title: RU109_1181_mammary


title: RU109_1187_mammary

status: Public on Jan 01 2014

type: RNA

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

country: USA

institute: UCSF

hyb_protocol: 90uL of hybridization sample were incubated in the Affymetrix GeneTitan Oven instrument for 17 hours at 48C. Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the 550039 fluidics script and the GeneTitan Hybridization Module for WT Array Plates.

scan_protocol: An Affymetrix GeneTitan instrument was used to acquire the microarray image data

data_processing: CEL files were background corrected and normalized with RMA using the oligo package. Batch effects for array plate and lymph node cluster were corrected using ComBat, using covariates described in sample metadata

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mammary fat pad

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were housed in standard conditions with chow and water ad libitum.

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: Mice were not treated

tag: tissue

value: mammay fat pads

tag: genetic background

value: [FVB/N x Spret/Ei] x FVB/N Backcross

tag: Sex

value: female

tag: age

value: 8 wk


title: mammary gland_milk removed 12h_rep3

city: Burlington

first: Emma

middle: Hull

last: Wall

state: VT

address: 89 Beaumont Ave

department: Medicine

institute: University of Vermont

description: Cow 3 full

hyb_protocol: The biotinylated cRNAs were fragmented into 50- to 200-base fragments and then hybridized to GeneChip Bovine Genome Arrays for 16h at 45°C in a rotating Affymetrix GeneChip Hybridization Oven 320.  After hybridization, arrays were washed and stained with streptavidin-phycoerythrin on an automated Affymetrix GeneChip Fluidic Station F450.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 2700 and the images quantified using Affymetrix GeneChip Operating Software.

data_processing: The signal intensity for each probe on each chip was calculated from scanned images using GeneChip Operating Software (Affymetrix), and signal intensities were analyzed using BioConductor (http://www.bioconductor.org).  Probe intensities were background corrected, normalized, and summarized using the Robust Multichip Average method described by Speed and coworkers (Bolstad et al., 2003; Irizarry et al., 2003).  An alternative normalization method based on housekeeping genes did not significantly change the results.  The false discovery rate (FDR) was calculated by performing distinct permutations of the sample labels (Benjamini et al., 2001; Storey and Tibshirani, 2003; Storey et al., 2005).  In experiment 1, probe sets were considered differentially expressed when the signed fold change (4X vs. 2X) was ≥ 2, the P-value was < 0.05, and the FDR was < 0.20.  In experiment 2, probe sets were considered differentially expressed when the signed fold change was ≥ 1.2 and the P-value was < 0.10.  The less stringent signed fold change and P-value cutoffs for experiment 2 were used to allow for identification of genes that were differentially expressed in experiment 1 and may have been differentially expressed in experiment 2, but to a lesser degree.  To protect against false positives, the results of experiment 1 were used as a filter and only those genes differentially expressed in that experiment were investigated for differential expression in experiment 2.

organism: Bos taurus

source_name: bovine mammary gland, 12h of milk stasis

label_protocol: RNA amplification and microarray analysis for both experiments was performed at the University of Vermont microarray core facility using previously described protocols (Affymetrix, 2005-2006).  Briefly, 2 ug of total RNA from each tissue sample were reverse transcribed to the single stranded cDNA using a T7-oligo(dT) primer.  T4 DNA polymerase was used to synthesize double-stranded cDNA, which served as a template for in vitro transcription using T7 RNA polymerase to produce biotinylated cRNA.

extract_protocol: Total RNA was isolated from each biopsy sample using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.  The RNA was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

tag: breed

value: Holstein

tag: tissue type

value: lactating mammary gland


title: mammary gland_milk removed 0h_rep2

description: Cow 2 empty

source_name: bovine mammary gland, milk just removed


title: mammary gland_milk removed 0h_rep4

description: Cow 4 empty


title: RU109_1172_mammary


title: RU109_1186_mammary


title: mammary gland_milk removed 0h_rep3

description: Cow 3 empty


title: RU109_1182_mammary


title: Naive_24_h_rep5

city: Bonn

first: Khalid

middle: A.

last: Abnaof

state: North Rhine-Westfalina

address: Dahlmann Straße 2

department: Algorithmic Bioinformatics

country: Germany

institute: Bonn-Aachen International Centre for Information Technology (B-IT)

hyb_protocol: Tecan hybridization stations with fully automated washing steps according to manufacturer instructions

scan_protocol: Imagene Scanner according to manufacturer instructions

data_processing:
norm exponential convulsion method was used for background correction and loess normalization for within array normalization and quantile normalization for between array normalization, spot quality weights are consided
Series supplementary file normalized.txt includes background-corrected and normalized log2 ratio (Cy5/Cy3)
miRBase 15.0

source_name: Hippocampal cells (wild-type mouse NMRI)

label_protocol: miRCURY LNATM microRNA Hi-Power Labeling Kit according to manufacturer instructions

extract_protocol: Total RNA was isolated from the sonicated tissue using miRVANA miRNA isolation kit According to manufacturer instructions

treatment_protocol: SE was induced in mice (NMRI) chemically by a single dose of Pilocarpine (300mg/kg;i.p.).

tag: strain

value: Naive

tag: time

tag: replicate

value: NMRI

tag: cell type

value: hippocampal cells

source_name: Total RNA from pooled hippocampal cells (wild-type mouse NMRI)


title: RU109_1171_mammary


title: Naive_24_h_rep4


title: mammary gland_milk removed 12h_rep4

description: Cow 4 full


title: Naive_24_h_rep3


title: mammary gland_milk removed 0h_rep1

description: Cow 1 empty


title: RU109_1169_mammary


title: mammary gland_milk removed 12h_rep2

description: Cow 2 full


title: RU109_1165_mammary


title: RU109_1166_mammary


title: Naive_24_h_rep1


title: RU109_1160_mammary


title: 6Hz_27_72h__rep_6

source_name: Hippocampal cells (sound-stimulated SE mouse NMRI)

treatment_protocol: After an electrically induced seizure, mice received electrical stimulation (current intensity 44 mA, 0.2 ms monopolar pulses at 6 Hz frequency for 3 s)

source_name: Total RNA from pooled hippocampal cells (sound stimulated SE mouse NMRI)


title: 6Hz_28_72h__rep_7


title: mammary gland_milk removed 12h_rep1

description: Cow 1 full


title: RU109_1158_mammary


title: RU109_1159_mammary


title: Naive_24_h_rep2


title: 6Hz_26_72h__rep_5


title: 6Hz_25_72h__rep_4


title: RU109_1163_mammary


title: IEC 144h vs. IEC Eimeria 144h (251486811179_1_4)

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: 144h experiment 3

hyb_protocol: Whole mouse genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.9.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

source_name: caeca, infected, 144h

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: The life cycle of E. falciformis was maintained by continuous passage in NMRI mice

extract_protocol: Total RNA was purified using PureLink RNA Mini Kit (Life Technologies)

treatment_protocol: Animals at the age of 8-12 weeks were orally infected with 1500 oocysts of E. falciformis suspended in 100 µl PBS. The infected (24 and 144 hrs post-infection) and uninfected caeca were washed in Ca++ and Mg++-free HBSS, longitudinally dissected into sections (5 mm) in culture dishes, collected in polypropylene tubes, and then incubated with DTT (1 mM) dissolved in HBSS for 30 min at 37°C on a horizontal rotation shaker. Supernatants were discarded and tissues were suspended in 1 mM EDTA/ HBSS solution. Samples were incubated for 30 min at 37°C, and shaken rigorously every 10 min. Subsequent supernatants were passed through a cell strainer (70 µm) into fresh polypropylene tubes and centrifuged at 1500 rpm for 5 min. Pellets were resuspended in 1 ml TRIzol reagent and stored at -80°C until further use

tag: infection

value: infected

source_name: caeca, uninfected, 144h

value: uninfected


title: IEC 144h vs. IEC Eimeria 144h (251486811179_1_3)

description: 144h experiment 3


title: RU109_1152_mammary


title: RU109_1151_mammary


title: RU109_1156_mammary


title: RU109_1153_mammary


title: IEC 144h vs. IEC Eimeria 144h (251486811177_1_4)

description: 144h experiment 2


title: 6Hz_24_72h__rep_3


title: RU109_1154_mammary


title: RU109_1140_mammary


title: RU109_1157_mammary


title: IEC 144h vs. IEC Eimeria 144h (251486811175rehyb_1_3)

description: 144h experiment 1


title: RU109_1141_mammary


title: RU109_1139_mammary


title: 6Hz_23_72h__rep_2


title: IEC 144h vs. IEC Eimeria 144h (251486811177_1_3)

description: 144h experiment 2


title: IEC 144h vs. IEC Eimeria 144h (251486811175rehyb_1_4)

description: 144h experiment 1


title: RU109_1150_mammary


title: 6Hz_22_72h__rep_1


title: RU109_1155_mammary


title: RU109_1143_mammary


title: IEC 24h vs. IEC Eimeria 24h (251486811179_1_1)

description: 24h experiment 3

source_name: caeca, uninfected, 24h

source_name: caeca, infected, 24h


title: RU109_1142_mammary


title: RU109_1133_mammary


title: 6Hz_21_24h__rep_7


title: 6Hz_20_24h__rep_6


title: IEC 24h vs. IEC Eimeria 24h (251486811177_1_2)

description: 24h experiment 2


title: 6Hz_19_24h__rep_5


title: RU109_1137_mammary


title: IEC 24h vs. IEC Eimeria 24h (251486811179_1_2)

description: 24h experiment 3


title: 6Hz_18_24h__rep_4


title: RU109_1125_mammary


title: RU109_1132_mammary


title: RU109_1131_mammary


title: RU109_1136_mammary


title: RU109_1130_mammary


title: IEC 24h vs. IEC Eimeria 24h (251486811177_1_1)

description: 24h experiment 2


title: IEC 24h vs. IEC Eimeria 24h (251486811175rehyb_1_1)

description: 24h experiment 1


title: RU109_1118_mammary


title: 6Hz_17_24h__rep_3


title: RU109_1120_mammary


title: RU109_1121_mammary


title: IEC 24h vs. IEC Eimeria 24h (251486811175rehyb_1_2)

description: 24h experiment 1


title: KO1 PAO

description: Gene expression total lung RNA.

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). The values are the 'gProcessedSignal' from the Agilent Technologies Feature Extraction and represent signal intensities left after multiplicatively detrended background subtraction. No inter-array normalization was done.

source_name: lung homogenates, AhR KO, P. aeruginosa infection

label_protocol: RNA was labeled with the single-color Quick amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Mice were 8-12 weeks of age at the beginning of the experiments, matched for age and sex, and kept under specific pathogen-free (SPF) conditions.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: Mice were infected intratracheally (i.t.) with 4 x 10^6 CFUs of P. aeruginosa strain PAO1 under light anesthesia.

tag: strain/background

tag: genotype/variation

value: AhR-deficient knockout (AhR-/-)

value: lung

tag: treatment

value: intratracheally infected with P. aeruginosa (PAO1)


title: RU109_1114_mammary


title: 6Hz_15_24h__rep_1


title: RU109_1112_mammary


title: WT5 PAO

description: Gene expression total lung RNA.

source_name: lung homogenates, WT, P. aeruginosa infection

value: wild type


title: RU109_1107_mammary


title: RU109_1113_mammary


title: KO4 PAO

description: Gene expression total lung RNA.


title: 6Hz_14_6h__rep_7


title: 6Hz_13_6h__rep_6


title: RU109_1119_mammary


title: 6Hz_16_24h__rep_2


title: 6Hz_12_6h__rep_5


title: RU109_1106_mammary


title: WT2 PBS

description: Gene expression total lung RNA.

source_name: lung homogenates, WT, PBS control

value: PBS control


title: 6Hz_11_6h__rep_4


title: RU109_1097_mammary


title: RU109_1104_mammary


title: WT2 PAO

description: Gene expression total lung RNA.


title: 6Hz_10_6h__rep_3


title: RU109_1095_mammary


title: WT1 PBS

description: Gene expression total lung RNA.


title: KO2 PBS

description: Gene expression total lung RNA.

source_name: lung homogenates, AhR KO, PBS control


title: RU109_1096_mammary


title: RU109_1099_mammary


title: RU109_1088_mammary


title: RU109_1098_mammary


title: 6Hz_9_6h__rep_2


title: RU109_1090_mammary


title: RU109_1087_mammary


title: KO1 PBS

description: Gene expression total lung RNA.


title: i.n. animal 4 2h

source_name: blood, flagellin, 2 hours

label_protocol: Total RNA labeling was performed with the single color Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Blood was sampled with heparin and red blood cell lysis was performed on the fresh blood. Subsequently, RNA extraction was performed on RNA II nucleospin columns (Macherey Nagel).

treatment_protocol: Female C57BL/6J (6 weeks old) were maintained in an accredited specific pathogen-free facility (#A59107, Institut Pasteur de Lille) and immunized with the TLR5 agonist Flagellin (1μg diluted in PBS) by intra nasal (i.n.) administration. Blood samples of four time points post immunization were taken at 2h, 4h, 18h and 48h.

tag: gender

value: 6 weeks

value: intranasal flagellin immunization

tag: time point

value: 2 hours post-intranasal immunization


title: RU109_1080_mammary

value: mammay fat pads

value: [FVB/N x Spret/Ei] x FVB/N Backcross

value: female


title: 6Hz_8_6h__rep_1


title: 6Hz_7_3h__rep_7


title: RU109_1089_mammary

value: 8 wk


title: i.n. animal 3 2h


title: i.n. animal 5 2h


title: RU109_1081_mammary


title: 6Hz_6_3h__rep_6


title: RU109_1103_mammary


title: RU109_1078_mammary


title: RU109_1091_mammary


title: RU109_1076_mammary


title: RU109_1077_mammary


title: RU109_1079_mammary


title: RU109_1075_mammary


title: i.n. animal 1 2h


title: i.n. animal 2 2h


title: RU109_1074_mammary


title: 6Hz_4_3h__rep_4


title: 6Hz_3_3h__rep_3


title: RU109_1070_mammary


title: RU109_1066_mammary


title: RU109_1067_mammary


title: i.n. animal 3 4h

source_name: blood, flagellin, 4 hours

value: 4 hours post-intranasal immunization


title: i.n. animal 5 4h


title: RU109_1060_mammary

source_name: Mammary fat pad


title: 6Hz_2_3h__rep_2

value: NMRI


title: RU109_1059_mammary


title: i.n. animal 4 4h


title: RU109_1058_mammary


title: RU109_1068_mammary


title: 6Hz_1_3h__rep_1

value: hippocampal cells


title: 6Hz_5_3h__rep_5


title: 6Hz_35_Kon__rep_7


title: i.n. animal 1 4h


title: RU109_1057_mammary


title: RU109_1056_mammary


title: 6Hz_34_Kon__rep_6


title: i.n. animal 2 4h


title: RU109_1052_mammary


title: RU109_1050_mammary


title: RU109_1049_mammary


title: RU109_1051_mammary


title: i.n. animal 4 18h

source_name: blood, flagellin, 18 hours

value: 18 hours post-intranasal immunization


title: 6Hz_32_Kon__rep_4


title: 6Hz_33Kon__rep_5

description: 6Hz_33 Kon


title: i.n. animal 5 18h


title: i.n. animal 3 18h


title: RU109_1055_mammary


title: 6Hz_31_Kon__rep_3


title: RU109_1048_mammary


title: i.n. animal 2 18h


title: i.n. animal 5 48h

source_name: blood, flagellin, 48 hours

value: 48 hours post-intranasal immunization


title: 6Hz_30_Kon__rep_2


title: 6Hz_29_Kon__rep_1


title: RU109_1031_mammary


title: RU109_1030_mammary


title: RU109_1042_mammary


title: RU109_1041_mammary


title: i.n. animal 4 48h


title: RU109_1032_mammary


title: RU109_1026_mammary


title: i.n. animal 3 48h


title: RU109_1043_mammary


title: RU109_1027_mammary


title: RU109_1025_mammary


title: RU109_1029_mammary


title: i.n. animal 1 18h


title: RU109_1020_mammary


title: RU109_1021_mammary


title: RU109_1018_mammary


title: RU109_1019_mammary


title: naive animal 5

source_name: blood, naive


title: i.n. animal 1 48h


title: naive animal 4


title: i.n. animal 2 48h


title: RU109_1007_mammary


title: RU109_1006_mammary


title: RU109_1024_mammary


title: RU109_1005_mammary


title: RU109_1017_mammary


title: naive animal 3


title: naive animal 2


title: RU109_1014_mammary


title: naive animal 1


title: RU109_1012_mammary


title: JMJD2A-3

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol for iScan scanner.

data_processing: The data were log base 2 transformed and normalized using quantile normalisation with Matlab.

label: streptavidin Cy-3

organism: Homo sapiens

source_name: LNCaP cells with  vector+JMJD2A-3 shRNA

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit (Ambion).

extract_protocol: Cells were harvested 3 days after infection. RNA was extracted with Trizol reagent and further extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Two different ETV1 shRNA, two different JMJD2A shRNA, and one non-targeting control construct were cloned into pSIREN-retroQ vector. These plus packaging plasmids were cotransfected into 293 T cells to prepare retroviral contructs. Supernatants  were collected 48 and 72 h after transfection, passed through a 0.45 micron filter, and concentrated with PEG.  LNCaP cells were infected twice during a 24 h timespan with 5 microgram/mL polybrene.

tag: cell line

value: LNCaP

tag: transfection

value: JMJD2A-3 shRNA


title: JMJD2A-5

source_name: LNCaP cells with  vector+JMJD2A-5 shRNA

value: JMJD2A-5 shRNA


title: Ruptured Aneurysm rep 42

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description:
Replicate 42
Sample 81

scan_protocol: Standard Illumina scanning protocol

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

source_name: Blood

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

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

tag: group

value: Ruptured Aneurysm

value: Female


title: ETV1-1

source_name: LNCaP cells with  vector+ETV-1-1 shRNA

value: ETV-1-1 shRNA


title: Ruptured Aneurysm rep 40

description:
Replicate 40
Sample 78

tag: Sex

value: Male


title: Ruptured Aneurysm rep 41

description:
Replicate 41
Sample 80


title: sh-cm

source_name: LNCaP cells with control vector

value: non-trageting control vector (sh-cm)


title: hESC H1 B2M KO c2

city: Seattle

first: Laura

last: Riolobos

state: WA

address: 1959 NE Pacific St

institute: University of Washington

description:
hESC H1 cells were targeted with AAV-based vectors to knock out B2M gene, clone 2
Sample name: B2MKOc2

hyb_protocol: cRNA samples were hybridized onto Human HT-12 v4 Expression BeadChip (Illumina) according to manufacture's protocols.

scan_protocol: Arrays were scanned by the Genomics Resource Lab at Fred Hutchinson Cancer Center with an Illumina BeadArray Reader.

data_processing: Raw expression files were loaded into Bioconductor. The Bioconductor package 'lumi' was used to read in the GenomeStudio Probe Level from unnormalized data, and quantile normalize the data.

source_name: Cultured hESC H1 B2M KO

label_protocol: All RNA samples were amplified and labelled using Illumina's TotalPrep RNA Amplification Kit according to manufacturer's protocol.

growth_protocol: All cells were cultured on Matrigel (BD Biosciences) in mTESR media (Stem Cell Technologies)

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent 2100 Bioanalyzers and NanoDrop DN-1000 spectrophotometer.

value: hESC H1 cells

value: B2M KO


title: Control rep 18

description:
Replicate 18
Sample 79

value: Control


title: hESC H1 wt rep1 (H1A)

description:
hESC H1 wt
Sample name: H1A

source_name: Cultured hESC H1

value: wt


title: hESC H1 B2M KO c1

description:
hESC H1 cells were targeted with AAV-based vectors to knock out B2M gene, clone 1
Sample name: B2MKOc1


title: hESC H1 wt rep2 (H1B)

description:
hESC H1 wt
Sample name: H1B


title: Control rep 17

description:
Replicate 17
Sample 74


title: Ruptured Aneurysm rep 43

description:
Replicate 43
Sample 83


title: Ruptured Aneurysm rep 37

description:
Replicate 37
Sample 73


title: ETV1-5

source_name: LNCaP cells with  vector+ETV-1-5 shRNA

value: ETV-1-5 shRNA


title: Ruptured Aneurysm rep 38

description:
Replicate 38
Sample 75


title: Ruptured Aneurysm rep 35

description:
Replicate 35
Sample 70


title: Ruptured Aneurysm rep 36

description:
Replicate 36
Sample 72


title: Control rep 16

description:
Replicate 16
Sample 66


title: Ruptured Aneurysm rep 33

description:
Replicate 33
Sample 67


title: Ruptured Aneurysm rep 32

description:
Replicate 32
Sample 65


title: Ruptured Aneurysm rep 31

description:
Replicate 31
Sample 63


title: Ruptured Aneurysm rep 30

description:
Replicate 30
Sample 62


title: Ruptured Aneurysm rep 28

description:
Replicate 28
Sample 57


title: Ruptured Aneurysm rep 29

description:
Replicate 29
Sample 59


title: Ruptured Aneurysm rep 26

description:
Replicate 26
Sample 54


title: Ruptured Aneurysm rep 34

description:
Replicate 34
Sample 68


title: MCF7_BI2536_E2_rep3

city: Barcelona

first: Michael

last: Wierer

address: c/ Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation (CRG)

description:
12_MA__1200252665211710__Cy3_Blp_1_2/4
Gene expression after 1h BI2536 and 6h E2

hyb_protocol: The labeled cRNA was hybridized to the Agilent Human whole genome 4X44k v2 microarray (G4845A) according to the manufacturer's protocol.

scan_protocol: Arrays were scanned on an Agilent G2565CA microarray scanner at 100% PMT and 5 µm resolution.

data_processing: The sample data table consists of the data processed by the Agi4x44PreProcess software in combination with the hgug4112a.db library file. The preprocessing steps were the following: Background correction, Normalization between samples, Filtering probes by their Quality Flag and Summarizing replicated probes. The dataset is thereforer the high quality probe set used for later differential expression analysis.

label_protocol: Aliquots of 100 ng of total RNA from three biological replicates were labelled using Low Input Quick Amp Labeling kit (Agilent) following manufacturer instructions. Briefly, mRNA was reverse transcribed with T7-oligo-dT primer. cDNA was then in vitro transcribed with T7 RNA polymerase in the presence of Cy3-CTP.

growth_protocol: MCF7 cells were cultured in DMEM  with 10% FBS

extract_protocol: RNA was extracted with the RNeasy extraction kit (Qiagen).

treatment_protocol: For hormonal starvation, MCF7 cells were cultured for 3 days in phenol-red free DMEM supplemented with 5% charcoal-dextran treated FBS. Cells were pretreated for 1h with 100nM BI2536 or vehicle (DMSO), followed by induction with 10 nM estradiol or vehicle (ethanol) for 6 h.

value: breast cancer cells

tag: pretreated with

value: 100nM BI2536 for 1h

tag: induced with

value: 10 nM estradiol for 6 h


title: Ruptured Aneurysm rep 27

description:
Replicate 27
Sample 55


title: MCF7_BI2536_E2_rep2

description:
11_MA__1100252665211709__Cy3_11Blp_1_1/4
Gene expression after 1h BI2536 and 6h E2


title: Control rep 13

description:
Replicate 13
Sample 53


title: Control rep 14

description:
Replicate 14
Sample 60


title: Ruptured Aneurysm rep 23

description:
Replicate 23
Sample 48


title: Ruptured Aneurysm rep 24

description:
Replicate 24
Sample 49


title: Ruptured Aneurysm rep 21

description:
Replicate 21
Sample 44


title: Ruptured Aneurysm rep 25

description:
Replicate 25
Sample 50


title: Control rep 15

description:
Replicate 15
Sample 61


title: MCF7_BI2536_ETOH_rep1

description:
07_MA__1300252665211708__Cy3_7Blm_1_3/3
Gene expression after 1h BI2536 and 6h EtOH

value: ethanol (vehicle) for 6 h


title: Control rep 12

description:
Replicate 12
Sample 47


title: MCF7_BI2536_E2_rep1

description:
10_MA__1400252665211708__Cy3_10Blp_1_4/4
Gene expression after 1h BI2536 and 6h E2


title: Ruptured Aneurysm rep 22

description:
Replicate 22
Sample 46


title: MCF7_DMSO_E2_rep2

description:
05_MA__1300252665211709__Cy3_5Cp_1_3/2
Gene expression after 1h DMSO and 6h E2

value: DMSO (vehicle) for 1hr


title: MCF7_BI2536_ETOH_rep2

description:
08_MA__1400252665211709__Cy3_8Blm_1_4/3
Gene expression after 1h BI2536 and 6h EtOH


title: Control rep 11

description:
Replicate 11
Sample 42


title: MCF7_BI2536_ETOH_rep3

description:
09_MA__1100252665211710__Cy3_9Blm_1_1/3
Gene expression after 1h BI2536 and 6h EtOH


title: MCF7_DMSO_E2_rep1

description:
04_MA__1200252665211708__Cy3_4Cp_1_2/2
Gene expression after 1h DMSO and 6h E2


title: Ruptured Aneurysm rep 20

description:
Replicate 20
Sample 41


title: Control rep 10

description:
Replicate 10
Sample 40


title: Ruptured Aneurysm rep 19

description:
Replicate 19
Sample 39


title: Muscle_grass_fed_rep7

city: Dublin 4

first: Marion

middle: Teresa

last: Ryan

address: Belfield

department: Veterinary Sciences

country: Ireland

institute: University College Dublin

hyb_protocol: The fragmented and labeled cDNA was added to the hybridisation cocktail in accordance with the NuGEN guidelines.  Following hybridisation for 18 hr at 45°C, the array was washed and stained on the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA), inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: The microarrays were processed using a custom pipeline written in R using bioconductor libraries. The arrays were read in using functions from simpleaffy, pre-processed and normalised using the Factor Analysis for Robust Microarray Summarization (FARMS) algorithm (Hochreiter et al., 2006). The data was normalised using the quantile normalisation technique as implemented in the qFarms function. The normalised probeset data was then filtered to retain only the informative probes as determined by FARMS.

source_name: M. longissimus dorsi (LD) muscle

label_protocol: Five μg of the amplified single-stranded cDNA was fragmented and labeled using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies, San Carlos, CA) in accordance with manufacturers guidelines.  The enzymatically and chemically fragmented products (50–100nt) were labeled via the attachment of biotinylated nucleotides onto the 3' end of the fragmented cDNA.

growth_protocol: Charolais × Limousin crossbred heifers were randomly assigned to one of two production systems a pasture-fed group (G) and a concentrate-fed group (C).

extract_protocol: Total RNA was extracted using Trizol® reagent (Sigma-Aldrich Corp., St. Louis, MO, USA) and Tissue Lyzer ™ (Qiagen, Hilden, Germany) according to the manufacturer's protocols. The extracted RNA was treated with DNase I (Qiagen, Hilden, Germany) at room temperature for 10 min to remove genomic DNA. Total RNA was quantified and assessed for purity on a NanoDrop™ 1000  Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and samples with a 260/280 ratio ≥ 2.0 were considered suitable for cDNA synthesis. Total RNA integrity number (RIN) was assessed on the Agilent 2100 Bioanalyser version A.02.12 (Agilent Technologies Inc., CA, USA) using an RNA 6000 Nano LabChip kit (Caliper Technologies Corp. MA, USA).

treatment_protocol: Animals were slaughtered in accordance with European regulations at Meadow Meats Limited, Rathdowney, Co Laois. Samples from the M. longissimus dorsi (LD) muscle were collected within 20 min postmortem. Muscle was stored in RNAlater™, (Ambion Ltd., Cambridge, UK) for 24 hr and transferred to -80°C for long term storage.

tag: tissue

value: M. longissimus dorsi (LD) muscle

tag: breed

value: Charolais × Limousin

tag: assigned group

value: pasture-fed


title: MCF7_DMSO_ETOH_rep3

description:
03_MA__1300252665211710__Cy3_3Cm_1_3/1
Gene expression after 1h DMSO and 6h EtOH


title: Muscle_grass_fed_rep1

scan_protocol: Following hybridisation for 18 hr at 45°C, the array was washed and stained on the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA), inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).


title: Ruptured Aneurysm rep 18

description:
Replicate 18
Sample 37

value: Ruptured Aneurysm

value: Female


title: Muscle_grass_fed_rep6


title: Control rep 8

description:
Replicate 8
Sample 29

value: Male


title: TQ M disc, replicate 14

city: College Park

first: Gerald

middle: S

last: Wilkinson

state: MD

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

description:
TqM_6.4g
Biological replicate 14 of 14.

hyb_protocol: Using Agilent's recommended protocol, hybridizations were mixed with equal amounts of labeled nucleic acid. The ratio of the amount of labeled dye to nucleic acid (pmol/ug) was adjusted so that the same amount of red and green signal was acquired in each channel.

scan_protocol: Scanned using an Agilent G2505C microarray scanner in an ozone scrubbed room. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used. This software flags spots if pixel variation is too high or if the spot intensity is an outlier. Flagged features were subsequently removed from further analysis.  The processed signal intensities were calculated using a spatial detrend value for background subtraction and a combination of linear and lowess dye normalization.

organism: Teleopsis quinqueguttata

source_name: 25 pairs of eye-antennal discs, male, third-instar larvae

label_protocol: We used T7 to amplify messenger RNA prior to labeling. This procedure uses reverse transcription to make single-stranded cDNA and then DNA polymerization to make double-stranded (ds) cDNA, which is then amplified using a linear amplification procedure. Each pair of samples was alternately labeled with Cy3 and Cy5 dyes with regard to sex.

growth_protocol: Each sample consisted of 25 eye discs sampled from male or female wandering larvae, or heads from 6 male or female adult flies, that were taken from population cages maintained at the University of Maryland, College Park, derived from flies originally collected from SE Asia.

extract_protocol: Total RNA was extracted from larval tissue using the SV Total RNA Isolation System (Promega). Adult heads were ground with a pestle under liquid nitrogen, and total RNA was extracted using the mirVANA Total RNA extraction kit (Ambion).

tag: population

value: Gombak

value: male

tag: age

value: third-instar (wandering) larvae

value: eye disc and brain


title: Ruptured Aneurysm rep 16

description:
Replicate 16
Sample 33


title: TQ M disc, replicate 13

description:
TqM_6.3r
Biological replicate 13 of 14.


title: Control rep 9

description:
Replicate 9
Sample 34

value: Control


title: Muscle_Concentrate_fed_rep6

value: concentrate-fed


title: Ruptured Aneurysm rep 14

description:
Replicate 14
Sample 28


title: MCF7_DMSO_ETOH_rep1

description:
01_MA__1100252665211708__Cy3_1Cm_1_1/1
Gene expression after 1h DMSO and 6h EtOH

tag: cell type

value: breast cancer cells


title: Ruptured Aneurysm rep 15

description:
Replicate 15
Sample 31


title: TQ F disc, replicate 13

description:
TqF_6.3g
Biological replicate 13 of 14.

source_name: 25 pairs of eye-antennal discs, female, third-instar larvae

value: female


title: MCF7_DMSO_ETOH_rep2

description:
02_MA__1200252665211709__Cy3_2Cm_1_2/1
Gene expression after 1h DMSO and 6h EtOH


title: Muscle_grass_fed_rep5


title: Muscle_Concentrate_fed_rep4


title: TQ F disc, replicate 14

description:
TqF_6.4r
Biological replicate 14 of 14.


title: Ruptured Aneurysm rep 13

description:
Replicate 13
Sample 26


title: Ruptured Aneurysm rep 12

description:
Replicate 12
Sample 23


title: Control rep 7

description:
Replicate 7
Sample 27


title: Ruptured Aneurysm rep 17

description:
Replicate 17
Sample 36


title: TQ F disc, replicate 12

description:
TqF_6.2r
Biological replicate 12 of 14.


title: Muscle_Concentrate_fed_rep5


title: Ruptured Aneurysm rep 11

description:
Replicate 11
Sample 22


title: Control rep 6

description:
Replicate 6
Sample 21


title: Muscle_grass_fed_rep4


title: Muscle_Concentrate_fed_rep1


title: Control rep 5

description:
Replicate 5
Sample 16


title: Ruptured Aneurysm rep 9

description:
Replicate 9
Sample 15


title: Control rep 4

description:
Replicate 4
Sample 14


title: TQ M disc, replicate 12

description:
TqM_6.2g
Biological replicate 12 of 14.


title: Muscle_Concentrate_fed_rep3


title: Ruptured Aneurysm rep 10

description:
Replicate 10
Sample 18


title: TQ M disc, replicate 11

description:
TqM_6.1r
Biological replicate 11 of 14.


title: TQ F disc, replicate 10

description:
TqF_5.4r
Biological replicate 10 of 14.


title: TQ F disc, replicate 11

description:
TqF_6.1g
Biological replicate 11 of 14.


title: Ruptured Aneurysm rep 7

description:
Replicate 7
Sample 12


title: Ruptured Aneurysm rep 6

description:
Replicate 6
Sample 10


title: Ruptured Aneurysm rep 8

description:
Replicate 8
Sample 13


title: Ruptured Aneurysm rep 3

description:
Replicate 3
Sample 5


title: Muscle_Concentrate_fed_rep2


title: TQ M disc, replicate 10

description:
TqM_5.4g
Biological replicate 10 of 14.


title: Ruptured Aneurysm rep 4

description:
Replicate 4
Sample 7


title: Ruptured Aneurysm rep 5

description:
Replicate 5
Sample 9


title: TQ M disc, replicate 9

description:
TqM_5.3r
Biological replicate 9 of 14.


title: Control rep 3

description:
Replicate 3
Sample 8


title: Control rep 2

description:
Replicate 2
Sample 3


title: TQ F disc, replicate 9

description:
TqF_5.3g
Biological replicate 9 of 14.


title: TQ F disc, replicate 8

description:
TqF_5.2r
Biological replicate 8 of 14.


title: Muscle_Concentrate_fed_rep7


title: Muscle_grass_fed_rep3


title: Ruptured Aneurysm rep 2

description:
Replicate 2
Sample 4


title: TQ M disc, replicate 8

description:
TqM_5.2g
Biological replicate 8 of 14.


title: Ruptured Aneurysm rep 1

description:
Replicate 1
Sample 2


title: TQ F disc, replicate 7

description:
TqF_5.1g
Biological replicate 7 of 14.


title: Muscle_grass_fed_rep2


title: TQ M disc, replicate 7

description:
TqM_5.1r
Biological replicate 7 of 14.


title: Control rep 1

description:
Replicate 1
Sample 1


title: mammary gland_four times daily milking 21 d_rep 6

description: Cow 6 4X time 1

source_name: bovine mammary gland, 4X milking

value: Lactating mammary gland

value: four times daily milking


title: mammary gland_control_40 d_rep6

description: Cow 6 2X time 3

source_name: bovine mammary gland, control

value: control


title: Ruptured Aneurysm rep 39

description:
Replicate 39
Sample 76


title: mammary gland_four times daily milking 23 d_rep 6

description: Cow 6 4X time 2


title: TQ M disc, replicate 6

description:
TqM_4.2g
Biological replicate 6 of 14.


title: mammary gland_four times daily milking 40 d_rep 6

description: Cow 6 4X time 3


title: 11168_Cj0480c mutant_4hr_rep4

city: SARANAC LAKE

first: Wayne

last: Muraoka

state: NY

address: 154 Algonquin Ave

institute: Trudeau Institute

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts of labeled cDNA of the fucose treated and non-treated were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 10 min. The hybridization mixture was loaded onto a microarray slide and hybridized in a shaking incubator at 42 ºC for 16 h. Slides were washed as the manufacture’s recommendations and dried by centrifugation.

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of  each slides was scanned at a 10 μm resolution using two or three predetermined laser power and photomultiplier gain settings. Thus for rep1, five scan were perfprmed, and for rep2 and rep3 six scans were performed.

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength of each spot. The fluorescentc intensities of all spots were log2 transformed. The median of the log2-transformed spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization. This slide version includes spots representing 8 strains of C. jejuni and two sets of controls. Data was filtered to represent only spots from NCTC 11168.

organism: Campylobacter jejuni

source_name: C. jejuni NCTC11168 wild-type, MH w/o fucose, 4hr

label_protocol: cDNA was synthesized using aminoallyl-dNTP according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with Cy-3/cy-5 mono-Reactive Dye Pack (Amersham Biosciences, Piscataway, NJ)

growth_protocol: 10^8 CFU wild-type NCTC 11168 was grown in 10mL MH broth with or without fucose (25 mM final concentration) at 37OC under microaerophilic conditions (5% O2, 10% CO2, 85% N2) with gentle agitation for 4 hr.

extract_protocol: Total RNA was isolated using RNAprotectTM bacteria reagent (Qiagen) and an RNeasy kit (Qiagen) according to the manufacturer’s protocol with an optional step of on-column DNase treatment with RNase-Free DNase (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE)

tag: strain

value: wild-type

source_name: C. jejuni Cj0480c mutant, MH w/o fucose, 4hr

value: Cj0480c mutant


title: TQ F disc, replicate 4

description:
TqF_3.4r
Biological replicate 4 of 14.


title: TQ M disc, replicate 5

description:
TqM_4.1r
Biological replicate 5 of 14.


title: TQ F disc, replicate 5

description:
TqF_4.1g
Biological replicate 5 of 14.


title: 11168_Cj0480c mutant_4hr_rep2

tag: genotype/variation


title: 11168_Cj0480c mutant_4hr_rep1


title: 11168_+/- fucose_4hr_rep4

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength of each spot. The fluorescentc intensities of all spots were log2 transformed. The median of the log2-transformed spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization. This slide version includes spots representing 8 strains of C. jejuni and two sets of control spots. Data was filtered to represent only spots from NCTC 11168.

treatment_protocol: Fucose was added to a final concentration of 25mM at the start of incubation.

value: NCTC11168 wild-type

tag: treatment

value: sham-treated

source_name: C. jejuni NCTC11168 wild-type, MH w/ fucose (25mM final), 4hr

value: 25mM fucose treated


title: mammary gland_control_23 d_rep6

description: Cow 6 2X time 2


title: TQ F disc, replicate 6

description:
TqF_4.2r
Biological replicate 6 of 14.


title: mammary gland_control_21 d_rep6

description: Cow 6 2X time 1


title: 11168_+/- fucose_4hr_rep3


title: TQ M disc, replicate 4

description:
TqM_3.4g
Biological replicate 4 of 14.


title: mammary gland_control_40 d_rep5

description: Cow 5 2X time 3


title: 11168_Cj0480c mutant_4hr_rep3


title: mammary gland_four times daily milking 23 d_rep 5

description: Cow 5 4X time 2


title: mammary gland_control_23 d_rep5

description: Cow 5 2X time 2


title: mammary gland_four times daily milking 40 d_rep 5

description: Cow 5 4X time 3

tag: time point:


title: mammary gland_four times daily milking 21 d_rep 5

description: Cow 5 4X time 1

tag: time point


title: mammary gland_control_21 d_rep5

description: Cow 5 2X time 1


title: TQ M disc, replicate 3

description:
TqM_3.3r
Biological replicate 3 of 14.


title: 11168_+/- fucose_4hr_rep1


title: 11168_+/- fucose_4hr_rep2


title: TQ M disc, replicate 1

description:
TqM_2.3r
Biological replicate 1 of 14.


title: TQ F disc, replicate 2

description:
TqF_2.4r
Biological replicate 2 of 14.


title: TQ M disc, replicate 2

description:
TqM_2.4g
Biological replicate 2 of 14.


title: TQ F disc, replicate 1

description:
TqF_2.3g
Biological replicate 1 of 14.


title: TQ F disc, replicate 3

description:
TqF_3.3g
Biological replicate 3 of 14.


title: mammary gland_four times daily milking 23 d_rep 4

description: Cow 4 4X time 2


title: mammary gland_four times daily milking 40 d_rep 4

description: Cow 4 4X time 3


title: mammary gland_control_40 d_rep4

description: Cow 4 2X time 3


title: mammary gland_control_40 d_rep3

description: Cow 3 2X time 3


title: mammary gland_control_40 d_rep2

description: Cow 2 2X time 3


title: mammary gland_control_21 d_rep2

description: Cow 2 2X time 1


title: mammary gland_four times daily milking 21 d_rep 4

description: Cow 4 4X time 1


title: mammary gland_control_23 d_rep4

description: Cow 4 2X time 2


title: mammary gland_control_23 d_rep3

description: Cow 3 2X time 2


title: mammary gland_four times daily milking 40 d_rep 3

description: Cow 3 4X time 3


title: mammary gland_four times daily milking 21 d_rep 3

description: Cow 3 4X time 1


title: mammary gland_four times daily milking 23 d_rep 3

description: Cow 3 4X time 2


title: mammary gland_four times daily milking 21 d_rep 2

description: Cow 2 4X time 1


title: mammary gland_control_21 d_rep4

description: Cow 4 2X time 1


title: mammary gland_four times daily milking 40 d_rep 1

description: Cow 1 4X time 3


title: mammary gland_four times daily milking 40 d_rep 2

description: Cow 2 4X time 3


title: mammary gland_four times daily milking 23 d_rep 2

description: Cow 2 4X time 2


title: S5_A1_N170_S_42A_647

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

description: Second generation, lab reared larvae, initially collected from Åland metapopulationk, exposed to temperature treatments during final instar stage.

hyb_protocol: Fragmentation and hybridization was done using Gene Expression Hybridization Kit (Agilent) with two samples (825 ng labelled aRNA each) hybridized (65°C for 17 h at 10 RPM) to the same array according to the manufacturer's protocols. The slides were washed with Gene Expression Wash Buffer Kit (Agilent) and dried.

scan_protocol: Slide scanned with Axon GenePix® Autoloader 4200AL (Molecular Devices), with laser power set 100% and PMT gain set manually, using GenePix pro 6.1.0.4 (Molecular Devices).

data_processing: Signal intensities were extracted with GenePix pro 6.1.0.4 (Molecular Devices). Spot quality was examined by visual inspection and bad spots (containing dust etc.) were flagged. Raw intensity values (median of spot) were read in R using Limma-package and log2-transformed. Spots that were flagged bad ("Flags" = -100) got zero weight and were treated as missing information. Probes that were consistantly (in 90% of the arrays in each channel) saturated or had low signal (<2 standard deviations from the average intensity of DarkCorner spots) were removed. Data was normalized using loess and quantile method for within and between array normalization, respectively, without background subtraction, using the default setting in Limma.

label: Alexa Fluor 647

organism: Melitaea cinxia

source_name: Larvae 42A from family N170 exposed to Standard treatment

label_protocol: First strand reverse transcription was carried out at 46°C and 50°C for 1 h each in the presence of 8 µg of total RNA, 1 µl of Spike A or B from Two-Color RNA Spike-In Kit (Agilent), 5 µM oligo(dT)24-T7 primer (primed at 70°C for 10 min and cooled on ice for 2 min), 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM DTT, 0.5 mM each dNTP Mix, 40 U RNaseOUT™ (Invitrogen) and 200 U SuperScript™ III RT (Invitrogen). Second strand synthesis was carried out at 16°C for 2 h in the presence of 20 mM Tris-HCl (pH 6.8), 90 mM KCl, 4.6 mM MgCl2, 10 mM (NH4)2SO4, 0.3 mM each dNTP Mix, 2 U RNase H, 10 U DNA Ligase (NEB) and 40 U DNA Polymerase I (NEB). 3' overhangs were removed with 10 U T4 DNA Polymerase (NEB) incubated at 16°C for 15 min. Each reaction was inactivated by a 20 min incubation at 75°C and cooled to 4°C. Double stranded DNA was purified with NucleoSpin Extract II (Macherey-Nagel) following the PCR purification protocol. Reverse trancription was confirmed with PCR using primers for MDH gene (5'-ACTGCTAACCCTGAGGAGGC-3' and 5'-CCAAGGAACCAGTCCCTCAT-3'). A 3 h in vitro transcription with aminoallyl-UTP incorporation at 37°C was done using Ampliscribe T7 kit (Epicenter), followed by purification with NucleoSpin® RNA II kit (Macherey-Nagel), labelling with Alexa Fluor® Reactive Dye Decapacks for Microarray Applications (Invitrogen) and additional purification with NucleoSpin® RNA II kit (Macherey-Nagel) to remove unincorporated dye according to the manufacturer's protocols.

extract_protocol: Larvae was frozen and pulverized in liquid nitrogen with pestle and mortar. Total RNA was extracted using Trizol-method (Invitrogen) and further purified with NucleoSpin® RNA II kit (Macherey-Nagel) and Illustra MicroSpin G-25 Columns (GE heathcare) according to the manufacturer's protocols.

treatment_protocol: The larvae was reared in standard lab conditions until 6th instar stage. At 7th instar the larvae was exposed to Standard treatment (temperature profile: 15°C 17:00-6:59, 18°C 7:00-8:59, 22°C 9:00-10:59 and 26°C 11:00-16:59) and snap frozen in liquid nitrogen after 5 days of rearing.

tag: slide

tag: array

tag: family

value: Standard

tag: larvae


title: S4_A4_O171_H_15A_647

source_name: Larvae 15A from family O171 exposed to Hot treatment

treatment_protocol: The larvae was reared in standard lab conditions until 6th instar stage. At 7th instar the larvae was exposed to Hot treatment (temperature profile: 8°C 20:00-7:59, 15°C 8:00-9:59, 35°C 10:00-17:59 and 15°C 18:00-19:59) and snap frozen in liquid nitrogen after 4 days of rearing.

value: Hot


title: mammary gland_control_21 d_rep3

description: Cow 3 2X time 1

tag: group


title: mammary gland_four times daily milking 23 d_rep 1

description: Cow 1 4X time 2


title: S5_A2_O171_S_14B_647

source_name: Larvae 14B from family O171 exposed to Standard treatment


title: mammary gland_control_23 d_rep2

description: Cow 2 2X time 2


title: mammary gland_control_40 d_rep1

description: Cow 1 2X time 3


title: S5_A3_O171_S_28_647

source_name: Technical replicate 2 of S2_A3_O171_S_28_555 with dye swap


title: S5_A4_O171_H_15A_647

source_name: Technical replicate of S4_A4_O171_H_15A_647


title: S4_A1_N74_C_9C_647

source_name: Larvae 9C from family N74 exposed to Cold treatment

treatment_protocol: The larvae was reared in standard lab conditions until 6th instar stage. At 7th instar the larvae was exposed to Cold treatment (temperature profile: 8°C 18:00-9:59, 14°C 10:00-11:59, 20°C 12:00-15:59 and 14°C 16:00-17:59) and snap frozen in liquid nitrogen after 6 days of rearing.

value: Cold


title: S4_A3_N170_S_20B_647

source_name: Larvae 20B from family N170 exposed to Standard treatment


title: Hs683 resistant subclone 2_cy3

city: Amsterdam

first: Lotte

last: Hiddingh

address: De Boelelaan 1117

country: Netherlands

institute: VU University Medical Center

description:
Hs683 R2_cy3
raw data file:
US22502676_251485064820_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: cRNA was hybridized using the Agilent Gene Expression Hybridization Kit (5188-5242) according to the manufacturer´s protocol.

scan_protocol: Slides were scanned using an Agilent Microarray scanner (G2565BA). Image analysis was performed using feature extraction software version 9.5 (Agilent Technologies). The Agilent GE2-v5_95 protocol was applied using default settings.

data_processing: Array normalization was performed with R-package Limma within the Bioconductor software (v.3.2.3). Two channel raw data has been converted to normalized one channel data.

source_name: Hs683_resistant subclone 2

label_protocol: RNA samples were Cy3- or Cy5-labeled using the Agilent Low RNA Input Linear Amplification Kit Plus, according to the manufacturer's protocol.

extract_protocol: RNA was prepared using the miRVana RNA Purification kit (Ambion) according to manufacturer's protocol. RNA was quantified and quality checked with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell line background

value: glioblastoma cells

tag: sample type

value: wild type cell line


title: S4_A2_N74_S_7A_647

source_name: Larvae 7A from family N74 exposed to Standard treatment


title: Hs683_rep2_cy3

description:
Hs683_2_cy3
raw data file:
US22502676_251485064820_S01_GE2-v5_95_Feb07_1_3.txt

source_name: Hs683_wild type

value: TMZ-resistant subclone


title: S3_A4_N170_S_31A_647

source_name: Larvae 31A from family N170 exposed to Standard treatment


title: Hs683 resistant subclone 1_cy3

description:
Hs683 R1_cy3
raw data file:
US22502676_251485064820_S01_GE2-v5_95_Feb07_1_2.txt

source_name: Hs683_resistant subclone 1


title: S3_A3_N74_H_18B_647

source_name: Larvae 18B from family N74 exposed to Hot treatment


title: LNZ308_ resistant subclone 2_cy3

description:
LNZ308 R2_cy3
raw data file:
US22502676_251485064818_S01_GE2-v5_95_Feb07_1_4.txt

source_name: LNZ308_resistant subclone 2


title: LNZ308_rep2_cy3

description:
LNZ308_2_cy3
raw data file:
US22502676_251485064818_S01_GE2-v5_95_Feb07_1_3.txt

source_name: LNZ308_wild type


title: U87 resistant subclone 2_cy3

description:
U87 R2_cy3
raw data file:
US22502676_251485064817_S01_GE2-v5_95_Feb07_1_4.txt

source_name: U87_resistant subclone 2


title: LNZ308_ resistant subclone 1_cy3

description:
LNZ308 R1_cy3
raw data file:
US22502676_251485064818_S01_GE2-v5_95_Feb07_1_2.txt

source_name: LNZ308_resistant subclone 1


title: S2_A3_O171_C_6A_647

source_name: Larvae 6A from family O171 exposed to Cold treatment


title: S2_A2_N74_S_7C_647

source_name: Larvae 7C from family N74 exposed to Standard treatment


title: U87_rep2_cy3

description:
U87_2_cy3
raw data file:
US22502676_251485064817_S01_GE2-v5_95_Feb07_1_3.txt

source_name: U87_wild type


title: S3_A2_O171_S_14A_647

source_name: Larvae 14A from family O171 exposed to Standard treatment


title: U87 resistant subclone 1_cy3

description:
U87 R1_cy3
raw data file:
US22502676_251485064817_S01_GE2-v5_95_Feb07_1_2.txt

source_name: U87_resistant subclone 1


title: S1_A2_N170_C_33_647

source_name: Larvae 33 from family N170 exposed to Cold treatment


title: Hs683 resistant subclone 2_cy5

description:
Hs683 R2_cy5
raw data file:
US22502676_251485064820_S01_GE2-v5_95_Feb07_1_3.txt


title: S1_A4_N74_C_9A_647

source_name: Larvae 9A from family N74 exposed to Cold treatment


title: S2_A4_N170_H_32B_647

source_name: Larvae 32B from family N170 exposed to Hot treatment


title: Hs683_rep2_cy5

description:
Hs683_2_cy5
raw data file:
US22502676_251485064820_S01_GE2-v5_95_Feb07_1_4.txt


title: U87_rep1_cy3

description:
U87_1_cy3
raw data file:
US22502676_251485064817_S01_GE2-v5_95_Feb07_1_1.txt


title: LNZ308_rep1_cy3

description:
LNZ308_1_cy3
raw data file:
US22502676_251485064818_S01_GE2-v5_95_Feb07_1_1.txt


title: S5_A4_N170_C_44A_555

label: Alexa Fluor 555

source_name: Technical replicate of S4_A3_N170_C_44A_555


title: Hs683_rep1_cy5

description:
Hs683_1_cy5
raw data file:
US22502676_251485064820_S01_GE2-v5_95_Feb07_1_2.txt

source_name: Hs683_wild type


title: S3_A1_O171_S_28_647

source_name: Technical replicate 1 of S2_A3_O171_S_28_555 with dye swap


title: Hs683_rep1_cy3

description:
Hs683_1_cy3
raw data file:
US22502676_251485064820_S01_GE2-v5_95_Feb07_1_1.txt


title: Hs683 resistant subclone 1_cy5

description:
Hs683 R1_cy5
raw data file:
US22502676_251485064820_S01_GE2-v5_95_Feb07_1_1.txt

source_name: Hs683_resistant subclone 1


title: S2_A1_N74_S_17C_647

description: Second generation, lab reared larvae, initially collected from Åland metapopulationk, exposed to temperature treatments during final instar stage.

source_name: Larvae 17C from family N74 exposed to Standard treatment


title: S1_A1_N170_H_21A_647

source_name: Larvae 21A from family N170 exposed to Hot treatment


title: LNZ308_rep2_cy5

description:
LNZ308_2_cy5
raw data file:
US22502676_251485064818_S01_GE2-v5_95_Feb07_1_4.txt

source_name: LNZ308_wild type


title: S5_A2_O171_C_6B_555

source_name: Larvae 6B from family O171 exposed to Cold treatment


title: LNZ308_ resistant subclone 2_cy5

description:
LNZ308 R2_cy5
raw data file:
US22502676_251485064818_S01_GE2-v5_95_Feb07_1_3.txt

source_name: LNZ308_resistant subclone 2


title: S4_A4_O171_S_4C_555

source_name: Larvae 4C from family O171 exposed to Standard treatment


title: S5_A1_N170_H_21C_555

source_name: Larvae 21C from family N170 exposed to Hot treatment


title: S1_A3_O171_H_29A_647

source_name: Larvae 29A from family O171 exposed to Hot treatment


title: S5_A3_N74_S_34_555

source_name: Technical replicate of S4_A1_N74_S_34_555


title: S4_A3_N170_C_44A_555

source_name: Larvae 44A from family N170 exposed to Cold treatment


title: LNZ308 resistant subclone 1_cy5

description:
LNZ308 R1_cy5
raw data file:
US22502676_251485064818_S01_GE2-v5_95_Feb07_1_1.txt

source_name: LNZ308_resistant subclone 1


title: U87 resistant subclone 1_cy5

description:
U87 R1_cy5
raw data file:
US22502676_251485064817_S01_GE2-v5_95_Feb07_1_1.txt

source_name: U87_resistant subclone 1


title: Asynch-Neurons-Rep A

city: Boulder

first: Minh

last: Than

state: CO

address: Campus Box 347

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado, Boulder/HHMI

description: IP RNA and Total RNA come from the same worms

hyb_protocol: Hybridization Application 1.0 PURPOSE: To provide a standard operating procedure for hybridization of fluorocein labeled probes to cDNA or oligonucleotide elements on microarray glass slides. 2.0 SPECIAL NOTES: 3.0 AUTHORS: Mike Heinz 4.0 RELATED DOCUMENTS: L3.0, L7.0, H4.0, H5.0, H6.0 5.0 REQUIRED MATERIALS AND EQUIPMENT: Labeled probe Hybridization chamber apparatus Hybridization oven Heat block 4xSSC Air gun/ canister Timers Microcentrifuge Hybridization buffer (check vendor) Forceps Microarray(s) Pipettes Coverslips (Erie Scientific) 6.0 DEFINITIONS: 7.0 PROCEDURE: 7.1 Set up 7.1.1 Using an air gun canister, blow off all hybridization chamber parts to ensure they are clean, especially the microarray and the coverslip. 7.1.2 Assemble microarray hybridization chamber/ microarray/ coverslip apparatus. Make sure that the coverslip is appropriately placed over the entire arrayed area. 7.1.3 Add 100ul of 4xSSC to the humidity well in each hybridization chamber. 7.1.4 If frozen, remove probes from the -20C freezer and thaw at room temperature in the dark if frozen. Ensure that each probe has enough volume for the hybridization (ie. For a 25x25mm coverslip, 20ul is needed to cover the array surface). Each probe should have at least +2ul of probe in the tube compared to that of the volume to be applied to the array. If a probe does not contain the appropriate volume, add hybridization buffer (use appropriate vendor) to reach desired volume. Make sure to mix the solution if adding hyb buffer. 7.1.5 By checking the paperwork/ jobticket, make sure that the appropriate probes have been thawed and that the appropriate arrays have been placed in the chambers. 7.1.6 Heat the probes for 5 min. at 65C in the dark (or check for appropriate denaturing temperatures and times). 7.1.7 Centrifuge the probes for 1 min. at max speed. 7.2 Application 7.2.1 Carefully pipette 20ul (or other amount) under the coverslip covering the arrayed surface. Ensure that the array is completely covered. If not completely covered, pipette additional probe under the coverslip in increments of 2ul. Note any bubbles or abnormalities. 7.2.2 Apply the coverglass and clamps. Using the torque wrench, tighten the clamps. Make sure that the metal arms of the clamps are not resting on the edge of the coverglass. Also, make certain that the wrench is set at 46 lb/in. 7.2.3 Place the hybridization chambers in the hybrization box, then place the hyb. box in the oven at 42C and hybridize overnight (minimum of 12 hours). Make certain to place the chambers in the hyb. box so that they are level and stable.

scan_protocol: Slides are scanned on a ScanArray Express HT Scanner to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively. Laser power is kept constant for Cy3/Cy5 scans, and photomultiplier tube values were set for optimal intensity with minimal background. An additional scan is often done for each slide with the PMT set such that <1% of the elements are saturated in order to characterize spots which are saturated at the higher PMT setting. Gridding and analysis of images is performed with ScanArray software Express V3.0.

data_processing: Signal of probes to C. elegans genes (median spot value - median local background value) was filtered by removing spots with a value of <25 (in either channel). The remaining probes in each channel were normalized to the mean signal of all remaining probes in each respective channel. The ratio of normalized IP/Total signal was calculated, the Log2 value of this ratio is represented here. Log2 values were converted to percent ranks for further analysis as this as been shown to be more reliable for IP-based experiments (Roy et al., 2002). mRNAs were considered testable if they were represented in at least two of the agilent experiments. P-values for enrichment was calculated by using a one-tailed t-test for each percent rank value compared to all percent rank values within the dataset. Further, for genes with multiple probes, we kept the probe with the lowest p-value for further analysis - filtering out multiple probes. These percent ranks were then supplemented with the percent ranks from another replicate (THIS REPLICATE) from another microarray platform.

organism: Caenorhabditis elegans

source_name: Neuronal miRISC IP RNA

label_protocol: Protocol was performed by GTAC at Washington University in St. Louis.   The samples were amplified once using the MessageAmp aRNA kit (Ambion) and labeled with cy3 or cy5 using the MicroMax ASAP kit (Perkin Elmer).

growth_protocol: Asynchronous worms were grown to high-density on HB101 at 20oC and harvested when well-fed, plates included some dauers due to high density.

extract_protocol: This was performed exactly as previously described (Kudlow et al. 2012, Zhang et al., 2009, Zhang et al., 2007).

treatment_protocol: Worms were crosslinked with formaldehyde. The antibody used for the IPs: anti-GFP monoclonal antibody 3E6 (Molecular Probes, Cat# A-11120). Total RNA was taken before application of the antibody. IP RNA was taken from RNA associated with miRISC::GFP and anti-GFP antibody.

tag: developmental stage

value: Asynchronous

source_name: Whole worm (total RNA)


title: S4_A2_N74_H_18A_555

source_name: Larvae 18A from family N74 exposed to Hot treatment


title: U87_rep1_cy5

description:
U87_1_cy5
raw data file:
US22502676_251485064817_S01_GE2-v5_95_Feb07_1_2.txt

source_name: U87_wild type


title: LNZ308_rep1_cy5

description:
LNZ308_1_cy5
raw data file:
US22502676_251485064818_S01_GE2-v5_95_Feb07_1_2.txt


title: H2009_shLUC

city: Palo Alto

first: Dedeepya

last: Vaka

address: 265 Campus Drive

department: Pediatrics

institute: Stanford

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

label_protocol: Standard Affymetrix biotinylation protocol

growth_protocol: NCI-H1299 and NCI-H2009 were maintained in standard conditions of RPMI media supplemented with 10% FBS

extract_protocol: Trizol was used to extract RNA, followed by DNAse treatment in a Qiagen RNA column.

treatment_protocol: Standard lentiviral production methods were used in 293FT cells. The shRNA lentivirus was used to infect the cell lines for 2 days, then subjected to 2 days of puromycin selection to ensure a pure population infected cells. RNA was collected at day 4 after infection.

tag: cell line

value: lung cancer cells

tag: transfected with

value: control hairpins targeting luciferase


title: H2009_shGFP

value: control hairpins targeting GFP


title: S4_A1_N74_S_34_555

source_name: Larvae 34 from family N74 exposed to Standard treatment


title: H2009_shPTK7-1

value: shPTK7 (PTK7 knockdown)


title: H2009_shPTK7-2


title: U87_rep2_cy5

description:
U87_2_cy5
raw data file:
US22502676_251485064817_S01_GE2-v5_95_Feb07_1_4.txt


title: iPSC_H1_NPC_i2_EB_mesend_p9

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: SAMPLE 19

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on a Surescan Microarray Scanner G2600D using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-1100-Jul11 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: iPSC H1 NPC i2 EB mesend p9

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

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells.  Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM -mercaptoethanol (-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.  Embryoid bodies were cultured in fibroblast medium (FBS; EB_mesend) or in hESC medium without bFGF (KSR:EB_ecto) in 60mm Corning Low Attachment dishes for a total of 8 days. Media were changed by sedimentation every 2 days.

extract_protocol: RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200l chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250l of isopropanol and 250l of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.

value: hiPSC

tag: condition

tag: state

value: EB mesoderm

tag: line

tag: passage

tag: gender

value: Male


title: H1299_shPTK7-2

tag: cell type


title: S3_A3_N74_S_7B_555

source_name: Larvae 7B from family N74 exposed to Standard treatment

tag: treatment


title: U87 resistant subclone 2_cy5

description:
U87 R2_cy5
raw data file:
US22502676_251485064817_S01_GE2-v5_95_Feb07_1_3.txt

source_name: U87_resistant subclone 2


title: HSC39_TRIM44-SiRNA9_2

city: Cambridge

first: Nicholas

middle: B

last: Shannon

address: Robinson Way

department: Oncology

country: United Kingdom

institute: Cambridge Research Institute

hyb_protocol: The libraries were hybridised to GeneChipR Human Gene ST 1.0 arrays (Affymetrix) for 18hrs using the GeneChipR Hybridisation wash and stain kit, according to Affymetrix standard protocol

scan_protocol: Scanning was performed using an Affymetrix GS300 7G microarray scanner, according to Affymetrix standard protocol

data_processing: R/Bioconductor: Normalised expression estimates were obtained from the raw intensity values using a probe level linear model pre-processing algorithm available in the Bioconductor library AffyPLM (fitPLM) using default parameters.  Differential expression of genes between cells treated with H2O2 and matched control cells was assessed using an empirical Bayes’ statistic and p-values were adjusted for multiple testing using the Bioconductor library limma (eBayes)

source_name: HSC39, TRIM44-SiRNA(9) treated

label_protocol: The samples were reverse transcribed and cRNA generated using a AmbionR WT Expression kit (Ambion) then single stranded sense cDNA libraries were generated using a GeneChip WT HT Terminal Labelling kit (Affymetrix) according to Affymetrix standard protocols

growth_protocol: HSC39 was grown in RPMI media supplemented with 10%FCS.

extract_protocol: mRNA was extracted from HSC39 cells using the RNeasy® Plus Micro Kit (Qiagen, Crawley, UK).  The purity and integrity of the samples were assessed using a Nanodrop spectrophotometer (260/280 ratios >2) and Bioanalyser RNA 6000 chips (RIN >9.3)

treatment_protocol: The cells were transfected with 100nm TRIM44 siRNA obtained from Qiagen for a period of 48 hours according to the manufacturer's recommendations.

value: TRIM44-SiRNA(9) treated


title: NPC_H1_p13

description: SAMPLE 22

source_name: NPC H1 p13

value: NPC


title: H1299_shLUC


title: S2_A3_O171_S_28_555

source_name: Larvae 28 from family O171 exposed to Standard treatment

tag: slide


title: S3_A4_N170_C_44B_555

source_name: Larvae 44B from family N170 exposed to Cold treatment

tag: array


title: iPSC_H1_NPC_i3_EB_mesend_p11

description: SAMPLE 20

source_name: iPSC H1 NPC i3 EB mesend p11


title: H1299_shPTK7-1


title: S3_A2_O171_C_16A_555

source_name: Larvae 16A from family O171 exposed to Cold treatment

tag: family


title: S2_A4_N170_S_42B_555

source_name: Larvae 42B from family N170 exposed to Standard treatment

tag: larvae


title: HSC39_TRIM44-SiRNA9_1


title: iPSC_H1_NPC_i3_EB_mesend_p17

description: SAMPLE 21

source_name: iPSC H1 NPC i3 EB mesend p17


title: S2_A2_N74_H_18C_555

source_name: Larvae 18C from family N74 exposed to Hot treatment


title: H1299_shGFP


title: S3_A1_O171_H_5A_555

source_name: Larvae 5A from family O171 exposed to Hot treatment


title: RNA from brain of stimulated silkworm_P6

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Gene Expression in brain of female-odor stimulated male silkworm

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Silkworm Custom EST Microarray 4x44K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014879_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bombyx mori

source_name: brain, stimulated, replicate5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The lavae of silkworms were fed with artificial diet (silkmate). The egg and larvae were raised at 25 degree and 12L/12D condition.

extract_protocol: The genomic DNA was removed with TurboDNA-free kit (Life Technologies Corporation, Carlsbad, CA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Adult male silkworm moth were stimulated with the female odor, which has sex pheromone components, for 30 min. The whole brains were collected by disecction.

tag: tissue

value: brain

value: male

tag: treatment protocol

value: female-odor stimulated


title: RNA from brain of stimulated silkworm_P5

source_name: brain, stimulated, replicate4


title: RNA from brain of stimulated silkworm_P2

source_name: brain, stimulated, replicate2


title: iPSC_H1_NPC_i2_EB_mesend_p15

description: SAMPLE 18

source_name: iPSC H1 NPC i2 EB mesend p15


title: S1_A1_N170_S_31B_555

data_processing: Signal intensities were extracted with GenePix pro 6.1.0.4 (Molecular Devices). Spot quality was examined by visual inspection and bad spots (containing dust etc.) were flagged. Raw intensity values ("F635 Median" and "F532 Median") were read in R using Limma-package and log2-transformed. Spots that were flagged bad ("Flags" = -100) got zero weight and were treated as missing information. Probes that were consistantly (in 90% of the arrays in each channel) saturated or had low signal (<2 standard deviations from the average intensity of DarkCorner spots) were removed. Data was normalized using loess and quantile method for within and between array normalization, respectively, without background subtraction, using the default setting in Limma.

source_name: Larvae 31B from family N170 exposed to Standard treatment

value: Standard


title: RNA from brain of stimulated silkworm_P1

source_name: brain, stimulated, replicate1


title: HSC39_Negative_3

source_name: HSC39, All stars negative SiRNA treated

value: All stars negative SiRNA treated


title: S2_A1_N74_C_9B_555

source_name: Larvae 9B from family N74 exposed to Cold treatment

value: Cold


title: HSC39_TRIM44-SiRNA7_1

source_name: HSC39, TRIM44-SiRNA(7) treated

value: TRIM44-SiRNA(7) treated


title: HSC39_TRIM44-SiRNA7_2


title: iPSC_H1_NPC_i1_EB_mesend_p9

description: SAMPLE 17

source_name: iPSC H1 NPC i1 EB mesend p9


title: RNA from brain of control silkworm_C6

description: Gene Expression in brain of no treatment male silkworm

source_name: brain, control, replicate5

value: control


title: RNA from brain of stimulated silkworm_P4

source_name: brain, stimulated, replicate3


title: iPSC_H1_NPC_i2_EB_ecto_p15

description: SAMPLE 13

source_name: iPSC H1 NPC i2 EB ecto p15

value: EB ectoderm


title: HSC39_Negative_4


title: S1_A2_N170_S_20A_555

source_name: Larvae 20A from family N170 exposed to Standard treatment


title: S1_A4_N74_S_17B_555

source_name: Larvae 17B from family N74 exposed to Standard treatment


title: iPSC_H1_NPC_i3_EB_ecto_p11

description: SAMPLE 15

source_name: iPSC H1 NPC i3 EB ecto p11


title: S1_A3_O171_S_4A_555

source_name: Larvae 4A from family O171 exposed to Standard treatment


title: HSC39_Negative_1


title: iPSC_H1_NPC_i3_EB_ecto_p17

description: SAMPLE 16

source_name: iPSC H1 NPC i3 EB ecto p17


title: RNA from brain of control silkworm_C5

source_name: brain, control, replicate4


title: iPSC_H1_NPC_i2_EB_ecto_p9

description: SAMPLE 14

source_name: iPSC H1 NPC i2 EB ecto p9


title: RNA from brain of control silkworm_C3

source_name: brain, control, replicate2


title: iPSC_H1_NPC_i3_UNDIFF_p17

description: SAMPLE 11

source_name: iPSC H1 NPC i3 UNDIFF p17

value: UNDIFF

value: undifferentiated


title: VCaP_siPSF_Veh

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description:
5-VE-PSF_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from VCaP cells treated with vehicle (ethanol) after transfectd with siPSF

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (v.1.1.1) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days. VCaP cells were cultured in DMEM containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free DMEM containing 5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or R1881 (10 or 1 nM).

value: VCaP

value: prostate cancer cells

value: siPSF (siRNAs targeting PSF)

tag: treated with

value: Vehicle


title: RNA from brain of control silkworm_C4

source_name: brain, control, replicate3


title: RNA from brain of control silkworm_C2

source_name: brain, control, replicate1


title: iPSC_H1_NPC_i2_UNDIFF_p9

description: SAMPLE 9

source_name: iPSC H1 NPC i2 UNDIFF p9

value: hiPSC

value: Male


title: VCaP_siCTBP1-AS #2_R1881

description:
4-VR_AS_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from VCaP cells treated with R1881 1 nM after trasfected with siCTBP1-AS#2

value: siCTBP1-AS (siRNAs targeting CTBP1-AS)


title: iPSC_H1_NPC_i1_UNDIFF_p9

description: SAMPLE 8

source_name: iPSC H1 NPC i1 UNDIFF p9


title: VCaP_siPSF_R1881

description:
6-VR-PSF_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from VCaP cells treated with R1881 1 nM after transfectd with siPSF


title: iPSC_H1_NPC_i3_UNDIFF_p11

description: SAMPLE 10

source_name: iPSC H1 NPC i3 UNDIFF p11


title: iPSC_H1_NPC_i1_EB_ecto_p9

description: SAMPLE 12

source_name: iPSC H1 NPC i1 EB ecto p9


title: subcutaneousadiposetissue_RFIplR_115kg_rep6

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

country: France

institute: INRA

description: Gene expression in 115 kg body weight pig subcutaneous adipose tissue with high residual feed intake restricted at low RFI feeding level

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb hybridization chambers containing 1.65 µg of Cy3-labeled cRNA sample per hybridization. Hybridization reactions were performed at 65°C for 17 h using Agilent’s Gene Expression Hybridization Kit

scan_protocol: After washing, microarrays were scanned at 5 µm/pixel resolution using the Agilent DNA Microarray Scanner G2505C, and images were analyzed with Agilent Feature Extraction Software (Version 10.7.3.1, protocol GE1_107_Sep09)

data_processing: All analyses were then performed using the R software version 2.10.0 (R Development Core Team, 2008). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg) or feed restriction effect (RFIpl or RFIplR)

organism: Sus scrofa

source_name: subcutaneous adipose tissue, restricted high-RFI, 115kg body weight

label_protocol: Total RNA (150 ng) from each sample was labeled with Cy3 dye using the low RNA input linear amplification kit (Agilent Technologies) following the manufacturer’s instructions. Briefly, a two-step procedure was used to generate fluorescent complementary RNA (cRNA) by using T7 RNA polymerase. Samples were then purified with an RNeasy mini elute kit (Qiagen, Hilden, Germany)

growth_protocol: The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum. The high restricted-RFI pigs were fed at the low-RFI (RFIneg) feeding level.

extract_protocol: For total RNA extraction, samples of frozen tissues (80 to 100 mg each) were homogenized in Trizol reagent (Invitrogen, Cergy-Pontoise, France) using a TissueLyser (Qiagen) and were then treated as previously described (Vincent et al., 2012). RNA was finally purified using a silica-membrane technology under vacuum (Nucleospin 8 RNA kit, Macherey Nagel, Hoerdt, France)

value: subcutaneous adipose tissue

tag: strain

value: RFIplR

tag: feed condition

value: Restricted at RFIneg feeding level


title: subcutaneousadiposetissue_RFIplR_115kg_rep8


title: VCaP_siControl_R1881

description:
2-VR_Ct_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from VCaP cells treated with R1881 1 nM after transfected with siControl

tag: cell line

tag: transfected with

value: siControl


title: VCaP_siCTBP1-AS #2_Veh

description:
3-VE_AS_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from VCaP cells treated with vehicle (ethanol) after trasfected with siCTBP1-AS#2


title: VCaP_siControl_Veh

description:
1-VE_Ct_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from VCaP cells treated with vehicle (ethanol) after transfected with siControl


title: hESC_H1_EB_mesend_p56

description: SAMPLE 6

source_name: hESC H1 EB mesend p56

value: hESC

tag: condition

tag: state

value: EB mesoderm


title: hESC_H1_EB_ecto_p56

description: SAMPLE 4

source_name: hESC H1 EB ecto p56

tag: line

tag: passage


title: subcutaneousadiposetissue_RFIplR_115kg_rep7


title: subcutaneousadiposetissue_RFIplR_115kg_rep5


title: iPSC_H1_NPC_i1_UNDIFF_p13

description: SAMPLE 7

source_name: iPSC H1 NPC i1 UNDIFF p13

tag: cell type

tag: gender


title: LNCaP_siPSF_R1881

description:
4-siPSF-R1881_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with R1881 10 nM after transfectd with siPSF

value: LNCaP


title: hESC_H1_EB_mesend_p52

description: SAMPLE 5

source_name: hESC H1 EB mesend p52


title: subcutaneousadiposetissue_RFIplR_115kg_rep4


title: hESC_H1_EB_ecto_p52

description: SAMPLE 3

source_name: hESC H1 EB ecto p52

value: EB ectoderm


title: subcutaneousadiposetissue_RFIplR_115kg_rep3


title: LNCaP_siPSF_Veh

description:
3-siPSF-Et_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfectd with siPSF


title: LNCaP_siControl_R1881_rep3

description:
2-Ct-R1881_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with R1881 10 nM after transfected with siControl_rep


title: LNCaP_siCTBP1-AS #2_R1881

description:
10-LR-B6_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with R1881 1 nM after trasfected with siCTBP1-AS#2


title: LNCaP_siControl_Veh_rep3

description:
1-Ct-Et_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siControl_rep


title: subcutaneousadiposetissue_RFIplR_115kg_rep2


title: 507812A03

type: genomic

city: Hangzhou

first: Ping

last: Yu

address: 359 Tiyuchang Road

country: China

institute: China National Rice Research Institute

description: test sample vs control sample

hyb_protocol: Labeled samples were co-hybridized with hybridization system(NimbleGen) according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

scan_protocol: The arrays were scanned using MS200 scanner(NimbleGen) with 2µm resolution according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 CGH data extraction and analysis

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: test DNA from leaf

label_protocol: Pairs of genomic DNA (1µg) was labeled with fluorescent dyes Cy5 (test samples) or Cy3(reference DNA) according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

extract_protocol: Genomic DNA was extracted and purified from fresh young leaves using the Plant Genomic DNA Kit (TianGen)

tag: subspecies

value: Japonica

tag: group

value: Temperate

source_name: reference DNA from leaf


title: LNCaP_siCTBP1-AS #2_Veh

description:
9-LE-B6_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with vehicle (ethanol) after trasfected with siCTBP1-AS#2


title: hESC_H1_UNDIFF_p52

description: SAMPLE 1

source_name: hESC H1 UNDIFF p52

value: UNDIFF

value: undifferentiated


title: 507811A02

description: test sample vs control sample

value: Tropical


title: HSC39_Negative_2

source_name: HSC39, All stars negative SiRNA treated

tag: treatment

value: All stars negative SiRNA treated


title: subcutaneousadiposetissue_RFIpl_115kg_rep8

description: Gene expression in 115 kg body weight pig subcutaneous adipose tissue with high residual feed intake

source_name: subcutaneous adipose tissue, high-RFI, 115kg body weight

value: RFIpl

value: Ad libitum


title: ahr 24h pht_1 vs. ahr 24h DMSO_2

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: Scramble (scr) control or aryl hydrocarbon receptor (ahr) Knock Downs of cells treated with 50 uM of the ligands pyocyanin (pyo), 1-hydroxyphenazine (hp), phthiocol (pht) or DMSO as solvent control.

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing:
Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA).
The values were normalized by the linear and LOWESS dye normalization method using rank consistent probes and settings according to the Agilent FE protocol GE2_1100_Jul11.

source_name: ahr 24h pht

label_protocol: RNA was labeled with the dual-color Quick amp Labeling Kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: A549 cells were grown in complete DMEM medium (Gibco) in the presence of 5 ug/mL Puromycin.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: A549 human epithelial cell line and Ahr Knock Down (KD) were stimulated with the different ligands for 24 hr or DMSO as control.

tag: sirna

value: AhR

value: phthiocol

source_name: ahr 24h DMSO

value: DMSO


title: 507811A01

description: test sample vs control sample


title: subcutaneousadiposetissue_RFIplR_115kg_rep1

tag: tissue

value: subcutaneous adipose tissue

value: RFIplR

value: Restricted at RFIneg feeding level


title: LNCaP_siControl_Veh_rep2

description:
7-LE_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siControl#2

value: prostate cancer cells

value: siControl

value: Vehicle


title: subcutaneousadiposetissue_RFIpl_115kg_rep6


title: LNCaP_siControl_R1881_rep2

description:
8-LR_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with R1881 1 nM after transfected with siControl#2

value: LNCaP


title: ahr 24h hp_1 vs. ahr 24h DMSO_2

source_name: ahr 24h hp


title: 507812A01

description: test sample vs control sample

value: Japonica

value: Temperate


title: subcutaneousadiposetissue_RFIpl_115kg_rep7


title: LNCaP_siCTBP1-AS_R1881

description:
4-SiAS-R_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells  treated with R1881 10 nM after trasfected with siCTBP1-AS

value: siCTBP1-AS (siRNAs targeting CTBP1-AS)


title: hESC_H1_UNDIFF_p56

description: SAMPLE 2

source_name: hESC H1 UNDIFF p56

value: hESC

value: UNDIFF

value: undifferentiated

value: Male


title: ahr 24h DMSO_1 vs. ahr 24h pht_2

value: AhR


title: 507764A02

description: test sample vs control sample

value: Aromatic


title: 507764A03

description: test sample vs control sample

value: Tropical


title: 507812A02

description: test sample vs control sample


title: LNCaP_siControl_R1881_rep1

description:
2-nc-R_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with R1881 10 nM after transfected with siControl


title: subcutaneousadiposetissue_RFIpl_115kg_rep4

value: subcutaneous adipose tissue

value: RFIpl

value: Ad libitum


title: subcutaneousadiposetissue_RFIpl_115kg_rep5


title: LNCaP_siCTBP1-AS_Veh

description:
3-SiAS-E_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with vehicle (ethanol) after trasfected with siCTBP1-AS

value: prostate cancer cells


title: ahr 24h pyo_1 vs. ahr 24h DMSO_2

source_name: ahr 24h pyo

value: pyocyanin

value: DMSO


title: 507811A03

description: test sample vs control sample


title: ahr 24h DMSO_1 vs. ahr 24h hp_2


title: subcutaneousadiposetissue_RFIpl_115kg_rep3


title: subcutaneousadiposetissue_RFIpl_115kg_rep2


title: ahr 24h DMSO_1 vs. ahr 24h pyo_2


title: 507764A01

description: test sample vs control sample


title: control sample 6

city: Sao Paulo

first: Lucas

last: Alvizi

state: Sao Paulo

address: Rua do Matao 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

description: gene expression data from dental pulp stem cells extracted from deciduos tooth

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and hybridized for 16 hr in the Affymetrix Hybridization Oven 640.

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

data_processing: Data were analyzed with Expression Console (Affymetrix) and normalized by RMA method.

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: Cells were cultured in DMEM-F12 (Life Technologies) supplemented with 15% Foetal Bovine Serum (HyClone), 1% Non-essential aminoacids solution (Life Technologies), 1% penicillin-streptomycin solution (Life Technologies), in a humidified incubator at 37oC and 5% CO2. For storage, cells were frozen in medium containing 90% FBS and 10% DMSO (LGC Biotecnologia). Protocols are also described in Bueno et al, 2011 Stem Cell Reviews and Reports.

extract_protocol: Total RNA isolation was performed with NucleoSpin RNA II kit (Macherey-Nagel), following manufacturer’s recommendations. RNA quality and concentration were assessed using Nanodrop 1000 and agarose gel electrophoresis. Only RNA samples with absorbance ratio 260/280 > 1.8, preserved rRNA ratio (28S/18S) and no signs of degradation were used.

treatment_protocol: No specific treatment was used in cells cultures. Growing cells were used in the media described above.

value: control

value: decidous teeth dental pulp

value: female


title: LNCaP_siControl_Veh_rep1

description:
1-nc-Et_(HuGene-1_0-st-v1).rma-gene-default-Signal
Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siControl

value: LNCaP

value: siControl

value: Vehicle


title: subcutaneousadiposetissue_RFIpl_115kg_rep1


title: control sample 5

source_name: dental pulp stem cells extracted from deciduos tooth


title: scr 24h pht_1 vs. scr 24h DMSO_2

source_name: scr 24h pht

value: scramble control

value: phthiocol

source_name: scr 24h DMSO


title: control sample 4

value: male


title: scr 24h hp_1 vs. scr 24h DMSO_2

source_name: scr 24h hp


title: BFA-2

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

institute: scinet company

hyb_protocol: The arrays were hybridized at 65℃ overnight

scan_protocol: The arrays were scaned using FLA-8000 (FUJIFILM).

data_processing: The signal intensities were quantified using ArrayGauge software (FUJIFILM). The ratio of the signal intensity for E2- or BFA-treated sample to that for the control sample was caculated for each gene, and then normalized using control genes .

source_name: breast cancer cells

label_protocol: Five mg of total RNA was reverse-transcribed and labeled with cy3 (GE Healthcare) using SuperScript Indirect cDNA labeling system (Invitrogen).

extract_protocol: Total RNA was extracted using RNeasy plus mini kit (QIAGEN).

value: BFA

value: breast cancer cells


title: scr 24h DMSO_1 vs. scr 24h pht_2


title: subcutaneousadiposetissue_RFIneg_115kg_rep8

description: Gene expression in 115 kg body weight pig subcutaneous adipose tissue with low residual feed intake

source_name: subcutaneous adipose tissue, low-RFI, 115kg body weight

value: subcutaneous adipose tissue

value: RFIneg


title: subcutaneousadiposetissue_RFIneg_115kg_rep7

value: Ad libitum


title: scr 24h DMSO_1 vs. scr 24h hp_2


title: control sample 3


title: 507670A02

description: test sample vs control sample

organism: Oryza sativa Indica Group

value: Indica

value: Japonica

value: Temperate


title: 507670A03

description: test sample vs control sample


title: control (BFA)

value: control


title: BFA-1


title: subcutaneousadiposetissue_RFIneg_115kg_rep6


title: scr 24h DMSO_1 vs. scr 24h pyo_2

value: DMSO

source_name: scr 24h pyo

value: pyocyanin


title: 507604A03

description: test sample vs control sample

source_name: test DNA from leaf

value: Rayada


title: subcutaneousadiposetissue_RFIneg_115kg_rep5


title: scr 24h pyo_1 vs. scr 24h DMSO_2


title: control sample 2

value: decidous teeth dental pulp


title: 507670A01

description: control sample self-to-self

source_name: reference DNA from leaf


title: control sample 1

value: female


title: 507604A01

description: test sample vs control sample

value: Aus


title: 507604A02

description: test sample vs control sample


title: subcutaneousadiposetissue_RFIneg_115kg_rep4


title: ABE-2

data_processing: The signal intensities were quantified using ArrayGauge software (FUJIFILM). The ratio of the signal intensity for E2- or ABE-treated sample to that for the control sample was calculated for each gene, and then normalized using control genes .

source_name: ABE-treated Cells

value: breast cancer


title: ABE-3


title: ABE-1


title: NSCL/P sample 7

value: Non-syndromic cleft lip/palate (NSCL/P)

value: male


title: NSCL/P sample 6


title: 507596A03

description: test sample vs control sample


title: monocytes_2 vs monocytes+platelets_2

description: biological replicate 2

hyb_protocol: After precipitation, purification and quantification of labeled samples, 1.25 µg of each labeled cRNA was fragmented and hybridized to whole human genome 4x44k multipack microarrays (AMADID 014850) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Jan09 FE protocol. The extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 7.2.2 SP1.31 (Rosetta Biosoftware). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.  The normalized ratio provided in the data table below is always cy5/cy3 log(REDsignal/GREENsignal) per feature (processed signals used). Color swap arrays comprise either test/ref for positive polarity and ref/test for negative polarity.

source_name: monocytes

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)

growth_protocol: Human mononuclear cells and human platelets were obtained from buffy coat of umbilical cord blood. Monocytes were prepared by density gradient centrifugation on Biocoll separation solution and enriched by immunoaffinity selection (Monocyte Isolation Kit II; Miltenyi Biotec, Germany) and  platelets were centrifuged at 430 g for 20 min, platelet-rich plasma was removed and added to Tyrodes-HEPES buffer [HEPES 2.5 mmol/L, NaCl 150 mmol/L, KCl 1 mmol/L, NaHCO3 2.5 mmol/L, NaH2PO4 0.36 mmol/L, glucose (Glc) 5.5 mmol/L, BSA 1 mg/ml, pH 6.5]. After centrifuged (900 g for 10 min) and after removal of the supernatant, the resulting platelet pellet was resuspended and washed in Tyrodes-HEPES buffer (pH 7.4).

extract_protocol: Total RNA was extracted with TRIzol according the suppliers protocol (Invitrogen) using Glycogen as carrier.

treatment_protocol: Monocytes were cultured in high glucose DMEM medium with GlutaMax (supplemented with 5% heat inactivated fetal calf serum, penicillin (100 U/mL)-streptomycin (100 mg/mL), 1% MEM-vitamins and 1% nonessential amino acids; Invitrogen, Karlsruhe, Germany) at 37°C and 5% CO2 in 24 well plates for 2 hours. After that, freshly isolated platelets (monocyte to platelet, 1:100) were added. Half of the culture medium was changed with fresh complete medium every two days. After culture for 5 days, floating cells or platelets were washed out with warm PBS-1% FCS.

value: monocytes

source_name: monocytes and platelets co-culture

value: monocytes and platelets


title: subcutaneousadiposetissue_RFIneg_115kg_rep1

value: subcutaneous adipose tissue

value: RFIneg


title: NSCL/P sample 5


title: Cont (E2)

source_name: Cont (E2)


title: monocytes+platelets_1 vs monocytes_1

description: color-swap of biological replicate 1


title: subcutaneousadiposetissue_RFIneg_115kg_rep2

value: Ad libitum