title: Candida_parapsilosis_upc2_rep1

status: Public on Nov 30 2011

type: RNA

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

hyb_protocol: Purified cDNA was denatured at 95 degree Celsius  for 2 min, and then chilled on ice for 10 sec. Two cDNA samples were mixed. The hybridization was carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacture's manual.

scan_protocol: Scanned with an Axon 4000B scanner at 10 µm resolution. Data was acquired using GenePix 5.0 software. The quality and concentration of the isolated RNA was analyzed using an Agilent 2100 Bioanalyzer.

data_processing: LOWESS normalized, no background correction using the LIMMA package from Bioconductor.

molecule: total RNA

organism: Candida parapsilosis

source_name: Total RNA from C. parapsilosis CLIB214

label_protocol: RNA was concentrated and readjusted to a concentration of 4 μg/μl with RNase free water. A mixture of 24 μg  RNA, 2 μl Candida albicans specific RT primers mix (0.1 pmol μl (Eurogentec)) and RNase free water to a volume of 18.5 μl was incubated at 70 degrees Celsius for 10 min. Tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. The cDNA synthesis step was carried out in dim light conditions because of the photosensitive properties of the Cyanine-3 (Cy3) dye. A mixture of 8 μll 5X  First Strand buffer, 4 μll 0.1 M Dithiothreitol (DTT), 3 μl 20 mM dNTP mix - dCTP (consisting of 6.67 mM each dATP, dGTP, and dTTP), 1 μl 2 mM dCTP and 2 μl (400 U) of Superscript II Reverse Transcriptase was added to the tubes. 2 μl of 1 mM Cy3 (Cy3-dCTP from Amersham Biosciences, 25 nmol) or Cy5 (Cy5-dCTP from Amersham Biosciences, 25 nmol) was added to the relevant tubes. Tubes were lightly mixed and centrifuged briefly in order to collect the contents of the tube. After 2 hours incubation at 42 degrees Celsius, the tubes were given a quick spin and another 2 μl (400 U) Superscript II Reverse Transcriptase was added. The reaction was incubated for an additional 1 hour at 42 degrees Celsius. Again, tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. Any remaining RNA was degraded by the addition of 1 μl NRase A (0.05 mg ml-1) and 1 μl NRase H (0.05 units ml-1) and incubated at 37 degrees Celsius for 30 min.

growth_protocol: Overnight cultures in YPD at 30 degree Celsius were diluted to an OD A600 of 0.2 in 250 ml YPD. Cultures were incubated at 200 RPM at 30 C for about 3.5 hours in YPD until reaching an OD A600 of 0.6. Cultures were then split into two groups, spun down and resuspended in 100 ml YPD media. One culture was incubated at 30 C, 200 RPM, 21 % O2, and the other one at 30 degree Celsius, 200 RPM, 1 % O2. Media in hypoxic condition had been preincubated in the hypoxic chamber overnight. Cells were grown for an additional 2 hours. Cells were pelleted and frozen in RNA Later at -80 degree Celsius.

extract_protocol: Total RNA was isolated using a RiboPure Yeast kit (Ambion). RNA concentration was checked using Nanodrop. RNA quality was checked using Agilent Bioanalyzer.

tag: age

value: 2 h

tag: growth

value: 30 degree Celsius and 1% Oxygen.

tag: medium

tag: strain

source_name: Total RNA from C. parapsilosis UPC2 delete , grown in YPD medium at 30 degree celsius at 1% Oxygen

value: YPD medium preconditioned overnight at 1% Oxygen.


title: Feproexpress HP 63

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from liver sample of offspring

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

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

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

label: biotin

organism: Sus scrofa

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

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

tag: breed

value: German Landrace

tag: tissue

value: liver

tag: ontogenetic stage

value: 188 dpn

tag: gestation diet

value: offspring of German Landrace gilts fed a gestational high protein diet


title: Feproexpress HP 59


title: Liver wild type High Fat Diet, replicate 4

city: Lausanne

first: Dionysios

last: Chartoumpekis

address: Ave de la Sallaz 8

department: Service of Endocrinology Diabetes and Metabolism

country: Switzerland

institute: Lausanne University Hospital CHUV

description: Gene expression after 6 months on high-fat diet

hyb_protocol: Hybridization was performed in Atlas Biolabs (Berlin,Germany) as follows;1.65 μg of Cy3-labelled cRNA were fragmented according to the manufacturer´s instructions, and 1.425 μg of fragmented cRNA were hybridized (conc: 15 ng/μl).  Hybridization conditions: 65°C, 10 rpm, 17 h; in an Agilent hybridization oven

scan_protocol: Scanning was performed using an Agilent DNA Microarray Scanner (Model G2505C) and Agilent´s Scan Control Software (version A.8.3.1) in Atlas Biolabs (Berlin,Germany).

data_processing: Primary data analysis was performed using Agilent´s Feature Extraction Software (version 10.7.3.1) in Atlas Biolabs (Berlin,Germany).

organism: Mus musculus

source_name: Liver wild type 6 months High Fat Diet, replicate 4

label_protocol: Labelling of total RNA was performed in Atlas Biolabs (Berlin, Germany) using the following kit: Low Input Quick Amp Labeling Kit, One Color (#5190-2305), Agilent Technologies, using  100 ng of total RNA as starting material, according to the manufacturer´s instructions (Manual  One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling,  Version 6.5, Mai 2010, Agilent Technologies).  cRNA synthesis was regarded successful provided that =1.65 μg of cRNA with a Cy3-incorporation  rate =8.0 pmol/μg cRNA were synthesized.

growth_protocol: Mice were housed in the animal facility in the University of Patras Medical School in temperature-, light- and humidity-controlled rooms with a 12-h light/dark cycle.

extract_protocol: Total RNA was isolated using a guanidinium thiocyanate based method using the Trizol reagent (Invitrogen, Carlsbad,CA) and was further purified using the Rneasy minikit (Qiagen,Hilden,Germany) following the manufacturer's instructions.

treatment_protocol: Liver from wild type and Nrf2-KO mice was excised after perfusion with ice-cold saline and then it was immersed in RNA later solution (Ambion,Foster City, CA).

tag: treatment

value: high fat diet

tag: genotype

value: wild type

tag: gender

value: male

tag: genetic background


title: Feproexpress HP 60


title: Liver wild type High Fat Diet, replicate 1

source_name: Liver wild type 6 months High Fat Diet, replicate 1


title: Liver Nrf2 knock-out High Fat Diet, replicate 1

source_name: Liver Nrf2 knock-out 6 months High Fat Diet, replicate 1

value: Nrf2 KO


title: Feproexpress HP 58


title: Feproexpress HP 57


title: Candida_parapsilosis_upc2_rep3

value: YPD medium preconditioned overnight at 1% Oxygen


title: Candida_parapsilosis_normoxia_vs_hypoxia_rep2

hyb_protocol: Purified cDNA was denatured at 95 degree Celsius  for 2 min, and then chilled on ice for 10 sec. Two cDNA samples were mixed. The hybridization was carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacturer's instruction.

source_name: Total RNA from C. parapsilosis CLIB214 grown in YPD medium at 30 degree celsius and 21% oxygen (normoxia)

label_protocol: RNA was concentrated and readjusted to a concentration of 4 μg/μl with RNase free water. A mixture of 24 μg  RNA, 100 pmol of oligo dT primers (Invitrogen) and RNase free water to a volume of 18.5 μl was incubated at 70 degrees Celsius for 10 min. Tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. The cDNA synthesis step was carried out in dim light conditions because of the photosensitive properties of the Cyanine-3 (Cy3) dye. A mixture of 8 μll 5X  First Strand buffer, 4 μll 0.1 M Dithiothreitol (DTT), 3 μl 20 mM dNTP mix - dCTP (consisting of 6.67 mM each dATP, dGTP, and dTTP), 1 μl 2 mM dCTP and 2 μl (400 U) of Superscript II Reverse Transcriptase was added to the tubes. 2 μl of 1 mM Cy3 (Cy3-dCTP from Amersham Biosciences, 25 nmol) or Cy5 (Cy5-dCTP from Amersham Biosciences, 25 nmol) was added to the relevant tubes. Tubes were lightly mixed and centrifuged briefly in order to collect the contents of the tube. After 2 hours incubation at 42 degrees Celsius, the tubes were given a quick spin and another 2 μl (400 U) Superscript II Reverse Transcriptase was added. The reaction was incubated for an additional 1 hour at 42 degrees Celsius. Again, tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. Any remaining RNA was degraded by the addition of 1 μl NRase A (0.05 mg ml-1) and 1 μl NRase H (0.05 units ml-1) and incubated at 37 degrees Celsius for 30 min.

growth_protocol: Overnight cultures in YPD at 30 degree Celsius were diluted to an A600 of 0.2 in 250 ml YPD. Cultures were incubated at 200 RPM at 30 C for about 3.5 hours in YPD until reaching an A600 of 0.6. Cultures were then split into two groups, spun down and resuspended in 100 ml YPD media. One culture was incubated at 30 C, 200 RPM, 21 % O2, and the other one at 30 degree Celsius, 200 RPM, 1 % O2. Media for hypoxic growth had been preincubated in the hypoxic chamber overnight. Cells were grown for an additional 2 hours. Cells were pelleted and frozen in RNA Later at -80 degree Celsius.

value: 30 degree Celsius and 21% Oxygen.

value: YPD medium

source_name: Total RNA from C. parapsilosis CLIB214 grown in YPD medium at 30 degree celsius and 1% oxygen (hypoxia)


title: Candida_parapsilosis_normoxia_vs_hypoxia_rep1


title: Candida_parapsilosis_upc2_rep4


title: Liver wild type High Fat Diet, replicate 2

source_name: Liver wild type 6 months High Fat Diet, replicate 2


title: Liver wild type High Fat Diet, replicate 3

source_name: Liver wild type 6 months High Fat Diet, replicate 3


title: Liver Nrf2 knock-out High Fat Diet, replicate 3

source_name: Liver Nrf2 knock-out 6 months High Fat Diet, replicate 3


title: Candida_parapsilosis_normoxia_vs_hypoxia_rep4


title: Feproexpress HP 56


title: Liver Nrf2 knock-out High Fat Diet, replicate 4

source_name: Liver Nrf2 knock-out 6 months High Fat Diet, replicate 4


title: Feproexpress HP 61


title: Candida_parapsilosis_normoxia_vs_hypoxia_rep3


title: Liver Nrf2 knock-out High Fat Diet, replicate 2

source_name: Liver Nrf2 knock-out 6 months High Fat Diet, replicate 2


title: Candida_parapsilosis_upc2_rep2


title: Feproexpress HP 62


title: Feproexpress HP 55


title: brain_zf Ac_rep3

city: Durham

first: Erina

last: Hara

state: NC

address: Rm 449 Bryan Research Building

country: USA

institute: Duke University Medical Center

description: gene expression brain

hyb_protocol: From the amplified cDNA reactions, 1.5 mg of amplified labeled product (probe) was denatured and hybridized to our custom designed songbird oligo spotted arrays (Agilent Technologies; Whitney et al, in preparation) containing oligos designed from over 44,000 relatively unique cDNA transcripts, including some splice variants. More detailed information on the arrays is available at http://aviangenomes.org/main/zebrafincholigoarray.

scan_protocol: After hybridization, the microarrays were scanned with the Axon GenePix 4000B scanner to acquire and analyze the expression data (Molecular Devices).

data_processing: For analysis, signal intensity on an axon array scanner was obtained in Agilent oligoarray format. The data was extracted in R using the Agi4x44PreProcess Bioconductor library.The values were normalized using median centered log2 transformation. Raw and normalized expression distributions were evaluated for sample quality control using the normalization centering profile, the normalization factor, and a cross-sample correlation analysis. Normalization was evaluated with VSN (variance stabilization normalization)-Scale Factor package in R (R Foundation for Statistical Computing, Vienna, Austria). VSN-Scale Factor was chosen because it performed the least manipulation of the original intensity profiles, and normalizes samples among themselves.

organism: Taeniopygia guttata

source_name: Ac zebra finch

label_protocol: Samples were labeled with Cy3-dCTP using the uMACS SuperAmp Kit (Miltenyi Biotec).

extract_protocol: After laser capture the samples, the cap membrane with nuclei were carefully removed and placed in a 0.65 ml tube of the PicoPure RNA isolation kit which contained 50ul of disruption buffer (Molecular Devices). Tubes were placed on a 42oC heat block for 30 min then placed in a -80 oC freezer until all desired samples were captured. Total RNA was then isolated according to the remaining protocol steps in the PicoPure isolation kit instructions (Molecular Devices). The concentration and integrity of total RNA were measured on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA USA) using the RNA Pico 6000 kit according to manufacturer instructions (Agilent Technologies).

tag: brain area

value: surrounding arcopallium

value: Male

value: Adult


title: Feproexpress HP 52


title: Pf0-2x_whole_genome_array_adnA_mutant_rep4

city: Boston

first: Matthew

last: Mastropaolo

state: MA

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts Universicty School of Medicine

description: This sample is of adnA mutant Pseudomonas fluorescens Pf0-2x. It is the second of two Pf0-2x biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Pseudomonas fluorescens

source_name: Pseudomonas fluorescens Pf0-2x adnA mutant

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Pseudomonas fluorescens Pf0-2x (adnA-) was grown overnight in 50 mL of PMM.

extract_protocol: Samples were treated with the RNAprotect reagent (Qiagen Inc., Valencia, CA, USA) and the total RNA was extracted using the RNeasy Mini kit (Qiagen).  RNA was treated with RQ1 RNase free DNase (Promega Corporation, Madison, WI, USA). RNA samples were quantified using a NanoDrop Spectrophotometer (Isogen Life Science, The Netherlands).  The quality of the RNA was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) at Tufts University Core Facility (Tufts University School of Medicine, Boston, MA, USA).  First strand cDNA was synthesized from 10 mg total RNA with random hexamer primers from Invitrogen (Carlsbad, CA) using SuperScript Double-Stranded cDNA Synthesis kits (Invitrogen Corporation, Carlsbad, California, USA). The cDNA synthesis was carried out according to the NimbleGen protocol for synthesis of doublestranded cDNA.

value: adnA (transcription regulator) deletion mutant

tag: phenotype

value: non-flagellated, non-motile


title: Feproexpress HP 50


title: brain_zf Ac_rep2

description: gene expression brain


title: Feproexpress HP 53


title: brain_zf RA_rep2

description: gene expression brain

source_name: Ac song nucleus zebra finch

value: arcopallium song nucleus


title: Feproexpress HP 54

value: German Landrace


title: Feproexpress HP 49

value: liver


title: brain_bg Ac_rep1

description: gene expression brain

organism: Melopsittacus undulatus

source_name: Ac budgerigar


title: brain_bg Ac_rep3

description: gene expression brain


title: brain_zf RA_rep1

description: gene expression brain


title: brain_zf RA_rep3

description: gene expression brain


title: brain_bg Ac_rep2

description: gene expression brain


title: brian_bg RA_rep2

description: gene expression brain

source_name: Ac song nucleus budgerigar


title: brain_zf Ac_rep1

description: gene expression brain


title: Feproexpress HP 45

value: 28 dpn


title: Feproexpress HP 46

value: offspring of German Landrace gilts fed a gestational high protein diet


title: brain_ah Ac_rep3

description: gene expression brain

organism: Calypte anna

source_name: Ac hummingbird


title: brain_ah Ac_rep2

description: gene expression brain


title: brain_bg RA_rep3

description: gene expression brain


title: brain_bg RA_rep1

description: gene expression brain


title: Feproexpress HP 47

source_name: Liver


title: Feproexpress HP 43


title: Feproexpress HP 44


title: Feproexpress HP 51

value: 188 dpn


title: Pf0-1_whole_genome_array_wildtype_adnA_rep4

description: This sample is of wild-type Pseudomonas fluorescens Pf0-1. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

organism: Pseudomonas fluorescens Pf0-1

source_name: Pseudomonas fluorescens Pf0-1 wild-type

growth_protocol: Pseudomonas fluorescens Pf0-1 (adnA+) was grown overnight in 50 mL of Pseudomonas Minimal Medium (PMM) Kirner, S., S et. al. 1996. Microbiology 142 ( Pt 8):2129-2135.

value: Wild-type

value: normal


title: Pf0-2x_whole_genome_array_adnA_mutant_rep3

description: This sample is of adnA mutant Pseudomonas fluorescens Pf0-2x. It is the first of two Pf0-2x biological replicates used in this experiment, each from separate cultures.


title: Pf0-1_whole_genome_array_wildtype_adnA_rep3

description: This sample is of wild-type Pseudomonas fluorescens Pf0-1. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: Feproexpress HP 48


title: Feproexpress HP 42


title: brain_ah RA_rep3

description: gene expression brain

source_name: Ac song nucleus hummingbird


title: Feproexpress HP 40


title: lsg1 null 2.5 hr nitrogen starvation

city: Tokyo

first: Akira

last: Yamashita

address: Hong

department: Department of Biophysics and Biochemistry

country: Japan

institute: University of Tokyo

description: This sample is of lsg1∆ Schizosaccharomyce pombe JT659 under nitrogen starvation.

hyb_protocol: Hybridization was performed by Roche Applied Science, Japan.

scan_protocol: Scanning was performed by Roche Applied Science, Japan.

data_processing: Data processing was performed by Roche Applied Science, Japan

organism: Schizosaccharomyces pombe

label_protocol: Labeling was performed by Roche Applied Science, Japan.

growth_protocol: Cells of the wild-type (JY450) and lsg1Δ (JT659) fission yeast strains were grown to the mid-log phase in liquid MM and shifted to nitrogen-free MM-N. The cells were harvested 2.5 h after this shift.

extract_protocol: total RNA was extracted by the hot phenol method.

value: h90 lsg1::kanR ade6-M216 leu1

value: nitrogen starvation for 2h


title: brain_ah RA_rep1

description: gene expression brain


title: brain_ah RA_rep2

description: gene expression brain


title: Feproexpress HP 41


title: brain_dove Ac_rep3

description: gene expression brain

organism: Streptopelia risoria

source_name: Ac dove


title: brain_quail Ac_rep2

description: gene expression brain

organism: Coturnix japonica

source_name: Ac quail


title: brain_ah Ac_rep1

description: gene expression brain


title: brain_quail Ac_rep1

description: gene expression brain


title: Feproexpress HP 39


title: Feproexpress HP 35


title: brain_dove iAc_rep2

description: gene expression brain

source_name: iAc dove

value: intermediate arcopallium


title: brain_quail iAc_rep2

description: gene expression brain

source_name: iAc quail


title: brain_dove Ac_rep2

description: gene expression brain


title: Feproexpress HP 38


title: Feproexpress HP 37


title: Feproexpress HP 36


title: brain_dove Ac_rep1

description: gene expression brain


title: brain_dove iAc_rep3

description: gene expression brain


title: brain_dove iAc_rep1

description: gene expression brain


title: Feproexpress HP 34


title: wild type 2.5 hr nitrogen starvation

description: This sample is of wild-type Schizosaccharomyce pombe JY450 under nitrogen starvation.

value: h90 ade6-M216 leu1


title: Feproexpress HP 33


title: Standard diet mouse

city: Nicosia

first: Apostolos

last: Zaravinos

state: Nicosia

address: Kallipoleos 75

department: Department of Biological Sciences

country: Cyprus

institute: University of Cyprus

hyb_protocol: Hybridization was performed according to the manufacturer protocol (http://www.exiqon.com/ls/Documents/Scientific/miRCURY-LNA%E2%84%A2-microRNA-Array-v11-other-species-manual.pdf)

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing: Image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: adipose tissue from standard fat diet mouse

label_protocol: Labelling was performed using the miRCURY LNA™ microRNA Power Labeling Kit, according to the manufacturer protocol http://www.exiqon.com/ls/Documents/Scientific/miRCURY-LNA%E2%84%A2-microRNA-Array-v11-other-species-manual.pdf)

extract_protocol: Total RNA extracted using guanidinium thiocyanate following manufacturer's instructions

value: Adipose tissue


title: High fat diet mouse2

description: Technical replicate 2 of 2.

source_name: adipose tissue from high fat diet mouse


title: High fat diet mouse1

description: Technical replicate 1 of 2.


title: Feproexpress HP 32

value: 1 dpn


title: brain_quail iAc_rep1

description: gene expression brain

value: Male

value: Adult


title: Feproexpress HP 31


title: Psoriasis-10 baseline

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

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

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

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

organism: Homo sapiens

source_name: Psoriasis-10 baseline

extract_protocol: Whole skin punch biopsies were homogenized in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: disease state

value: psoriasis

tag: group

value: baseline


title: Lung_disease_sensitization_rep10

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: Biological replicate 10 of 10. Lung biopsy at sensitization from HDM-treated subject.

hyb_protocol: 18 hours at 60°C with constant rotation on Agilent WHG

scan_protocol: Agilent scanner according to the manufacturer’s protocol

data_processing: the data were extracted and normalized according to the default settings of Agilent Feature Extraction 7.5. LOWESS normalization, background subtraction, and ratio computation.

organism: Macaca mulatta

source_name: rhesus lung biopsy

label_protocol: T7 RNA polymerase single round of linear amplification

extract_protocol: micro total RNA isolation from animal tissues protocol (Qiagen, Valencia, CA)

treatment_protocol: sensitized to HDM antigen

tag: subject id

value: HDM exposure model of asthma

value: lung

tag: protocol

value: sensitized to HDM antigen

tag: timepoint

value: 15 weeks post-sensitization

tag: biological replicate

source_name: Stratagene Universal Human Reference

tag: reference

value: Stratagene Universal Human Reference


title: Feproexpress HP 28

tag: breed

value: German Landrace

value: liver

value: offspring of German Landrace gilts fed a gestational high protein diet


title: Feproexpress HP 29

tag: tissue


title: Feproexpress HP 26

tag: ontogenetic stage


title: Psoriasis-9 +placebo

source_name: Psoriasis-9 +placebo

label_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

value: placebo


title: Feproexpress HP 27

tag: gestation diet


title: Healthy-9 +placebo

source_name: Healthy-9 +placebo

value: healthy


title: Feproexpress HP 23


title: Lung_disease_sensitization_rep9

description: Biological replicate 9 of 10. Lung biopsy at sensitization from HDM-treated subject.


title: Healthy-9 +IFN-γ

source_name: Healthy-9 +IFN-γ

value: IFN-γ


title: Feproexpress HP 24


title: Feproexpress HP 30


title: Lung_disease_sensitization_rep7

description: Biological replicate 7 of 10. Lung biopsy at sensitization from HDM-treated subject.


title: Psoriasis-8 +IFN-γ

source_name: Psoriasis-8 +IFN-γ


title: Lung_disease_sensitization_rep4

description: Biological replicate 4 of 10. Lung biopsy at sensitization from HDM-treated subject.


title: Psoriasis-9 +IFN-γ

source_name: Psoriasis-9 +IFN-γ


title: Lung_disease_sensitization_rep8

description: Biological replicate 8 of 10. Lung biopsy at sensitization from HDM-treated subject.


title: Psoriasis-8 baseline

source_name: Psoriasis-8 baseline


title: Lung_disease_sensitization_rep5

description: Biological replicate 5 of 10. Lung biopsy at sensitization from HDM-treated subject.


title: Psoriasis-9 baseline

source_name: Psoriasis-9 baseline


title: Feproexpress HP 25

source_name: Liver


title: Lung_disease_sensitization_rep3

description: Biological replicate 3 of 10. Lung biopsy at sensitization from HDM-treated subject.


title: Psoriasis-8 +placebo

source_name: Psoriasis-8 +placebo


title: Psoriasis-10 +placebo

source_name: Psoriasis-10 +placebo


title: Psoriasis-7 +IFN-γ

source_name: Psoriasis-7 +IFN-γ


title: Lung_disease_sensitization_rep6

description: Biological replicate 6 of 10. Lung biopsy at sensitization from HDM-treated subject.


title: Psoriasis-7 baseline

source_name: Psoriasis-7 baseline


title: Feproexpress HP 22


title: Psoriasis-7 +placebo

source_name: Psoriasis-7 +placebo


title: Psoriasis-6 +placebo

source_name: Psoriasis-6 +placebo


title: Lung_control_sensitization_rep7

description: Biological replicate 7 of 8. Lung biopsy at sensitization from control-treated subject.

value: control

value: 7 of 8


title: Psoriasis-6 +IFN-γ

source_name: Psoriasis-6 +IFN-γ


title: Healthy-7 +placebo

source_name: Healthy-7 +placebo


title: Lung_control_sensitization_rep5

description: Biological replicate 5 of 8. Lung biopsy at sensitization from control-treated subject.

source_name: rhesus lung biopsy

value: 5 of 8

source_name: Stratagene Universal Human Reference


title: Healthy-8 +placebo

source_name: Healthy-8 +placebo


title: Healthy-6 +placebo

source_name: Healthy-6 +placebo


title: Feproexpress HP 16

description: Gene expression data from liver sample of offspring

value: 94 dpc


title: Lung_disease_sensitization_rep1

description: Biological replicate 1 of 10. Lung biopsy at sensitization from HDM-treated subject.


title: Feproexpress HP 19

value: 1 dpn


title: Feproexpress HP 21


title: Psoriasis-5 +placebo

source_name: Psoriasis-5 +placebo

value: psoriasis


title: Feproexpress HP 20


title: Lung_control_sensitization_rep8

description: Biological replicate 8 of 8. Lung biopsy at sensitization from control-treated subject.

value: 8 of 8


title: Lung_control_sensitization_rep6

description: Biological replicate 6 of 8. Lung biopsy at sensitization from control-treated subject.

value: lung

value: 6 of 8


title: Feproexpress HP 18


title: Lung_control_sensitization_rep4

description: Biological replicate 4 of 8. Lung biopsy at sensitization from control-treated subject.

value: sensitized to HDM antigen

value: 15 weeks post-sensitization

value: 4 of 8


title: Healthy-8 +IFN-γ

source_name: Healthy-8 +IFN-γ


title: Psoriasis-5 baseline

source_name: Psoriasis-5 baseline

value: baseline


title: Lung_disease_sensitization_rep2

description: Biological replicate 2 of 10. Lung biopsy at sensitization from HDM-treated subject.

value: HDM exposure model of asthma

value: Stratagene Universal Human Reference


title: Psoriasis-6 baseline

source_name: Psoriasis-6 baseline


title: Feproexpress HP 15

source_name: Liver

value: German Landrace

value: liver

value: offspring of German Landrace gilts fed a gestational high protein diet


title: Psoriasis-5 +IFN-γ

source_name: Psoriasis-5 +IFN-γ

value: IFN-γ


title: Healthy-7 +IFN-γ

source_name: Healthy-7 +IFN-γ

value: healthy


title: Feproexpress HP 17


title: Lung_control_sensitization_rep3

description: Biological replicate 3 of 8. Lung biopsy at sensitization from control-treated subject.

value: control

value: 3 of 8


title: Healthy-6 +IFN-γ

source_name: Healthy-6 +IFN-γ

value: placebo


title: Psoriasis-4 +IFN-γ

source_name: Psoriasis-4 +IFN-γ

value: psoriasis


title: Feproexpress HP 14

value: 94 dpc


title: Feproexpress HP 13


title: Healthy-5 +placebo

source_name: Healthy-5 +placebo


title: Psoriasis-3 +placebo

source_name: Psoriasis-3 +placebo


title: Lung_control_sensitization_rep1

description: Biological replicate 1 of 8. Lung biopsy at sensitization from control-treated subject.

value: lung

value: 1 of 8


title: Healthy-5 +IFN-γ

source_name: Healthy-5 +IFN-γ


title: Feproexpress HP 11


title: Psoriasis-3 +IFN-γ

source_name: Psoriasis-3 +IFN-γ


title: Psoriasis-4 baseline

source_name: Psoriasis-4 baseline


title: Feproexpress HP 12


title: Lung_disease_baseline_rep9

description: Biological replicate 9 of 9. Lung biopsy at baseline from HDM-treated subject.

source_name: rhesus lung biopsy

treatment_protocol: mock-sensitized (PBS)

value: mock-sensitized (PBS)

value: 9 of 9

source_name: Stratagene Universal Human Reference


title: Lung_disease_baseline_rep7

description: Biological replicate 7 of 9. Lung biopsy at baseline from HDM-treated subject.

value: baseline

value: 7 of 9


title: Lung_disease_baseline_rep8

description: Biological replicate 8 of 9. Lung biopsy at baseline from HDM-treated subject.

value: HDM exposure model of asthma

value: 8 of 9

value: Stratagene Universal Human Reference


title: Psoriasis-3 baseline

source_name: Psoriasis-3 baseline


title: Healthy-4 +placebo

source_name: Healthy-4 +placebo


title: Psoriasis-4 +placebo

source_name: Psoriasis-4 +placebo


title: Feproexpress HP 09

value: German Landrace

value: liver

value: offspring of German Landrace gilts fed a gestational high protein diet


title: Lung_control_sensitization_rep2

description: Biological replicate 2 of 8. Lung biopsy at sensitization from control-treated subject.

value: control

value: sensitized to HDM antigen

value: 15 weeks post-sensitization

value: 2 of 8


title: Healthy-4 +IFN-γ

source_name: Healthy-4 +IFN-γ

value: healthy

value: IFN-γ


title: Lung_disease_baseline_rep5

description: Biological replicate 5 of 9. Lung biopsy at baseline from HDM-treated subject.

value: lung

value: 5 of 9


title: Feproexpress HP 08

value: 94 dpc


title: Feproexpress HP 10


title: Healthy-3 +IFN-γ

source_name: Healthy-3 +IFN-γ


title: Lung_disease_baseline_rep6

description: Biological replicate 6 of 9. Lung biopsy at baseline from HDM-treated subject.

value: mock-sensitized (PBS)

value: baseline

value: 6 of 9


title: Feproexpress HP 07

source_name: Liver


title: Healthy-3 +placebo

source_name: Healthy-3 +placebo

value: placebo


title: Lung_disease_baseline_rep2

description: Biological replicate 2 of 9. Lung biopsy at baseline from HDM-treated subject.

value: HDM exposure model of asthma

value: 2 of 9

value: Stratagene Universal Human Reference


title: Lung_disease_baseline_rep3

description: Biological replicate 3 of 9. Lung biopsy at baseline from HDM-treated subject.

value: 3 of 9


title: Feproexpress HP 05

value: German Landrace

value: liver

value: offspring of German Landrace gilts fed a gestational high protein diet


title: Psoriasis-2 baseline

source_name: Psoriasis-2 baseline

value: psoriasis


title: Psoriasis-1 baseline

source_name: Psoriasis-1 baseline


title: Psoriasis-2 +IFN-γ

source_name: Psoriasis-2 +IFN-γ


title: Psoriasis-1 +placebo

source_name: Psoriasis-1 +placebo


title: Feproexpress HP 03


title: Feproexpress HP 06


title: Feproexpress HP 04


title: Lung_control_baseline_rep8

description: Biological replicate 8 of 8. Lung biopsy at baseline from control-treated subject.

value: control

value: 8 of 8


title: Feproexpress HP 02

description: Gene expression data from liver sample of offspring


title: Psoriasis-2 +placebo

source_name: Psoriasis-2 +placebo


title: Lung_control_baseline_rep5

description: Biological replicate 5 of 8. Lung biopsy at baseline from control-treated subject.

value: lung

value: 5 of 8


title: Lung_disease_baseline_rep1

description: Biological replicate 1 of 9. Lung biopsy at baseline from HDM-treated subject.

value: 1 of 9


title: Lung_control_baseline_rep7

description: Biological replicate 7 of 8. Lung biopsy at baseline from control-treated subject.

value: mock-sensitized (PBS)

value: 7 of 8


title: Psoriasis-1 +IFN-γ

source_name: Psoriasis-1 +IFN-γ

value: IFN-γ


title: Healthy-1 +IFN-γ

source_name: Healthy-1 +IFN-γ

value: healthy


title: Healthy-1 +placebo

source_name: Healthy-1 +placebo

value: placebo


title: Feproexpress AP 60

value: 188 dpn

value: offspring of German Landrace gilts fed a gestational adequate protein diet


title: Feproexpress HP 01

value: 94 dpc


title: Healthy-2 +IFN-γ

source_name: Healthy-2 +IFN-γ


title: Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy3) vs Input (Cy5) #2

type: genomic

city: Stony Brook

first: Hana

middle: S.

last: Fukuto

address: CMM rm350, Stony Brook University

department: Microbiology and Molecular Genetics/Center for Infectious Diseases

institute: Stony Brook University

description: Yersinia pestis KIM6+ Transposon Library “Output” vs Library “Input”

hyb_protocol: The microarray slides were prehybridized, washed, and dried immediately before hybridization by using the recommended protocol (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).  For hybridization, RNA labeled with Cy3 or Cy5 were dye-matched to 200-250 pmol and resuspended in 130µl of hybridization solution containing 25% (vol/vol) formamide, 5X SSC, 0.1% sodium dodecyl sulfate (SDS), and 300 µg/ml of sheared salmon sperm DNA (1X SSC is 0.15 M NaCl plus 0.015 M sodium citrate). Samples were heated at 95oC for 10 minutes prior to hybridization.  Hybridization was performed on a Tecan HS4800 Pro hybridization station as per manufacturer’s instructions. Hybridized arrays were sequentially washed with 5X SSC-0.1% SDS, 2X SSC-0.1% SDS, 0.1X SSC-0.1% SDS, 0.1% SDS, 95% ethanol, and deionized water.

scan_protocol: Arrays were directly scanned after the last wash using an Agilent G2505B DNA Microarray scanner controlled by Agilent scan control software, with a pixel size of 5 µm on a single-pass sequential line. The laser power was set to 100% for both red and green channels, and PMT gains were automatically adjusted by the scanner. Slide spots were gridded using GenePix Pro 6 software.  Lossless image files were stored for later analysis.

data_processing: The microarray data were analyzed using the Limma module of the Bioconductor package for the R statistical environment.  The microarray data for each gene was fitted to a linear model, and statistics were generated using the lmFit and eBayes functions.  The P values displayed were adjusted for multiple testing using the Benjamini and Hochberg method within Limma.  Annotations for microarray data were derived from the annotation files in a GenePix Array List (GAL) format provided by PFGRC.

molecule: genomic DNA

organism: Yersinia pestis

source_name: Yersinia pestis KIM6+ transposon library unselected input

label_protocol: Two µg of sheared purified gDNA was used for transcription with the amino-allyl MEGAscript kit (Ambion) and amino allyl UTP.  The transcription reaction was allowed to proceed for 14 hours at 37oC to make amino allyl-modified RNA.  The allyl-modified RNA was purified using the Qiagen nucleotide removal kit (Qiagen), and subsequently coupled with Cyanine 3 (Cy3) or Cyanine 5 (Cy5; GE Healthcare).

growth_protocol: A sample of the KIM6+ transposon library from the frozen stock was grown in HI broth culture at 28oC overnight with shaking.  A portion of the bacterial culture was harvested for use as an unselected “input” control.

extract_protocol: Genomic DNA (gDNA) was isolated from the “input” pool of KIM6+ using Genomic-tip 100/G reagents per the manufacturers protocol (Qiagen).  Twenty µg of purified gDNA was sheared by sonication, precipitated with ammonium acetate and ethanol, and resuspended in H2O containing DEPC

tag: sample type

value: yersinia pestis kim6+ transposon library, unselected input control (location in HI broth, Time overnight)

tag: library

tag: selection

value: input

source_name: Yersinia pestis KIM6+ transposon library output after selection inside macrophage

growth_protocol: A sample of the KIM6+ transposon library from the frozen stock was grown in HI broth culture at 28oC overnight with shaking. A portion of the culture was used to infect approximately 10^7 bone marrow-derived macrophages (BMMs) at a multiplicity of infection (MOI) of 2 for 15 minutes.  The infected BMMs were then washed with PBS, and incubated in tissue culture media containing 8 µg/ml gentamicin to kill extracellular bacteria.  The gentamicin concentration was reduced to 2 µg/ml after 1 hr.  At 8 hours post infection, the BMMs were washed with PBS and lysed with H2O containing 0.1% Triton-X 100. Bacteria were harvested by centrifugation and resuspended in HI, and an outgrowth step was performed overnight at 28oC with shaking.  The bacteria were then collected as the selected “output.”

extract_protocol: Genomic DNA (gDNA) was isolated from the “output” pool of KIM6+ using Genomic-tip 100/G reagents per the manufacturers protocol (Qiagen).  Twenty µg of purified gDNA was sheared by sonication, precipitated with ammonium acetate and ethanol, and resuspended in H2O containing DEPC

value: yersinia pestis kim6+ transposon library output after selection inside macrophage (location inside BMMs, Time 8hrs)

value: intracellular BMMS


title: Lung_disease_baseline_rep4

description: Biological replicate 4 of 9. Lung biopsy at baseline from HDM-treated subject.

source_name: rhesus lung biopsy

value: HDM exposure model of asthma

value: baseline

value: 4 of 9

source_name: Stratagene Universal Human Reference

value: Stratagene Universal Human Reference


title: Lung_control_baseline_rep3

description: Biological replicate 3 of 8. Lung biopsy at baseline from control-treated subject.

value: control

value: lung

value: 3 of 8


title: Lung_control_baseline_rep6

description: Biological replicate 6 of 8. Lung biopsy at baseline from control-treated subject.

value: mock-sensitized (PBS)

value: 6 of 8


title: Healthy-2 +placebo

source_name: Healthy-2 +placebo

value: healthy

value: placebo


title: Feproexpress AP 59

value: German Landrace

value: liver

value: 188 dpn

value: offspring of German Landrace gilts fed a gestational adequate protein diet


title: Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy3) vs Input (Cy5) #1

value: yersinia pestis kim6+ transposon library, unselected input control (location in HI broth, Time overnight)

value: input

value: yersinia pestis kim6+ transposon library output after selection inside macrophage (location inside BMMs, Time 8hrs)


title: Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy5) vs Input (Cy3)#2

extract_protocol: Genomic DNA (gDNA) was isolated from the “output” pool of KIM6+ using Genomic-tip 100/G reagents per the manufacturers protocol (Qiagen).  Twenty µg of purified gDNA was sheared by sonication, precipitated with ammonium acetate and ethanol, and resuspended in H2O containing DEPC.

value: yersinia pestis kim6+ transposon library

value: intracellular BMMS

extract_protocol: Genomic DNA (gDNA) was isolated from the “input” pool of KIM6+ using Genomic-tip 100/G reagents per the manufacturers protocol (Qiagen).  Twenty µg of purified gDNA was sheared by sonication, precipitated with ammonium acetate and ethanol, and resuspended in H2O containing DEPC.


title: Feproexpress AP 58


title: Feproexpress AP 56


title: Lung_control_baseline_rep2

description: Biological replicate 2 of 8. Lung biopsy at baseline from control-treated subject.

value: baseline

value: 2 of 8

value: Stratagene Universal Human Reference


title: Feproexpress AP 57


title: Lung_control_baseline_rep4

description: Biological replicate 4 of 8. Lung biopsy at baseline from control-treated subject.

value: control

value: lung

value: 4 of 8


title: Feproexpress AP 55


title: retina, adult, Csf2rb2, biological rep 2

city: Basel

first: Sandra

last: Siegert

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

description: GFP

hyb_protocol: Hybridization was performed with 5 μg biotinylated target, which was incubated with the GeneChip Gene 1.0 ST array (Affymetrix) at 45°C for 16 h. GeneChip Mouse Exon 1.0 ST array was used for the developmental study. Following hybridization, non-specifically bound nucleotides were removed by washing and the specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) and CEL files acquired using a GeneChip Command Console Software (Affymetrix).

data_processing: Data analysis of gene arrays was done in R (version 2.11.1) using bioconductor as well as in Mathematica (Wolfram Research). For gene arrays, after obtaining the CEL files for each gene array, the files were normalized using the rma function in the oligo package. The resulting text file for gene arrays contained the normalized expression values for 35’556 probes at log2 scale. Mouse gene annotation was downloaded from Affymetrix (MoGene-1_0-st- v1.na30.1.mm9.transcript.txt). Probes were only analyzed when a gene entry was annotated and duplicated annotated genes were removed. All genes are referred to by their NCBI gene symbols. Rod mixtures. In a first pre-screen of the gene expression data, expression of known rod-specific genes was recorded in the transcriptomes of almost all cell groups, despite a lack of GFP- or RFP-labeling in rod photoreceptors in these mouse lines. To eliminate this rod contamination, we used the separation method described above treating rods as type 1 cells. Note that despite a priori knowledge of several cell type-specific genes in other groups, we did not find these genes expressed in “incorrect” cell groups, suggesting that contamination was only by rods. For example, we did not find cone opsin (Opn1mw, Opn1sw) or melanopsin (Opn4) expression in cell groups in which the corresponding retinas had no cone or melanopsin labeling, respectively. Cone mixtures. In the mouse lines Lhx4, Chrna3, and Ier5 both cones and other cell types were labeled. We separated these mixtures into cone (Type 1) and other cell type (Type 2) components by the procedure described above. We used the predicted transcriptome of the Type 2 component in our analysis.

label_protocol: We used transgenic mouse lines that showed fluorescent-protein expression (RFP or GFP) in distinct cell types within the retina.

growth_protocol: Mice obtained from Mutant Mouse Regional Resource Centers (MMRRC) were FVB/N-Swiss Webster hybrids that are known to harbor a recessive mutation causing photoreceptor degeneration. These were backcrossed into the C57BL/6J background (RCC) and the F2 generation was used for transcriptome analysis. All other mouse lines had already been in the C57BL/6J background for several previous generations.

extract_protocol: Retinal cells were dissociated using a modified Papain-dissociation protocol of Morrow et al. with a process time of only 15 min. Cells from the retina were sorted. Cell sorting was performed using a MoFlo (Cytomation, Fort Collins, USA) with HQ515/30 (GFP) and HQ616/26 (RFP) bandpass filters. After recording several thousand events the fluorescence gate was set using Summit V 4.3.01 Build 2449 software and a population of events selected. Size and granularity of this population were determined using the forward and side scatter values, respectively, and cell debris discarded by setting a second gate. Finally, after determination of the duration of the events (pulse-width), a third gate was selected that served to exclude cell doublets or clumps. Using these three gates, cells were sorted in single-cell drop mode. A total of 200 cells were sorted at room temperature (RT) into a low-binding tube (Eppendorf) containing 60 µl cell lysis buffer (TRI reagent, Sigma-Aldrich).

tag: cell type

value: Retinal Microglia

tag: batch

tag: genetic background

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J

tag: line


title: retina, adult, Csf2rb2, biological rep 1

description: GFP


title: Lung_control_baseline_rep1

description: Biological replicate 1 of 8. Lung biopsy at baseline from control-treated subject.

tag: disease state

value: mock-sensitized (PBS)

value: 1 of 8


title: Feproexpress AP 54

value: German Landrace

value: liver

value: 188 dpn


title: retina, adult, Grik4, biological rep 1

description: RFP

value: Retinal Grik4 ganglion cell


title: Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy5) vs Input (Cy3)#1

value: yersinia pestis kim6+ transposon library output after selection inside macrophage (location inside BMMs, Time 8hrs)

value: yersinia pestis kim6+ transposon library, unselected input control (location in HI broth, Time overnight)

value: input


title: retina, adult, Opn4, biological rep 2

description: RFP

source_name: mOpn4-Cre1D4 × Rosa26-LSL-RFP

value: Retinal Melanopsin ganglion cell

value: mOpn4-Cre1D4 × Rosa26-LSL-RFP


title: Feproexpress AP 52

source_name: Liver

value: offspring of German Landrace gilts fed a gestational adequate protein diet


title: retina, adult, Grik4, biological rep 3

description: RFP


title: retina, adult, Opn4, biological rep 3

description: RFP


title: retina, adult, Grik4, biological rep 2

description: RFP


title: retina, adult, Opn4, biological rep 1

description: RFP


title: retina, adult, Csf2rb2, biological rep 3

description: GFP


title: Feproexpress AP 53


title: retina, adult, Drd4, biological rep 1

description: RFP

value: Retinal Drd4 ganglion cell


title: Feproexpress AP 49


title: Feproexpress AP 51


title: MCF-7_sh-CCN5

city: paris

first: Michèle

last: SABBAH

address: 184 rue du faubourg Saint-Antoine

country: France

institute: INSERM U938

hyb_protocol: Ten micrograms of biotin-labeled aRNA was fragmented using 5 µl of fragmentation buffer in a final volume of 20 µl, then was mixed with 240 µl of Amersham hybridization solution (GE Healthcare Europe GmbH, Freiburg, Germany) and injected onto CodeLink Human Whole Genome bioarrays containing human oligonucleotide gene probes targeting 57000 transcripts and EST (both from GE Healthcare Europe GmbH, Freiburg, Germany). Arrays were hybridized overnight at 37°C at 300 rpm in an incubator. The slides were washed in stringent TNT buffer at 46°C for 1 hour, and then a streptavidin-Cy5 (GE Healthcare) detection step was performed. Each slide was incubated for 30 min in 3.4 ml of streptavidin-Cy5 solution, then was washed 4 times in 240 ml of TNT buffer, rinsed twice in 240 ml of water containing 0.2% Triton X-100, and dried by centrifugation at 600 rpm.

scan_protocol: The slides were scanned using a Genepix 4000B scanner (Axon, Union City, USA) and Genepix software, with the laser set at 635 mm, the laser power at 100%, and the photomultiplier tube voltage at 60%.

data_processing:
The scanned image files were analyzed using CodeLink expression software, version 4.2 (GE Healthcare), which produces both a raw and normalized hybridization signal for each spot on the array.
CodeLink software was used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control probes in the array; spots with signal intensities below this threshold are referred to as "absent".

source_name: MCF-7, sh-CCN5

label_protocol: Total RNA (100 ng) were amplified and biotin-labeled by in vitro transcription (IVT) with a Message Amp aRNA kit (Ambion, Austin, Texas, USA).

extract_protocol: Total RNA were extracted from frozen cells with the RNeasy minikit (Qiagen, Hilden, Germany).

tag: cell line

value: breast cancer cells

tag: sh-rna


title: retina, adult, PV, biological rep 3

description: GFP

source_name: 129SVCB6(PV-CRE#32)SA-09 x ThyStopY

value: Retinal PV ganglion cell

value: 129SVCB6(PV-CRE#32)SA-09 x ThyStopY


title: Feproexpress AP 50


title: retina, adult, Drd4, biological rep 3

description: RFP

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: retina, adult, PV, biological rep 2

description: GFP


title: retina, adult, PV, biological rep 1

description: GFP


title: retina, adult, Ier5, biological rep 2

description: GFP

value: Retinal Ier5 amacrine cell


title: retina, adult, Drd4, biological rep 2

description: RFP


title: retina, adult, Ier5, biological rep 3

description: GFP


title: pre-senescent WI-38 AGO_2of2

first: Moussa

last: BENHAMED

address: Institut pasteur

institute: Institut Pasteur

description: Chip-chip input/AGO ChIP DNA

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: Input DNA from pre-senescent WI-38 AGO_2of2

label_protocol: 1 µg Input DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (Input DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Culturing of cells of primary human diploid fibroblasts strain WI38 were performed at physiological oxygen concentration of 3%

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: no treatment

value: primary human fibroblast WI-38

value: pre-senescent fibroblast

tag: chip antibody

value: none, input DNA

source_name: AGO ChIP DNA from WI-38 pre-senescent human fibroblast

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

value: pan AGO antibody


title: senescent WI-38 AGO_2of2

description: Chip-chip input/AGO ChIP DNA

source_name: Input DNA from senescent WI-38 AGO_2of2

treatment_protocol: transformed by Retroviral vector pBABE-RASV12

value: senescent fibroblast


title: retina, adult, Fbxo32, biological rep 1

description: GFP

value: Retinal Fbxo32 amacrine cell


title: Feproexpress AP 48

value: German Landrace

value: liver

value: 188 dpn


title: retina, adult, Fam81a, biological rep 1

description: GFP

value: Retinal Fam81a amacrine cell


title: Feproexpress AP 46

value: offspring of German Landrace gilts fed a gestational adequate protein diet


title: retina, adult, Ier5, biological rep 1

description: GFP


title: retina, adult, Fbxo32, biological rep 2

description: GFP


title: retina, adult, Fam81a, biological rep 2

description: GFP


title: transgenic line A vs. Wild type, 8 weeks, rep 2

city: Pretoria

first: Steven

middle: Grant

last: Hussey

state: Gauteng

address: Lynnwood Road, Hatfield

department: Genetics

country: South Africa

institute: University of Pretoria

description: Biological rep 2

hyb_protocol: Labeled cDNA was fragmented, hybridized and washed according to manucfacturer's specifications (Agilent Protocol for Two-Colour Microarray-Based Gene Expression Analysis, V. 5.7., March 2008)

scan_protocol: Slides were scanned with a Genepix™ 4000B scanner (Axon Instruments, Foster City, CA, USA).  Separate images were acquired for each fluorophore at a percentage saturation of 1%

data_processing: Scanned images of each fluorophore were imported and combined using GenePix Pro v.6.0 software, where all features on a superimposed GAL grid were automatically aligned. Spot checking was manually performed based on the criteria that noncircular or heterogeneous spots were included, as well as spots affected by slide artifacts. Results were analyzed in limmaGUI (Wettenhall & Smyth, 2004) using R, where background was subtracted and arrays were subjected to within-array and inter-array quantile normalization. 4 and 8 week time points were treated as separate experiments. Significanctly differentially expressed genes between three biological replicates of transgenic line A and three biological replicates of wild type were defined as those with an adjusted P-value (Pc) of less than 0.05, based on the Benjamini and Hochberg (1995) correction for experiment-wise multiple testing.

organism: Arabidopsis thaliana

source_name: transgenic line A, 8 weeks

label_protocol: cDNA was labeled indirectly with Ambion 5-(3-aminoallyl)-2'deoxyuridine-5'-triphosphate (aa-dUTP; cat # 8439) followed by dye coupling with Amersham CyDye Post-Labeling Reactive Dye Packs (GE Healthcare cat # RPN5661), according to the ACGT Microarray Facility Standard Operating Procedure (available online at http://www.microarray.up.ac.za/MA008_indirect_labelling_version3.pdf)

growth_protocol: Transgenic and wild type seeds were grown on hygromycin (transgenics: 50 µg/ml hygromycin B) for 2 weeks before transfer to jiffies. Plants were grown under articifical illumination (16 h days), 22oC and ~75% humidity. Plants were fertilized weekly

extract_protocol: Total RNA was extracted from inflorescence stems after grinding material to powder in liquid nitrogen, as described by Chang et al. (1993)

tag: genotype/variation

value: transgenic line A

value: inflorescence stem

tag: ecotype

tag: sample age

value: 8 weeks

source_name: wild type, 8 weeks

value: wild type


title: retina, adult, Chrna3, biological rep 3

description: GFP

value: Retinal Chrna3 amacrine cell

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: transgenic line A vs. Wild type, 8 weeks, rep 3

description: Biological rep 3

tag: tissue


title: transgenic line A vs. Wild type, 8 weeks, rep 1 tech rep 2

description: Biological rep 1


title: Feproexpress AP 45

tag: breed

tag: ontogenetic stage


title: MCF-7_sh-scrambled

source_name: MCF-7, sh-scrambled

value: breast cancer cells

value: scrambled


title: retina, adult, Fbxo32, biological rep 3

description: GFP


title: retina, adult, Chrna3, biological rep 2

description: GFP


title: Feproexpress AP 47

tag: gestation diet


title: retina, adult, Fam81a, biological rep 3

description: GFP


title: retina, adult, ChAT, biological rep 1

description: RFP

value: Retinal Starburst amacrine cell


title: Feproexpress AP 44

value: 28 dpn


title: transgenic line A vs. Wild type, 4 weeks, rep 1 tech rep 2

description: Biological rep 1

source_name: transgenic line A, 4 weeks

value: 4 weeks

source_name: wild type, 4 weeks


title: retina, adult, ChAT, biological rep 3

description: RFP


title: transgenic line A vs. Wild type, 4 weeks, rep 3

description: Biological rep 3


title: retina, adult, ChAT, biological rep 2

description: RFP


title: Feproexpress AP 43


title: Feproexpress AP 40


title: retina, adult, Chrna3, biological rep 1

description: GFP


title: Feproexpress AP 42


title: retina, adult, Crh, biological rep 2

description: RFP

value: Retinal Crh amacrine cell


title: transgenic line A vs. Wild type, 8 weeks, rep 1 tech rep 1

description: Biological rep 1


title: transgenic line A vs. Wild type, 4 weeks, rep 1 tech rep 1

description: Biological rep 1


title: Feproexpress AP 41

value: German Landrace


title: retina, adult, Crh, biological rep 1

description: RFP


title: Feproexpress AP 39

value: liver


title: retina, adult, Crh, biological rep 3

description: RFP


title: transgenic line A vs. Wild type, 4 weeks, rep 2

description: Biological rep 2


title: retina, adult, Rgs5, biological rep 3

description: GFP

value: Retinal Rgs5 amacrine cell


title: Feproexpress AP 37


title: retina, adult, Igfbp2, biological rep 1

description: GFP

value: Retinal Igfbp2 amacrine cell


title: Feproexpress AP 38

value: offspring of German Landrace gilts fed a gestational adequate protein diet


title: retina, adult ,Igfbp2, biological rep 2

description: GFP


title: retina, adult, Arc 3rd, biological rep 3

description: GFP

value: Retinal Arc amacrine cell


title: Feproexpress AP 36


title: retina, adult, Igfbp2, biological rep 3

description: GFP


title: retina, adult, Arc 2nd, biological rep 2

description: GFP


title: retina, adult, Arc 3rd, biological rep 1

description: GFP


title: Feproexpress AP 35


title: retina, adult, Rgs5, biological rep 2

description: GFP


title: retina, adult, Rgs5, biological rep 1

description: GFP


title: retina, adult, Arc 3rd, biological rep 2

description: GFP


title: retina, adult, Arc 2nd, biological rep 3

description: GFP


title: retina, adult, Arc 1st, biological rep 2

description: GFP


title: Feproexpress AP 33


title: retina, adult, Arc 1st, biological rep 1

description: GFP


title: retina, adult, Arc 1st, biological rep 3

description: GFP


title: Feproexpress AP 32


title: retina, adult, Lhx4, biological rep 3

description: GFP

value: Retinal Bipolar cell


title: retina, adult, Arc 2nd, biological rep 1

description: GFP


title: retina, adult, Pcp2, biological rep 2

description: GFP

value: Retinal Rod bipolar cell

tag: developmental stage

value: adult


title: retina, adult, Lhx4, biological rep 2

description: GFP


title: retina, adult, Kcng4, biological rep 2

description: RFP

source_name: B6Cf1-Tg(Kcng4-CreERT2, #)BR × Rosa26-LSL-RFP


title: retina, adult, Lhx4, biological rep 1

description: GFP


title: retina, adult, Kcng4, biological rep 1

description: RFP

value: B6Cf1-Tg(Kcng4-CreERT2, #)BR × Rosa26-LSL-RFP


title: Feproexpress AP 31


title: Feproexpress AP 29

value: 1 dpn


title: retina, adult, Kcng4, biological rep 3

description: RFP

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: Feproexpress AP 30


title: Feproexpress AP 28


title: HCT116_siCtrl

city: Sydney

first: Hamish

last: Campbell

state: NSW

address: 214 Hawkesbury Rd

country: Australia

institute: Children's Medical Research Institute

description: HCT116 Cells transfected with control siRNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: For normalization the array that had the lowest Euclidean distance from the median of all arrays was chosen as the index array, and all other arrays were normalized to this array using loess intensity-dependent smoothing.

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

growth_protocol: A549 lung adenocarcinoma and MCF7 breast cancer cell lines , and HCT116 colorectal carcinoma were validated for authenticity by CellBank Australia (www.cellbankaustralia.com).   All cell lines were cultured in RPMI-1640 supplemented with 10% v/v fetal bovine serum (FBS) (both from Invitrogen Corporation, Carlsbad, CA) in humidified air with 5% v/v CO2 at 37°C.

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

treatment_protocol: Stealth™ siRNAs were reverse transfected at a final concentration of  5 nM using Lipofectamine RNAiMax (Invitrogen), total RNA was extracted 48hrs post transfection.

tag: transfected

value: control siRNA


title: HCT116_siYB-2

description: HCT116 Cells transfected with 5nM siRNA2 targeting YB1. RNA was extracted 48hrs post transfection

value: siRNA2 YB1


title: retina, adult, mGluR6, biological rep 2

description: RFP

source_name: B6Cf1-Tg(mGlur6-Cre)BR × Rosa26-LSL-RFP

tag: cell type

value: Retinal ON-bipolar cell

value: B6Cf1-Tg(mGlur6-Cre)BR × Rosa26-LSL-RFP


title: retina, adult, Gja10, biological rep 3

description: RFP

source_name: B6Cf1-Tg(Gja10-Cre, #14)BR × Rosa26-LSL-RFP

value: Retinal Horizontal cell

tag: batch


title: retina, adult, Pcp2, biological rep 1

description: GFP

tag: genetic background


title: HCT116_siYB-1

description: HCT116 Cells transfected with 5nM siRNA1 targeting YB1. RNA was extracted 48hrs post transfection

value: siRNA1 YB1


title: retina, adult, Pcp2, biological rep 3

description: GFP

tag: line


title: retina, adult, Gja10, biological rep 1

description: RFP

value: B6Cf1-Tg(Gja10-Cre, #14)BR × Rosa26-LSL-RFP


title: Feproexpress AP 26

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

value: German Landrace

value: liver


title: HCT116_Cells

description: HCT116 Cell control

tag: treatment


title: retina, adult, mGluR6, biological rep 3

description: RFP


title: retina, adult, mGluR6, biological rep 1

description: RFP


title: retina, adult, Gja10, biological rep 2

description: RFP


title: Feproexpress AP 27

value: offspring of German Landrace gilts fed a gestational adequate protein diet


title: MCF7_siYB-2

description: MCF7 Cells transfected with 5nM siRNA2 targeting YB1. RNA was extracted 48hrs post transfection

tag: cell line


title: retina, adult, d4, biological rep 3

description: RFP

source_name: d4-Cre × Rosa26-LSL-RFP

value: Retinal Cone photoreceptor

value: d4-Cre × Rosa26-LSL-RFP


title: Feproexpress AP 25


title: retina, adult, d4, biological rep 2

description: RFP


title: Feproexpress AP 24


title: Feproexpress AP 23


title: retina, adult, Chrnb4, biological rep 2

description: GFP


title: retina, adult, Chrnb4, biological rep 1

description: GFP


title: MCF7_siYB-1

description: MCF7 Cells transfected with 5nM siRNA1 targeting YB1. RNA was extracted 48hrs post transfection


title: MCF7_siCtrl

description: MCF7 Cells transfected with control siRNA


title: retina, adult, Chrnb4, biological rep 3

description: GFP


title: retina, adult, b2 single, biological rep2

description: RFP

source_name: b2-Cre × Rosa26-LSL-RFP

value: Retinal Rod photoreceptor

value: b2-Cre × Rosa26-LSL-RFP


title: Feproexpress AP 34

description: Gene expression data from liver sample of offspring

value: 28 dpn


title: retina, adult, b2 single, biological rep1

description: RFP

value: adult


title: retina, adult, d4, biological rep 1

description: RFP

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: retina, adult, b2 single, biological rep3

description: RFP


title: Feproexpress AP 21

value: 1 dpn


title: Feproexpress AP 19


title: retina, adult, b2 2nd, biological rep3

description: RFP


title: retina, adult, b2 2nd, biological rep2

description: RFP


title: A549_siCtrl

description: A549 Cells transfected with control siRNA

value: control siRNA


title: A549_siYB-2

description: A549 Cells transfected with 5nM siRNA2 targeting YB1. RNA was extracted 48hrs post transfection

value: siRNA2 YB1


title: Feproexpress AP 20


title: MCF7_Cells

description: MCF7 Cell control


title: Feproexpress AP 22


title: A549_siYB-1

description: A549 Cells transfected with 5nM siRNA1 targeting YB1. RNA was extracted 48hrs post transfection


title: Feproexpress AP 18


title: retina, adult, b2 1st, biological rep3

description: RFP


title: Feproexpress AP 17


title: WT_116h_rep3

city: Bielefeld

first: Anh Vu

last: Nguyen

state: NRW

address: G2-154, CEBITEC, Universitaetsstr. 27

department: Cell and Molecular Biology

institute: Bielefeld University

description: WT T6 116h biological replicate 3 of 3

hyb_protocol: Mixtures of two different labeled cDNA samples were hybridized to DNA probes on Chlamydomonas microarray slides version 2 (Eberhard et al. 2006). The microarray slides were immobilized, prehybridized, hybridized and washed following as instructed in the supplier’s protocol. Just prior to hybridization, probe DNA was cross-linked (immobilization) to the slide by using a UV crosslinker (UVC500, Hoefer, USA) by 6000 mJoules. Slides were incubated in pre-warmed prehybridization solution (5× SSC, 0.1% SDS, 0.1 mg/ml BSA, 25% formamide; filtered and autoclaved) in a slide container at 42°C for one hour. They were then washed two times with 0.1× SSC (prewarmed at 42°C; filtered and autoclaved) by gentle agitation for 5 minutes. The sides were then washed in 42°C prewarmed water, then in isopropanol and finally dried by centrifugation (185 × g, 3 min). The suitable pair of previously labeled cDNA samples was mixed and dried in a vacuum-centrifuge with a foil-covered lid. Dried cDNA was resuspended in 65 μL of EasyHyb solution (Roche Diagnostics) supplemented with sonicated salmon sperm DNA at 50 μg/ml, then boiled for 3 minutes. The denatured sample was hybridized to a prepared slide in a HS 4800 hybridization station (Tecan) at 42°C for 2 h.

scan_protocol: After hybridization, the microarray slide was washed once in 2× SSC, 0.2% SDS (5 min, 42°C), twice in 0.2× SSC, 0.1% SDS (2 min, 21°C), and twice in 0.2× SSC (2 min, 21°C) and then dried by centrifugation (3 min, 185 × g, 20°C). The dried slide was scanned with a pixel size of 10 μm using the ScanArray 4000 microarray scanner (Perkin-Elmer, Boston).

data_processing: Median signal and median local background intensities were determined for each spot on the microarray images using the ImaGene 6.0 software for spot detection, image segmentation, and signal quantification (Biodiscovery Inc., Los Angeles, California, USA)

organism: Chlamydomonas reinhardtii

source_name: Reference: WT S replete culture prior to S starvation

label_protocol: 10 micro gram of total RNA were used for cDNA synthesis and labeling using Promega Chipshot Indirect Labeling and Clean-up system following manufacturer's instructions

growth_protocol: Cultures were grown in 1L flasks containing 400 ml TAP medium placed on an orbital shaker with 50 micro Enstein/m2/s illumination until late stationary phase

extract_protocol: Total RNA extracted using Promega SV Total RNA Isolation System following manufacturer's protocol

treatment_protocol: Cells were harvested by centrifugation ( 2500 x g, 4 min). The cell pellets were washed 3 times with TAP-S then were resuspended in TAP-S to a cell density of approximately 12 millions cells per milliliter. The cell suspension was then aliquoted into 330ml custom-made photobioreactors. The bioreactors were sealed and were illumiated with cool white light (300 micro Enstein/m2/s).

tag: strain

tag: time point

tag: oxygen availability

value: yes

tag: hydrogen production

value: no

source_name: WT, -S for H2 production, 116h


title: A549_Cells

description: A549 Cell control


title: retina, adult, b2 1st, biological rep2

description: RFP


title: Feproexpress AP 16

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).


title: retina, adult, b2 2nd, biological rep1

description: RFP


title: WT_T0_vs_Stm6Glc4_T0_rep3

description: WT T0 vs Stm6Glc4 T0 biological replicate 3 of 3

source_name: Sample: Stm6Glc4 S replete culture prior to S starvation


title: WT_T0_vs_Stm6Glc4_T0_rep2

description: WT T0 vs Stm6Glc4 T0 biological replicate 2 of 3


title: WT_T0_vs_Stm6Glc4_T0_rep1

description: WT T0 vs Stm6Glc4 T0 biological replicate 1 of 3


title: Feproexpress AP 14

value: 94 dpc


title: WT_116h_rep1

description: WT T6 116h biological replicate 1 of 3


title: WT_116h_rep2

description: WT T6 116h biological replicate 2 of 3


title: retina, adult, Arc, biological rep2

description: GFP

data_processing: Data analysis of gene arrays was done in R (version 2.11.1) using bioconductor as well as in Mathematica (Wolfram Research). For gene arrays, after obtaining the CEL files for each gene array, the files were normalized using the rma function in the oligo package. The resulting text file for gene arrays contained the normalized expression values for 35’556 probes at log2 scale. Mouse gene annotation was downloaded from Affymetrix (MoGene-1_0-st- v1.na30.1.mm9.transcript.txt). Probes were only analyzed when a gene entry was annotated and duplicated annotated genes were removed. All genes are referred to by their NCBI gene symbols.

value: Retinal Arc amacrine cell

tag: cell mixture

value: retina, adult, Arc


title: retina, adult, b2 1st, biological rep1

description: RFP


title: Feproexpress AP 15

value: German Landrace

tag: tissue

value: liver


title: WT_92h_rep3

description: WT T5 92h biological replicate 3 of 3

source_name: WT, -S for H2 production, 92h


title: HepG2_Stearic acid_rep3

city: Aarhus

first: Toke

middle: Krogager

last: Hansen

address: gustav wieds vej 10c

department: Molecular Biology

country: Denmark

institute: Aarhus University

description:
SC
raw data file technical rep1: H029-0607002926.gpr
raw data file technical rep2: H030-0607002929.gpr

hyb_protocol: Fragmented aRNA was hybridized at 42° C overnight using the HybBag mixing system with 1× OneArray Hybridization Buffer (Phalanx Biotech), 0.01 mg/mL sheared salmon sperm DNA (Promega) and 0.025 mg/mL labeled target. After hybridization, the arrays were washed according to the OneArray protocol

scan_protocol: Raw intensity signals from each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format

data_processing: The data from all microarrays in each experimental set were passed to Rosetta Resolver (Rosetta Biosoftware) for analysis. Testing was performed by combining the technical replicates and performing statistical analyses using Rosetta Resolver's proprietary modeling techniques

source_name: HepG2, Stearic acid, 7 days

label_protocol: RNA was converted to double-stranded cDNA and amplified using an in vitro transcription reaction that included aminoallyl-UTP, and the aRNA product was conjugated with Cy5T NHS ester

extract_protocol: Total RNA Purification Kit (NORGEN BIOTEK CORPORATION) Distribubed by Phalanx Biotech

treatment_protocol: Incubation for seven days with 100 µM fatty acid (oleic, elaidic or stearic acid)

tag: incubated fatty acid

value: Stearic acid


title: retina, adult, Arc, biological rep3

description: GFP


title: retina, adult, ChAT 17, cone 183, biological rep3

description: RFP/GFP

source_name: ChAT-Cre × Rosa26-LSL-RFP  : Chrnb4-GFP

value: Retinal Starburst amacrine cell and cone photoreceptor mixture

value: ChAT 17, cone 183

value: ChAT-Cre × Rosa26-LSL-RFP  :Chrnb4-GFP


title: Feproexpress AP 13

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

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

tag: breed

tag: ontogenetic stage

value: offspring of German Landrace gilts fed a gestational adequate protein diet


title: HepG2_Stearic acid_rep4

description:
SD
raw data file technical rep1: H031-0607002930.gpr
raw data file technical rep2: H032-0607002931.gpr


title: retina, adult, Arc, biological rep1

description: GFP

tag: developmental stage

value: adult


title: HepG2_Elaidic acid_rep4

description:
ED
raw data file technical rep1: H023-0607008703.gpr
raw data file technical rep2: H024-0607008704.gpr

source_name: HepG2, Elaidic acid, 7 days

value: Elaidic acid


title: WT_92h_rep1

description: WT T5 92h biological replicate 1 of 3


title: Feproexpress AP 12

tag: gestation diet


title: retina, adult, ChAT 17, cone 183, biological rep2

description: RFP/GFP

tag: cell type

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: WT_92h_rep2

description: WT T5 92h biological replicate 2 of 3


title: HepG2_Stearic acid_rep2

description:
SB
raw data file technical rep1: H027-0607002924.gpr
raw data file technical rep2: H028-0607002925.gpr


title: Feproexpress AP 11


title: HepG2_Elaidic acid_rep3

description:
EC
raw data file technical rep1: H021-0607002936.gpr
raw data file technical rep2: H022-0607002937.gpr


title: Feproexpress AP 10


title: Feproexpress AP 09


title: retina, adult, ChAT 125, cone 75, biological rep3

description: RFP/GFP

value: ChAT 125, cone 75


title: WT_68h_rep3

description: WT T4 68h biological replicate 3 of 3

source_name: WT, -S for H2 production, 68h


title: WT_68h_rep1

description: WT T4 68h biological replicate 1 of 3


title: HepG2_Elaidic acid_rep1

description:
EA
raw data file technical rep1: H017-0607002932.gpr
raw data file technical rep2: H018-0607002933.gpr


title: WT_68h_rep2

description: WT T4 68h biological replicate 2 of 3


title: retina, adult, ChAT 17, cone 183, biological rep1

description: RFP/GFP


title: WT_52h_rep3

description: WT T3 52h biological replicate 3 of 3

source_name: WT, -S for H2 production, 52h


title: Feproexpress AP 07


title: HepG2_Elaidic acid_rep2

description:
EB
raw data file technical rep1: H019-0607008699.gpr
raw data file technical rep2: H020-0607008700.gpr


title: Feproexpress AP 08


title: retina, adult, ChAT 125, cone 75, biological rep2

description: RFP/GFP


title: WT_52h_rep2

description: WT T3 52h biological replicate 2 of 3


title: Feproexpress AP 06


title: HepG2_Oleic acid_rep4

description:
OD
raw data file technical rep1: H015-0607008712.gpr
raw data file technical rep2: H016-0607008713.gpr

source_name: HepG2, Oleic acid, 7 days

value: Oleic acid


title: HepG2_Oleic acid_rep2

description:
OB
raw data file technical rep1: H011-0607008694.gpr
raw data file technical rep2: H012-0607008695.gpr


title: retina, adult, ChAT 0, cone 200, biological rep3

description: GFP

value: Retinal Cone photoreceptor

value: ChAT 0, cone 200


title: retina, adult, ChAT 125, cone 75, biological rep1

description: RFP/GFP


title: Feproexpress AP 03

value: 94 dpc


title: HepG2_Oleic acid_rep1

description:
OA
raw data file technical rep1: H009-0607008690.gpr
raw data file technical rep2: H010-0607008693.gpr


title: retina, adult, ChAT 43, cone 157, biological rep2

description: RFP/GFP

value: ChAT 43, cone 157


title: WT_52h_rep1

description: WT T3 52h biological replicate 1 of 3

value: yes

value: no


title: Feproexpress AP 05

description: Gene expression data from liver sample of offspring

value: German Landrace

value: liver


title: HepG2_control_rep4

description:
CD
raw data file technical rep1: H007-0607008144.gpr
raw data file technical rep2: H008-0607008145.gpr

source_name: HepG2, control, 7days


title: Feproexpress AP 04


title: WT_28h_rep3

description: WT T2 28h biological replicate 3 of 3

source_name: WT, -S for H2 production, 28h


title: WT_28h_rep2

description: WT T2 28h biological replicate 2 of 3


title: WT_28h_rep1

description: WT T2 28h biological replicate 1 of 3


title: Feproexpress AP 02


title: HepG2_Oleic acid_rep3

description:
OC
raw data file technical rep1: H013-0607008696.gpr
raw data file technical rep2: H014-0607008698.gpr


title: retina, adult, ChAT 43, cone 157, biological rep1

description: RFP/GFP

value: Retinal Starburst amacrine cell and cone photoreceptor mixture


title: retina, adult, ChAT 43, cone 157, biological rep3

description: RFP/GFP


title: HepG2_control_rep2

description:
CB
raw data file technical rep1: H003-0607008687.gpr
raw data file technical rep2: H004-0607008688.gpr


title: HepG2_control_rep3

description:
CC
raw data file technical rep1: H005-0607008682.gpr
raw data file technical rep2: H006-0607008683.gpr


title: retina, adult, ChAT 0, cone 200, biological rep2

description: GFP


title: HepG2_control_rep1

description:
CA
raw data file technical rep1: H001-0607008711.gpr
raw data file technical rep2: H002-0607008676.gpr


title: Feproexpress AP 01


title: WT_16h_rep2

description: WT T1 16h biological replicate 2 of 3

source_name: WT, -S for H2 production, 16h


title: WT_16h_rep1

description: WT T1 16h biological replicate 1 of 3


title: Stm6Glc4_52h_rep3

description: Stm6Glc4 T3 52h biological replicate 3 of 3

source_name: Reference: Stm6Glc4 S replete culture prior to S starvation

source_name: Stm6Glc4, -S for H2 production, 52h


title: WT_16h_rep3

description: WT T1 16h biological replicate 3 of 3


title: retina, adult, ChAT 50, cone 150, biological rep3

description: RFP/GFP

value: ChAT 50, cone 150


title: HepG2_Stearic acid_rep1

description:
SA
raw data file technical rep1: H025-0607002938.gpr
raw data file technical rep2: H026-0607002939.gpr

value: Stearic acid


title: Stm6Glc4_76h_rep3

description: Stm6Glc4 T4 76h biological replicate 3 of 3

source_name: Stm6Glc4, -S for H2 production, 76h


title: retina, adult, ChAT 50, cone 150, biological rep1

description: RFP/GFP

value: ChAT-Cre × Rosa26-LSL-RFP  :Chrnb4-GFP


title: retina, adult, ChAT 100, cone 100, biological rep3

description: RFP/GFP

value: ChAT 100, cone 100

value: adult


title: retina, adult, ChAT 50, cone 150, biological rep2

description: RFP/GFP

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: retina, adult, ChAT 150, cone 50, biological rep1

description: RFP/GFP

value: ChAT 150, cone 50


title: AML13_6H_Fenretinide

city: Shanghai

first: Hui

last: Zhang

address: 197 Ruijin Rd II

department: Shanghai Institute of Hematology

country: China

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

hyb_protocol: Array control targets and hybridization buffer were added, and samples (fragmented cRNA ) were applied to microarrays enclosed. After hybridization, slides were washed sequentially.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner.

data_processing: Data was processed using GenePattern software available at the Broad Insititute. MAS5.0 processing was used with quantile normalization.

label_protocol: 1 µg of total RNA were primed with 2 μl (100pmol) of T7-(d7)24 primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 1 μl SuperScript II (Invitrogen Life Technologies ), and 3μl of 10 mM dNTP (200μM each), 12μl IVT Labeling NTP Mix (Affymetrix ).

growth_protocol: The AML CD34+ cell derived from two primarily diagnosed AML were cultured in serum-free medium (StemCell technologies, Vancouver BC, Canada) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted and purified using miRNeasy (QIAGEN) isolation kit according to the manufacturer’s instructions.

treatment_protocol: 5 μM fenretinide

tag: culture intensity

value: AML C34+ cells from primarily diagnosed AML

tag: disease type

value: acute myelogenous leukemia


title: retina, adult, ChAT 100, cone 100, biological rep2

description: RFP/GFP

tag: genetic background

tag: line


title: retina, adult, ChAT 150, cone 50, biological rep3

description: RFP/GFP


title: Stm6Glc4_52h_rep2

description: Stm6Glc4 T3 52h biological replicate 2 of 3


title: Stm6Glc4_52h_rep1

description: Stm6Glc4 T3 52h biological replicate 1 of 3


title: Stm6Glc4_76h_rep2

description: Stm6Glc4 T4 76h biological replicate 2 of 3


title: retina, adult, ChAT 0, cone 200, biological rep1

description: GFP

value: Retinal Cone photoreceptor

value: ChAT 0, cone 200


title: AML12_12H_Fenretinide


title: retina, adult, ChAT 150, cone 50, biological rep2

description: RFP/GFP


title: AML13_12H_Fenretinide


title: Stm6Glc4_76h_rep1

description: Stm6Glc4 T4 76h biological replicate 1 of 3


title: Huh-7 cells control

first: Filip

last: Bebek

address: Molecular Microbiology Laboratory Rm 262, School of Biotechnology and Biomolecular Sciences (BABS), University of new South Wales

institute: Molecular Microbiology Laboratory

description: Gene expression data from untreated huh-& cells

hyb_protocol: Following fragmentation, labelled cRNA was  hybridised to the GeneChip®  HG-U133 plus 2.0 probe array during a 16 hr incubation (45°C). Following hybridisation, each probe array underwent automated washing and staining steps.

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

data_processing: The image obtained from scanned arrays was acquired using the Affymetrix® GeneChip® Operating Software (GCOS), converting the signal derived from each probe set into a raw intensity value. Probe set values were quantile normalised with the aid of RMAexpress software.

label: Biotin

source_name: Untreated Huh-7 cells

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

growth_protocol: Huh-7 cells were maintained at 37°C in a humidified atmosphere containing 5% CO2 and cultured in Dulbecco’s modified Eagle Medium (DMEM) supplemented with 10% (v/v) heat inactivated (56°C, 30 min) Fetal Bovine Serum (FBS), 4.5 g/L Glucose, and 2 mM glutamax.

extract_protocol: Total cellular RNA was extracted from each sample using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions, and included DNase I treatment on column (15 min at RT).

treatment_protocol: Following a 24hr incubation period, IFNa terated Huh-7 cells had the existing growth medium replaced with fresh growth medium containing recombinant human IFN-alpha 2b at a final concentration of 100 U/mL. The cells in the ‘Untreated’ flask simply had the growth media exchanged.

tag: cell line


title: retina, adult, ChAT 100, cone 100, biological rep1

description: RFP/GFP


title: AML12_6H_Fenretinide


title: RV_NF_6

city: Bad Oeynhausen

first: Patrick

last: Schwientek

address: Georgstr. 11

department: Klinik f. Thorax- & Kardiovaskularchirurgie

institute: Herz- & Diabeteszentrum NRW

description: Gene expression data from non-failing control hearts

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: right ventricle of NF patient 6

growth_protocol: Myocardial tissue was directly taken from non-failing and failing hearts.

extract_protocol: Samples were pruned from the left ventricle near the apex. RNA extraction has been carried out with TRIzol reagent and tissue was homogenized using a rotor-stator homogenizer. Homogenates were transferred to a Phase Lock Gel (PLG) Heavy tube (Eppendorf), chloroform was added, and the mixture was centrifuged. Supernatants were collected, and isopropanol was added to precipitate the RNA. The RNA pellet was washed with 80% ethanol, then air-dried before dissolving in 100 l of RNase-free H2O. RNA was further purified using the RNeasy Mini protocol according to the manufacturer’s directions (Qiagen).

treatment_protocol: The samples were frozen in liquid nitrogen directly after pruning and defrosted only for microarray analysis.

tag: age

tag: indication

value: Non-Failing

tag: gender

value: f

tag: ventricle

value: right


title: Huh-7 cells + IFNa

department: School of Biotechnology and Biomolecular Sciences (BABS)

description: Gene expression data from IFN-alpha treated (100 U/mL for 6 hours) Huh-7 cells

source_name: IFN-alpha treated Huh-7 cells


title: AML12_0H_Con

treatment_protocol: untreated


title: Stm6Glc4_28h_rep3

description: Stm6Glc4 T2 28h biological replicate 3 of 3

tag: strain

tag: time point

tag: oxygen availability

value: yes

tag: hydrogen production

value: no

source_name: Stm6Glc4, -S for H2 production, 28h


title: AML13_0H_Con


title: retina, adult, ChAT 200, cone 0, biological rep3

description: RFP

value: Retinal Starburst amacrine cell

tag: cell mixture

value: ChAT 200, cone 0


title: Stm6Glc4_28h_rep2

description: Stm6Glc4 T2 28h biological replicate 2 of 3


title: retina, adult, ChAT 200, cone 0, biological rep2

description: RFP

tag: developmental stage


title: Stm6Glc4_16h_rep1

description: Stm6Glc4 T1 16h biological replicate 1 of 3

source_name: Stm6Glc4, -S for H2 production, 16h


title: LV_NF_6

source_name: left ventricle of NF patient 6

value: left


title: Stm6Glc4_16h_rep2

description: Stm6Glc4 T1 16h biological replicate 2 of 3


title: Stm6Glc4_16h_rep3

description: Stm6Glc4 T1 16h biological replicate 3 of 3


title: Cornea plus DT infected

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The 2% trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Whole corneas from bone marrow chimeric mice

label_protocol: Biotinylated cRNA were prepared from 2 - 2.5 ug total RNA using the Affymetrix 3’ IVT express kit (#901229, Affymetrix Inc., Santa Clara, CA)

extract_protocol: Total RNA was isolated from pooled whole corneas using RNeasy and Qiashredder kits (Qiagen, Valencia, CA)

tag: tissue

value: Cornea

tag: infection

value: plus DT infected

tag: host strain

value: BALB/cJ


title: RV_NF_5

source_name: right ventricle of NF patient 5


title: retina, ChAT P18, biological rep2

description: RFP

data_processing:
Data analysis of gene arrays was done in R (version 2.11.1) using bioconductor. For exon arrays, the transcript cluster expression was calculated with the rma function using the command expr <- rma(read.celfiles[filenames, pkgname=pd.moex.1.0.st.v1]). Annotations for transcript clusters were downloaded from Affymetrix (MoEx-1_0-st-v1.na24.mm8.transcript.csv). The Arc-GFP time-course data was created in two batches: batch A contained samples P6-P16; batch B contained two non-contiguous sets of samples, P1-P6 and P17-P43. Correlation analysis revealed extensive batch effects between the samples. Because time-course batch A was surrounded on both sides by batch B, we shifted (in log2 space) the expression values for each transcript in batch A so that the average expression in batch A corresponded to the average expression in batch B. That is why we have in the matrix file only 1 value per Data point for Arc
MoEx-1_0-st-v1.r2_core.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.core.mps

tag: cell type

tag: batch

value: B

tag: age (day)

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: retina, ChAT P18, biological rep3

description: RFP

tag: genetic background

tag: line


title: Cornea no DT infected

value: no DT infected


title: Stm6Glc4_28h_rep1

description: Stm6Glc4 T2 28h biological replicate 1 of 3


title: Cornea no DT mock infected

value: no DT mock infected


title: retina, ChAT P18, biological rep1

description: RFP


title: Cornea plus DT mock infected

value: plus DT mock infected


title: retina, adult, ChAT 200, cone 0, biological rep1

description: RFP

value: adult


title: NIH-3T3 TMPRSS2/ERG (tERG) (replicate 3)

city: Monza

first: Vera

last: Magistroni

address: via Cadore 48

department: Clinical Medicine and Prevention

country: Italy

institute: University of Milano-Bicocca

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures using Gene ChIP Scanner 3000

data_processing: RMA Background adjustment, normalization and summarization of the raw data (.CEL files) were analyzed using the R package 'aroma.affymetrix' (H. Bengtsson; K. Simpson; J. Bullard; K. Hansen, aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008). The CDF annotation file used was a binary-converted version of the 'unsupported' CDF that is provided by Affymetrix (http://www.aroma-project.org/node/32).

source_name: NIH-3T3 cell line

label_protocol: Standard Affymetrix procedures.

growth_protocol: cells were maitained in DMEM supplemented with 10% FBS, in a humidified chamber with 5% CO2 supply

extract_protocol: RNA was extracted with TRIzol Reagent (Invitrogen) according to manufacturer's instuctions

treatment_protocol: cells were stably transfected with either TMPRSS2/ERG, FUS/ERG or EWS/ERG fusion cDNA and kept under selection for resistance to G418

tag: cell line

tag: transfection

value: TMPRSS2-ERG fusion


title: Macrophages_rep1

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

description:
Gene expression data from B to M transdifferentiation
2344_BM_Macs_1.CEL

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data have been normalized with RMA method, using Bioconductor in R

source_name: Cultured macrophages

label_protocol: RNAs were processed for Affymetrix 430.2 arrays as described in the manufacturer's instructions

growth_protocol: Pre-B cells were isolated, placed in duplicate on stromal cells plus cytokines, infected with an C/EBPaER-GFP retrovirus, GFP pos. cells sorted and after re-seeding on stroma induced with b-Est. Green cells were sorted at different times

extract_protocol: RNA was isolated by Trizol

treatment_protocol: GFP pos. cells were sorted and afetr re-seeding on stroma induced with b-Est. GFP pos cell were sorted at different imes thereafter

value: Macrophages


title: RV_NF_4

source_name: right ventricle of NF patient 4

tag: age

tag: indication

value: Non-Failing

tag: gender

value: m

tag: ventricle

value: right


title: pre-B_120h_b-Est_rep2

description:
Gene expression data from B to M transdifferentiation
2396_aER_120h_bEST_2.CEL

source_name: B to M transdifferentiation sample

value: Bone marrow derived cells (pre-B)

value: C/EBPaER-GFP retrovirus

tag: agent

value: b-Est

tag: time


title: LV_NF_3

source_name: left ventricle of NF patient 3

value: left


title: NIH-3T3 TMPRSS2/ERG (tERG) (replicate 2)


title: NIH-3T3  FUS-ERG (replicate 1)

value: FUS-ERG fusion


title: LV_NF_4

source_name: left ventricle of NF patient 4


title: LV_NF_5

source_name: left ventricle of NF patient 5


title: pre-B_120h_b-Est_rep1

description:
Gene expression data from B to M transdifferentiation
2343_aER_120h_bEST_1.CEL


title: NIH-3T3 EWS-ERG (replicate 3)

value: EWS-ERG fusion


title: NIH-3T3  FUS-ERG (replicate 2)


title: NIH-3T3  FUS-ERG (replicate 3)


title: RV_NF_3

source_name: right ventricle of NF patient 3


title: LV_NF_2

source_name: left ventricle of NF patient 2

value: f


title: RV_NF_1

source_name: right ventricle of NF patient 1


title: retina, ChAT P3, biological rep3

description: RFP

value: Retinal Starburst amacrine cell

value: B

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: retina, Arc, P43

description: GFP

value: Retinal Arc amacrine cell

value: A and B


title: retina, ChAT P3, biological rep1

description: RFP


title: pre-B_48h_b-Est_rep1

description:
Gene expression data from B to M transdifferentiation
2341_aER_48h_bEST_1.CEL


title: NIH-3T3 EWS-ERG (replicate 2)


title: Macrophages_rep2

description:
Gene expression data from B to M transdifferentiation
2397_BM_Macs_2.CEL


title: pre-B_12h_b-Est_rep2

description:
Gene expression data from B to M transdifferentiation
2392_aER_12h_bEST_2.CEL


title: retina, ChAT P3, biological rep2

description: RFP


title: retina, Arc, P20

description: GFP


title: NIH-3T3  EWS-ERG (replicate 1)


title: NIH-3T3 empty (replicate 3)

value: empty vector


title: retina, Arc, P19

description: GFP


title: RV_DCM_7

description: Gene expression data from dilated failing hearts

source_name: right ventricle of DCM patient 7

value: Dilated cardiomyopathy


title: retina, Arc, P18

description: GFP


title: NIH-3T3 empty (replicate 2)


title: LV_DCM_7

source_name: left ventricle of DCM patient 7


title: pre-B_3h_b-Est_rep1

description:
Gene expression data from B to M transdifferentiation
2338_aER_3h_bEST_1.CEL


title: RV_DCM_6

source_name: right ventricle of DCM patient 6


title: pre-B_3h_b-Est_rep2

description:
Gene expression data from B to M transdifferentiation
2391_aER_3h_bEST_2.CEL


title: pre-B_48h_b-Est_rep2

description:
Gene expression data from B to M transdifferentiation
2394_aER_48h_bEST_2.CEL


title: RV_NF_2

description: Gene expression data from non-failing control hearts

source_name: right ventricle of NF patient 2

value: Non-Failing


title: LV_DCM_6

source_name: left ventricle of DCM patient 6

value: m


title: pre-B_12h_b-Est_rep1

description:
Gene expression data from B to M transdifferentiation
2339_aER_12h_bEST_1.CEL


title: pre-B_3h_EtOH_rep2

description:
Gene expression data from B to M transdifferentiation
2390_aER_3h_EtOH_2.CEL

value: EtOH


title: LV_NF_1

source_name: left ventricle of NF patient 1


title: NIH-3T3 empty (replicate 1)


title: MIWI -/-  biological replicate 2

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with RMA from aroma.affy normalization method.

source_name: purified Round Spermatids total RNA, adult

label_protocol: Affymetrix protocol

growth_protocol: no specific treatment of mice, testes dissection at room temperature, testes kept in cold PBS before cell fractionation

extract_protocol: Trizol extraction of total RNA from round spermatids pooled from the respective gradient fractions

treatment_protocol: removal tunica albuginea, collagenase treatment in PBS, cell extraction from seminiferous tubules by pipetting with pasteur pipette, cell fractionation with BSA gradient 2-4%

tag: genotype/variation

value: MIWI -/-

tag: strain


title: retina, Arc, P16

description: GFP


title: MIWI +/KI biological replicate 1

value: MIWI +/KI


title: RV_DCM_5

source_name: right ventricle of DCM patient 5

value: right


title: MIWI +/KI biological replicate 2


title: retina, Arc, P15

description: GFP


title: retina, Arc, P14

description: GFP


title: LV_DCM_5

source_name: left ventricle of DCM patient 5

value: left


title: pre-B_3h_EtOH_rep1

description:
Gene expression data from B to M transdifferentiation
2337_aER_3h_EtOH_1.CEL

value: Bone marrow derived cells (pre-B)

tag: infection

value: C/EBPaER-GFP retrovirus


title: retina, Arc, P12

description: GFP


title: MIWI +/- biological replicate 2

value: MIWI +/-


title: RV_DCM_4

source_name: right ventricle of DCM patient 4

value: f


title: LV_DCM_4

source_name: left ventricle of DCM patient 4


title: retina, Arc, P10

description: GFP


title: retina, Arc, P13

description: GFP


title: MIWI -/KI biological replicate 2

value: MIWI -/KI