title: 24h-mmg-B

source_name: PBL of healthy donor B irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 24h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named B, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then incubated in modelled microgravity (mmg) for 24h.


title: miR-7_HEY 1

status: Public on Apr 09 2012

type: RNA

city: Atlanta

first: Shubin

last: Shahab

state: GA

address: 310 Ferst Drive

department: Biology

country: USA

institute: Georgia Institute of Technology

description: Biological replicate 1 of 2.

hyb_protocol: Hybridization with GeneChip miRNA Array chips (Affymetrix, Santa Clara, CA) was carried out according to the manufacturer's instructions.

scan_protocol: Scanning was performed according to Affymetrix-recommended procedures using the GeneChip scanner 3000.

data_processing: Raw data in the form of CEL files were produced by the Affymetrix GeneChip Operating System (GCOS) software and analyzed using miRNA QC Tool software (Affymetrix). Normalization was performed using the default workflow of the miRNA QC Tool software. Briefly, probesets were tested for detection above background using a Wilcoxon Rank-Sum test (p <0.06) and then normalized using quantile normalization. Probesets with ‘FALSE’ call in all groups were removed from statistical analysis. A constant (16) is added for variance stabilization and then values are summarized using the median polish method. The log base 2 transformed expression values were then normalized across samples by Z-score calculations using Spotfire DecisionSite for Microarray Analysis (DSMA). Probeset intensities were filtered with DSMA using a modulation threshold of 0.5 to include only those probesets with at least a fold change ≥ 1.4. Differentially expressed probesets were identified using the SAM algorithm at a threshold 5% false discovery rate correction.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Cultured HEY epithelial ovarian carcinoma cell line, miR7 transfected

label_protocol: MiRNAs were labeled with the Genisphere FlashTag HSR Biotin RNA labeling kit (Genisphere, Hatfield, PA).

growth_protocol: The cells (duplicates or triplicates per transfection, 1.5 × 10^5 per well) were seeded on six-well plates in growth medium RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10 % v/v heat-inactivated fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM L-glutamine (Mediatech), 10 mM HEPES buffer (Mediatech), penicillin (100 U/ml), and streptomycin (100 μg/mL) and were allowed to adhere overnight at 37°C in a 5 % CO2 atmosphere.

extract_protocol: Total RNA was isolated from the transfected HEY cells using the mirVana miRNA isolation kit according to the manufacturer's instructions (Applied Biosystems, Foster City, CA).

treatment_protocol: Approximately 16h after seeding, the wells were washed with PBS and the growth medium was replaced with Opti-MEM (Invitrogen), followed by transfection of hsa-miR-7 miRIDIAN mimic or miRIDIAN miRNA mimic negative control #1 (miR-NC, a C.elegans miRNA, cel-miR-67, with confirmed minimal sequence identity in humans) using the Lipofectamine 2000 transfection agent (Invitrogen) according to the manufacturer's instructions at a final concentration of 25nM. Following 4 hours of  incubation in the reduced serum Opti-MEM medium, the cells were switched back to complete growth medium (RPMI 1640) and allowed to grow for another 48 hours before RNA extraction.

tag: cell line

value: HEY

tag: cell type

value: epithelial ovarian carcinoma

tag: treatment

value: hsa-miR-7 mimic


title: Subject 55, Day0+16h stimulated NBCs

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

description: Gene expression of Subject 55, Day0+16h stimulated NBCs

hyb_protocol: Extracted RNAs were hybridized onto Illumina Human HT-12 v4 Whole-Genome Gene Expression BeadChips according to standard Illumina protocols (Illumina Inc., San Diego, CA)

scan_protocol: Standard Illumina scanning protocol (iScan system)

data_processing: Raw data is the output from Illumina GenomeStudio version 1.7.0. Processed data is log2 transformed and batch effect corrected (Partek GS, St Louis, MO). The processed data were not normalized for the analysis.

source_name: in vitro cultivated naive B cells (NBCs)

label_protocol: Total RNA was amplified and labeled with biotinylated nucleotides using the Illumina TotalPrep RNA Amplification Kit from Ambion (PN AMIL1791)

growth_protocol: We developed a two-step B cell culture model. CD19+CD27- NBCs were first cultured with F(ab’)2 anti-Ig(A+G+M), CD40L, CpG and IL-2. At D4, activated B cells were washed and then reseeded with IL-2, IL-4 & IL-10 in the absence of CD40L

extract_protocol: Total RNA was extracted with Qiagen RNeasy kit (Qiagen Inc.)

tag: pathology

value: Healthy donor

tag: subject

value: purified naive B cells from blood

tag: growth protocol

value: stimulated

tag: il-2 treatment

value: no IL-2

tag: time point


description: Gene expression of Subject 55, Day0+22h stimulated NBCs, IL-2 positive

value: 50 U/ml IL-2 (added at Day0+16h)


description: Gene expression of Subject 55, Day0+22h stimulated NBCs, IL-2 negative


title: Subject 55, unstimulated NBCs

description: Gene expression of Subject 55, unstimulated NBCs

value: unstimulated


title: RH server number 20

type: genomic

city: Los Angeles

first: Richard

middle: T

last: Wang

state: CA

address: 650 Charles E Young Drive South

institute: UCLA

description: US23502366_251469327145_S01_CGH-v4_95_Feb07.txt

hyb_protocol: The samples were hybridized for 40 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software version 9.5.1.1

data_processing: Data from each array was mean centered. The data across all arrays was aggregated and bimodal. The data was scaled so that the second mode was centered at log10(3/2) for autosomes and log10(2/1) for sex chromosomes.

molecule: genomic DNA

organism:
Homo sapiens
Cricetulus griseus

source_name: RH server number 20

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating cy5/cy3 labeled dUTP.

growth_protocol: Cells were grown in alpha MEM with 10% FBS, 1x ampicillin and 1x HAT

extract_protocol: DNA was extracted using the Qiagen DNeasy Tissue kit according to the manufacturer's instructions

value: G3 radiation hybrid

tag: gender

value: male/male

organism: Cricetulus griseus

source_name: A23 cell line

value: male


description: Gene expression of Subject 55, Day4 stimulated NBCs, CSFElo fraction, IL-2 negative

tag: cell fraction

value: CSFElo


description: Gene expression of Subject 55, Day4 stimulated NBCs, CSFEhi fraction, IL-2 negative

value: CSFEhi


description: Gene expression of Subject 55, Day4 stimulated NBCs, CSFElo fraction, IL-2 positive


title: IDR-1018-treated, mouse 13 (infected), Brain

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

hyb_protocol: A total of 1.5ug of labelled cRNA was then prepared for hybridisation to the Sentrix Mouse-6 Expression Beadchip (v1.1) by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip). A total hybridisation volume of 30ul is prepared for each sample and 30ul loaded into a single array on the Sentrix Mouse-6 Expression Beadchip (v1.1).  A total of 6 different labelled samples can be loaded into 6 individual arrays per beadchip.  The chip is hybridised at 58C for 16 hours in an oven with a rocking platform.  After hybridisation, the chip is washed using the appropriate protocols as outlined in the Illumina manual.

scan_protocol: Upon completion of the washing, the chips are then coupled with Cy3 and scanned in the illumina BeadArray Reader.  The scanner operating software, BeadStudio, converts the signal on the array into a TXT file for analysis.

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma package of Bioconductor open-source software project (http://www.bioconductor.org). Brain and spleen samples were processed separately, where raw intensities were neqc background corrected with offset 50, quantile normalized then log2-transformed.

organism: Mus musculus

source_name: IDR-1018-treated, infected, Brain

label_protocol: A total of 500ng was labelled using the Ambion Total Prep RNA amplification kit (Cat. No. – IL1791).  The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

growth_protocol: Female 8-week-old C57BL/6 mice, were maintained under conventional conditions. The two infected groups were injected i.p. with 1x10^5 P. berghei ANKA-infected red blood cells. IDR-1018 or saline was injected i.v. into the tail vein at 8 mg/kg in 200 µL saline at 48-hour intervals starting 24 h prior to infection. Brains and spleens were taken from three uninfected mice, three saline-treated infected mice and nine IDR-1018-treated infected mice at day 3 of infection.

extract_protocol: Up to one third of the brain or spleen was macerated in 1 ml Trizol with a tissue homogenizer and extracted with chloroform and isopropanol. Samples were washed twice in 75% ethanol and resuspended in RNAse-free water. A maximum of 100 µg RNA was purified by spin columns using the RNeasy Mini kit (Qiagen), following the manufacturer’s instructions and including DNAse digestion. Quality and quantity of RNA was assessed using a Bioanalyser 2100 (Agilent Technologies, Forest Hill, Victoria, Australia).

treatment_protocol: Tissue was stored in RNAlater (Ambion, Applied Biosystems, CA, USA) for 1 day at 4˚C and then at -20˚C until processing.

tag: background strain

tag: mouse

tag: tissue

value: Brain

tag: p. berghei anka-infected

value: infected

tag: brain section

value: front

tag: beadchip barcode

tag: beadchip section

value: D


description: Gene expression of Subject 52, Day4 stimulated NBCs, CSFElo fraction, IL-2 negative


description: Gene expression of Subject 52, Day4 stimulated NBCs, CSFElo fraction, IL-2 positive


description: Gene expression of Subject 52, Day4 stimulated NBCs, CSFEhi fraction, IL-2 positive


title: RH server number 19

description: US23502366_251469327170_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 19

tag: cell line


title: RH server number 16

description: US23502366_251469327012_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 16


title: RH server number 18

description: US23502366_251469327135_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 18


description: Gene expression of Subject 52, Day4 stimulated NBCs, CSFEhi fraction, IL-2 negative

tag: cell type


title: RH server number 14

description: US23502366_251469327010_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 14


title: RH server number 13

description: US23502366_251469327037_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 13


title: 24h-mmg-A

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

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

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

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 60% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were and inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.

source_name: PBL of healthy donor A irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 24h.

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

extract_protocol: Total RNA was isolated from 107 cells by using Trizol® Reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 20% were used for microarray analysis.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named A, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then incubated in modelled microgravity (mmg) for 24h.


title: 4h-mmg-A

source_name: PBL of healthy donor A irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 4h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named A, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then incubated in modelled microgravity (mmg) for 4h.


title: 24h-1g-A

source_name: PBL of healthy donor A irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 24h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named A, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then kept parallel ground conditions (1g) for 24h.


title: 4h-1g-A

source_name: PBL of healthy donor A irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 4h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named A, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then kept parallel ground conditions (1g) for 4h


title: RH server number 15

description: US23502366_251469327011_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 15


title: Subject 52, unstimulated NBCs

description: Gene expression of Subject 52, unstimulated NBCs


title: RH server number 11

description: US23502366_251469327035_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 11


title: Subject 52, Day0+16h stimulated NBCs

description: Gene expression of Subject 52, Day0+16h stimulated NBCs


description: Gene expression of Subject 52, Day0+22h stimulated NBCs, IL-2 positive


description: Gene expression of Subject 52, Day0+22h stimulated NBCs, IL-2 negative


title: 24h-1g-P

source_name: PBL of healthy donor P irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 24h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named P, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then kept parallel ground conditions (1g) for 24h.


description: Gene expression of Subject 51, Day4 stimulated NBCs, CSFEhi fraction, IL-2 negative


description: Gene expression of Subject 51, Day0+22h stimulated NBCs, IL-2 positive


title: 4h-mmg-P

source_name: PBL of healthy donor P irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 4h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named P, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then incubated in modelled microgravity (mmg) for 4h.


title: RH server number 17

description: US23502366_251469327169_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 17


description: Gene expression of Subject 51, Day4 stimulated NBCs, CSFEhi fraction, IL-2 positive

source_name: in vitro cultivated naive B cells (NBCs)


title: RH server number 12

description: US23502366_251469327036_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 12

source_name: A23 cell line


title: 24h-mmg-P

source_name: PBL of healthy donor P irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 24h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named P, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then incubated in modelled microgravity (mmg) for 24h.


description: Gene expression of Subject 51, Day4 stimulated NBCs, CSFElo fraction, IL-2 negative


description: Gene expression of Subject 51, Day4 stimulated NBCs, CSFElo fraction, IL-2 positive


title: 4h-1g-P

source_name: PBL of healthy donor P irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 4h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named P, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then kept parallel ground conditions (1g) for 4h


description: Gene expression of Subject 51, Day0+22h stimulated NBCs, IL-2 negative


title: RH server number 10

description: US23502366_251469326990_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 10


title: RH server number 8

description: US23502366_251469327004_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 8


title: Subject 51, unstimulated NBCs

description: Gene expression of Subject 51, unstimulated NBCs


title: Subject 51, Day0+16h stimulated NBCs

description: Gene expression of Subject 51, Day0+16h stimulated NBCs


title: RH server number 7

description: US23502366_251469327003_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 7


title: RH server number 9

description: US23502366_251469326989_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 9


title: RH server number 3

description: US23502366_251469327134_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 3


title: Bone biopsy_post_8

status: Public on Apr 08 2012

city: Oslo

first: Tove

last: Lekva

address: Sognsvannsveien 20

department: Section of Specialized Endocrinology and Institute for Internal Medicine

country: Norway

institute: OUS-HF, Rikshospitalet

description: Post TAH 16_1.CEL

hyb_protocol: The cRNA was hybridized to HG U133 plus 2.0 Arrays (Affymetrix) followed by washing and staining on the GeneChips Fluidics Station 450 (Affymetrix)

scan_protocol: Signal intensities were detected by  Affymetrix GeneChip Scanner 3000

data_processing: The scanned images were processed using GCOS 1.4 (Affymetrix) according to the manufacturer. The resulting data sets (CEL files) were imported into ArrayAssist Expression Software (v5.2.0;Iobion Informatics LLC) and normalized using the PLIER algorithm in Array Assist to calculate relative signal values for each probe set.

source_name: Bone biopsy post

label_protocol: Double-stranded cDNA and biotin-labeled cRNA probes were made from 5 μg of total RNA by use of GeneChip® Expression 3' Amplification One-Cycle Target Labeling kit (Affymetrix).

extract_protocol: Trizol extraction followed by Rneasy clean up kit (qiagen) was performed according to the manufacturer´s instruction

tag: age

tag: adenoma

value: pituitary

value: bone

tag: biopsy collection

value: post-surgery

tag: time pre_post surgery (years)


title: Bone biopsy_post_9

description: RM Post 24_1.CEL

value: female


title: Bone biopsy_post_7

description: Post ECA 4_1.CEL

value: adrenal


title: RH server number 2

description: US23502366_251469327077_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 2


title: RH server number 6

description: US23502366_251469327002_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 6


title: RH server number 4

description: US23502366_251469327116_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 4


title: Bone biopsy_post_5

description: MAH Post 18_1.CEL


title: Bone biopsy_pre_5

description: MAH Pre 17_1.CEL

source_name: Bone biposy pre

value: pre-surgery


title: Bone biopsy_post_6

description: KHJ Post 36_1.CEL


title: Bone biopsy_post_4

description: AGVA Prost 2_1.CEL


title: Acute infection 1452_AI

city: Beltsville

first: Robert

middle: W

last: Li

state: MD

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

hyb_protocol: single dye

scan_protocol: Axon GenePix 4000B at 5 uM resolution

data_processing: The data presented here are average fluorescent intensity from either 4 or 8 perfect match oligos that represent a single unique sequence. These data are usually log transformed and subject to quantile normalization method using the R package before analyzed. see Li & Li, BMC Genomics 2006, 7:234

organism: Bos taurus

source_name: Jejunum, Acute Infection

label_protocol: incorporation

extract_protocol: Trizol following by Qiagen RNeasy clean-up

value: 2-4 months old

tag: infection

value: Acute infection with Giardia

value: jejunum


title: Bone biopsy_post_2

description: Bus Post 66_1.CEL


title: Bone biopsy_pre_7

description: Pre ECA 3_1.CEL


title: Bone biopsy_pre_4

description: AGVA Pre 1_1.CEL


title: Bone biopsy_pre_6

description: KHJ Pre 35_1.CEL


title: Bone biopsy_post_1

description: ENS Post 12_1.CEL


title: Bone biopsy_pre_9

description: RM Pre 23_1.CEL


title: Bone biopsy_pre_8

description: Pre TAH 15_1.CEL


title: Bone biopsy_pre_1

description: ENS Pre 11_1.CEL


title: Control 8980_CT

source_name: Jejunum, Uninfected control

value: Uninfected control


title: Bone biopsy_pre_2

description: Bus Pre 65_1.CEL


title: Bone biopsy_pre_3

description: LJB Pre 21_1.CEL


title: Acute infection 9749_AI

source_name: Jejunum, Acute infection


title: Acute infection 6069_AI

source_name: jejunum, acute infection


title: Control 0466_CT


title: Control 6099_CT

source_name: Jejunum, uninfected control

value: uninfected control


title: Bone biopsy_post_3

description: LJB Post 22_1.CEL


title: RH server number 1

description: US23502366_251469327076_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 1

value: G3 radiation hybrid

value: male/male

source_name: A23 cell line

value: male


title: BTX623 2hr sucrose repeat II

city: Singapore

first: Shu-Ye

last: Jiang

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory, National University of Singapore

description: Gene expression after 2hr in 5% sucrose solution

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5

organism: Sorghum bicolor

source_name: BTX623 2hr Repeat II

label_protocol: labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Both grain and sweet sorghum (Sorghum bicolor L. Moench cultivars BT×623 and Keller were used for all experiments in this study. Their seeds were imbibed in water. After germination, they were planted in greenhouse and were grown under natural light and temperature conditions.

extract_protocol: Total RNA samples were prepared using RNeasy Plant mini kit (Qiagen). Total RNA quality was analyzed by nanodrop reading and Agilent Bioanalyzer running

treatment_protocol: The two-week old seedlings of grain (BTX623) and sweet (Keller) sorghum lines were subjected to 5% of sucrose solution, and samples were then collected in 0, 2, and 6 h intervals respectively.

value: whole seedling

tag: treatment

value: 5% sucrose

tag: time

tag: cultivar

value: Two-week old


title: BTX623 6hr sucrose repeat II

description: Gene expression after 6hr in 5% sucrose solution

source_name: BTX623 6hr Repeat II


title: BTX623 0hr sucrose repeat II

description: Gene expression after 0hr in 5% sucrose solution

source_name: BTX623 0hr Repeat II


title: Acute infection 1096_AI

value: 2-4 montyhs old


title: BTX623 2hr sucrose repeat I

source_name: BTX623 2hr Repeat I


title: Keller 6hr sucrose repeat II

source_name: Keller 6hr Repeat II

value: Keller


title: BTX623 6hr sucrose repeat I

source_name: BTX623 6hr Repeat I


title: Keller 0hr sucrose repeat II

source_name: Keller 0hr Repeat II


title: Keller 2hr sucrose repeat II

source_name: Keller 2hr Repeat II


title: Gettys06_MR_LIVER4

city: Baton Rouge

first: Kirsten

middle: P

last: Stone

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

hyb_protocol: 10 ug of fragmented DIG-labeled cRNA used for array hybridization according to Applied Biosystems protocol

scan_protocol: Chemiluminescence detection, imaging, and image analysis performed according to Applied Biosystems protocols and using the 1700 Chemiluminescent Microarray Analyzer Software v 1.0.3

label: DIG-UTP

organism: Rattus norvegicus

source_name: liver, MR diet

label_protocol: 1 ug of total RNA was transcribed to DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT kit v2.0

extract_protocol: RNA extracted using TriReagent (Molecular Research Center, Inc. Cincinnati, OH), with added purification of the aqueous layer using Qiagen Rneasy MiniKit. Concentration and quality of RNA assessed using Agilent Bioanalyzer.

treatment_protocol: Livers flash frozen in liquid nitrogen immediately after dissection; stored at -80C

tag: strain

value: Fischer 344

tag: gender

value: Male

value: Liver


title: Control 6770_CT

tag: tissue


title: BTX623 0hr sucrose repeat I

source_name: BTX623 0hr Repeat I


title: Gettys06_MR_LIVER3


title: Keller 6hr sucrose repeat I

source_name: Keller 6hr Repeat I


title: Drosophila melanogaster larval female rep3

city: Houston

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: Biological replicate 3 of 3

hyb_protocol: 825ng of Cy3 labelled cDNA was fragmented and hybridized to the Agilent-018972 D. melanogaster Oligo Microarray 4x44K G2519F (GPL6385), following the manufacturer's instructions. After 17 hrs of hybridization at 65C, arrays were washed using the Agilent wash buffers per the manufacturer's instructions.

scan_protocol: Slides were scanned on the Axon 4000B scanner using the Agilent HD_GX_1Color setting (scan area 61x21.5 mm, scan resolution 5 um, and Green PMT set to XDR hi 100% and XDR low 10%).

data_processing: Scanned images were analyzed with the Agilent Feature Extraction Software version 10.5.1.1 (protocol GE1_105_DEC08) to obtain background substracted and spatially detrended processed signal intensities.

organism: Drosophila melanogaster

source_name: larval female

label_protocol: 1000ng of total RNA in 10ul of RNase-free water was used to generate double-stranded cDNA using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion, Inc., Austin, TX), following the manufacter's instructions. The cDNA was then coupled to Cy3 reactive dye using the same kit, followed by a column purification using the kit-supplied equipment and reagents. Dye incorporation and cDNA yield were checked on a NanoDrop Spectrophotometer.

growth_protocol: Flies were grown at 22C on cornmeal media. Male and female larva were separately flash frozen on dry ice and stored at -80C. Virgin male and female newly eclosed flies were collected, aged for 3-5 days at 22C, and then frozen at -80C.

extract_protocol: Total RNA was extracted from the samples using TRIzol (Invitrogen Inc, Carlsbad, CA), following the manufacter's instructions.

value: Oregon R

tag: Sex

value: female

tag: developmental stage

value: larval

value: whole organism


title: Gettys06_MR_LIVER1


title: Drosophila melanogaster larval male rep2

description: Biological replicate 2 of 3

source_name: larval male


title: Gettys06_CON_LIVER4

source_name: liver, CON diet


title: Drosophila melanogaster larval male rep1

description: Biological replicate 1 of 3


title: Gettys06_CON_LIVER3


title: Drosophila melanogaster larval female rep1

description: Biological replicate 1 of 3


title: Keller 2hr sucrose repeat I

source_name: Keller 2hr Repeat I


title: Gettys06_MR_LIVER2


title: Drosophila melanogaster adult male rep1

description: Biological replicate 1 of 1

source_name: adult male

value: adult


title: Keller 0hr sucrose repeat I

source_name: Keller 0hr Repeat I


title: Drosophila melanogaster larval female rep2

description: Biological replicate 2 of 3


title: Drosophila melanogaster larval male rep3

description: Biological replicate 3 of 3


title: Drosophila melanogaster adult female rep1

description: Biological replicate 1 of 1

source_name: adult female


title: WT MeDIP

status: Public on Apr 07 2012

first: Aik

last: Ooi

address: 650 Charles E Young Dr S, Factor 9-240

department: Pediatrics

hyb_protocol: Arrays were hybridized for 16-18 h at 42C, and then washed. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: The MeDIP array data were processed and visualized using the Affymetrix Integrated Genome Browser (www.affymetrix.com/partners_programs/programs/developer/tools/download_igb.affx)

label: Cy 5

source_name: WT mouse lung

label_protocol: MeDIP DNA was labeled per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Lung tissues were homogenized using tissue homogenizer, followed by treatment with cell lysis buffer, proteinase K, and Rnase. DNA was extracted using standard isopropanol precipitation method.

value: mouse lung left lower lobe

value: 6-10 weeks old mouse

tag: antibody

tag: genotype/variation

value: wild type

label: Cy 3

source_name: WT mouse lung input


title: TG MeDIP

source_name: TG mouse lung

value: CC10-rtTA-IL13 transgenic

source_name: TG mouse lung input


title: RH server number 5

description: US23502366_251469327117_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 5

tag: cell line

value: G3 radiation hybrid

value: male/male

source_name: A23 cell line

value: male


title: Gettys06_CON_LIVER2


title: Gettys06_CON_LIVER1


title: Myeloma_MM1.S_18hpo24hPD_rep1

city: New York

first: Xiangao

last: Huang

state: New York

address: 1300 York Avenue

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medical College

description: Gene expression after 18 h-release from G1 block induced by treatment with PD for 24 h

hyb_protocol: 825 ng of Cy3-labelled cRNA was hybridized to Agilent 4×44K Whole Human Genome Microarray and washed, according to manufacturer's protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. The data were further analyzed by GeneSpring11.5 (Agilent) using the workflow type of Advanced Analysis with Normalization Algorithm of Normalize to Control Genes (ACTB) and Preprocess Baseline Option of Baseline to median of all samples.

source_name: MM1.S cells at 18 h-release from G1 block induced by treatment with PD for 24 h

label_protocol: 1 ug of total RNA, each from 3 independent isolations, was amplified and labeled with Cy3 using Ambion's MessageAmp kit (Life Technologies, Grand Island, NY).

extract_protocol: Total RNA was isolated using an RNeasy® Plus Mini Kit (Qiagen, Valencia, CA). The RNA purity and integrity were determined on the 2001 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: disease

value: Multiple Myeloma


title: Myeloma_MM1.S_18hpo24hPD_rep3


title: Myeloma_MM1.S_4hpo24hPD_rep1

description: Gene expression after 4 h-release from G1 block induced by treatment with PD for 24 h

source_name: MM1.S cells at 4 h-release from G1 block induced by treatment with PD for 24 h


title: Myeloma_MM1.S_18hpo24hPD_rep2


title: Myeloma_MM1.S_36hPD_rep1

description: Gene expression after treatment with PD for 36 h

source_name: MM1.S cells treated with PD for 36 h


title: 14054269 - invA2 vs mock2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Transcriptomic analysis between Salmonella wt and differents mutants in type3 secretion system.

hyb_protocol: mock2 Cy5 / invA2 Cy3 : 30pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - MS 22°C Long day

treatment_protocol: no treatment

tag: ecotype

tag: age

tag: dev.stage (boyes et al. plant cell 2001)

value: mock


title: 14054268 - mock2 vs invA2

hyb_protocol: invA2 Cy5 / mock2 Cy3 : 30pmol.


title: Myeloma_MM1.S_36hPD_rep2


title: Myeloma_MM1.S_36hPD_rep3


title: 13968868 - A2 rep2 vs H1 rep2

description: What are the transcriptional consequences of the allelic contrast at SG3, SG1 and EGO3 loci mapped for its effect on shoot growth and identified at the gene level

hyb_protocol: H1 rep2 Cy5 / A2 rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

source_name: H1 rep2

growth_protocol: aerial - N/A

extract_protocol: H1 rep2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:60mM mannitol - abiotic stress - compound addition,mannitol:quantity 60mM .

value: 60mM mannitol

value: H1 is Col allele containing HIF

source_name: A2 rep2

extract_protocol: A2 rep2:5ug. (Qiagen_RNeasy.pdf)

value: cape verde islands

value: A2 is Cvi allele containing HIF


title: Myeloma_MM1.S_4hpo24hPD_rep3


title: 13968869 - H1 rep2 vs A2 rep2

hyb_protocol: A2 rep2 Cy5 / H1 rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14119476 - invA1 vs mock1

hyb_protocol: mock1 Cy5 / invA1 Cy3 : 30pmol.


title: 14119474 - mock1 vs invA1

hyb_protocol: invA1 Cy5 / mock1 Cy3 : 30pmol.


title: Myeloma_MM1.S_24hPD_rep2

description: Gene expression after treatment with PD for 24 h

source_name: MM1.S cells treated with PD for 24 h


title: Myeloma_MM1.S_24hPD_rep3


title: Myeloma_MM1.S_4hpo24hPD_rep2


title: 13968866 - A2 rep1 vs H1 rep1

hyb_protocol: H1 rep1 Cy5 / A2 rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: H1 rep1

extract_protocol: H1 rep1:5ug. (Qiagen_RNeasy.pdf)

source_name: A2 rep1

extract_protocol: A2 rep1:5ug. (Qiagen_RNeasy.pdf)


title: Myeloma_MM1.S_24hPD_rep1


title: Myeloma_MM1.S_12hPD_rep3

description: Gene expression after treatment with PD for 12 h

source_name: MM1.S cells treated with PD for 12 h


title: Myeloma_MM1.S_12hPD_rep1


title: Myeloma_MM1.S_12hPD_rep2


title: 13968867 - H1 rep1 vs A2 rep1

hyb_protocol: A2 rep1 Cy5 / H1 rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Myeloma_MM1.S_Cntl_rep2

description: Gene expression in untreated MM1.S cells

source_name: Untreated MM1.S cells


title: Myeloma_MM1.S_Cntl_rep1


title: Myeloma_MM1.S_Cntl_rep3


title: MCF7 control 6.20

city: Ithaca

first: Scott

last: Coonrod

state: NY

address: 1 Hungerford Hill

department: J.A. Baker Institute for Animal Health

institute: Cornell University

description: Gene expression after PAD2 knockdown

hyb_protocol: Hybridization was done following a One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling protocol from Agilent Technologies.  Briefly, 825ng per sample 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 55 ul containing 11ul 25x Agilent fragmentation buffer and 2.2 ul 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized 100ul to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red & Green and both the Red and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using parameters (protocol GE1-105_DEC8 and Grid: 014850_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: MCF-7 cells

label_protocol: Labeling was done using the Amino Allyl MessageAmpTM II ARNA Amplication Kit from Ambion following the manufacture's protocol.

growth_protocol: MCF7 control and PAD2 knockdown cells were grown with DMEM, 10% FBS, 1% antibiotic/antimycoctic in a humidified atmosphere of 5% CO2 at 37 degrees celcius.  Stable clones were selected with 2ug/mL of puromycin

extract_protocol: Total RNA was prepared using a Qiagen Rneasy mini kit including the on-column DNase digestion.  Quality of RNA was assessed using an Agilent Bioanalyzer 2100.

value: control


title: MCF7 PAD2kd 3.31

description: Gene expression after PAD2 knockdown

value: PAD2 KD


title: MCF7 control 1a1.6.22

description: Gene expression after PAD2 knockdown


title: Leaf rep3

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description: 20-day leaves (Col-0)

hyb_protocol: Fragmentation of the labeled aRNA prepares the target for hybridization to GeneChip® 3’ expression arrays with GeneChip® hybridization oven 640.

scan_protocol: Wash and stain the arrays with GeneChip® fluidics station 450, Scan the arrays with the GeneArray scanner 3000 by the GeneChip® Operating  Software (GCOS) or Command Console® (AGCC) Software.

data_processing: RMA data were obtained by using Partek GS 6.4.

source_name: leaf

label_protocol: In Vitro Transcription to Synthesize Biotin-Modified aRNA with IVT Labeling Master Mix generates multiple copies of biotin-modified aRNA from  the double-stranded cDNA templates; this is the amplification step.aRNA Purification removes unincorporated NTPs, salts, enzymes, and  inorganic phosphate to improve the stability of the biotin-modified aRNA.

growth_protocol: 16 h light, 8 h dark, 21°C

extract_protocol: Extract and purify the total RNA by the Qiagen RNeasy Mini Kit.Reverse Transcription to Synthesize First-Strand cDNA is primed with  T7 oligo(dT) primer to synthesize cDNA containing a T7 promoter sequence.Second-Strand cDNA Synthesis converts the single-stranded cDNA into  a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA polymerase and RNase H to simultaneously degrade the RNA  and synthesize second strand cDNA.

treatment_protocol: Calli were induced on the CIM plate.

tag: genetic background

value: leaf

value: 20 day


title: Leaf rep1

description: 20-day leaves (Col-0)


title: MCF7 control 3.31

description: Gene expression after PAD2 knockdown


title: leaves_12hpi_Rep2

status: Public on Apr 06 2012

city: Lisboa

first: Andreia

last: Figueiredo

address: Campo Grande

department: UMBPB

country: Portugal

institute: ICAT/FCUL

description:
Rep_2 _12hpi
Biological replicate 2 of 3. Comparison of 'Regent' vs. 'Trincadeira' at 12hpi. Both files coming from Versarray and edited for GEPAS are presented.

hyb_protocol: The hybridization mix consisted of 40μL labelled cDNA, 1.7 μL of poly-A DNA (10 mg mL-1) (Sigma), 1.6 μL salmon sperm DNA (5 mg mL-1) (Invitrogen), 1.6 μL of 50X Denhardt´s solution (1% Ficoll (type 400), 1% PVP-40, 1% BSA), 8.45 μL of 20X SSC and 1.69 μL of 10% SDS(w/v). The mixture was denatured at 97ºC for 2 min and cooled to 60ºC, and then 1μl of 10X DIG blocking (Roche Diagnostic GmbH, Mannheim, Germany) buffer was added. Hybridization was carried out at 60º C for 17 hours in chambers ArrayIt (Telechem International).

scan_protocol: Slides were scanned using VersArray ChipReader® vs 3.1. build 1.68 (Bio-Rad, USA), and spot and background intensities were quantified using VersArray AnalyserTM software vs 4.5.1.46 (Bio-Rad, USA).

data_processing:
Data files were imported into GEPAS (http://gepas.bioinfo.cipf.es) and log2-transformed prior to normalization (DNMAD). Print-tip Lowess was used for within-slide normalization considering background subtraction. Impute missing values (median). Patterns with less than 70% were removed.

VersArray file: Raw data file retrieved by VersArray Analyser software (Bio-Rad).
GEPAS file: Raw data file (with flags indicated) ready to go for GEPAS software for normalization.

organism: Vitis vinifera

label_protocol: Fifty micrograms of RNA from each biological replicate were reverse transcribed using amino allyl-modified dUTP to produce cDNA modified with reactive primary amines (Amino Allyl cDNA Labeling Kit). Then, the Amino modified cDNA was labelled with either Cy3 or Cy5 dye molecules with the Amino Allyl cDNA Labeling Kit (Ambion Inc, Applied Biosystems, California, USA) according to manufacturer’s instructions.

growth_protocol: Grapevine plants from ‘Regent’ and ‘Trincadeira’ cultivars were grown under greenhouse conditions.

extract_protocol: Total RNA was isolated from young leaves of Vitis vinifera ‘Regent’ and ‘Trincadeira’ essentially as described by Zeng et al. (2002). Briefly, RNA purification was carried out with DNAse (Invitrogen, San Diego, CA, USA) and with the RNeasy Plant Mini kit according to the supplier’s instructions (Qiagen, Valencia, CA, USA).

treatment_protocol: RNA was extracted from leaves of non-inoculated and inoculated plants 6hpi and 12hpi.

value: Trincadeira

tag: susceptibility to p. viticola

value: susceptible

value: leaves

tag: condition

value: Plasmopara viticola infection

value: Regent

value: resistant


title: leaves_12hpi_Rep1fw

description:
Rep_1fwd_12hpi
Technical replicate 1 of 1. Repetition of labelling and hybridization from biological replicate 1 at 12hpi. Both files coming from Versarray and edited for GEPAS are presented.

tag: time


title: Leaf rep2

description: 20-day leaves (Col-0)


title: Callus rep3

description: 20-DAC calli from 20-day leaf blade explants (Col-0)

source_name: callus

value: callus

value: 20 days after culture


title: leaves_12hpi_Rep3fw

description:
Rep_3fw _12hpi
Technical replicate 1 of 2. Repetition of labelling and hybridization from biological replicate 3 at 12hpi. Both files coming from Versarray and edited for GEPAS are presented.

tag: cultivar


title: Callus rep2


title: MCF7 PAD2kd 4A1.6.22

description: Gene expression after PAD2 knockdown

tag: treatment


title: MCF7 control 2.6.1

description: Gene expression after PAD2 knockdown


title: Wild type replicate 2

first: Jun

last: Xu

address: 1230 york avenue

institute: Rockefeller University

hyb_protocol: hybridization buffer (Agilent Gene expression hybridization kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially in Buffer 1 and Buffer 2.

scan_protocol: Scanned on an Agilent G2565A scanner. 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 for background subtraction and LOWESS normalization.

organism: Arabidopsis

source_name: WT

label_protocol: 100ng of each sample was labeled together with two-color spike in RNAs using Lowinput quickamp labeling kit (Agilent)

growth_protocol: Plants were grown on sterile solid half-strength Murashige-Skoog (MS) medium for 12 days (22°C, 16/8h photoperiod cycles).

extract_protocol: Total RNA extracted using plant RNeasy mini kit (Qiagen) following manufacturer's instructions

treatment_protocol: Seedlings were transferred onto 3MM papers (Whatman) at 22°C exposed to 60% humidity at room temperature under dim light. After 30 min fresh weight of dehydrated seedlings was reduced to about 60%.

value: 12-day old seedlings

value: time 0

value: dehydration 30min


title: leaves_12hpi_Rep3

description:
Rep_3 _12hpi
Biological replicate 3 of 3. Comparison of 'Regent' vs. 'Trincadeira' at 12hpi. Both files coming from Versarray and edited for GEPAS are presented.


title: Wild type replicate dye-swap 1


title: leaves_12hpi_Rep3fw2

description:
Rep_3 fw2_12hpi
Technical replicate 2 of 2. Repetition of labelling and hybridization from biological replicate 3 at 12hpi. Both files coming from Versarray and edited for GEPAS are presented.


title: dcp5-1 replicate dye-swap 2


title: MCF7 PAD2kd 2.6.1

description: Gene expression after PAD2 knockdown


title: dcp5-1 replicate 2


title: Wild type replicate 1


title: Wild type replicate dye-swap 2


title: dcp5-1 replicate dye-swap 1


title: leaves_6hpi_Rep3

description:
Rep_3 _6hpi
Biological replicate 3 of 3. Comparison of 'Regent' vs. 'Trincadeira' at 6hpi. Both files coming from Versarray and edited for GEPAS are presented.


title: leaves_6hpi_Rep2

description:
Rep_2 _6hpi
Biological replicate 2 of 3. Comparison of 'Regent' vs. 'Trincadeira' at 6hpi. Both files coming from Versarray and edited for GEPAS are presented.


title: leaves_12hpi_Rep1

description:
Rep_1_12hpi
Biological replicate 1 of 3. Comparison of 'Regent' vs. 'Trincadeira' at 12hpi. Both files coming from Versarray and edited for GEPAS are presented.


title: Callus rep1


title: dcp5-1 replicate 1


title: Ly-6Clo monocyte, steady state - sample 6

city: Boston

first: Martin

last: Etzrodt

state: MA

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Massachusetts General Hospital

description: Ly-6Clo 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scan protocol.

data_processing: Raw data were exported and normalized using Gene Pattern 3.3.2, Build ID 9695, IlluminaNormalizer (normalization method: quantile)

source_name: monocyte

label_protocol: Standard Illumina label protocol.

growth_protocol: 6-8 wk old C57BL/6 mice, on regular chow diet.

extract_protocol: Total RNA was isolated using the miRVANA microRNA isolation kit (Ambion).

treatment_protocol: Spleens were homogenized in ice cold PBS with 0.5% BSA and 1mM EDTA, stained with fluorophore conjugated monoclonal antibodies and sorted directly in RLT lysis buffer on a FACS Aria (BD Biosystems). A negative selection (lineage depletion step) on a MACS LD magnetic column (Miltenyi) preceeded the sort. Total processing time <2h.

value: spleen

tag: gender

value: female

tag: strain

value: 6-8 weeks

tag: cell type

value: monocyte

tag: monocyte subset


title: leaves_0h_Rep1

description:
Rep_1 _0h
Biological replicate 1 of 2. Comparison of 'Regent' vs. 'Trincadeira' at 0h. Both files coming from Versarray and edited for GEPAS are presented.

tag: tissue

value: control


title: Ly-6Clo monocyte, steady state - sample 5

description: Ly-6Clo 2


title: leaves_6hpi_Rep1

description:
Rep_1 _6hpi
Biological replicate 1 of 3. Comparison of 'Regent' vs. 'Trincadeira' at 6hpi. Both files coming from Versarray and edited for GEPAS are presented.


title: leaves_0h_Rep2

description:
Rep_2 _0h
Biological replicate 2 of 2. Comparison of 'Regent' vs. 'Trincadeira' at 0h. Both files coming from Versarray and edited for GEPAS are presented.


title: adult cardiac fibroblasts transduced with GHMT-retroviruses for 2 weeks

city: Dallas

first: Kunhua

last: Song

state: Texas

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label_protocol: cRNA were prepared for Illumina arrays

growth_protocol: cells were cultured in 10-cm dish

extract_protocol: Total RNA were extracted with Trizol reagent

treatment_protocol: cells were infected with retroviruses

value: 2 months

value: heart


title: MCF7 PAD2kd 6.20

description: Gene expression after PAD2 knockdown

value: PAD2 KD


title: Ly-6Clo monocyte, steady state - sample 4

description: Ly-6Clo 1


title: adult cardiac fibroblasts transduced with empty retroviral vector for 2 weeks


title: Monocyte_Ly6Clo_Blood_04

hyb_protocol: Labeled cDNA was assessed using the Nanodrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE) and the Agilent 2100 Bioanalyzer; equal amounts of Cy3-labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays. Hybridizations were performed for 14 h according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner. Raw signal intensities were extracted with their Feature Extraction v9.1 software.

data_processing: The dataset was normalized using the quantile normalization method. No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization. All procedures were carried out using functions in the R package limma in Bioconductor.

source_name: Monocyte Ly-6Clo, Blood

label_protocol: RNA was amplified using the NuGen WT-Ovation Pico System, and the amplified cDNA was labeled using the FL-Ovation cDNA Fluorescent Module (NuGen Technologies, San Carlos, Ca). 5ng of input total RNA was reverse–transcribed into cDNA and then amplified using a linear isothermal amplification process (SPIA). The amplified products were CY-3 labeled and fragmented according to manufacturer’s guidelines.

growth_protocol: CHOW

extract_protocol:
Monocyte subsets from blood and spleen of a group of four mice were isolated by fluorescence activated cell sorting (FACS) as CD11bhi (CD90/B220/CD49b/NK1.1/Ly-6G)lo (F4/80/I-Ab/CD11c)lo Ly-6Chi  cells.
Samples of 1,000 Ly-6Clo blood monocytes were collected directly into 20 µl lysis buffer of the PicoPure RNA isolation kit (Arcturus). RNA extraction was subsequently performed according to the manufacturer’s instructions (Arcturus).
Total RNA quality was assessed using RNA pico lab chips on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RIN (RNA integrity number) >=  8.

treatment_protocol: healthy mice, no treatment

value: 8-12 weeks

value: Blood

tag: cell signature

value: Ly-6Clo monocytes were identified as CD11b hi (CD90/B220/CD49b/NK1.1/Ly-6G)lo (F4/80/I-Ab/CD11c)lo


title: Ly-6Chi monocyte, steady state - sample 3

description: Ly-6Chi 3


title: adult cardiac fibroblasts transduced with empty retroviral vector for 4 weeks


title: adult heart

source_name: adult heart


title: Monocyte_Ly6Clo_Blood_03


title: adult cardiac fibroblasts

source_name: adult cardiac fibroblasts


title: Ly-6Chi monocyte, steady state - sample 2

description: Ly-6Chi 2


title: Ly-6Chi monocyte, steady state - sample 1

description: Ly-6Chi 1


title: adult cardiac fibroblasts transduced with GHMT-retroviruses for 4 weeks


title: Monocyte_Ly6Clo_Blood_02


title: Monocyte_Ly6Clo_Blood_01


title: ulcerative colitis peripheral blood 127

status: Public on Apr 05 2012

first: R.

middle: Alan

last: Harris

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Ulcerative colitis peripheral blood sample

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: GenomeStudio software version 2010.3.0.30128

label: Cy5 and Cy3

source_name: peripheral blood 127

label_protocol: Standard Illumina protocol

extract_protocol: For twin samples, genomic DNA was extracted and purified from peripheral blood samples using the Maxwell® 16 system from Promega with the Blood DNA purification kit. In order to increase the concentration of the extracted DNA, Milipore microcon filters were used. For other samples, either Gentra Puregene (Qiagen) for whole blood according to manufacturers recommendation, or the QuiAmp DNA mini kit (Qiagen) on isolated peripheral blood mononuclear cells (PBMCs) was used. BD Vacutainer® CPT™ Cell Preparation Tube with Sodium Citrate was used in the later case to isolate PBMCs from PBL.

value: Male

tag: age (y)

value: Peripheral Blood

tag: disease state

value: ulcerative colitis

tag: twin


title: ulcerative colitis peripheral blood 164

source_name: peripheral blood 164


title: ulcerative colitis peripheral blood 145

source_name: peripheral blood 145

value: Female


title: ulcerative colitis peripheral blood 125

source_name: peripheral blood 125


title: normal peripheral blood 11B

description: Normal peripheral blood sample

source_name: peripheral blood 11B

value: normal

value: Twin of sample 11A


title: Crohn's disease peripheral blood 186

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 186

value: Crohn's disease


title: Crohn's disease peripheral blood 217

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 217


title: Crohn's disease peripheral blood 189

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 189


title: Crohn's disease peripheral blood 301

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 301


title: normal peripheral blood 10A

description: Normal peripheral blood sample

source_name: peripheral blood 10A

value: Twin of sample 10B


title: Crohn's disease peripheral blood 224

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 224


title: ulcerative colitis peripheral blood 11A

source_name: peripheral blood 11A

value: Twin of sample 11B


title: ulcerative colitis peripheral blood 10B

source_name: peripheral blood 10B

value: Twin of sample 10A


title: ulcerative colitis peripheral blood 84

source_name: peripheral blood 84


title: normal peripheral blood 195

description: Normal peripheral blood sample

source_name: peripheral blood 195


title: ulcerative colitis peripheral blood 142

source_name: peripheral blood 142


title: Crohn's disease peripheral blood 284

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 284


title: Crohn's disease peripheral blood 152

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 152


title: ulcerative colitis peripheral blood 278

source_name: peripheral blood 278


title: normal peripheral blood 310

description: Normal peripheral blood sample

source_name: peripheral blood 310


title: Crohn's disease peripheral blood 151

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 151


title: normal peripheral blood 12

description: Normal peripheral blood sample

source_name: peripheral blood 12


title: Crohn's disease peripheral blood 32

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 32


title: normal peripheral blood 8B

description: Normal peripheral blood sample

source_name: peripheral blood 8B

value: Twin of sample 8A


title: Crohn's disease peripheral blood 272

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 272


title: Crohn's disease peripheral blood 255

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 255


title: ulcerative colitis peripheral blood 8A

source_name: peripheral blood 8A

value: Twin of sample 8B


title: Crohn's disease peripheral blood 124

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 124


title: Crohn's disease peripheral blood 299

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 299


title: normal peripheral blood 308

description: Normal peripheral blood sample

source_name: peripheral blood 308


title: Crohn's disease peripheral blood 150

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 150


title: ulcerative colitis peripheral blood 264

source_name: peripheral blood 264


title: Genmascq_Pig_LL_N65

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 300 ng of cyanine 3-labeled cRNA sample per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. Slides were disassembled and washed for 1 minute at room temperature in SSPE wash solution 1 (6x SSPE + 0.005% Sarcosine) and in SSPE wash solution 2 (0.06x SSPE + 0.005% Sarcosine) for one minute at room temperature. The microarrays were then treated with Agilent Stabilization and Drying Solution at room temperature for 30 seconds.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Raw data from 15198 probes fluorescent hybridization signal intensities were log transformed and centered within sample by subtraction of sample median from all raw values.

organism: Sus scrofa

source_name: Longissimus lumborum

label_protocol: Total RNA (500 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit  following the manufacturer’s instructions.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Longissimus lumborum

tag: ChIP


title: normal peripheral blood 181

description: Normal peripheral blood sample

source_name: peripheral blood 181


title: Genmascq_Pig_LL_N66


title: Genmascq_Pig_LL_N62


title: Genmascq_Pig_LL_N73


title: Genmascq_Pig_LL_N87


title: Genmascq_Pig_LL_N88


title: Genmascq_Pig_LL_N83


title: Genmascq_Pig_LL_N64


title: Genmascq_Pig_LL_N93


title: Genmascq_Pig_LL_N75


title: Genmascq_Pig_LL_N89


title: normal peripheral blood 14

description: Normal peripheral blood sample

source_name: peripheral blood 14


title: normal peripheral blood 2

description: Normal peripheral blood sample

source_name: peripheral blood 2


title: Genmascq_Pig_LL_N55


title: normal peripheral blood 239

description: Normal peripheral blood sample

source_name: peripheral blood 239


title: normal peripheral blood 19

description: Normal peripheral blood sample

source_name: peripheral blood 19


title: normal peripheral blood 1B

description: Normal peripheral blood sample

source_name: peripheral blood 1B

value: Twin of sample 1A


title: normal peripheral blood 10

description: Normal peripheral blood sample

source_name: peripheral blood 10


title: normal peripheral blood 13

description: Normal peripheral blood sample

source_name: peripheral blood 13


title: normal peripheral blood 3B

description: Normal peripheral blood sample

source_name: peripheral blood 3B

value: Twin of sample 3A


title: Crohn's disease peripheral blood 3A

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 3A

value: Twin of sample 3B


title: Crohn's disease peripheral blood 1A

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 1A

value: Twin of sample 1B


title: normal peripheral blood 2A

description: Normal peripheral blood sample

source_name: peripheral blood 2A

value: Twin of sample 2B


title: Genmascq_Pig_LL_N54


title: Genmascq_Pig_LL_N25


title: Genmascq_Pig_LL_N45


title: Genmascq_Pig_LL_N37


title: Genmascq_Pig_LL_N51


title: Genmascq_Pig_LL_N17


title: Genmascq_Pig_LL_N23


title: Genmascq_Pig_LL_N36


title: normal peripheral blood 200

description: Normal peripheral blood sample

source_name: peripheral blood 200

value: Male

value: Peripheral Blood


title: Genmascq_Pig_LL_N35


title: Genmascq_Pig_LL_N59


title: Crohn's disease peripheral blood 2B

description: Crohn's disease peripheral blood sample

source_name: peripheral blood 2B

value: Female

value: Twin of sample 2A


title: Genmascq_Pig_LL_N22


title: Genmascq_Pig_LL_N53


title: Genmascq_Pig_LL_N29


title: Genmascq_Pig_LL_N27


title: Genmascq_Pig_LL_N24


title: normal peripheral blood 3

description: Normal peripheral blood sample

source_name: peripheral blood 3

value: normal


title: Genmascq_Pig_LL_N33


title: normal peripheral blood 5

description: Normal peripheral blood sample

source_name: peripheral blood 5


title: Genmascq_Pig_LL_N12

source_name: Longissimus lumborum


title: Genmascq_Pig_LL_N14


title: Genmascq_Pig_LL_N04


title: Genmascq_Pig_LL_N08


title: Genmascq_Pig_LL_N07


title: Genmascq_Pig_LL_N06


title: Genmascq_Pig_LL_N09


title: Genmascq_Pig_LL_M97


title: Genmascq_Pig_LL_N15


title: Genmascq_Pig_LL_N01


title: Genmascq_Pig_LL_N05


title: Genmascq_Pig_LL_M99


title: Genmascq_Pig_LL_M96


title: Genmascq_Pig_LL_M87


title: Genmascq_Pig_LL_M92


title: Genmascq_Pig_LL_M93


title: Genmascq_Pig_LL_M83


title: Genmascq_Pig_LL_M88


title: Genmascq_Pig_LL_M82


title: Genmascq_Pig_LL_M95


title: Genmascq_Pig_LL_M98


title: Genmascq_Pig_LL_M84


title: A508285-R

first: Hon-chiu

middle: Eastwood

last: Leung

address: 1102 Bates Street  Room C1030.09

hyb_protocol: Illumina hybridizatio protocol (default protocol), repeat samples were another repeat of the labeled aRNA loaded onto another chip

scan_protocol: Illumina Beadarray Reader default protocol using Beadscan software

data_processing: Image files and sample sheets were loaded into GenomeStudio version 2010.1 to compile the project. The intensity values were averaged normalization and background subtracted

label: Biotin

source_name: Adult cerebellum repeat

label_protocol: Illumina totalprep RNA amplification protocol (Ambion Inc)

extract_protocol:
Illumina totalprep RNA amplification protocol
Total RNA molecules from primary tumors and xenograft models were purified using Trizol, RNA was quantified using Nanodrop 1000 spectrophotometer.

value: Adult cerebellum


title: A508112-R


title: Genmascq_Pig_LL_M89


title: Genmascq_Pig_LL_M91


title: Genmascq_Pig_LL_M81


title: A508285

source_name: Adult cerebellum


title: A602127

source_name: normal fetal brain

value: normal fetal brain


title: A508112


title: A602126


title: Genmascq_Pig_LL_M73


title: Genmascq_Pig_LL_M77


title: A602126-R

source_name: normal fetal brain repeat


title: A602127-R


title: Genmascq_Pig_LL_M67


title: A911105


title: Genmascq_Pig_LL_M54


title: A911105-R


title: Genmascq_Pig_LL_M70


title: Genmascq_Pig_LL_M53


title: Genmascq_Pig_LL_M52


title: NFb-R

source_name: normal fetal brain  repeat


title: Genmascq_Pig_LL_M44


title: Genmascq_Pig_LL_M40


title: NFb


title: Genmascq_Pig_LL_M43


title: Genmascq_Pig_LL_M30


title: NCb-2-R

source_name: normal adult cerebellum repeat

value: normal adult cerebellum


title: NCb-2

source_name: normal adult cerebellum


title: NCb-1-R

source_name: normal adult cerebellum  repeat


title: Genmascq_Pig_LL_M39


title: Genmascq_Pig_LL_M31


title: Genmascq_Pig_LL_M47


title: Genmascq_Pig_LL_M34


title: Genmascq_Pig_LL_M32


title: Genmascq_Pig_LL_M38


title: NCb-1


title: Genmascq_Pig_LL_M26


title: Genmascq_Pig_LL_M27


title: NT-1197


title: Genmascq_Pig_LL_M37


title: A317

city: Cambridge

last: Zhou

address: 16 Divinity Ave. Rm2112

department: Organismic and Evolutionary Biology

institute: Harvard University

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: Total RNA from Harwich5 Y-chromosome introgression male genotype.

label_protocol: 3DNA procedure

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

tag: genotype

tag: Sex

value: male (XY)

tag: age

value: adult, 3 days old

source_name: Total RNA from Harwich7 Y-chromosome introgression male genotype.


title: NT-1197-R


title: Genmascq_Pig_LL_M12


title: Genmascq_Pig_LL_M14


title: Genmascq_Pig_LL_M28


title: Genmascq_Pig_LL_M24


title: A318

description: Biological replicate


title: Genmascq_Pig_LL_M15


title: A314

description: Biological replicate

source_name: Total RNA from Harwich15 Y-chromosome introgression male genotype.

source_name: Total RNA from Harwich23 Y-chromosome introgression male genotype.


title: Genmascq_Pig_LL_M22


title: A316

description: Biological replicate


title: Genmascq_Pig_LL_M04


title: Genmascq_Pig_LL_M11


title: Genmascq_Pig_LL_M18


title: A311

description: Biological replicate


title: icb-1595-iii-R

source_name: Xenograft of patient 1595, passage III repeat

value: Xenograft

tag: patient id

value: patient 1595

tag: cell passage

value: passage III

tag: patient age

value: 15 m old

tag: patient sex

value: male

tag: initial diagnosis

tag: final diagnosis

value: MB (anaplastic)


title: Genmascq_Pig_LL_M06

value: Longissimus lumborum


title: Genmascq_Pig_LL_M09


title: icb-1595-iii

source_name: Xenograft of patient 1595, passage III


title: ICb-1595-I

source_name: Xenograft of patient 1595, passage I

value: passage I


title: A313

description: Biological replicate


title: Genmascq_Pig_LL_M19


title: Genmascq_Pig_LL_M10


title: A315

description: Biological replicate


title: A312

description: Biological replicate


title: ICb-1595-I-R

source_name: Xenograft of patient 1595, passage I repeat


title: ICb-1572-V-R

source_name: Xenograft of patient 1572, passage V repeat

value: patient 1572

value: passage V

value: 14 yr 9 m old

value: MB (large cell)


title: pt-1595

source_name: Patient 1595

value: primary medulloblastoma tissue

value: Patient 1595


title: pt-1595-R

source_name: Patient 1595 repeat


title: Genmascq_Pig_LL_M03

source_name: Longissimus lumborum


title: Genmascq_Pig_LL_M02


title: Genmascq_Pig_LL_988


title: T18

description: Biological replicate


title: ICb-1572-V

source_name: Xenograft of patient 1572, passage V


title: A320

description: Biological replicate


title: T17

description: Biological replicate


title: A300

description: Biological replicate


title: Genmascq_Pig_LL_984


title: Genmascq_Pig_LL_963


title: Genmascq_Pig_LL_986


title: T16

description: Biological replicate


title: Genmascq_Pig_LL_993


title: ICb-1572-III-R

source_name: Xenograft of patient 1572, passage III repeat


title: A319

description: Biological replicate


title: Genmascq_Pig_LL_958


title: Genmascq_Pig_LL_945


title: Genmascq_Pig_LL_980


title: ICb-1572-III

source_name: Xenograft of patient 1572, passage III


title: Genmascq_Pig_LL_961


title: T19

description: Biological replicate


title: Genmascq_Pig_LL_923


title: Genmascq_Pig_LL_922


title: A299

description: Biological replicate


title: ICb-1572-I-R

source_name: Xenograft of patient 1572, passage I repeat


title: Pt-1572-R

source_name: Patient 1572 repeat

value: Patient 1572


title: Genmascq_Pig_LL_952


title: Genmascq_Pig_LL_999


title: Genmascq_Pig_LL_962


title: ICb-1494-V-R

source_name: Xenograft of patient 1494, passage V repeat

value: patient 1494

value: 5 yr 2 m old

value: female

value: Medulloblastoma_Anaplastic/large cell MB with nodular background


title: Genmascq_Pig_LL_920


title: ICb-1572-I

source_name: Xenograft of patient 1572, passage I

value: Xenograft


title: Pt-1572

source_name: Patient 1572


title: Genmascq_Pig_LL_919


title: A215

description: Biological replicate

source_name: Total RNA from Harwich7 Y-chromosome introgression male genotype.

value: male (XY)

value: adult, 3 days old

source_name: Total RNA from Harwich15 Y-chromosome introgression male genotype.


title: Genmascq_Pig_LL_918


title: A214

description: Biological replicate


title: A213

description: Biological replicate


title: Genmascq_Pig_LL_911


title: ICb-1494-V

source_name: Xenograft of patient 1494, passage V

value: MB (anaplastic)


title: A212

description: Biological replicate


title: A211

description: Biological replicate

source_name: Total RNA from Harwich5 Y-chromosome introgression male genotype.

source_name: Total RNA from Harwich23 Y-chromosome introgression male genotype.


title: Genmascq_Pig_LL_909

value: Longissimus lumborum


title: Genmascq_Pig_LL_912


title: ICb-1494-I-R

source_name: Xenograft of patient 1494, passage I repeat

value: passage I


title: Genmascq_Pig_LL_913


title: Genmascq_Pig_LL_914


title: Genmascq_Pig_LL_889


title: Genmascq_Pig_LL_893


title: Genmascq_Pig_LL_891


title: Genmascq_Pig_LL_906


title: Genmascq_Pig_LL_916


title: Genmascq_Pig_LL_892


title: Genmascq_Pig_LL_882


title: ICb-1494-III-R

source_name: Xenograft of patient 1494, passage III repeat

value: passage III


title: ICb-1487-III

source_name: Xenograft of patient 1487, passage III

value: patient 1487

value: 6 yr 11 m old

value: male

value: medulloblastoma with focal anaplastic features arising in a background of nodular pattern

value: MB (classic)


title: A210

description: Biological replicate


title: Genmascq_Pig_LL_883

source_name: Longissimus lumborum


title: ICb-1494-III

source_name: Xenograft of patient 1494, passage III


title: ICb-1487-III-R

source_name: Xenograft of patient 1487, passage III repeat


title: Genmascq_Pig_LL_879


title: Yap+/-

city: Kansas City

first: Udayan

last: Apte

state: KS

address: 3901 Rainbow Blvd, MS1018

department: Pharmacology

institute: University of Kansas Medical Center

description: gene expression data from postnatal day 30 livers

hyb_protocol: 200ul hybridization solution per GeneChip using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Single Scan; Affymetrix GeneChip Scanner 3000 7G with Autoloader; Affymetrix GeneChip Command Console (AGCC) ver. 1.1

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 (RMA) using RMA default analysis settings: RMA Background Correction; Quantile Normalization; Median Polish probeset summarization.

source_name: postnatal day 30 liver of Yap+/-

label_protocol: Biotinylated In-vitro Transcription using the GeneChip 3` IVT Express Kit

growth_protocol: Yap+/- mice were bred on C57BL/6 backgournd for at least 6 generations before use in these experiments. Yap+/+ and Yap+/- mice were sacrificed at PND30, livers were removed and stored at -80 deg. C. Pooled livers from 5 mice per group were used for gene array experiments.

extract_protocol: Trizol / Phase lock gel protocol

treatment_protocol: No treatments were given to the mice.

value: liver

tag: strain

tag: genotype/variation

value: Yap+/-

value: postnatal day 30


title: Genmascq_Pig_LL_881

tag: tissue


title: Genmascq_Pig_LL_878


title: A208

description: Biological replicate


title: Pt-1494-R

source_name: Patient 1494 repeat

value: primary medulloblastoma tissue

value: Patient 1494

value: 5 yr 2 m old

value: female


title: A209

description: Biological replicate

value: male (XY)

value: adult, 3 days old


title: Genmascq_Pig_LL_886

value: Longissimus lumborum


title: Genmascq_Pig_LL_804


title: Genmascq_Pig_LL_880


title: Yap+/+

source_name: wild type liver

value: Yap+/+


title: Pt-1494

source_name: Patient 1494

value: Medulloblastoma_Anaplastic/large cell MB with nodular background

value: MB (anaplastic)


title: ICb-1487-I

source_name: Xenograft of patient 1487, passage I

value: Xenograft

value: patient 1487

value: passage I

value: 6 yr 11 m old


title: ICb-1494-I

source_name: Xenograft of patient 1494, passage I

value: patient 1494


title: Genmascq_Pig_LL_782


title: ICb-1487-I-R

source_name: Xenograft of patient 1487, passage I repeat

value: male

value: medulloblastoma with focal anaplastic features arising in a background of nodular pattern

value: MB (classic)


title: Genmascq_Pig_LL_778


title: Genmascq_Pig_LL_773


title: Genmascq_Pig_LL_781


title: Genmascq_Pig_LL_777


title: Genmascq_Pig_LL_768


title: Genmascq_Pig_LL_801


title: Genmascq_Pig_LL_746


title: Genmascq_Pig_LL_741


title: Genmascq_Pig_LL_752


title: Genmascq_Pig_LL_765


title: ICb-1338-III-R

source_name: Xenograft of patient 1338, passage III repeat

value: patient 1338

value: passage III

value: 0 yr 6 m old

value: Medulloblastoma_Nodular (desmoplastic) medulloblastoma with prominent extensively nodular componet

value: MB (nodular)


title: Genmascq_Pig_LL_747

value: Longissimus lumborum


title: Pt-1338-R

source_name: Patient 1338 repeat

value: primary medulloblastoma tissue

value: Patient 1338

value: female


title: L1-RFK

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo

country: Japan

institute: Kumamoto University

description: 3T3-L1, rfk siRNA

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: differentiating 3T3-L1 cells with rfk-specific siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT Express Kit User Manual, Affymetrix).

growth_protocol: Cells were grown in DMEM containing 25mM glucose and 10% FBS. For adipogenic induction, insulin, dexamethaone and 3- isobutyl-1-methylxanthine were added.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to manufacturer's protocol.

treatment_protocol: Cells were washed twice with PBS, and were collected in cell lysis buffer RLT (RNeasy Mini Kit) and homogenized.

tag: cell type

value: differentiating 3T3-L1 adipocytes


title: ICb-1338-III

source_name: Xenograft of patient 1338, passage III

value: Xenograft


title: L1-AOF2

description: 3T3-L1, aof2 siRNA

source_name: differentiating 3T3-L1 cells with aof2-specific siRNA


title: Pt-1487

source_name: Patient 1487

value: Patient 1487


title: L1-TC

description: 3T3-L1, TC-treated

source_name: differentiating 3T3-L1 cells treated with tranylcypromine


title: Genmascq_Pig_LL_739

source_name: Longissimus lumborum


title: L1-PHF21A

description: 3T3-L1, phf21a siRNA

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: differentiating 3T3-L1 cells with phf21a-specific siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: Pt-1487-R

source_name: Patient 1487 repeat

value: 6 yr 11 m old


title: Genmascq_Pig_LL_720


title: Genmascq_Pig_LL_726


title: Genmascq_Pig_LL_761


title: ICb-1338-I-R

source_name: Xenograft of patient 1338, passage I repeat

value: passage I


title: Genmascq_Pig_LL_728


title: L1-GL3-1

description: 3T3-L1, control siRNA

source_name: differentiating 3T3-L1 cells with control siRNA


title: ICb-1338-I

source_name: Xenograft of patient 1338, passage I


title: L1-GL3-2

description: 3T3-L1, control siRNA


title: Pt-1338

source_name: Patient 1338


title: Genmascq_Pig_LL_715


title: Genmascq_Pig_LL_708


title: Genmascq_Pig_LL_719


title: Genmascq_Pig_LL_707


title: Genmascq_Pig_LL_697


title: Genmascq_Pig_LL_691


title: Genmascq_Pig_LL_703


title: ICb-1299-IV

source_name: Xenograft of patient 1299, passage IV

value: patient 1299

value: passage IV

value: 2 yr 9 m old

value: Medulloblastoma_Anaplastic/large cell with focal nodular features

value: MB (anaplastic)


title: Genmascq_Pig_LL_713


title: ICb-1299-III

source_name: Xenograft of patient 1299, passage III

value: passage III


title: ICb-1299-IV-R

source_name: Xenograft of patient 1299, passage IV repeat


title: ICb-1299-III-R

source_name: Xenograft of patient 1299, passage III repeat


title: Pt-1299

source_name: Patient 1299

value: Patient 1299


title: Genmascq_Pig_LL_677


title: Genmascq_Pig_LL_676


title: Genmascq_Pig_LL_688


title: Genmascq_Pig_LL_663


title: Genmascq_Pig_LL_680


title: Genmascq_Pig_LL_671


title: ICb-1197-III-R

source_name: Xenograft of patient 1197, passage III repeat

value: patient 1197

value: 5 yr old

value: male

value: Medulloblastoma_Nodular Medulloblastoma with Focal Anaplastic Features

value: MB (nodular)


title: ICb1299-I

source_name: Xenograft of patient 1299, passage I

value: female


title: ICb1299-I-R

source_name: Xenograft of patient 1299, passage I repeat

value: Xenograft


title: Genmascq_Pig_LL_668

value: Longissimus lumborum


title: ICb-1197-III

source_name: Xenograft of patient 1197, passage III


title: Genmascq_Pig_LL_667


title: Genmascq_Pig_LL_674


title: Genmascq_Pig_LL_661


title: Genmascq_Pig_LL_662


title: Pt-1299-R

source_name: Patient 1299 repeat

value: primary medulloblastoma tissue


title: Genmascq_Pig_LL_653

source_name: Longissimus lumborum


title: Genmascq_Pig_LL_672


title: Genmascq_Pig_LL_660


title: Genmascq_Pig_LL_652


title: Genmascq_Pig_LL_646


title: Genmascq_Pig_LL_642


title: ICb-1197-I-R

source_name: Xenograft of patient 1197, passage I repeat

value: passage I


title: Genmascq_Pig_LL_639


title: Genmascq_Pig_LL_629


title: Genmascq_Pig_LL_630


title: Genmascq_Pig_LL_626


title: Genmascq_Pig_LL_618


title: Genmascq_Pig_LL_625


title: ICb-1192-V-R

source_name: Xenograft of patient 1192, passage V repeat

value: patient 1192

value: passage V

value: 12 yr 5 m  old

value: Medulloblastoma

value: MB (classic)


title: ICb-1197-I

source_name: Xenograft of patient 1197, passage I


title: ICb-1192-V

source_name: Xenograft of patient 1192, passage V


title: Genmascq_Pig_LL_620


title: Genmascq_Pig_LL_619


title: ICb1192-III-R

source_name: Xenograft of patient 1192, passage III repeat

value: passage III


title: Genmascq_Pig_LL_607


title: Genmascq_Pig_LL_622


title: ICb1192-III

source_name: Xenograft of patient 1192, passage III


title: Genmascq_Pig_LL_615


title: Genmascq_Pig_LL_612


title: Genmascq_Pig_LL_609


title: ICb1192-I

source_name: Xenograft of patient 1192, passage I


title: ICb1192-I-R

source_name: Xenograft of patient 1192, passage I repeat


title: Genmascq_Pig_LL_613


title: Pt-1192

source_name: Patient 1192

value: Patient 1192


title: Genmascq_Pig_LL_604


title: Genmascq_Pig_LL_605


title: Pt-1192-R

source_name: Patient 1192 repeat


title: Genmascq_Pig_LL_590


title: ICb-1140-III-R

source_name: Xenograft of patient 1140, passage III repeat

value: patient 1140

value: 6 yr  old

value: MB (Anaplastic)


title: Genmascq_Pig_LL_616


title: Genmascq_Pig_LL_587


title: ICb-1140-III

source_name: Xenograft of patient 1140, passage III

value: male


title: Genmascq_Pig_LL_602


title: Genmascq_Pig_LL_593


title: Genmascq_Pig_LL_565


title: ICb-1140-II

source_name: Xenograft of patient 1140, passage II

value: passage II


title: ICb-1140-II-R

source_name: Xenograft of patient 1140, passage II repeat


title: Genmascq_Pig_LL_564


title: Genmascq_Pig_LL_573


title: Genmascq_Pig_LL_583


title: Genmascq_Pig_LL_559


title: Pt-1140MB-R

source_name: Patient 1140 repeat

value: Patient 1140


title: Genmascq_Pig_LL_572


title: Pt-1140MB

source_name: Patient 1140


title: Genmascq_Pig_LL_576

source_name: Longissimus lumborum


title: Genmascq_Pig_LL_550


title: Genmascq_Pig_LL_551


title: Genmascq_Pig_LL_547


title: Genmascq_Pig_LL_552


title: Genmascq_Pig_LL_556


title: Genmascq_Pig_LL_542


title: ICb-1078-V

source_name: Xenograft of pateint 1078, passage V

value: Xenograft

value: pateint 1078

value: 11 yr 9 m old


title: ICb-1078-V-R

source_name: Xenograft of pateint 1078, passage V repeat


title: Genmascq_Pig_LL_555

value: Longissimus lumborum


title: Genmascq_Pig_LL_532


title: Genmascq_Pig_LL_531


title: ICb-1078-III-R

source_name: Xenograft of pateint 1078, passage III repeat


title: ICb-1078-I

source_name: Xenograft of pateint 1078, passage I

value: passage I


title: Genmascq_Pig_LL_534


title: Genmascq_Pig_LL_537


title: Genmascq_Pig_LL_530


title: ICb-1078-I-R

source_name: Xenograft of pateint 1078, passage I repeat


title: Genmascq_Pig_LL_516


title: ICb-1078-III

source_name: Xenograft of pateint 1078, passage III


title: Pt-1078-R

source_name: Patient 1078 repeat

value: primary medulloblastoma tissue

value: Patient 1078


title: Genmascq_Pig_LL_493


title: Genmascq_Pig_LL_509


title: Genmascq_Pig_LL_535


title: Genmascq_Pig_LL_517


title: Pt-1078

source_name: Patient 1078


title: Genmascq_Pig_LL_424


title: Genmascq_Pig_LL_539


title: Genmascq_Pig_LL_490


title: Genmascq_Pig_LL_498


title: ICb984-V-R

source_name: Xenograft of patient 984, passage V repeat

value: patient 984

value: passage V

value: 7 yr 10 m old

value: female


title: IC984-III-R

source_name: Xenograft of patient 984, passage III repeat

value: passage III


title: Genmascq_Pig_LL_420


title: ICb984-V

source_name: Xenograft of patient 984, passage V


title: IC984-I-R

source_name: Xenograft of Patient 984, passage I repeat

value: Patient 984


title: Genmascq_Pig_LL_499


title: Genmascq_Pig_LL_546


title: Genmascq_Pig_LL_417


title: Genmascq_Pig_LL_492


title: Genmascq_Pig_LL_419


title: Genmascq_Pig_LL_422


title: Genmascq_Pig_LL_413


title: Genmascq_Pig_LL_415


title: Genmascq_Pig_LL_394


title: Genmascq_Pig_LL_388


title: IC984-III

source_name: Xenograft of patient 984, passage III

value: MB (Anaplastic)


title: Genmascq_Pig_LL_412


title: IC984-I

source_name: Xenograft of Patient 984, passage I


title: Genmascq_Pig_LL_406


title: Genmascq_Pig_LL_389


title: Genmascq_Pig_LL_414


title: Genmascq_Pig_LL_384


title: Genmascq_Pig_LL_398


title: Genmascq_Pig_LL_392


title: Genmascq_Pig_LL_386


title: Genmascq_Pig_LL_390


title: Genmascq_Pig_LL_410


title: Genmascq_Pig_LL_403


title: Genmascq_Pig_LL_387


title: Genmascq_Pig_LL_391


title: Genmascq_Pig_LL_374


title: Genmascq_Pig_LL_341


title: Genmascq_Pig_LL_373


title: Genmascq_Pig_LL_357


title: Genmascq_Pig_LL_338


title: Genmascq_Pig_LL_377


title: Genmascq_Pig_LL_378


title: Genmascq_Pig_LL_354


title: Genmascq_Pig_LL_368


title: Genmascq_Pig_LL_347


title: Genmascq_Pig_LL_314


title: Genmascq_Pig_LL_309


title: Genmascq_Pig_LL_313


title: Genmascq_Pig_LL_315


title: Genmascq_Pig_LL_303


title: Genmascq_Pig_LL_336


title: Genmascq_Pig_LL_305


title: Genmascq_Pig_LL_310


title: Genmascq_Pig_LL_299


title: Genmascq_Pig_LL_298


title: Genmascq_Pig_LL_339


title: Genmascq_Pig_LL_365


title: Genmascq_Pig_LL_304


title: Genmascq_Pig_LL_296


title: Genmascq_Pig_LL_302


title: Genmascq_Pig_LL_297


title: Genmascq_Pig_LL_408


title: Genmascq_Pig_LL_294


title: Genmascq_Pig_LL_287


title: Genmascq_Pig_LL_275


title: Genmascq_Pig_LL_285


title: Genmascq_Pig_LL_282


title: CFT073 NaCl biological rep 1

city: Dayton

first: Oleg

last: Paliy

state: OH

address: 3640 Colonel Glenn

department: Biochemistry and Molecular Biology

institute: Wright State University

description: Gene expression data from bacteria in K-medium + 0.3M NaCl

hyb_protocol: 2 µg of biotin Labeled cDNA was hybridized to an E. coli Genome 2 array (Affymetrix, Inc). Independent array hybridizations were carried out for three biological replicates of each of the three conditions.

scan_protocol: The gene chips were scanned using the GCOS software package.

data_processing: GCOS was used to obtain detection calls for each microarray.  The statistical difference for mRNA expression were analyzed using CarmaWeb. Affymetrix GeneChip analysis was performed using MAS for background correction, VSN for normalization, MAS for PM correction and Medianpolish for Expression.  VSN normalized data not provided by submitter.

organism: Escherichia coli CFT073

source_name: CFT073 in NaCl

label_protocol: cDNA synthesis, fragmentation, and labeling and washing and scanning of the E. coli GeneChip arrays were performed according to Affymetrix instructions.

growth_protocol: Cells from single colonies were grown on LB agar and then inoculated into liquid LB and grown to saturation. Then 50 µl was inoculated into 5 ml of K-medium and grown to saturation again. The cultures were then inoculated into the separate media as follows: 25 μl into K-medium, 50 µl into K-medium + 0.3M NaCl, 75 µl into K-medium + 0.6M urea; the final volume was 5ml in all cases. These cultures were grown overnight. The cultures were incubated in 250 ml Erlenmeyer flasks in the three media in a water bath at 30ºC.

extract_protocol: Total RNA was extracted by the hot phenol–chloroform method.

treatment_protocol: When the samples had reached an OD600 of 0.4-0.5, 25 ml of each culture was added to a 2.5 ml mixture of cold 95% ethanol and 5% phenol to preserve the mRNA. The cells were cooled rapidly on ice and immediately harvested by centrifugation at 4°C, and the pellet was frozen on dry ice.

tag: growth condition

value: 50 µl into K-medium + 0.3M NaCl


title: Genmascq_Pig_LL_300


title: CFT073 urea biological rep 3

description: Gene expression data from bacteria in K-medium + 0.6M urea

source_name: CFT073 in urea

value: 75 µl into K-medium + 0.6M urea


title: Genmascq_Pig_LL_276

source_name: Longissimus lumborum


title: Genmascq_Pig_LL_291


title: Genmascq_Pig_LL_280


title: Genmascq_Pig_LL_288


title: CFT073 urea biological rep 2


title: Genmascq_Pig_LL_272


title: Genmascq_Pig_LL_278


title: Genmascq_Pig_LL_279


title: CFT073 NaCl biological rep 3


title: Genmascq_Pig_LL_274


title: Genmascq_Pig_LL_284


title: Genmascq_Pig_LL_289


title: CFT073 urea biological rep 1


title: CFT073 K-med biological rep 3

description: Gene expression data from bacteria in K-medium

source_name: CFT073 in K-med

value: 25 μl into K-medium


title: CFT073 K-med biological rep 1


title: A-OsMADS29 (line14) rep2

city: shanghai

first: linlin

last: yin

address: 300 fenglin road

institute: SIPPE

description: Gene expression in nucellar projection of 3 DAF A-OsMADS29 (line14) seed

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression 4*44K Microarrays for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 015241_D_F_20081112) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Oryza sativa

source_name: Nucellar projection cells, A-OsMADS29 (line14),3 DAF, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 4 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: ZH11 and A-OsMADS29 (line2 and line14) were growth in the same conditon.The rice seeds were germinated in sterilized water and then grown in pots in a phytotron with a 12-h light (26℃) / 12-h dark (18℃) cycle.

extract_protocol: Nucellar projection cells of seeds at 3 DAF were isolated using a Veritas Microdissection System (Arcturus/Molecular Devices).The RNA was extracted with the PicoPure RNA Isolation Kit (Arcturus/Molecular Devices) and amplified using a TargetAmp 2-round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnologies) following the manufacturer's recommendations. RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genetic background

value: OsMADS29 mutant

tag: source tissue

value: seed

value: Nucellar projection cells

value: 3 DAF


title: Genmascq_Pig_LL_269

value: Longissimus lumborum

tag: ChIP


title: CFT073 NaCl biological rep 2


title: A-OsMADS29 (line14) rep1

source_name: Nucellar projection cells, A-OsMADS29 (line14),3 DAF, replicate 1

tag: genotype


title: Genmascq_Pig_LL_263


title: Genmascq_Pig_LL_255


title: Genmascq_Pig_LL_267


title: Genmascq_Pig_LL_257


title: A-OsMADS29 (line2) rep2

description: Gene expression in nucellar projection of 3 DAF A-OsMADS29 (line2) seed

source_name: Nucellar projection cells, A-OsMADS29 (line2),3 DAF, replicate 2


title: ZH11 rep1

description: Gene expression in nucellar projection of 3 DAF ZH11 seed

source_name: Nucellar projection cells, ZH11,3 DAF, replicate 1

value: wild type


title: Genmascq_Pig_LL_256


title: CFT073 K-med biological rep 2