanArrayTM microarray analysis system (Perkin Elmer®, MA).

data_processing:
To determine signal intensity of fluorescence for each spot, the 16-bit TIFF scanned images were analyzed by the software ImaGene 6.1 (Biodiscovery Inc., EI Segundo, CA). Microarray data were analyzed as previously described by Mukhopadhyay et al. (Mukhopadhyay et al., 2006; He et al., 2009b). Briefly, it includes the following major steps. (i) Empty spots with SNR <2.0 (SNR, signal-to-noise ratio), and bad spots were flagged and removed before normalization. (ii) The net signal of each spot was calculated by subtracting the background signal and adding a pseudo signal of 100 to obtain a positive value. For resulting net signals of <50, a value of 50 was used. (iii) The total signal intensity of all microarray (slides) in this experiment was normalized with the genomic DNA signal (Cy3 signal), and a normalization factor was calculated for each slide. (iv) Both Cy3 and Cy5 signal intensity of each spot were adjusted by multiplying the normalization factor calculated above. Therefore, the resultant Cy5 signal of each probe presents the normalized signal intensity for each gene. (v) A ratio R of Cy5/Cy3 signal was calculated for each spot on each array. (vi) To compare genomic analysis, the control and treatment conditions were defined respectively so as to identify the control (Rc) and treatment (Rt) ratios. And then log2 R value was calculated for each gene. (vii) Finally, to access the significant change between treatment and control, a Z score was calculated via following equation: , where 0.25 is a pseudovariance term. Typically, a cutoff |Log2R|≥1.0 and |Z|≥ 2.0 was used to determine changes with significance.
The column headers for the raw data are (separated by ;): id;probe_ID;gene_ID;pos;flag;signal_mean;bg_mean;net_sig;bg_stdev;SNR;SBR;demo;sig_stdev;meta_row;meta_col;sub_row;sub_col

organism: Thermoanaerobacter sp. X514

source_name: X514 (Xe) was collected at mid-log in the presence of 6% (v/v) ethanol

label_protocol: Ten microgram of total RNA was reverse-transcribed using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 1 mM Cy5 dUTP (Invitrogen) according to previous  description (He et al., 2006). The purified 500 ng genomic DNA was fluorescently labeled by random priming using Klenow fragment of DNA polymerase  in the presence of 1mM Cy3 dUTP as described elsewhere (He et al., 2005).

growth_protocol: Thermoanaerobacter sp. X514 wt, Xm and Xe were grown anaerobically in defined medium supplement either with or without ethanol.

extract_protocol: Total cellular RNA was isolated using Trizol Reagent (Invitrogen). RNA samples were treated with Rnase-free DNaseI and purifed using the total RNA Isolation Kit (NucleoSpin RNAII, Macherey-Nagel Inc. Genomic DNA was isolated and purified from Thermoanaerobacter sp. X514 by CTAB (hexadecyltrimethylammonium bromide)-NaCl method (Zhou et al., 1995).

value: Thermoanaerobacter sp. X514 ethanol tolerant mutant Xe

value: in the presence of 6% (v/v) ethanol

source_name: pool of genomic DNA extracted from control organisms for all samples

value: Thermoanaerobacter sp. X514

value: control


title: E9.5 embryos, Hipk1-/- rep 2


title: MAS98.12 bevacizumab day3 mouse No1 Right Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumab day3

value: Bevacizumab

value: Basal

tag: rna concentration (ng/ul)

tag: rin value

value: primary human breast cancer


title: E9.5 embryos, Hipk1-/- rep 1


title: MAS98.12 doxorubicin day3 mouse No16 Right Side

value: Doxorubicin

value: Basal breast cancer xenograft tumor

tag: amplification date

tag: hybridization date


title: Xe-6%_1

tag: treatment


title: MAS98.06 bevacizumab-doxorubicin day10 mouse No60 Left Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab-doxorubicin day10

value: Left Side

value: Bevacizumab Doxorubicin

value: Luminal

tag: tissue

value: Luminal breast cancer xenograft tumor

tag: donor tissue


title: MAS98.12 bevacizumab day10 mouse No25 Left Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumab day10


title: E9.5 embryos, Hipk2-/- rep 1

tag: strain

value: C57B6/129svj mixed background

value: whole embryo

tag: genotype/variation


title: MAS98.12 bevacizumab day10 mouse No55 Left Side

tag: xenograft model

tag: mouse #


title: Xe-0%_3

source_name: X514 (Xe) was collected at mid-log without ethanol

value: in the absence of ethanol


title: MAS98.06 bevacizumab day3 mouse No46 Right Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab day3

tag: side graft

value: Right Side

tag: time (d)


title: MAS98.12 doxorubicin day3 mouse No23 Right Side

source_name: Breast Cancer Xenograft MAS98.12 doxorubicin day3


title: Xe-6%_3

value: Thermoanaerobacter sp. X514 ethanol tolerant mutant Xe


title: E9.5 embryos, Control rep 3

value: Control


title: MAS98.06 bevacizumab-doxorubicin day3 mouse No13 Right Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab-doxorubicin day3


title: E9.5 embryos, Control rep 2

source_name: E9.5 embryo


title: E9.5 embryos, Hipk1-/- rep 3


title: MAS98.06 doxorubicin day3 mouse No45 Left Side

source_name: Breast Cancer Xenograft MAS98.06 doxorubicin day3


title: Phc2 L307R MEF_2

tag: age

value: embryonic day 12.5

tag: passage no.

tag: sample type

value: input

tag: antibody

value: Ring 1B


title: wild type MEF_promoter_2

tag: genotype

value: wild type


title: Xe-0%_2

value: Thermoanaerobacter sp. X514

value: control


title: Xm-0%_3

source_name: X514 (Xm) was collected at mid-log without ethanol

value: Thermoanaerobacter sp. X514 ethanol tolerant mutant Xm


title: Xm-2%_1

source_name: X514 (Xm) was collected at mid-log in the presence of 2% (v/v) ethanol

value: in the presence of 2% (v/v) ethanol


title: Xm-0%_2


title: Xm-2%_3


title: Control vs. cadmium-treated cells rep6

city: São Paulo

first: Paulo

last: Zaini

address: Av. Prof. Lineu Prestes, 748 - Butantã

department: Bioquímica

institute: Universidade de São Paulo

description: Biological replicate 2 of 2. Technical replicate 2 of 4.

hyb_protocol: AF555 and AF647 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (GE Healthcare, USA) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning, USA) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were soaked in water for 10s and dried with nitrogen gas.

scan_protocol: Scanned on a GenePix scanner (Agilent, USA). Fluorescence intensity mean and surrounding mean background from each spot were obtained with the software Array Vision 6.0 (Imaging Research, Inc., USA). Unreliable spots were manually flagged.

data_processing:
Spots presenting mean intensity below 2 times the standard deviation of its background in AF555 and AF647 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the iron stress time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((F555+F647)/2)].
Raw data files contain the platform columns listed below, plus the last two columns containing the raw data; one for channel 1 (labelled with AF647, red fluorescence) and one for channel 2 (labelled with AF555, green fluorescence).

organism: Gracilaria tenuistipitata

source_name: Gracilaria tenuistipitata Chang-Xia were cultivated in seawater enriched with von Stosch solution.

label_protocol: 10 µg of total RNA were used for cDNA synthesis with ImPromII Reverse Transcription System (Promega, USA) according to manufacturer's instructions. The cDNAs were labeled with the fluorophores Alexa Fluor 555 and 647 by using the kit Super Script Plus cDNA Indirect Labeling System, according to the instructions provided by the manufacturer (Invitrogen, USA).

growth_protocol: Specimens of the tetrasporophyte of Gracilaria tenuistipitata Chang-Xia were cultivated in seawater enriched with von Stosch solution (Edwards, 1970) and final ph adjusted to 7.5, at a temperature of 24ºC, with a plant density of 5 g.L-1, under a light/dark cycle of 12-h, and at an irradiance of 120 µmol photons/m-2 s-1 provided by a white fluorescent lamp (GE Healthcare, USA). The medium was renewed every six days.

extract_protocol: Total RNA extracted using Concert Plant RNA Reagent (Invitrogen, USA). Quality control of RNA was performed using a Bioanalyzer equipment (Agilent, USA)

treatment_protocol: Cells were cultured in the medium described in the growth protocol, containing 0.95ppm of copper (CuSO4) or 1ppm of cadmium (CdCl2), all from (Sigma-Aldrich, USA).

tag: growth condition

value: seawater enriched with Von Stosch solution.

value: 1ppm of cadmium (CdCl2)

value: seawater enriched with Von Stosch solution, plus 1ppm of cadmium (CdCl2).


title: Control vs. cadmium-treated cells rep7

description: Biological replicate 2 of 2. Technical replicate 3 of 4 (dye swap).


title: Control vs. cadmium-treated cells rep8

description: Biological replicate 2 of 2. Technical replicate 4 of 4 (dye swap).


title: Control vs. cadmium-treated cells rep5

description: Biological replicate 2 of 2. Technical replicate 1 of 4.


title: Xm-0%_1


title: Xm_control_3

source_name: X514 (Xm) was collected at mid-log after addition ddH2O 2 hour as control

value: as the control of 0.15% ethanol treated 2 hour


title: Control vs. cadmium-treated cells rep4

description: Biological replicate 1 of 2. Technical replicate 4 of 4 (dye swap).


title: Xm_control_2


title: Xm-2%_2


title: Xm_control_1


title: MAS98.06 bevacizumab day3 mouse No6 Right Side

value: Bevacizumab

tag: intrinsic subtype

value: Luminal

value: Luminal breast cancer xenograft tumor

tag: rna extraction date

tag: rna concentration (ng/ul)

tag: rin value

tag: amplification date

value: primary human breast cancer


title: MAS98.06 doxorubicin day10 mouse No32 Right Side

source_name: Breast Cancer Xenograft MAS98.06 doxorubicin day10

value: Right Side

tag: treatment

value: Doxorubicin

tag: tissue

tag: hybridization date

tag: donor tissue


title: 015_Xm_3

source_name: X514 (Xm) was collected at mid-log after addition 0.15% ethanol 2 hour

tag: strain

value: 0.15% ethanol treated 2 hour


title: MAS98.12 bevacizumab day3 mouse No3 Left Side

tag: xenograft model

tag: mouse #

tag: side graft

value: Left Side

tag: time (d)

value: Basal

value: Basal breast cancer xenograft tumor

tag: comment bioanalyzer

value: Bioanalyzer:looks good


title: MAS98.06 control day10 mouse No23 Right Side

source_name: Breast Cancer Xenograft MAS98.06 control day10

value: Control


title: MAS98.06 bevacizumab-doxorubicin day10 mouse No35 Right Side

value: Bevacizumab Doxorubicin


title: Control vs. cadmium-treated cells rep3

description: Biological replicate 1 of 2. Technical replicate 3 of 4 (dye swap).

value: seawater enriched with Von Stosch solution.


title: Control vs. cadmium-treated cells rep2

description: Biological replicate 1 of 2. Technical replicate 2 of 4.

value: 1ppm of cadmium (CdCl2)


title: 015_Xm_1

value: Thermoanaerobacter sp. X514 ethanol tolerant mutant Xm

source_name: pool of genomic DNA extracted from control organisms for all samples

value: Thermoanaerobacter sp. X514

value: control


title: 015_Xm_2


title: MAS98.06 bevacizumab-doxorubicin day10 mouse No71 Right Side

value: Luminal


title: MAS98.06 control day10 mouse No16 Left Side

value: Luminal breast cancer xenograft tumor


title: C_4h_3

source_name: X514 (wt) was collected at mid-log after addition ddH2O 4 hour as control

value: as the control of 0.15% ethanol treated 4 hour


title: C_4h_2


title: Control vs. cadmium-treated cells rep1

description: Biological replicate 1 of 2. Technical replicate 1 of 4.

value: seawater enriched with Von Stosch solution, plus 1ppm of cadmium (CdCl2).


title: C_4h_1


title: Control vs. copper-treated cells rep8

value: seawater enriched with Von Stosch solution, plus 0.95ppm of copper (CuSO4).

value: 0.95ppm of copper (CuSO4)


title: Control vs. copper-treated cells rep6


title: Control vs. copper-treated cells rep7


title: 015_4h_2

source_name: X514 (wt) was collected at mid-log after addition 0.15% ethanol 4 hour

value: 0.15% ethanol treated 4 hour


title: Control vs. copper-treated cells rep5


title: 015_4h_1


title: C_2h_2

source_name: X514 (wt) was collected at mid-log after addition ddH2O 2 hour as control

value: as the control of 0.15% ethanol treated 2 hour


title: 015_2h_3

source_name: X514 (wt) was collected at mid-log after addition 0.15% ethanol 2 hour

value: 0.15% ethanol treated 2 hour


title: C_1h_3

source_name: X514 (wt) was collected at mid-log after addition ddH2O 1 hour as control

value: as the control of 0.15% ethanol treated 1 hour


title: C_2h_1


title: 015_2h_2


title: C_1h_2


title: Control vs. copper-treated cells rep4


title: MAS98.06 control-without Estradiol day10 mouse No31 Left Side

source_name: Breast Cancer Xenograft MAS98.06 control-withoutEstradiol day10

value: Left Side

value: Control without Estradiol

value: Bioanalyzer:looks good

value: primary human breast cancer


title: MAS98.12 doxorubicin day10 mouse No6 Left Side

source_name: Breast Cancer Xenograft MAS98.12 doxorubicin day10

value: Doxorubicin

value: Basal

value: Basal breast cancer xenograft tumor

value: Bioanalyzer:more baseline, but ribosomal peaks visible


title: Control vs. copper-treated cells rep2

value: seawater enriched with Von Stosch solution.


title: 015_4h_3

value: Thermoanaerobacter sp. X514

value: control


title: 015_2h_1


title: C_1h_1


title: MAS98.12 bevacizumab-doxorubicin day3 mouse No63 Left Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumab-doxorubicin day3

value: Bevacizumab Doxorubicin


title: MAS98.12 control day10 mouse No36 Right Side

source_name: Breast Cancer Xenograft MAS98.12 control day10

value: Right Side

value: Control


title: Xe-0%_1

source_name: X514 (Xe) was collected at mid-log without ethanol

value: Thermoanaerobacter sp. X514 ethanol tolerant mutant Xe

value: in the absence of ethanol


title: 015_1h_1

source_name: X514 (wt) was collected at mid-log after addition 0.15% ethanol 1 hour

value: 0.15% ethanol treated 1 hour


title: MAS98.12 bevacizumab-doxorubicin day10 mouse No2 Right Side

source_name: Breast Cancer Xenograft MAS98.12 bevacizumab-doxorubicin day10


title: C_30min_3

source_name: X514 (wt) was collected at mid-log after addition ddH2O 30 minutes as control

value: as the control of 0.15% ethanol treated 30 minutes


title: C_30min_2