title: DAC-treated Cord Blood CD34+ progenitors

status: Public on Dec 31 2017

type: RNA

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

country: USA

institute: Johns Hopkins School of Medicine

description: Individual sample

hyb_protocol: Agilent Gene Expression Hybridization Kit using the manufacturer's protocol.

scan_protocol: Microarrays are scanned with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: Loess normalization as implemented in the Limma package from Bioconductor.

molecule: total RNA

organism: Homo sapiens

source_name: DAC-treated CD34+ CB

label_protocol: Agilent low RNA input linear amplification kit.

extract_protocol: Trizol extraction based on the manufacturer's instructions, followed by RNeasy cleanup as per the manufacturer's instructions.

tag: cell type

value: CD34+ CB

tag: sample type

value: Obtained from ALLCELLS (Emeryville, CA), stimulated with Flt3L, TPO, SCF X 3 days

tag: treatment

value: 5 micromolar 5-AZA (DAC) for 96 hours

source_name: Control-treated CD34+ CB

value: 1x PBS for 96 hours


title: TSA-treated viral 4F Adult Fibroblast iPSC clone HUF5 p23

description: Individual sample

source_name: TSA-treated AdF_iPSC-HUF5-4FV p23

value: AdF_iPSC-HUF5-4FV p23

tag: passage

value: Provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009)

value: 300 nanomolar TSA for 18 hour

source_name: Control-treated AdF_iPSC-HUF5-4FV p23


title: TSA-treated Cord Blood CD34+ progenitors

description: Individual sample

source_name: TSA-treated CD34+ CB


title: TSA-treated nonviral 7F Neonatal fibroblast iPSC clone 7ta p47

description: Individual sample

source_name: TSA-treated AdF_iPSC-7ta-7FE p47

value: AdF_iPSC-7ta-7FE p47

value: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 324:797-801 (2009).

source_name: Control-treated AdF_iPSC-7ta-7FE p47


title: DAC-treated retroviral 4F MSC iPSC p25

description: Individual sample

source_name: DAC-treated MMW2 iPS p25

value: MMW2 iPS p25

value: retroviral mesenchymal stem cell iPSC (Ohm et al. 2011 Cancer Res 70:7662-7673 2010)

source_name: Control-treated MMW2 iPS p25


title: TSA-treated viral 4F Adult Fibroblast iPSC clone HUF3 p25

description: Individual sample

source_name: TSA-treated AdF_iPSC-HUF3-4FV p25

value: AdF_iPSC-HUF3-4FV p25

source_name: Control-treated AdF_iPSC-HUF3-4FV p25


title: DAC-treated nonviral 7F Neonatal fibroblast iPSC clone 7ta p47

description: Individual sample

source_name: DAC-treated AdF_iPSC-7ta-7FE p47


title: TSA-treated nonviral 7F Adult fibroblast iPSC clone 6.1 p26

description: Individual sample

source_name: TSA-treated fF_iPSC-6.1-7FE p26

value: fF_iPSC-6.1-7FE p26

value: non-integrated fetal Fibroblast iPSC generated in the Zambidis laboratory

source_name: Control-treated fF_iPSC-6.1-7FE p26


title: DAC-treated viral 4F Adult Fibroblast iPSC clone HUF3 p25

description: Individual sample

source_name: DAC-treated AdF_iPSC-HUF3-4FV p25


title: DAC-treated hESC (H9) p56

description: Individual sample

source_name: DAC-treated hESC (H9) p56

value: hESC (H9) p56

value: Undifferentiated hESC

source_name: Control-treated hESC (H9) p56


title: DAC-treated hESC (ESO3) p85

description: Individual sample

source_name: DAC-treated hESC (ESO3) p85

value: hESC (ESO3) p85

source_name: Control-treated hESC (ESO3) p85


title: DAC-treated viral 4F Adult Fibroblast iPSC clone HUF5 p23

description: Individual sample

source_name: DAC-treated AdF_iPSC-HUF5-4FV p23


title: TSA-treated nonviral Keratinocyte iPSC clone 1 p14

description: Individual sample

source_name: TSA-treated Ker_iPSC-KA.3-7FE p14

value: Ker_iPSC-KA.3-7FE p14

value: non-integrated keratinocyte iPSC generated in the Zambidis laboratory

source_name: Control-treated Ker_iPSC-KA.3-7FE p14


title: TSA-treated nonviral 7F stromal primed cord blood iPSC clone 19.11 p25

description: Individual sample

source_name: TSA-treated sp-CB_iPSC-19.11-7FE p25

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: TSA-treated nonviral 7F stromal primed cord blood iPSC clone 19.11 p18

description: Individual sample

source_name: TSA-treated sp-CB_iPSC-19.11-7FE p18

value: 1x PBS for 96 hours


title: TSA-treated nonviral 7F stromal primed cord blood iPSC clone 6.2 p29

description: Individual sample

source_name: TSA-treated sp-CB_iPSC-6.2-7FE p29

value: sp-CB_iPSC-6.2-7FE p29

source_name: Control-treated sp-CB_iPSC-6.2-7FE p29


title: DAC-treated nonviral 7F stromal primed cord blood iPSC clone 19.11 p18

description: Individual sample

source_name: DAC-treated sp-CB_iPSC-19.11-7FE p18

value: 5 micromolar 5-AZA (DAC) for 96 hours


title: TSA-treated hESC (H9) p56

description: Individual sample

source_name: TSA-treated hESC (H9) p56

value: 300 nanomolar TSA for 18 hour


title: DAC-treated nonviral 7F stromal primed cord blood iPSC clone 6.2 p29

description: Individual sample

source_name: DAC-treated sp-CB_iPSC-6.2-7FE p29


title: DAC-treated nonviral 7F Adult fibroblast iPSC clone 6.1 p26

description: Individual sample

source_name: DAC-treated fF_iPSC-6.1-7FE p26


title: TSA-treated retroviral 4F MSC iPSC p25

description: Individual sample

source_name: TSA-treated MMW2 iPS p25

source_name: Control-treated MMW2 iPS p25


title: DAC-treated nonviral Keratinocyte iPSC clone 1 p14

description: Individual sample

source_name: DAC-treated Ker_iPSC-KA.3-7FE p14


title: TSA-treated hESC (ESO3) p85

description: Individual sample

source_name: TSA-treated hESC (ESO3) p85


title: DAC-treated nonviral 7F stromal primed cord blood iPSC clone 19.11 p25

description: Individual sample

source_name: DAC-treated sp-CB_iPSC-19.11-7FE p25


title: TSA-treated H1 human Embryonic Stem Cells, Passage 42 (NIH Code WA01)

description: Individual sample

source_name: TSA-treated hESC (H1) p42

value: hESC (H1) p42

source_name: Control-treated hESC (H1) p42


title: FAMI Control N. 4 (C)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 5% sensitivity settings.

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Images were obtained with ScanArray Lite (PerkinElmer) scanner, using the ScanArray Express software (PerkinElmer), with a 635 nm laser, maintaining constant laser power (85%) and constant photomultiplier gain (55%).

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 86% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were and inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.

source_name: Platelets from 42 normal controls

label_protocol: We performed miRNA expression profiling from 200 ng of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies). Total RNA was dephosphorylated and ligated with pCp-Cy3. Unincorporated dyes were removed with MicroBioSpin6 columns (BioRad) . Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes.

extract_protocol: Peripheral blood (40 ml) from controls was collected in EDTA, and platelets were isolated within 1 hour by differential centrifugation. Purity of platelet preparations was checked with a Cell-Dyn Coulter counter (Abbot Diagnostics, Abbott Park). A fraction of platelets was resuspended in TRIzol reagent (Invitrogen) for total RNA isolation according to the manufacturer's guidelines. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip (Agilent Technologies, Palo Alto, CA). Platelet purification was also checked after total RNA extraction by quantitative RT-PCR on the platelet specific marker, integrin alpha 2b, and the leukocyte specific marker T cell receptor (TCR). Good samples, used for further analysis and experiments, showed < 1% TCR purity level.

tag: blood donor volunteers

tag: age groups

tag: Sex

value: equal number of male and female subjects for each age group. Blood donors were excluded from any cardiovascular sufferance by appropriate clinical tests.


title: FAMI Control N. 4 (A)


title: DAC-treated H1 human Embryonic Stem Cells, Passage 42 (NIH Code WA01)

description: Individual sample

source_name: DAC-treated hESC (H1) p42


title: FAMI patient N. 16

source_name: Platelets from patient with acute MI within 6 hours of the onset of symptoms

extract_protocol: Peripheral blood (40 ml) from patients was collected in EDTA, and platelets were isolated within 1 hour by differential centrifugation. Purity of platelet preparations was checked with a Cell-Dyn Coulter counter (Abbot Diagnostics, Abbott Park). A fraction of platelets was resuspended in TRIzol reagent (Invitrogen) for total RNA isolation according to the manufacturer's guidelines. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip (Agilent Technologies, Palo Alto, CA). Platelet purification was also checked after total RNA extraction by quantitative RT-PCR on the platelet specific marker, integrin alpha 2b, and the leukocyte specific marker T cell receptor (TCR). Good samples, used for further analysis and experiments, showed < 1% TCR purity level.

treatment_protocol: Patients were all with the same clinical presentation: acute MI within 6 hours of the onset of symptoms, without any previous evidence of coronary disease, except for the retrospective report of possible episodes of angina in the previous week and potentially eligible for thrombolysis or other coronary reperfusion strategie.

tag: age (years)

tag: gender

value: male

tag: bmi

tag: n. diseased vessels

tag: ck peak

tag: tnl on admission (pg/ml)

tag: crp on admission (mg/dl)

tag: il-6 on admission (ng/dl)


title: FAMI patient N. 33


title: FAMI patient N. 27


title: TSA-treated nonviral 7F Adult fibroblast iPSC clone 6.6 p17

description: Individual sample

source_name: TSA-treated fF_iPSC-6.6-7FE p17

value: fF_iPSC-6.6-7FE p17

source_name: Control-treated fF_iPSC-6.6-7FE p17


title: DAC-treated nonviral 7F Adult fibroblast iPSC clone 6.6 p17

description: Individual sample

source_name: DAC-treated fF_iPSC-6.6-7FE p17


title: Control_2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: adult cardiac endothelial cells (EC)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Qiagen RNAeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genetic

value: wild type


title: G2_EC_KO_1

value: Gata2 knock out


title: G2_EC_KO_2


title: FAMI Control N. 4 (B)


title: Control_1


title: Mammary fat pad-Pxmp mouse 3

city: Oulu

first: Vasily

middle: D.

last: Antonenkov

address: Kottinkangas

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

description: Mammary fat pad #4 and #9

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: dChip

label: biotin

source_name: Mammary fat pad-Pxmp mouse

label_protocol: Affymetrix standard protocol

extract_protocol: Rneasy Lipid tissue Mini Kit (Qiagen)

tag: strain background

tag: genotype/variation

value: female


title: Mammary fat pad-WT mouse 2

description: Mammary fat pad #4 and #9

source_name: Mammary fat pad-WT mouse


title: Wt_Mtb_5mM_Lysin_V_3

hyb_protocol: After cDNA fragmentation and terminal labeling with  biotinylated GeneChip®DNA Labeling Reagent  labeled cDNA were hybridized for 16 hr at 50°C on GeneChip MTbH37Rva520456F (Custom Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to manufactures recommendations.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

data_processing: Image analysis was done by Command Console Software (Affymetrix). Probeset summarization and microarray normalization was performed by RMA algorithm.

organism: Mycobacterium tuberculosis

source_name: Wt Mt

label_protocol: cDNA was labeled using the terminal deoxynucleotidyl transferase (Promega) together with the GeneChip DNA Labeling Reagent (Affymetrix) according to the protocol of the manufacturer.

growth_protocol: For gene expression experiments, Mt was grown in minimal medium [26] containing 3.4 µM CaCl2, 0.35 µM ZnSO4, 7.3 mM KH2PO4, 2 mM MgSO4, 17.6 mM Na2HPO4, 190.8 µM ferric ammonium citrate, 0.05% Tween 80 supplemented with 100 mM glycerol and 5 mM lysine as sole nitrogen source.

extract_protocol: RNA from bacteria was extracted form a growing culture at OD600 of ~0.3. The cells were incubated with an equal amount of 5 M GTC buffer (5 M guanidinium isothiocyanate, 0.5% n-laurylsarcosine, 0.7% sodium citrate, 0.7% β-mercaptoethanol) for 15 min at room temperature and harvested by centrifugation at 4,500 x g for 15 min. The pellet was resuspended in 1 ml of TRIzol RNA Isolation Reagent (Life Technologies, Darmstadt, Germany) and incubated for further 15 min at room temperature. Cell lysis was done in a Lysing Matrix B tube (MP Biomedicals, Illkirch, France) using the Hybaid RiboLyser. The tubes were centrifuged at 13,000 x g for 3 min and the supernatant was transferred in a new reaction tube for chloroform extraction. The aqueous solution, consisting of the RNA, was mixed with an equal volume of 70% ethanol and the purification was performed with the RNeasy Mini Kit according to the protocol given by the manufacturer (Qiagen, Hilden, Germany). In deviation from the protocol, the optional DNase I digestion (DNase I supplied by Qiagen) was extended to 1 h and a second DNase I digestion (DNase I supplied by NEB) was performed after elution from the columns. A second RNA cleanup was done using the RNeasy Mini Kit.

tag: genotype

value: wildtype


title: Mammary fat pad-WT mouse 1

description: Mammary fat pad #4 and #9


title: FAMI patient N. 26


title: Mammary fat pad-Pxmp mouse1

description: Mammary fat pad #4 and #9


title: Mammary fat pad-Pxmp mouse 2

description: Mammary fat pad #4 and #9


title: Mammary fat pad-WT mouse 3

description: Mammary fat pad #4 and #9


title: Wt_Mtb_5mM_Lysin_V_2


title: 1985c_5mM_Lysin_V_3


title: Wt_Mtb_5mM_Lysin_V_1


title: 1985c_5mM_Lysin_V_2


title: CD31+/CD146+/- vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 6.13 p21 [Fig7]

description: Individual sample

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series.

scan_protocol: Fluorescent signals were obtained by scanning with the iScan System.

data_processing: Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were quantile normalized without background subtraction to obtain normalized data as deposited.

source_name: CD31+/CD146+/- vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 6.13 passage 21

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).

tag: cell type

tag: sample type

value: CD31+/CD146+/- vascular progenitors derived by the Zambidis laboratory, by the method of Park et al. Cytometry Part A 83(1):114-26. (2013).


title: 1985c_5mM_Lysin_V_1


title: E11.5Hoxb7-GFP-positive_Flk1-negative-UB

city: Kumamoto

first: Atsuhiro

last: Taguchi

state: Kumamoto

department: IMEG

country: Japan

institute: Kumamoto Univ.

description: Gene expression

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

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocolGE1_107_Sep09 and Grid: 028005_D_F_20100804) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: E11.5 ureteric bud

label_protocol: 10ng of total RNA was amplified using WT–Ovation Pico RNA　Amplification System (NuGEN Technologies, Inc., Cat.3300) according to the manufacturer's instructions. Amplified cDNA were labeled with Cyanine 3 (Cy3) using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Cat.5190-0449) according to the manufacturer's instructions, followed by Microcon YM-30 column purification (Millipore Corporation, Billerica, MA, USA). After amplification and labeling, cDNA quantity and cyanine incorporation were determined using a Nanodrop ND-1000 spectrophometer and an Agilent Bioanalyzer.

growth_protocol: nothing

extract_protocol: Each embryonic progenitor cells were sorted by a FACS SORP Aria (Becton Dickinson). Total RNA was extracted using Rneasy Plus Micro Kit purchased from QIAGEN following manufacture's protocol.

treatment_protocol: nothing

value: embryo, ICR, Hoxb7-GFP


title: CD31+/CD146+/- vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 19.11 p19 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 19.11 passage 19


title: CD31+/CD146+/- vascular progenitors derived from hESC (H9) p56 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from H9 human Embryonic Stem Cells, Passage 56 (NIH Code WA09)


title: E9.5Wt1-GFP-positive-rostral part

description: Gene expression

source_name: E9.5 rostral part of the embryo

value: embryo, ICR, Wt1-GFP


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 1 [Fig7]

description: Individual sample

source_name: neonatal cord blood CD34+ cells, treated as described

value: neonatal cord blood CD34+ cells

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero (D0); co-cultured with BMSC from day zero to +3, then harvested


title: CD31+/CD146+/- vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF1 p12 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF1 passage 12

value: CD31+/CD146+/- vascular progenitors derived by the Zambidis laboratory, by the method of Park et al. Cytometry Part A 83(1):114-26. (2013). VP-AdF_iPSC-HUF1-4FV provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009).


title: CD31+/CD146+/- vascular progenitors derived from hESC (H9) p52 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from H9 human Embryonic Stem Cells, Passage 52 (NIH Code WA09)


title: E10.5Hoxb7-GFP-positive_Flk1-negative-caudal part

description: Gene expression

source_name: E10.5 caudal part of the WD


title: CD31+/CD146+/- vascular progenitors derived from hESC (ES03) p80 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from ES03 human Embryonic Stem Cells, Passage 80 (ES Cell International)


title: CD31+/CD146+/- vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 6.2 p31 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 6.2 passage 31


title: E9.5Wt1-GFP-positive-caudal part

description: Gene expression

source_name: E9.5 caudal part of the embryo


title: Fibroblast Day zero, Sample 2 [Fig7]

description: Individual sample

source_name: adult fibroblasts, Coriell Institute, Cat # AG07714, treated as described

value: adult fibroblasts

tag: cell line

value: Fibroblasts passaged 2-3 days prior to day 0 and then harvested on day zero


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 3 [Fig7]

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured with BMSC from day zero to +3, then harvested


title: E9.5Hoxb7-GFP-positive_Flk1-negative-caudal part

description: Gene expression

source_name: E9.5 caudal part of the WD


title: CD31+/CD146+/- vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF5 p29 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF5 passage 29

value: CD31+/CD146+/- vascular progenitors derived by the Zambidis laboratory, by the method of Park et al. Cytometry Part A 83(1):114-26. (2013). VP-AdF_iPSC-HUF5-4FV provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009).


title: CD31+/CD146+/- vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF3 p30 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF3 passage 30

value: CD31+/CD146+/- vascular progenitors derived by the Zambidis laboratory, by the method of Park et al. Cytometry Part A 83(1):114-26. (2013). VP-AdF_iPSC-HUF3-4FV provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009).


title: E9.5Hoxb7-GFP-positive_Flk1-negative-rostral part

description: Gene expression

source_name: E9.5 rostral part of the WD


title: E10.5Hoxb7-GFP-positive_Flk1-negative-rostral part

description: Gene expression

source_name: E10.5 rostral part of the WD


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 2 [Fig7]

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured with BMSC from day zero to +3, then harvested


title: E8.75Hoxb7-GFP-positive

description: Gene expression

source_name: E8.75 embryo


title: Fibroblast Day zero, Sample 3 [Fig7]

description: Individual sample


title: CD31+/CD146+/- vascular progenitors derived from hESC (H9) p51 [Fig7]

description: Individual sample

source_name: CD31+/CD146+/- vascular progenitors derived from H9 human Embryonic Stem Cells, Passage 51 (NIH Code WA09)


title: Fibroblast Day zero, Sample 1 [Fig7]

description: Individual sample


title: OS_6h_rep3

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL13527 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Quantile normalization and the log2 transformation were performed on all raw microarray data using the R package “Agi4x44PreProcess”. Controls were removed from the list. All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: leaves

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata wild type plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of Manduca sexta oral secretions diluted 1/5 (v/v) in water.

tag: tissue

value: leaves

tag: time point

tag: treatment

value: induced with oral secretions (OS) of Manduca sexta larvae


title: OS_6h_rep1

value: wild type


title: OS_1h_rep1


title: OS_6h_rep2


title: OS_2h_rep2


title: OS_0.5h_rep2


title: OS_1h_rep3


title: OS_0.5h_rep1


title: OS_11h_rep3


title: OS_5h_rep3


title: OS_2h_rep3


title: OS_13h_rep2


title: OS_2h_rep1


title: Control_6h_rep3

value: control


title: OS_11h_rep1


title: OS_5h_rep1


title: OS_1h_rep2


title: OS_5h_rep2


title: OS_0.5h_rep3


title: Control_5h_rep3


title: Control_5h_rep1


title: OS_13h_rep1


title: Control_6h_rep2


title: OS_11h_rep2


title: Control_0.5h_rep2


title: OS_13h_rep3


title: Control_5h_rep2


title: Control_6h_rep1


title: Control_0.5h_rep3


title: Control_0.5h_rep1


title: Control_2h_rep2


title: Control_11h_rep2


title: Control_2h_rep3


title: Control_1h_rep3


title: Control_1h_rep1


title: Control_2h_rep1


title: Control_13h_rep3


title: Control_1h_rep2


title: Renal response to dietary phosphorus intake [Niere_Phosphor_11]

city: Dummerstorf

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

description: Gene expression data from kidney

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Sus scrofa

source_name: kidney

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma-Aldrich,Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was column-purified using the NucleoSpin RNA II-Kit (Macherey-Nagel,Düren, Germany)

treatment_protocol: Diets varying in phosphate content

tag: dietary group (low-intake, medium-intake, high-intake)

value: low-intake

tag: Sex

value: m

tag: age (days post natum)


title: Renal response to dietary phosphorus intake [Niere_Phosphor_13]

description: Gene expression data from kidney


title: Control_13h_rep1


title: Renal response to dietary phosphorus intake [Niere_Phosphor_07]

description: Gene expression data from kidney

value: high-intake

value: w


title: Renal response to dietary phosphorus intake [Niere_Phosphor_10]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_14]

description: Gene expression data from kidney

value: medium-intake


title: Renal response to dietary phosphorus intake [Niere_Phosphor_18]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_16]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_15]

description: Gene expression data from kidney


title: Control_13h_rep2


title: Renal response to dietary phosphorus intake [Niere_Phosphor_05]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_19]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_09]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_12]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_17]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_03]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_08]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_06]

description: Gene expression data from kidney


title: Control_11h_rep1


title: Renal response to dietary phosphorus intake [Niere_Phosphor_04]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_02]

description: Gene expression data from kidney


title: Renal response to dietary phosphorus intake [Niere_Phosphor_01]

description: Gene expression data from kidney


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_19]

description: Gene expression data from jejunum

source_name: jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_18]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_17]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_12]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_14]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_16]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_09]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_15]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_07]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_08]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_03]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_01]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_05]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_06]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_04]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_10]

description: Gene expression data from jejunum


title: Colon response to dietary phosphorus intake [Colon_Phosphor_18]

description: Gene expression data from colon

source_name: colon


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_13]

description: Gene expression data from jejunum


title: Colon response to dietary phosphorus intake [Colon_Phosphor_19]

description: Gene expression data from colon


title: Control_11h_rep3


title: Colon response to dietary phosphorus intake [Colon_Phosphor_16]

description: Gene expression data from colon


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_02]

description: Gene expression data from jejunum


title: Jejunal response to dietary phosphorus intake [Jeju_Phosphor_11]

description: Gene expression data from jejunum


title: Colon response to dietary phosphorus intake [Colon_Phosphor_14]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_17]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_12]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_10]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_08]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_06]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_15]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_02]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phophor_13]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_07]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_09]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_04]

description: Gene expression data from colon


title: Colon response to dietary phosphorus intake [Colon_Phosphor_11]

description: Gene expression data from colon


title: Control shRNA expressing cells treated with Doxycyline -rep2

city: Sydney

first: Tao

last: Liu

state: NSW

address: C25 Lowy Cancer Research Center Gate 9 High St UNSW

department: Histone Modifications

country: Australia

institute: Children's Cancer Institute

description: MYCN-amplified neuroblastoma cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: Expression Console used to generate rma-gene-full-Signal

label: Biotin

source_name: Neuroblastoma BE(2)-C cells expressing doxycyline inducible SCRAMBLE shRNA treated with Doxycycline -2

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

growth_protocol: Neuroblastoma BE(2)-C cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum

extract_protocol: RNA was extracted from the cells ninety six hours after treatment with RNeasy mini kit (Qiagen, Hamburg, Germany).

treatment_protocol: Neuroblastoma BE(2)-C cells expressing control (SCRAMBLE) shRNA or DOT1L shRNA were treated with control vehicle (DMSO) or Doxycyline for 96 hours.

value: Peripheral nervous system tumour cells

tag: expression

value: doxycyline inducible SCRAMBLE shRNA

value: doxycycline


title: DOT1L shRNA expressing cells treated with Doxycyline -rep1

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells expressing doxycyline inducible DOT1L shRNA treated with Doxycycline -1

value: doxycyline inducible DOT1L shRNA


title: DOT1L shRNA expressing cells treated with DMSO -rep2

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells expressing doxycyline inducible DOT1L shRNA treated with DMSO control -2

value: control vehicle (DMSO)


title: DOT1L shRNA expressing cells  treated with Doxycyline -rep2

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells expressing doxycyline inducible DOT1L shRNA treated with Doxycycline -2


title: Control shRNA expressing cells treated with Doxycyline -rep1

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells expressing doxycyline inducible SCRAMBLE shRNA treated with Doxycycline -1


title: Control shRNA expressing cells treated with DMSO -rep2

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells expressing doxycyline inducible SCRAMBLE shRNA treated with DMSO control -2


title: Control shRNA expressing cells treated with DMSO -rep1

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells expressing doxycyline inducible SCRAMBLE shRNA treated with DMSO control -1


title: Colon response to dietary phosphorus intake [Colon_Phosphor_01]

description: Gene expression data from colon


title: LYAR siRNA-6

description: MYCN-amplified neuroblastoma cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human HuGene-2_0-st Array. GeneChips were washed and stained.

data_processing:
Expression Console used to generate rma-gene-full-Signal
Results were further analyzed in R (http://www.r-project.org/) with bioconductor package (http://www.bioconductor.org/).

source_name: Neuroblastoma BE(2)-C cells transfected with LYAR siRNA-10

growth_protocol: BE(2)-C neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted using Rneasy kit (Qiagen, Hamburg, Germany) according to the manufacturer's instructions.

treatment_protocol: BE(2)-C neuroblastoma cells were transfected with Control siRNA, LYAR siRNA-6 or LYAR siRNA-10 with transfection reagent Lipofectamine2000 and Opti-MEM for 32 hours

value: BE(2)-C neuroblastoma cell line

value: Peripheral nervous system tumor cells

tag: transfection

value: LYAR siRNA-10


title: Colon response to dietary phosphorus intake [Colon_Phosphor_05]

description: Gene expression data from colon


title: DOT1L shRNA expressing cells treated with DMSO -rep1

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells expressing doxycyline inducible DOT1L shRNA treated with DMSO control -1


title: Colon response to dietary phosphorus intake [Colon_Phosphor_03]

description: Gene expression data from colon


title: LYAR siRNA-10

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells transfected with LYAR siRNA-6

value: LYAR siRNA-6


title: Control siRNA

description: MYCN-amplified neuroblastoma cells

source_name: Neuroblastoma BE(2)-C cells transfected with Control siRNA

value: Control siRNA


title: Hippocampal_neurons_untreated_rep4

city: Freiburg

first: Henriette

last: Franz

address: Alberstr: 17

department: Anatomy and Cellbiology

institute: University Freiburg

description: Hippocampal neurons were isolated at day E18.5, cultured for 11 days in vitro and then treated with or without 55mM KCL, then the total RNA was isolated

hyb_protocol: Labeled targets were hybridised to the arrays according to the manufacturers protocol (Affymetrix). Arrays were washed and stained using the Affymetrix Hyb and Stain kit

scan_protocol: Arrays were scanned using the Affymetrix Scanner 3000 7G and CEL files were processed using Command Console software (Affymetrix)

data_processing: We used Partek Genomics Suite software for further analysis: Pre-background Adjustment was done for GC Content and probe sequence. We used RMA background correction and Quantile normalization. Probes were log2 transformed and probeset summarization was done with median polish. Probe values were log2 transformed.

source_name: hippocampal neurons

label_protocol: We used the Affymetrix WT Plus kit for labeling as described by the manufacturer.

extract_protocol: C57BL/6J (Janvier Labs, France) hippocampi of E18.5 embryos were dissected and collected in 15 ml Hanks’ Balanced Salt Solution (HBSS, PAA, Germany). After centrifugation (5min; 800xg) hippocampi were dissociated by adding 1ml 0.05% trypsin-ethylenediaminetetracetic acid (PAA) at 37°C for 15min. After adding 1ml of fetal bovine serum (FBS, Life Technologies) and 1ml of neurobasal (NB) medium supplemented as previously described (Vezzali R et al. 2016) samples were homogenized by repeated passages through a pipette tip. After 10min centrifugation at 1000Xg, cells were resuspended in complete NB medium containing 22µM L-glutamic acid (Sigma, Germany), counted, and seeded on poly-ornithine (0.1 mg/ml, Sigma) and laminin (1μg/ml, Sigma) coated plates. Medium change was performed every 96h by exchanging half of the volume of the medium with fresh NB medium with complements and AraC (1µg/ml for the first, and 0.5µg/ml for the second medium change, Sigma). At day in vitro (DIV) 11 cells were treated with 55mM KCl at 37ºC, 5%CO2 at different time points before harvesting.

treatment_protocol: samples treated or untreated with 55mM KCl

value: cultured hippocampal neurons

tag: differentiation state in vitro

value: 11 days

tag: developmental stage

tag: mouse number

tag: strain


title: Hippocampal_neurons_4h_KCL_rep2

growth_protocol: 1000Xg, cells were resuspended in complete NB medium containing 22µM L-glutamic acid (Sigma, Germany), counted, and seeded on poly-ornithine (0.1 mg/ml, Sigma) and laminin (1μg/ml, Sigma) coated plates. Medium change was performed every 96h by exchanging half of the volume of the medium with fresh NB medium with complements and AraC (1µg/ml for the first, and 0.5µg/ml for the second medium change, Sigma).


title: Hippocampal_neurons_4h_KCL_rep3


title: Hippocampal_neurons_untreated_rep1


title: Hippocampal_neurons_4h_KCL_rep1


title: Hippocampal_neurons_4h_KCL_rep4


title: HSC Pool 3 treated without TPO and IR. Biological rep.2

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were preprocessed and analyzing using Partek Genomic Suite.

source_name: HSC Pool 3 treated without TPO and IR

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: 10,000 HSCs were sorted in StemSpan medium supplemented with recombinant Flt3-ligand (100 ng/ml), interleukin-3 (10 ng/ml), interleukin-6 (10ng/ml), Stem cell factor (100 ng/ml), in the presence (+T) or absence (-T) of 50 ng/ml TPO and cutlured for 45 min before being subjected to irradiation at 2Gy. Total RNA was extracted 45 min after irradiation (IR).

extract_protocol: Total RNA was extracted using RNeasy plus micro kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: 45 min fater irradiation, the cells were washed in PBS and lyzed and homogenized in denaturing guanidine-isothiocyanate–containing Buffer RLT Plus (Qiagen, Hilden, Germany)

value: HSC


title: Hippocampal_neurons_untreated_rep2


title: HSC Pool 4 treated  with TPO and IR. Biological rep.3

source_name: HSC Pool 4 treated  with TPO and IR


title: plasma_ITP_10

city: Suzhou

first: yang

last: he

state: Jiangsu

address: 1 Shizi Street

country: China

institute: Soochow University

description: miRNA expression in peripheral blood

hyb_protocol: Each slide was hybridized with 100ng Cy3‐labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190‐0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃, 20rpm for 20 hours according to the manufacturer's instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA， Agilent technologies, Santa Clara, CA, US)

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: peripheral blood

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190‐0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer's instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVanaTM PARISTM (Cat#AM1556, Ambion, Austin, TX, US) following the manufacturer's instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers and ITP patients.

value: blood plasma

tag: gender

value: female

tag: age

tag: diagnosis

value: ITP

tag: platelet count （×10^9/l）


title: plasma_ITP_9

description: miRNA expression in peripheral blood

tag: sample type


title: plasma_ITP_8

description: miRNA expression in peripheral blood


title: plasma_ITP_1

description: miRNA expression in peripheral blood

value: male


title: HSC Pool 3 treated with TPO and IR. Biological rep.2

source_name: HSC Pool 3 treated with TPO and IR

tag: cell type


title: plasma_ITP_7

description: miRNA expression in peripheral blood


title: HSC Pool 2 treated without TPO and IR. Biological rep.1

source_name: HSC Pool 2 treated without TPO and IR


title: Hippocampal_neurons_untreated_rep3

tag: tissue


title: plasma_ITP_3

description: miRNA expression in peripheral blood


title: plasma_ITP_5

description: miRNA expression in peripheral blood


title: plasma_ITP_4

description: miRNA expression in peripheral blood


title: plasma_control_6

description: miRNA expression in peripheral blood

value: healthy control


title: HSC Pool 2 treated with TPO and IR. Biological rep.1

source_name: HSC Pool 2 treated with TPO and IR


title: HSC Pool 4 treated without TPO and IR. Biological rep.3

source_name: HSC Pool 4 treated without TPO and IR


title: plasma_ITP_6

description: miRNA expression in peripheral blood


title: plasma_ITP_2

description: miRNA expression in peripheral blood


title: plasma_control_2

description: miRNA expression in peripheral blood


title: plasma_control_5

description: miRNA expression in peripheral blood


title: plasma_control_4

description: miRNA expression in peripheral blood


title: plasma_control_3

description: miRNA expression in peripheral blood


title: plasma_control_1

description: miRNA expression in peripheral blood


title: Candida albicans orf19.4531 KO_6hr_biological rep 2

city: New Delhi

first: Nitesh

middle: Kumar

last: Khandelwal

state: Delhi

address: Near Munirka

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

description: Gene expression after 6hr in orf19.4531 KO Candida albicans cells

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Agilent Candida albicans 8x15k Microarray Gene expression  (AMADID: 026377) designed by Genotypic Technology Private Limited. 600ng of cy3 labeled samples were  fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift ( Gene based Analysis was performed)

organism: Candida albicans

source_name: Candida albicans cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: C.albicans strains were grown over night in YEPD in biological duplicates. From primary cultures, cells of  0.2 OD600 were inoculated in 15 ml YEPD and allowed to grow for  6 hrs to reach log phase

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit following the manufacturer's recommendations.

tag: genotype


title: Candida albicans orf19.4531 KO_6hr_biological rep 1


title: eye disc of UAS-wge, biologic rep 2

city: Sendai

first: Keita

last: Masuko

address: Aoba 6-3, Aramaki, Aoba-ku,

department: Pharmaceutical Science

institute: Tohoku University

hyb_protocol: Following fragmentation, 12 ug of aRNA were hybridized for 16 hr at 45˚C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymeteix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 30.

organism: Drosophila melanogaster

source_name: eye disc of UAS-wge

label_protocol: Biotinylated aRNA were prepared by in vitto transcription of two-round synthesized cDNA, according to the standard protocol of GeneChip 3' IVT Express Kit, from 100 ng total RNA.

growth_protocol: Flies for each genotype were raised on a standerd cornmeal medium at room temperture. Third instar wandering larvae were dissected.

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

treatment_protocol: Thirty pairs of eye-antennal imaginal discs were dissected in cold PBS, and put them into Trizol reagent (Thermo Fisher Scientific).

tag: genotype/variation

value: UAS-wge

value: wandering 3rd instar larvae

value: eye-antennal imaginal disc


title: arr1,10,12, salt, replicate 2

city: Yokohama

first: Rie

last: Nishiyama

address: Tsurumi, Suehiro-cho 1-7-22

department: CSRS

institute: Riken

description: Gene expression data from arr1,10,12 under high salinity condition

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer's instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX12.6.11 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: arr1,10,12, salt, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The ahp2,3,5, arr1,10,12, and Col-0 plants were grown on MS media for 10 days. (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the 11 d-old whole seedlings using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: 10-day-old ahp2,3,5, arr1,10,12, and Col-0 plants were transferred to 0.5 x MS supplemented with 200 mM NaCl (salt stress) or 0 mM NaCl (control), collected just after 24 hours.

value: Whole seedlings

value: 11 day-old

tag: treatment

value: 200 mM NaCl


title: ahp2,3,5, salt, replicate 2

description: Gene expression data from ahp2,3,5 under high salinity condition

source_name: ahp2,3,5, salt, replicate 2


title: eye disc of UAS-wge, biologic rep 3


title: eye disc of ey > wge, biologic rep 1

source_name: eye disc of ey > wge

value: ey-Gal4 UAS-wge


title: eye disc of ey > wge; Su(var)3-9[1]/[2], biologic rep 2

source_name: eye disc of ey > wge; Su(var)3-9[1]/[2]

value: ey-Gal4 UAS-wge; Su(var)3-9[1]/[2]


title: eye disc of ey > wge, biologic rep 3


title: eye disc of ey > wge; Su(var)3-9[1]/[2], biologic rep 3


title: eye disc of ey-Gal4, biologic rep 1

source_name: eye disc of ey-Gal4


title: arr1,10,12, salt, replicate 1

source_name: arr1,10,12, salt, replicate 1


title: eye disc of ey-Gal4, biologic rep 3


title: eye disc of UAS-wge, biologic rep 1


title: eye disc of ey > wge; Su(var)3-9[1]/[2], biologic rep 1


title: ahp2,3,5, salt, replicate 1

source_name: ahp2,3,5, salt, replicate 1


title: eye disc of ey > wge, biologic rep 2


title: WT, salt, replicate 1

description: Gene expression data from WT under high salinity condition

source_name: WT, salt, replicate 1


title: eye disc of ey-Gal4, biologic rep 2


title: WT, salt, replicate 2

source_name: WT, salt, replicate 2


title: ahp2,3,5, salt, replicate 3

source_name: ahp2,3,5, salt, replicate 3


title: WT, salt, replicate 3

source_name: WT, salt, replicate 3


title: arr1,10,12, salt, replicate 3

source_name: arr1,10,12, salt, replicate 3


title: ahp2,3,5, control, replicate 3

description: Gene expression data from ahp2,3,5 under control condition

source_name: ahp2,3,5, control, replicate 3

value: 0 mM NaCl


title: ahp2,3,5, control, replicate 1

source_name: ahp2,3,5, control, replicate 1


title: arr1,10,12, control, replicate 2

description: Gene expression data from arr1,10,12 under control condition

source_name: arr1,10,12, control, replicate 2


title: arr1,10,12, control, replicate 1

source_name: arr1,10,12, control, replicate 1


title: ahp2,3,5, control, replicate 2

source_name: ahp2,3,5, control, replicate 2


title: WT, control, replicate 3

description: Gene expression data from WT under control condition

source_name: WT, control, replicate 3


title: arr1,10,12, control, replicate 3

source_name: arr1,10,12, control, replicate 3


title: WT, control, replicate 2

source_name: WT, control, replicate 2


title: COUP-red CT G+/M- 2

city: Enschede

last: Passier

address: Building Zuidhorst

department: MIRA Institute for Biomedical Technology and Technical Medicine

country: Netherlands

institute: University of Twente

description: SAMPLE 10

hyb_protocol: Standard Illumina protocol: Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: Samples were scanned with illumina iscan array scanner using standard Illumina protocol

data_processing: The data was normalized using quantile normalization in Genespring GX  v12.5

source_name: Human embryonic stem cells

label_protocol: Biotin-labeled (Biotin-16-UTP) amplified cRNA was generated using Illumina Totalprep-96 RNA Amplification Kit

growth_protocol: Differentiation of COUP-TFIImCherry/+-NKX2.5eGFP/+, COUP-TFIImCherry/--NKX2.5eGFP/+ and NKX2.5eGFP/+ hESCs to cardiomyocytes using the Spin-Embryoid body method.

extract_protocol: RNA was extracted using Macherey-Nagel Nucleospin Kit.

treatment_protocol: To direct differentiation to the atrial lineage cells were treated with 1 uM Retinoic acid (Sigma) from day 4 - 7 of differentiation. Cells were sorted for GFP and mCherry.

value: COUP-TFII mCherry/+

value: Human embryonic stem cells

value: CT

tag: timepoint

value: week 3 of differentiation


title: COUP-red RA G+/M+ 2

description: SAMPLE 11

value: Retinoic acid


title: WT, control, replicate 1

source_name: WT, control, replicate 1


title: COUP-red RA G-/M+ 1

description: SAMPLE 9


title: WT NKX-GFP CT G+

description: SAMPLE 5


title: COUP-red RA G+/M+ 1

description: SAMPLE 8


title: COUP-KO 1 RA G+/M+

description: SAMPLE 4

value: COUP-TFII mCherry/-


title: N2

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description:
replicate 2
SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: MCF-7 cell line

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

growth_protocol: To construct NDRG1-OT1 overexpression plasmid pcDNA3.1(+)-NDRG1-OT1, the NDRG1-OT1 was digested from pUC57 plasmid(GenScript) by BamH1 and EcoR1 and ligated into pcDNA3.1(+) plasmid

extract_protocol: Total RNA was extracted by TRIpure reagent(Roche) according to the manufacturer’s protocol.

treatment_protocol: To over-express NDRG1-OT1, the MCF7 cell line was transfected with pcDNA3.1(+)-NDRG1-OT1 plasmid using jetPRIME transfection reagent(Polyplus-transfection SA) according to manufacturer’s instructions.

value: breast cancer cells

tag: cell line


title: COUP-red CT G+/M- 1

description: SAMPLE 7


title: N3

description:
replicate 3
SAMPLE 6

tag: transfection


title: COUP-KO 2 RA G+/M+

description: SAMPLE 3


title: E3

description:
replicate 3
SAMPLE 3


title: COUP-KO 1 CT G+/M-

description: SAMPLE 2


title: N1

description:
replicate 1
SAMPLE 4


title: COUP-red RA G-/M+ 2

description: SAMPLE 12


title: E1

description:
replicate 1
SAMPLE 1


title: WT NKX-GFP RA G+

description: SAMPLE 6


title: E2

description:
replicate 2
SAMPLE 2


title: COUP-KO 2 CT G+/M-

description: SAMPLE 1


title: Arabidopsis incubated with yeast Replicates 1,2 and 3

city: Brisbane

first: chanyarat

last: Paungfoo-Lonhienne

state: QLD

address: The University of Queensland

department: Science

institute: The University of Queensland

hyb_protocol: standard protocols by AGRF, Australia

scan_protocol: Scanned on an Agilent Technologies DNA Microarray Scanner and the program associated with it was Agilent Scan Control. Images were quantified using Agilent Feature Extraction v. 10.1.1.1.

data_processing: Partek Genomics suite was used for background subtraction and quantile normalization.

source_name: root

label_protocol: standard protocols by AGRF, Australia

growth_protocol: Arabidopsis plant were grown axenically in hydroponic culture for 4 weeks before yeast was added into the medium solution.  Control received no yeast. After 24 h, plant roots were harvested.

extract_protocol: Total RNA of Arabidopsis roots grown in hydroponic culture were extracted using NucleoSpin® Plant Kits (BD Biosciences Clontech, Japan).

tag: cultivar

value: Columbia

tag: culture

value: hydroponic

value: 5 weeks

value: incubated with yeast for 24 h

value: no incubation with yeast


title: FAMI Control N. 2

description: Images were analyzed using CodeLink expression software version 4.2, and raw data analysis was exported to GeneSpring format (tab-delimied text format).

hyb_protocol: Arrays were hybridized for 21 hours at 37°C at 300 rpm on a Thermomixer comfort (Eppendorf) and washed according to manufacturer’s protocol. The bioarrays were stained with incubation in 3.4 mL of streptavidin-Cy5 solution for 30 minutes, washed, and dried by centrifugation at 640 rpm.

scan_protocol: Images were obtained with ScanArray Lite (PerkinElmer) scanner, using the ScanArray Express software (PerkinElmer), with a 635 nm laser, maintaining constant laser power (85%) and constant photomultiplier gain (55%).

data_processing: Raw intensity signals were analyzed with the GeneSpring GX 7.3.1 software (Agilent Technologies). Normalization steps included: data transformation, setting measurements less than 0.01 to 0.01; per chip and per gene median polishing; per gene normalization to specific samples (i.e. normal controls). Before performing the statistical analysis we filtered genes with the “present” or “marginal” quality flag values (automatically assigned to each spot by the CodeLink software, according to a signal to noise computation) in 28 out of 38 conditions for platelet data.

source_name: Platelets from patient with acute MI within 6 hours of the onset of symptoms

label_protocol: We performed microarray experiments using the CodeLink Expression Bioarray System (GE Healthcare). Total RNA (1.5 µg) was amplified and biotin-labeled using the CodeLink Expression Assay Reagent Kit following the manufacturer’s protocol. Before amplification, mRNA control spikes were added to all tubes. These controls were used to verify the quality of the process. Biotin-labeled aRNA (10 µg) was fragmented and loaded into a CodeLink Human Whole Genome Bioarray, containing about 55,000 human oligonucleotide gene probes, matching more than 45,000 human genes and transcript targets

extract_protocol: Peripheral blood (40 ml) from controls was collected in EDTA, and platelets were isolated within 1 hour by differential centrifugation. Purity of platelet preparations was checked with a Cell-Dyn Coulter counter (Abbot Diagnostics, Abbott Park). A fraction of platelets was resuspended in TRIzol reagent (Invitrogen) for total RNA isolation according to the manufacturer's guidelines. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip (Agilent Technologies, Palo Alto, CA). Platelet purification was also checked after total RNA extraction by quantitative RT-PCR on the platelet specific marker, integrin alpha 2b, and the leukocyte specific marker T cell receptor (TCR). Good samples, used for further analysis and experiments, showed < 1% TCR purity level.

tag: blood donor volunteers

tag: age groups

tag: Sex

value: equal number of male and female subjects for each age group. Blood donors were excluded from any cardiovascular sufferance by appropriate clinical tests.


title: FAMI Control N. 4


title: FAMI patient N. 41 (B)

label_protocol: We performed microarray experiments using the CodeLink Expression Bioarray System (GE Healthcare). Total RNA (1.5 µg) was amplified and biotin-labeled using the CodeLink Expression Assay Reagent Kit following the manufacturer’s protocol. Before amplification, mRNA control spikes were added to all tubes. These controls were used to verify the quality of the process. Biotin-labeled aRNA (10 µg) was fragmented and loaded into a CodeLink Human Whole Genome Bioarray, containing about 55,000 human oligonucleotide gene probes, matching more than 45,000 human genes and transcript targets

extract_protocol: Peripheral blood (40 ml) from patients was collected in EDTA, and platelets were isolated within 1 hour by differential centrifugation. Purity of platelet preparations was checked with a Cell-Dyn Coulter counter (Abbot Diagnostics, Abbott Park). A fraction of platelets was resuspended in TRIzol reagent (Invitrogen) for total RNA isolation according to the manufacturer's guidelines. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip (Agilent Technologies, Palo Alto, CA). Platelet purification was also checked after total RNA extraction by quantitative RT-PCR on the platelet specific marker, integrin alpha 2b, and the leukocyte specific marker T cell receptor (TCR). Good samples, used for further analysis and experiments, showed < 1% TCR purity level.

tag: age (years)

tag: gender

value: male

tag: bmi

tag: n. diseased vessels

tag: ck peak

tag: tnl on admission (pg/ml)

tag: crp on admission (mg/dl)

tag: il-6 on admission (ng/dl)


title: FAMI patient N. 41 (A)


title: FAMI patient N. 42 (A)

value: female


title: FAMI Control N. 3


title: FAMI Control N. 1

value: equal number of male and female subjects for each age group.  Blood donors were excluded from any cardiovascular sufferance by appropriate clinical tests.


title: FAMI patient N. 42 (B)


title: FAMI patient N. 33 (A)


title: FAMI patient N. 40 (B)


title: FAMI patient N. 29 (B)


title: FAMI patient N. 31 (A)


title: FAMI patient N. 40 (A)


title: FAMI patient N. 26 (B)


title: FAMI patient N. 24 (A)


title: FAMI patient N. 29 (A)


title: FAMI patient N. 25 (A)


title: FAMI patient N. 39 (B)


title: FAMI patient N. 27 (B)


title: FAMI patient N. 24 (B)


title: FAMI patient N. 25 (B)


title: FAMI patient N. 33 (B)


title: FAMI patient N. 32 (B)


title: FAMI patient N. 26 (A)


title: FAMI patient N. 31 (B)


title: FAMI patient N. 39 (A)


title: FAMI patient N. 27 (A)


title: FAMI patient N. 23 (A)


title: FAMI patient N. 32 (A)


title: FAMI patient N. 23 (B)


title: FAMI patient N. 21 (A)


title: FAMI patient N. 19 (B)


title: FAMI patient N. 21 (B)


title: FAMI patient N. 15 (A)

value: not available


title: FAMI patient N. 16 (A)


title: FAMI patient N. 16 (B)


title: FAMI patient N. 15 (B)


title: FAMI patient N. 19 (A)


title: P.f. incubated U CM 2hrs Rep 3

city: Parkville

first: Karen

last: Day

state: VIC

address: Building 155, University of Melbourne

department: Faculty of Science

institute: University of Melbourne

hyb_protocol: For each sample, biotinylated, fragmented cRNA was used to prepare the hybridization cocktail, which was heated and pipetted into an equilibrated probe array and hybridized for 16 hours.  (See GeneChip Expression Analysis Technical Manual; Eukaryotic Target Hybridization

scan_protocol: Samples were scanned using the Affymetrix GeneChip 3000 7G (See GeneChip® Expression Wash, Stain and Scan User Manual, P/N 702731)

data_processing:
Non-Anopheles probe-sets were pre-processed and expression measures were calculated using the GeneChip multi-array average (GCRMA) method. The analysis was performed using R (version 2.15.0) with the affy (version 1.34.0) and gcrma (version 2.28.0) packages that are part of the Bioconductor project. The R package limma (version 3.12.0) was used for calculation of differential expression by linear modeling and empirical Bayes statistics.
Plasmodium_Anopheles.cdf
Affy_plasmoKEY.csv

organism: Plasmodium falciparum

source_name: P.f. incubated U CM 2hrs

label_protocol: cDNA created from extracted TRIzol-purified RNA was used to generate biotin-labeled cRNA using the GeneChip IVT labeling kit and the samples were then fragmented by metal-induced hydrolysis (See GeneChip Expression Analysis Technical Manual; SYNTHESIS OF BIOTIN-LABELED cRNA FOR BOTH THE ONE-CYCLE AND TWO-CYCLE TARGET LABELING ASSAYS)

growth_protocol: Plasmodium falciparum blood stages were cultured for 18 hours in vitro at densities of >3x10^4 parasites per microliter (High Parasite Density) or < 5x10^3 parasites per microliter (Low Parasite Density).  Conditioned medium was harvested by removing supernantant from high and low parasite density cultures.

extract_protocol: Cell pellets from late stage Plasmodium falciparum cultures were lysed in TRIzol reagent and the aqueous phase separated by centrifugation.  RNA was precipitated with isopropyl alcohol and resuspended in Rnase-free water.

treatment_protocol: In vitro cultures of late stage Plasmodium falciparum were incubated with conditioned medium harvested from high and low parasite density cultures and uninfected erythrocyte cultures.  RNA was extracted after 2 hours of incubation.

tag: conditioned medium

value: Uninfected Erythrocyte


title: P.f. incubated U CM 2hrs Rep 1


title: P.f. incubated HD CM 2hrs Rep 3

source_name: P.f. incubated HD CM 2hrs

value: High Parasite Density


title: P.f. incubated LD CM 2hrs Rep 2

source_name: P.f. incubated LD CM 2 hrs

value: Low Parasite Density


title: P.f. incubated LD CM 2hrs Rep 1


title: P.f. incubated LD CM 2hrs Rep 3


title: P.f. incubated HD CM 2hrs Rep 2


title: P.f. incubated U CM 2hrs Rep 2


title: P.f. incubated HD CM 2hrs Rep 1


title: ap1_PAC_mock_30_rep2

city: Freising-Weihenstephan

first: Claus

last: Schwechheimer

address: WZW - Lehrstuhl Systembiologie der Pflanzen, Am Hochanger 4

institute: Claus Schwechheimer

hyb_protocol: The probes were hybridized in rotating hybridization chambers (Agilent Technologies) and incubated at 65 °C for 17 h in a hybridization oven. Subsequently, the arrays were washed according to manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cy3-labeled cRNA was prepared from 150 ng total RNA

growth_protocol: Arabidopsis thaliana (Col-0) and ap1-15 seedlings were grown for 15 days on GM-Medium at 22 °C 120 µE continuous light. After 15 days the seedlings, were transferred to GM-Medium containing 10 µM paclobutrazol (PAC). After additional 2 days seedlings were sprayed with either mock-solution or 100 µM GA3.

extract_protocol: Total RNA was prepared using the Macherey-Nagel Nucleo Spin RNA Plant Kit was prepared from three biological replicate samples for each GA3 or mock treatment.

treatment_protocol: Seedlinges were sprayed with either mock-solution or 100 µM GA3 and collected after 30 min (30) and 60 min (60) GA3 (GA3) or mock (mock) treatment.

tag: ecotype background

value: Col

tag: genotype/variation

value: ap1 mutant

tag: tissue

value: 17 days-old seedlings

tag: treated with

value: mock-solution

tag: time point

value: 30 min after mock treatment


title: ap1_PAC_GA3_60_rep3

value: 100 µM GA3

value: 60 min after GA3 treatment


title: ap1_PAC_mock_60_rep2

value: 60 min after mock treatment


title: ap1_PAC_mock_60_rep1


title: ap1_PAC_GA3_30_rep2

value: 30 min after GA3 treatment


title: ap1_PAC_mock_60_rep3


title: wild type (Col)_PAC_GA3_60_rep3

source_name: wild type (Col)_PAC_GA3_60

value: wild type


title: ap1_PAC_mock_30_rep3


title: ap1_PAC_GA3_30_rep3


title: ap1_PAC_GA3_30_rep1


title: wild type (Col)_PAC_GA3_30_rep2

source_name: wild type (Col)_PAC_GA3_30


title: ap1_PAC_GA3_60_rep2


title: ap1_PAC_GA3_60_rep1


title: ap1_PAC_mock_30_rep1


title: wild type (Col)_PAC_mock_60_rep1

source_name: wild type (Col)_PAC_mock_60


title: wild type (Col)_PAC_GA3_60_rep1


title: Breast biopsy sample_R15406_T115

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were pre-hybridized in prewarmed 5X SCC, 0.1% SDS and 0.1% BSA at 42ºC for 45 min, rinsed under milliQ water and spun dry using a centrifuge for 5 min at 1500 rpm. Labeled samples were redissolved in 42ºC prewarmed 12 microliter of Hybridization buffer A (50% formamide, 6X SSC, 0.5% SDS and 5X Denhardt’s applied to a glass coverslip, covered with the spotted glass slide. Arrays were incubated in a corning hybridization chamber for 18 hr at 42ºC in a humid environment (In Slide Out oven, Boeckel). Arrays were washed at room temperature using an orbital shaker for 10 min with a high stringency wash buffer (0.1X SSC, 0.1% SDS), twice for 10 min with a low stringency wash buffer (0.1X SSC), rinsed for 5 min in milliQ water and spun dry for 5 min at 1500 rpm using a centrifuge.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004, Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays were scaled so that every array has the same median intensity and same absolute standard deviation, in order to give the same weight to every gene on the array.
After normalization, replicated spots of the same gene were average.

source_name: Breast biopsy sample_R15406_T115

label_protocol:
Linear T7-oligodT mediated mRNA amplification (described by Van Gelder et al. 1990 and Eberwine et al. 1992)
3 microgram of the in vitro amplified aRNA samples were reverse transcribed with 4 microliter 5X first strand buffer, 2 microliter 0.1 M DTT, 0.4 microliter low dT-dNTP mix (25 mM dA, dC, dG, 10 mM dT), 1.5 microliter Superscript II (Invitrogen) and 2 microliter 25 mM Cy3-dUTP or Cy5-dUTP (Amersham). The reaction was incubated at 42ºC for 2 hr, chilled on ice and quick spun to bring down condensation. To stop the reaction 1 microliter 1 M NaOH/20 mM EDTA, was added followed by 80 microliter MilliQ-H20 and 10 microliter 3M NaOAc pH 5. Labeled samples were purified with Quiaquick PCR purification columns (Qiagen) and eluted twice with 50 microliter EB (10 mM Tris pH 8.5). Labeling efficiency was calculated by quantification with Nanodrop, obtaining between 50-80 pmol/microliter of Cy3 or Cy5 labeled probes. Labeled samples for the same array were combined, 1 microliter 1 microgram/microliter Human Cot DNA (Invitrogen) was added, and the labeled mix was desiccated by Speed-Vac centrifugation.

extract_protocol:
Frozen tumor samples come from surgical biopsies provided by the Hospital del Mar (Barcelona). Total RNA was prepared by using Ultraspec® RNA isolation system (Biotecx laboratories Inc.) following manufacturer’s instructions.
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

tag: age

value: 36 years-old patient

tag: cancer type

value: Infiltrating ductal carcinoma (IDC)

tag: reproductive stage

value: premenopausal

tag: tumor stage

tag: depth

value: vascular invasion

tag: histological grade

tag: treatment

value: chemotherapy and hormonal therapy

tag: status

value: free of disease

tag: marker

tag: receptor

value: ER+,PR+.

source_name: Universal human reference RNA Stratagene® (cat.no.740000)

tag: type

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R15407_T116

source_name: Breast biopsy sample_R15407_T116

value: 68 years-old patient

value: postmenopausal


title: Breast biopsy sample_R15404_T113

source_name: Breast biopsy sample_R15404_T113

value: ER+,PR-.


title: Breast biopsy sample_R15376_T106

source_name: Breast biopsy sample_R15376_T106

value: 76 years-old patient

value: Infiltrating lobulillarl carcinoma (ILC)

value: no vascular invasion

value: hormonal therapy


title: Breast biopsy sample_R15405_T114

source_name: Breast biopsy sample_R15405_T114

value: 72 years-old patient


title: Breast biopsy sample_R15371_T102

source_name: Breast biopsy sample_R15371_T102

value: 67 years-old patient

value: p53-,HER 2+ (2+AMPLIFIED)


title: Breast biopsy sample_R15374_T104

source_name: Breast biopsy sample_R15374_T104

value: 50 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: chemotherapy and hormonal therapy and HERCEPTIN

value: p53-,HER2+ (3+AMPLIFIED FISH)

value: ER-,PR-.


title: wild type (Col)_PAC_mock_30_rep2

source_name: wild type (Col)_PAC_mock_30

value: Col

value: wild type

value: 17 days-old seedlings

value: mock-solution

value: 30 min after mock treatment


title: Breast biopsy sample_R15375_T105

source_name: Breast biopsy sample_R15375_T105

value: 47 years-old patient

value: premenopausal

value: vascular invasion

value: chemotherapy and hormonal therapy

value: free of disease

value: ER+,PR+.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R15402_T112

source_name: Breast biopsy sample_R15402_T112

value: 74 years-old patient

value: Mucinous carcinoma

value: postmenopausal


title: Breast biopsy sample_R15372_T103

source_name: Breast biopsy sample_R15372_T103

value: 63 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: no vascular invasion

value: with disease

value: ER+,PR-.


title: wild type (Col)_PAC_mock_30_rep3

value: Col

value: wild type

value: 17 days-old seedlings

value: mock-solution


title: wild type (Col)_PAC_mock_60_rep2

value: 60 min after mock treatment


title: Breast biopsy sample_R15399_T109

source_name: Breast biopsy sample_R15399_T109

value: 5 years-old patient

value: NORMAL BREAST.


title: wild type (Col)_PAC_GA3_60_rep2

value: 100 µM GA3

value: 60 min after GA3 treatment


title: Breast biopsy sample_R15400_T110

source_name: Breast biopsy sample_R15400_T110

value: 75 years-old patient

value: vascular invasion

value: chemotherapy

value: free of disease

value: ER-,PR-.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R15398_T108

source_name: Breast biopsy sample_R15398_T108

value: 72 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: postmenopausal

value: no vascular invasion

value: chemotherapy and hormonal therapy

value: ER+,PR+.


title: wild type (Col)_PAC_GA3_30_rep1

source_name: wild type (Col)_PAC_GA3_30

value: Col

value: wild type

value: 17 days-old seedlings

value: 30 min after GA3 treatment


title: Breast biopsy sample_R15408_T117

source_name: Breast biopsy sample_R15408_T117

value: 52 years-old patient

value: premenopausal


title: wild type (Col)_PAC_mock_60_rep3

source_name: wild type (Col)_PAC_mock_60

value: mock-solution

value: 60 min after mock treatment


title: wild type (Col)_PAC_GA3_30_rep3

value: 100 µM GA3


title: Breast biopsy sample_R15401_T111

source_name: Breast biopsy sample_R15401_T111

value: 74 years-old patient

value: vascular invasion

value: free of disease

source_name: Universal human reference RNA Stratagene® (cat.no.740000)


title: wild type (Col)_PAC_mock_30_rep1

value: 30 min after mock treatment


title: Breast biopsy sample_R15328_T94

source_name: Breast biopsy sample_R15328_T94

value: 62 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: postmenopausal

value: chemotherapy

value: ER-,PR-.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R15326_T93

source_name: Breast biopsy sample_R15326_T93

value: 60 years-old patient

value: NORMAL BREAST.


title: Breast biopsy sample_R15336_T101

source_name: Breast biopsy sample_R15336_T101

value: no vascular invasion

value: hormonal therapy

value: ER+,PR+.


title: Breast biopsy sample_R15333_T98

source_name: Breast biopsy sample_R15333_T98

value: chemotherapy and hormonal therapy


title: Breast biopsy sample_R15335_T100

source_name: Breast biopsy sample_R15335_T100

value: Infiltrating lobulillarl carcinoma (ILC)


title: Breast biopsy sample_R15334_T99

source_name: Breast biopsy sample_R15334_T99

value: 46 years-old patient

value: premenopausal


title: Breast biopsy sample_R15378_T107

source_name: Breast biopsy sample_R15378_T107

value: 61 years-old patient

value: free of disease


title: Breast biopsy sample_R15332_T97

source_name: Breast biopsy sample_R15332_T97

value: 34 years-old patient

value: chemotherapy, hormonal therapy and HERCEPTIN

value: p53-,HER2+ (3+AMPLIFIED FISH)


title: Breast biopsy sample_R15330_T95

source_name: Breast biopsy sample_R15330_T95

value: 59 years-old patient

value: Infiltrating lobulillar carcinoma (ILC)

value: postmenopausal

value: no vascular invasion,-


title: Breast biopsy sample_R15331_T96

source_name: Breast biopsy sample_R15331_T96

value: NORMAL BREAST.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R15309_T92

source_name: Breast biopsy sample_R15309_T92

value: 58 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: no vascular invasion

value: with disease

value: p53-,HER2+ (3+++ AMPLIFIED FISH)

value: ER-,PR-.


title: Breast biopsy sample_R15306_T89

source_name: Breast biopsy sample_R15306_T89

value: 73 years-old patient

value: Infiltrating ductal carcinoma (IDC) + "in situ" intraductal carcinoma

value: hormonal therapy

value: ER+,PR+.


title: Breast biopsy sample_R15304_T87

source_name: Breast biopsy sample_R15304_T87

value: 66 years-old patient

value: chemotherapy  NEOADJUVANT

value: free of disease


title: Breast biopsy sample_R13719_T81

source_name: Breast biopsy sample_R13719_T81

value: 56 years-old patient

value: postmenopausal

value: chemotherapy


title: Breast biopsy sample_R15308_T91

source_name: Breast biopsy sample_R15308_T91

value: chemotherapy and hormonal therapy

value: ER+,PR-.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R13715_T80

source_name: Breast biopsy sample_R13715_T80

value: 61 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: vascular invasion


title: Breast biopsy sample_R15307_T90

source_name: Breast biopsy sample_R15307_T90

value: 59 years-old patient

value: no vascular invasion

source_name: Universal human reference RNA Stratagene® (cat.no.740000)


title: Breast biopsy sample_R13721_T82

source_name: Breast biopsy sample_R13721_T82

value: 60 years-old patient

value: Infiltrating lobulillar carcinoma (ILC)

value: no vascular invasion,-

value: ER+,PR- ,


title: Breast biopsy sample_R15301_T84

source_name: Breast biopsy sample_R15301_T84

value: 42 years-old patient

value: Infiltrating ductal carcinoma (IDC)+Ca intraductal no infilt

value: premenopausal

value: chemotherapy , hormonal therapy and HERCEPTIN


title: Breast biopsy sample_R13626_T70

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004, Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays

source_name: Breast biopsy sample_R13626_T70

value: 66 years-old patient

value: NORMAL BREAST.


title: Breast biopsy sample_R15305_T88

source_name: Breast biopsy sample_R15305_T88

value: 64 years-old patient

value: Infiltrating ductal carcinoma (IDC) + "in situ" intraductal carcinoma

value: postmenopausal

value: chemotherapy and hormonal therapy

value: free of disease

value: ER+,PR+.


title: Breast biopsy sample_R13722_T83

source_name: Breast biopsy sample_R13722_T83

value: 41 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: no vascular invasion

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R12861_T69

source_name: Breast biopsy sample_R12861_T69

value: vascular invasion

value: hormonal therapy

value: ER-.


title: Breast biopsy sample_R12849_T64

source_name: Breast biopsy sample_R12849_T64

value: 57 years-old patient

value: premenopausal

value: chemotherapy

value: ER-,PR-.


title: Breast biopsy sample_R12856_T67

source_name: Breast biopsy sample_R12856_T67

value: 78 years-old patient

value: ER+ ,PR+.


title: Breast biopsy sample_R12853_T65

source_name: Breast biopsy sample_R12853_T65

value: 60 years-old patient

value: postmenopausal

value: EXITUS

value: ER+,PR-.


title: Breast biopsy sample_R13629_T73

source_name: Breast biopsy sample_R13629_T73

value: 67 years-old patient

value: HG1, hormonal therapy

value: free of disease

value: ER+,PR+.


title: Breast biopsy sample_R13631_T75

source_name: Breast biopsy sample_R13631_T75

value: 54 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: no vascular invasion

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R13628_T72

source_name: Breast biopsy sample_R13628_T72

value: 41 years-old patient

value: premenopausal

value: chemotherapy and hormonal therapy


title: Breast biopsy sample_R13630_T74

source_name: Breast biopsy sample_R13630_T74

value: 59 years-old patient

value: chemotherapy

value: ER-,PR- ,


title: Breast biopsy sample_R13632_T76

source_name: Breast biopsy sample_R13632_T76

value: 66 years-old patient

value: postmenopausal


title: Breast biopsy sample_R13714_T79

source_name: Breast biopsy sample_R13714_T79

value: 51 years-old patient

value: vascular invasion

value: EXITUS APRIL/2007

value: ER-,PR-.


title: Breast biopsy sample_R13633_T77

source_name: Breast biopsy sample_R13633_T77

value: 72 years-old patient

value: hormonal therapy

value: free of disease

value: ER+,PR+.


title: Breast biopsy sample_R13713_T78

source_name: Breast biopsy sample_R13713_T78

value: 73 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: no vascular invasion

source_name: Universal human reference RNA Stratagene® (cat.no.740000)

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R12854_T66

source_name: Breast biopsy sample_R12854_T66

value: 79 years-old patient

value: celullar neuroendocrine carcinoma

value: vascular invasion,_

value: EXITUS


title: Breast biopsy sample_R15302_T85

source_name: Breast biopsy sample_R15302_T85

value: 71 years-old patient

value: postmenopausal

value: chemotherapy and hormonal therapy


title: Breast biopsy sample_R12860_T68

source_name: Breast biopsy sample_R12860_T68


title: Breast biopsy sample_R13627_T71

source_name: Breast biopsy sample_R13627_T71

value: 66 years-old patient

value: vascular invasion

value: chemotherapy and hormonal therapy neoadjuvant


title: Breast biopsy sample_R15303_T86

source_name: Breast biopsy sample_R15303_T86

value: chemotherapy  NEOADJUVANT

value: ER-,PR-.


title: Breast biopsy sample_R6345_T46

source_name: Breast biopsy sample_R6345_T46

value: 46 years-old patient

value: Infiltrating ductal carcinoma (IDC) + Intraductal carcinoma

value: premenopausal

value: hormonal therapy

value: free of disease

value: ER+,PR-.


title: Breast biopsy sample_R6267_T43

source_name: Breast biopsy sample_R6267_T43

value: 78 years-old patient

value: Infiltrating ductal carcinoma (IDC)+ "in situ" intraductal

value: ER+,PR+.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7170_T51

source_name: Breast biopsy sample_R7170_T51

value: 69 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: postmenopausal

value: no vascular invasion

value: chemotherapy


title: Breast biopsy sample_R7346_T61

source_name: Breast biopsy sample_R7346_T61

value: 40 years-old patient

value: Infiltrating ductal carcinoma (IDC)+ "in situ" intraductal carcinoma

value: chemotherapy and hormonal therapy

value: ER+ (LOW),PR+.


title: Breast biopsy sample_R6265_T42

source_name: Breast biopsy sample_R6265_T42

value: 53 years-old patient

value: Infiltrating ductal carcinoma (IDC) + "in situ" intraductal

value: vascular invasion

value: with disease

value: ER-,PR-.


title: Breast biopsy sample_R7335_T59

source_name: Breast biopsy sample_R7335_T59

value: 60 years-old patient

value: Ductal carcinoma with apocrine differentiation + intraductal carcinoma

value: HG1,-,NO FOLLOW-UP


title: Breast biopsy sample_R7343_T60

source_name: Breast biopsy sample_R7343_T60

value: 84 years-old patient

value: hormonal therapy

value: EXITUS

value: ER+,PR-.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R6256_T47

source_name: Breast biopsy sample_R6256_T47

value: 81 years-old patient

value: Infiltrating lobulillarl carcinoma (ILC)

value: postmenopausal

value: chemotherapy


title: Breast biopsy sample_R6255_T41

source_name: Breast biopsy sample_R6255_T41

value: 77 years-old patient

value: Infiltrating ductal carcinoma (IDC)


title: Breast biopsy sample_R6254_T40

source_name: Breast biopsy sample_R6254_T40

value: vascular invasion


title: Breast biopsy sample_R7322_T55

source_name: Breast biopsy sample_R7322_T55

value: 82 years-old patient

value: "in situ" lobulilar carcinoma

value: vascular invasion,-,no therapy,-


title: Breast biopsy sample_R7328_T56

source_name: Breast biopsy sample_R7328_T56

value: 57 years-old patient

value: vascular invasion,NO VALORABLE

value: chemotherapy and hormonal therapy

value: ER+,PR+.

source_name: Universal human reference RNA Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7331_T57

source_name: Breast biopsy sample_R7331_T57

value: 58 years-old patient

value: Infiltrating ductal carcinoma (IDC) + "in situ" intraductal carcinoma

value: no vascular invasion

value: free of disease

value: ER-,PR-.


title: Breast biopsy sample_R6285_T45

source_name: Breast biopsy sample_R6285_T45

value: 62 years-old patient

value: Infiltrating ductal carcinoma (IDC)+Ca intraductal

value: postmenopausal

value: p53-,HER2+ (2+)/POLISOME AMPLIFIED

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7156_T54

source_name: Breast biopsy sample_R7156_T54

value: 66 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: chemotherapy

value: p53-,HER2 (3+)/POLISOME AMPLIFIED


title: Breast biopsy sample_R6283_T38

source_name: Breast biopsy sample_R6283_T38

value: 89 years-old patient

value: Infiltrating ductal carcinoma (IDC) + intraductal solid type

value: hormonal therapy


title: Breast biopsy sample_R7351_T63

source_name: Breast biopsy sample_R7351_T63

value: 53 years-old patient

value: ER-,PR- ,BRCA2+.


title: Breast biopsy sample_R6277_T35

source_name: Breast biopsy sample_R6277_T35

value: no vascular invasion

value: p53-,HER2 3+/POLISOME AMPLIFIED


title: Breast biopsy sample_R6250_T39

source_name: Breast biopsy sample_R6250_T39

value: 68 years-old patient

value: free of disease

value: ER-,PR-.


title: Breast biopsy sample_R10117_T33

source_name: Breast biopsy sample_R10117_T33

value: 42 years-old patient

value: premenopausal

value: chemotherapy and hormonal therapy

value: ER+,PR-.


title: Breast biopsy sample_R7142_T49

source_name: Breast biopsy sample_R7142_T49

value: 57 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: postmenopausal

value: ER+,PR+.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7143_T50

source_name: Breast biopsy sample_R7143_T50

value: 66 years-old patient

value: Infiltrating lobulillarl carcinoma (ILC)

value: vascular invasion

value: chemotherapy

value: EXITUS


title: Breast biopsy sample_R7140_T48

source_name: Breast biopsy sample_R7140_T48

value: 81 years-old patient


title: Breast biopsy sample_R7334_T58

source_name: Breast biopsy sample_R7334_T58

value: 60 years-old patient

value: NORMAL BREAST.


title: Breast biopsy sample_R6282_T37

source_name: Breast biopsy sample_R6282_T37

value: 69 years-old patient

value: Infiltrating lobulillarl carcinoma (ILC) + "in situ" lobulillar carcinoma

value: no vascular invasion

value: chemotherapy .