title: BT549_sic-Jun_rep3

city: Stockholm

first: Chunyan

last: Zhao

address: Hälsovägen 7-9

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description:
CZ9 jun3_ 3_G09
Gene expression in si_c-Jun treated cells

hyb_protocol: Hybridization to Human Gene 1.1 ST array plates was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.

scan_protocol: Array plates were scanned using a GeneTitan scanner.

data_processing: Preprocessing in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: BT549 cells, c-Jun knockdown, 72h

label_protocol: Total RNA was converted to sense strand cDNA using Ambion WT Expression kit. For fragmentation and labeling, WT GeneChip WT target Labeling kit was used.

growth_protocol: The human breast cancer cell line BT549 was maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: BT549 cells were transfected with a control siRNA or with the pool of siRNAs targeting Fra-1 or c-Jun. Cells were harvested and total RNA was extracted 72h after transfection.

value: breast cancer cells

tag: sirna

value: c-Jun


title: H5882

status: Public on Jun 30 2014

type: RNA

city: Niigata

first: Masayuki

last: Nashimoto

state: Niigata

address: Higashijima 265-1, Akihaku

country: Japan

institute: Niigata University of Pharmacy and Applied Life Sciences

description: Gene expression after 18-hour incubation in the presence of 1 μM of the heptamer-type sgRNA H5882.

hyb_protocol: 1.65 μg 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 manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo 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 (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Scaled signal intensity that adjusts the average intensity value to 2500.

molecule: total RNA

organism: Homo sapiens

source_name: HL60, H5882 (UUGCCGU)

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

growth_protocol: HL60 cells were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in 5% CO2 humidified incubator.

extract_protocol: After 18 hours, total RNA was extracted with ISOGEN (Nippon Gene, Tokyo, Japan) from the cells.

treatment_protocol: HL60 cells were plated at 8 × 104 cells/500 μl/well on a 24-well dish in RPMI-1640 media containing 1 μM of various naked heptamer-type sgRNAs.

tag: treatment

tag: cell line

tag: origin

value: Acute promyelocytic leukemia


title: H1885

description: Gene expression after 18-hour incubation in the presence of 1 μM of the heptamer-type sgRNA H1885.

source_name: HL60, H1885 (AUCUUCA)


title: H10927

description: Gene expression after 18-hour incubation in the presence of 1 μM of the heptamer-type sgRNA H10927.

source_name: HL60, H10927 (GGGGGCG)


title: PBMC_SNG001_visit4_rep5

city: Southampton

first: Phillip

last: Monk

address: Tremona Road

department: Southampton General Hospital

country: United Kingdom

institute: Synairgen Research Ltd

hyb_protocol: The 8 pack format mastermixes were followed (Two color microarray-based gene expression analysis: Low input quick amp labeling (v 6.5, May 2010))

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C US84300231 using protocol GE2_107_Sep09.

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

source_name: Peripheral blood mononuclear cells, SNG001

label_protocol: Followed the protocol described in Two color microarray-based gene expression analysis: Low input quick amp labeling (v 6.5, May 2010) using 200ng of total RNA

extract_protocol: Total RNA extracted using Qiagen PAXgene RNA extraction kit following manufacturer's instructions

tag: agent

tag: timepoint

value: Day 7

tag: cell type

value: Peripheral blood mononuclear cells

source_name: Stratagene Universal Human Reference RNA

tag: reference


title: BT549_sic-Jun_rep1

description:
CZ7 jun3_ 1_H0
Gene expression in si_c-Jun treated cells

label: biotin


title: PBMC_SNG001_visit3_rep5

value: Day 4

value: Stratagene Universal Human Reference RNA


title: Normal Volunteer, Replicate 21

city: Bethesda

first: Eric

last: Billings

state: MD

address: 10 Center Drive

country: USA

institute: NHLBI

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: The data were analyzed with Affymetrix apt version 1.12, GeneSpring 11.5.1 .  Apt was used to determine present/absent calls and GeneSpring RMA normalization was applied.

source_name: Alveolar macrophage isolated from Normal Volunteer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Affymetrix Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: Total RNA extraction.

tag: diagnosis

value: Normal

tag: tissue

value: Alveolar Macrophage


title: Liver d150 high protein diet during lactation biological rep6

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

country: Germany

description:
the mouse outbred line DUK, which is a cross-breed line generated at our Institute (Leibniz Institute for Farm Animal Biology (FBN), in 18196 Dummertorf, Germany) from the following 4 outbred and 4 inbred lines:    NMRI (white)  Han:NMRI (white)  Han:CFW (white)  Han:CF1 (white)  CBA/Bln (agouti)   AB/Bln (white)  C57BL/Bln (black)  XVII/Bln (white).
Sample pools, livers from three animals

hyb_protocol: The fragmented cRNA was hybridized overnight (45°C) in the GeneChipR Hybridisation Oven 640 (Affymetrix) to the Affymetrix Mouse Genome 430_2.0 expression arrays. Washing and staining protocols were performed with the Affymetrix Fluidics Station 450. For signal enhancement, an antibody amplification was carried out using a biotinylated antistreptavidin antibody (Vector Laboratories, Peterborough, UK), which was cross-linked by a goat IgG (Sigma–Aldrich, Taufkirchen, Germany) followed by a second staining with streptavidin–phycoerythrin conjugate (Molecular Probes, Invitrogen, Karlsruhe, Germany)

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 (Affymetrix) at 1.56 micron resolution

data_processing: Data analysis was performed with the MAS 5.0 (Microarray Suite statistical algorithm, Affymetrix) probe level analysis using GeneChip Operating Software (GCOS 1.4), and the final data extraction was done with the Data Mining Tool 3.1 (Affymetrix)

label: Biotin

organism: Mus musculus

source_name: Liver at postnatal day 150 after control diet during pregnancy and maternal high protein diet during lactation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: Mice were kept in Makrolon-cages of 30 x 12.5 x 12.5 cm with free access to pellet concentrate and water. The light regime was LD 12:12, the room temperature was standardized to 21 °C.

extract_protocol: Total RNA from liver samples was prepared using the RNeasy Mini Kit with simultaneous removal of genomic DNA with RNAse free DNAse I (both from Qiagen). Varying amounts of RNA from four (d21) or three to four samples (d150) were then combined to pools of 5 µg RNA per pool considering equal contributions of individual samples.

treatment_protocol: Female mice were randomly allocated to feeding groups receiving one of two experimental isoenergetic diets with control (20% w/w) and high protein (40% w/w) levels, respectively

tag: outbred line

value: DUK

value: liver


title: PBMC_SNG001_visit2_rep5

value: Day 1


title: BT549_sic-Jun_rep2

description:
CZ8 jun3_ 2_F07
Gene expression in si_c-Jun treated cells


title: BT549_siFra-1_rep3

description:
CZ6 fra3_E09
Gene expressionin si_Fra-1 treated cells

source_name: BT549 cells, Fra-1 knockdown, 72h


title: PBMC_SNG001_visit3_rep3


title: Liver d150 high protein diet during lactation biological rep5

institute: Leibniz Institute for Farm Animal Biology


title: PBMC_SNG001_visit4_rep7


title: BT549_siFra-1_rep2

description:
CZ5 fra2_D07
Gene expressionin si_Fra-1 treated cells


title: Liver d21 high protein diet during lactation biological rep3

source_name: Liver at postnatal day 21 after control diet during pregnancy and maternal high protein diet during lactation


title: Liver d150 high protein diet during lactation biological rep4


title: Liver d21 high protein diet during lactation biological rep2


title: PBMC_SNG001_visit4_rep3


title: BT549_sicontrol_rep3

description:
CZ2 ctrl2_C05
Gene expression in si_control treated cells

source_name: BT549 cells, siControl, 72h

value: control


title: BT549_sicontrol_rep4

description:
CZ3 ctrl3_A09
Gene expression in si_control treated cells


title: BT549_sicontrol_rep2

description:
CZ10 ctrl2_B07
Gene expression in si_control treated cells


title: BT549_siFra-1_rep1

description:
CZ4 fra1_A07
Gene expressionin si_Fra-1 treated cells


title: PBMC_SNG001_visit2_rep2


title: Liver d150 high protein diet during pregnancy biological rep2

source_name: Liver at postnatal day 150 after maternal high protein diet during pregnancy and control diet during lactation


title: PBMC_SNG001_visit2_rep3


title: estrogen receptor negative BC sample 10

city: Torrevieja

first: Ramon

middle: G

last: Manzano

state: Alicante

address: Partida la Loma s/n

department: Unidad de Consejo Genetico, Plataforma de Oncologia

country: Spain

institute: Hospital Quiron Torrevieja

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: sampleJ

hyb_protocol: Hybridization was done with the Agilent Hybridization kit, according to the manufacturer´s instructions in a hybridization oven for 17 hours at 65Âº C.

scan_protocol: Agilent whole human genome 4x44K microarrays were scanned with a G2505B scanner from Agilent Technologies and data were extracted with the Agilent Feature Extraction software (version 9.5) according to standard Agilent protocols

data_processing: Cy3 data from feature extraction files (both 2 color arrays and 1 color arrays) were background corrected (normexp), quantile normalized and log2 transformed using the limma package (Bioconductor project) in the R statistical environment (version 2.10.1).

source_name: Primary breast tumor biopsy after surgery

label_protocol: Labelling was performed with Agilent QuickAmp labelling kit according to the manufacturer´s instructions

extract_protocol: Total RNA was extracted with Rneasy columns (QIAGEN)

tag: gender

value: Female

tag: erbb2 status (by ihc)

value: Negative

tag: age

tag: tumor grade

tag: tumor diameter


title: Liver d21 high protein diet during lactation biological rep1


title: PBMC_SNG001_visit4_rep2


title: Liver d150 high protein diet during pregnancy biological rep3


title: PBMC_SNG001_visit4_rep1


title: PBMC_SNG001_visit3_rep2


title: Liver d21 high protein diet during pregnancy biological rep3

source_name: Liver at postnatal day 21 after maternal high protein diet during pregnancy and control diet during lactation


title: Liver d21 high protein diet during pregnancy biological rep2


title: PBMC_SNG001_visit3_rep1


title: STC273

type: genomic

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

description: AGC MSS

hyb_protocol: Each dye-labeled DNA was purified and mixed with hybridization reagents, applied on the array and incubated for 24 hours at 65ºC in a hybridization oven (Agilent). After hybridization, slides were washed sequentially.

scan_protocol: The arrays were scanned using Agilent microarray scanner.

data_processing: Raw data were generated from scanned images of Agilent array data using Agilent Feature Extraction Software 10.7.3.1.

molecule: genomic DNA

label_protocol: 1 µg of genomic DNA were labeled with fluorescent dye at 37°C for 2 hours. BioPrime aCGH labeling system (Invitrogen) was used for labeling step.

extract_protocol: genomic DNA extracted using DNeasy Blood & Tissue Kit (Qiagen) following manufacturer's instructions.

tag: disease state

value: normal

value: Stomach

value: Male

value: tumor


title: Liver d150 control diet biological rep3

source_name: Liver at postnatal day 150 after maternal control diet during pregnancy and lactation


title: Liver d150 high protein diet during pregnancy biological rep1


title: STC265

description: AGC MSS


title: STC248

description: AGC MSS


title: Liver d150 control diet biological rep1


title: EGC28

description: EGC MSS


title: PBMC_placebo_visit4_rep31

source_name: Peripheral blood mononuclear cells, placebo

value: placebo


title: Liver d150 control diet biological rep2


title: STC243

description: AGC MSS


title: PBMC_placebo_visit3_rep31


title: EGC23

description: EGC MSS


title: Liver d21 high protein diet during pregnancy biological rep1


title: EGC20

description: EGC MSS


title: PBMC_placebo_visit2_rep31


title: PBMC_placebo_visit4_rep30

value: Day 7


title: BT549_sicontrol_rep1

description:
CZ1 ctrl1_G05
Gene expression in si_control treated cells

value: breast cancer cells

tag: sirna


title: PBMC_SNG001_visit2_rep1

value: Peripheral blood mononuclear cells


title: Liver d21 control diet biological rep3

source_name: Liver at postnatal day 21 after maternal control diet during pregnancy and lactation


title: EGC10

description: EGC MSS


title: PBMC_placebo_visit3_rep30

value: Day 4

value: Stratagene Universal Human Reference RNA


title: Liver d21 control diet biological rep1


title: PBMC_placebo_visit2_rep30


title: STC291

description: AGC MSI-H

tag: tag


title: SRC-2OE, biological replicate 3

city: Houston

first: Hui-Ju

last: Lee

state: Texas

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: Hybridization cocktails containing Affymetrix spike-in controls and 15.0 μg of each fragmented, labeled cRNA were loaded onto Affymetrix GeneChip® Mouse 430 2.0 arrays.  The arrays were hybridized for 16 hours at 45°C with rotation at 60 rpm in the Affymetrix GeneChip® Hybridization Oven 640. The arrays were washed and stained with a streptavidin, R-phycoerythrin conjugate stain using the Affymetrix GeneChip® Fluidics Station 450 using fluidics protocol FS450_0001. Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000.

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

source_name: SRC-2OE/+ prostate

label_protocol: Samples were labeled using the standard Affymetrix linear amplification protocol using the 3’ IVT Express Kit.  250 ng of total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was tested for integrity on the Agilent Bioanalyzer and quantified using the NanoDrop® ND-1000 spectrophotometer.  15.0 µg of the labeled cRNA was fragmented and re-checked for concentration and size.

extract_protocol: Trizol extraction followed by Qiagen RNeasy purification

value: Prostate

tag: genotype

value: Probasin-cre; PTENflox/+; SRC-2OE/+

value: 7 months


title: Liver d21 control diet biological rep2

value: DUK

value: liver


title: PBMC_placebo_visit4_rep29


title: PBMC_placebo_visit3_rep29


title: STC263

description: AGC MSI-H


title: STC297

description: EGC MSI-H

value: Female


title: PBMC_placebo_visit4_rep28


title: SRC-2OE, biological replicate 2


title: SRC-2OE, biological replicate 1


title: STC252

description: AGC MSI-H


title: PBMC_placebo_visit2_rep29

value: Day 1


title: Control, biological replicate 2

source_name: Control prostate

value: Probasin-cre; PTENflox/+


title: STC246

description: EGC MSI-H

value: normal

value: Stomach


title: Control, biological replicate 1


title: EGC15

description: EGC MSI-H

value: tumor


title: EGC3

description: EGC MSI-H


title: PBMC_placebo_visit3_rep28

value: placebo


title: EGC8

description: EGC MSI-H


title: PBMC_placebo_visit2_rep28


title: Control, biological replicate 3


title: PBMC_placebo_visit3_rep26


title: MaSC-enriched Wnt1-Tg  SPI-2

city: Little Rock

first: Rosalia

middle: CM

last: Simmen

state: Arkansas

address: 15 Children's Way Slot 512-20B

department: Physiology and Biophysics

institute: University of Arkansas for Medical Sciences

description: Mammary Basal gene expression

hyb_protocol: Fifteen microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Mouse Genome 430 2.0 Array (N = 2/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing:
Cel files were generated using GCOS and utilized for analysis using GeneSpring GX v 11
Summarization Algorithm: RMA    Technology: Affymetrix.GeneChip.Mouse430_2   Normalization: Quantile   Baseline Transformation: median of all samples

source_name: Mouse Basal (MaSC-enriched) population

label_protocol: First- and second- strand cDNA synthesis (from 0.1 ug total RNA), biotin-labeled aRNA synthesis, and fragmentation of cRNA  reactions were performed following protocols described by Affymetrix. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Total RNA was isolated from freshly sorted mammary Basal population using the Arcturus PicoPure RNA isolation kit (Life Technologies Corporation, Carlsbad, CA)

tag: strain

value: B66SJL/HEV/J (mixed background)

tag: genotype/variation

value: MMTV-Wnt1-Transgenic (Wnt1-Tg)

value: Mammary gland

value: Basal (stem cells, myoepithelial cells, myoepithelial progenitors)

tag: diet

value: soy protein isolate (SPI) diet


title: PBMC_placebo_visit4_rep26

tag: agent

tag: timepoint

value: Day 7

tag: cell type

value: Peripheral blood mononuclear cells

value: Stratagene Universal Human Reference RNA


title: PBMC_placebo_visit4_rep25

tag: reference


title: MaSC-enriched Wnt1-Tg  SPI-1

description: Mammary Basal gene expression

tag: tissue


title: PBMC_placebo_visit2_rep26


title: PBMC_placebo_visit3_rep25

value: Day 4


title: MaSC-enriched Wnt1-Tg  CAS-2

description: Mammary Basal gene expression

value: control casein (CAS) diet


title: PBMC_placebo_visit2_rep25


title: im 25 dpa vs. TM-1 25 dpa rep1

city: Nanjing

first: Cheng

last: Wang

address: Weigang No.1

country: China

institute: Nanjing Agricultural University

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 25 dpa, replicate 1

hyb_protocol: Cy3 and Cy5-labeled cDNA resolved in 80 µL hybridization solution (3×SSC, 0.2% SDS, 5 × Denhart’s, 25% formamide). DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Slides were hybridized at 42°C overnight and transferred to fresh containers with Wash Solution 1 (0.2% SDS, 2 × SSC) at 42°C for 5 min and then immersed in Wash Solution 2 (0.2 × SSC) at room temperature for 5 min.

scan_protocol: All microarrays were scanned with a LuxScan scanner using the LuxScan 3.0 software (Captalbio Corp).

data_processing: Data were filtered and corrected for bias using the following steps: (1) Low quality spots (dust particles, scratches, high background, or irregularly shaped spots) were manually flagged and excluded. (2) Faint spots with intensity < 400 units after subtraction of the background were removed. (3) Statistical analyses were carried out using the LIMMA package (version 3.4.5) in R (version2.12.2). All operations were performed according to those described in the user’s guide of LIMMA. The data were normalized within arrays using the “LOWESS” method (Yang et al., 2002) and across arrays by the “Aquantile” method (Yang et al., 2003). Normalized data were fitted to linear models in LIMMA to analyze DEGs using a moderated t-statistic (eBays) method (Symth et al., 2004). The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

organism: Gossypium hirsutum

source_name: im 25 dpa

label_protocol: RNA amplification and labeling were performed using the cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China) per the manufacturer’s protocol. Briefly, total RNA was reverse transcribed into double-stranded cDNA using the CbcScript enzyme. Subsequently, cRNA was synthesized from cDNA products using the T7 Enzyme Mix in the cRNA Amplification and Labeling Kit and purified using the NucleoSpin® RNA clean-up kit. After the cRNA was synthesized, the new cDNA was generated with random primers from the cRNA using CbcScript II enzyme in the kit. Finally, the transcription products were purified with the Nucleospin® Extract II Kit (MACHEREY-NAGEL), and fluorescent dye-labeled (Cy5 and Cy3-dCTP) cDNA was synthesized with the Klenow enzyme

extract_protocol: Total RNA of fibers from 13–25 DPA of TM-1 and the im mutant were extracted using a modified CTAB-sour phenol extraction method.

value: Fiber

tag: developmental stage

value: 25 dpa (days post anthesis)

tag: material

value: immature fiber mutant (im)

source_name: TM-1 25 dpa

value: Gossypium hirsutum L. acc. TM-1


title: im 25 dpa vs. TM-1 25 dpa rep2

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 25 dpa, replicate 2


title: im 25 dpa vs. TM-1 25 dpa rep3

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 25 dpa, replicate 3


title: STC232

description: AGC MSI-H

value: normal

value: Stomach

tag: gender

value: Female


title: im 22 dpa vs. TM-1 22 dpa rep2

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 22 dpa, replicate 2

source_name: TM-1 22 dpa

value: 22 dpa (days post anthesis)

source_name: im 22 dpa


title: MaSC-enriched Wnt1-Tg  CAS-1

description: Mammary Basal gene expression

value: B66SJL/HEV/J (mixed background)

value: MMTV-Wnt1-Transgenic (Wnt1-Tg)


title: PBMC_placebo_visit2_rep24

value: placebo

value: Day 1

source_name: Stratagene Universal Human Reference RNA


title: PBMC_placebo_visit4_rep24

value: Day 7


title: PBMC_placebo_visit3_rep24

value: Peripheral blood mononuclear cells


title: GP EWS-FLI1 at 48h, rep2

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

institute: Japanese Foundation for Cancer Research

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 GeneChip Scanner 3000 7G.

source_name: Mouse GP cells, 48h after transduced with EWS-FLI1 virus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: FZ and GP cells were microdissected from long bones of 18.5 dpc mouse embryo, and cultured in IMDM with 15% FBS

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: FZ and GP cells were transduced with pMY retroviral vectors with or without the EWS-FLI1 insert

tag: source tissue

value: embryo joint

value: growth place (GP)-derived cells

tag: transfection

value: EWS-FLI1 virus

tag: time

tag: genetic background

value: BALB/cAJcl


title: GP EWS-FLI1 at 48h, rep3


title: GP EWS-FLI1 at 48h, rep1


title: im 22 dpa vs. TM-1 22 dpa rep1

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 22 dpa, replicate 1

value: Fiber


title: PBMC_placebo_visit4_rep23

value: Stratagene Universal Human Reference RNA


title: FZ EWS-FLI1 at 48h, rep2

source_name: Mouse FZ cells, 48h after transduced with EWS-FLI1 virus

value: osteochondrogenic progenitors derived from the facial zone (FZ) of murine long bone


title: FZ EWS-FLI1 at 48h, rep1


title: im 22 dpa vs. TM-1 22 dpa rep3

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 22 dpa, replicate 3

value: Gossypium hirsutum L. acc. TM-1

value: immature fiber mutant (im)


title: im 19 dpa vs. TM-1 19 dpa rep1

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 19 dpa, replicate 1

source_name: im 19 dpa

value: 19 dpa (days post anthesis)

source_name: TM-1 19 dpa


title: FZ EWS-FLI1 at 48h, rep3


title: MPC_3

first: Uma

middle: T

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Data were processed using Affymetrix Expression Console software. Gene level expression were summarized using RMA quantile normalization method.

source_name: Pheochromocytoma metastatic to liver

label_protocol: The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin.

growth_protocol: Viable MTT cells were collected at 80% confluence and snap frozen

extract_protocol: Extraction of RNA from normal and tumor tissue was performed following a protocol that combines separation of the RNA fraction of tissue homogenized in TRIZOL with subsequent column-based RNA purification.

tag: disease status

value: Metastasis

value: MPC cells


title: MPC_2


title: im 19 dpa vs. TM-1 19 dpa rep3

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 19 dpa, replicate 3


title: im 16 dpa vs. TM-1 16 dpa rep2

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 16 dpa, replicate 2

source_name: TM-1 16 dpa

value: 16 dpa (days post anthesis)

source_name: im 16 dpa


title: im 16 dpa vs. TM-1 16 dpa rep1

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 16 dpa, replicate 1


title: im 19 dpa vs. TM-1 19 dpa rep2

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 19 dpa, replicate 2


title: GP empty at 48h, rep3

source_name: Mouse GP cells, 48h after transduced with empty virus

value: empty virus


title: PBMC_placebo_visit3_rep22

source_name: Peripheral blood mononuclear cells, placebo

value: placebo

value: Day 4


title: PBMC_placebo_visit3_rep23

value: Peripheral blood mononuclear cells


title: PBMC_placebo_visit2_rep23

value: Day 1


title: im 13 dpa vs. TM-1 13 dpa rep3

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 13 dpa, replicate 3

source_name: im 13 dpa

value: 13 dpa (days post anthesis)

source_name: TM-1 13 dpa


title: GP empty at 48h, rep2

value: embryo joint

value: growth place (GP)-derived cells


title: MPC_1


title: MTT_3

value: MTT cells


title: PBMC_placebo_visit4_rep22

value: Day 7

value: Stratagene Universal Human Reference RNA


title: im 16 dpa vs. TM-1 16 dpa rep3

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 16 dpa, replicate 3

value: Fiber

value: Gossypium hirsutum L. acc. TM-1


title: FZ empty at 48h, rep3

source_name: Mouse FZ cells, 48h after transduced with empty virus

value: osteochondrogenic progenitors derived from the facial zone (FZ) of murine long bone

value: BALB/cAJcl


title: GP empty at 48h, rep1


title: MTT_2

value: Metastasis


title: im 13 dpa vs. TM-1 13 dpa rep2

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 13 dpa, replicate 2

value: immature fiber mutant (im)


title: MTT_1


title: PBMC_placebo_visit2_rep22


title: FZ empty at 48h, rep2

value: empty virus


title: mammary basal cells pre-culture17.02.2010_Basal cells

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

description:
5282035042_F
RNA extracted from mouse mammary basal cells sorted at high purity (~95%) by flow cytometry. Basal cells consist predominantly of myoepithelial cells intermixed with rare mammary stem cells which occur at a frequency of 1 in every ~300 basal cells.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log base 2 quantile normalised using the beadarray package in R

source_name: 10-14 week old, female, virgin C57BL/6J mice (Charles River)

label_protocol: BeadArrays were washed and stained with streptavidin Cy3 following the Illumina WGGX DirectHyb Assay Guide (11286331 RevA)

growth_protocol: Mammary glands from 10-14 week old, female, virgin C57BL/6J mice were dissociated into single cells and basal cells were sorted by flow cytometry at a purity of ~95%. Inducing basal cell proliferation in vitro causes mammary stem cell expansion over 7 days in culture. Basal cells were cultured on Matrigel-coated cell culture plastic in a keratinocyte stem cell media supplemented with the Rho kinase inhibitor Y-27632 and were co-seeded with irradiated NIH 3T3 fibroblast feeder cells. In order to determine the molecular changes that occur during culture that may contribute to mammary stem cell expansion, gene expression profiling was conducted on basal cells pre-culture and after 1- or 7-day-culture

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen) following the manufacturer’s instructions. The RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific) and quality checked using a 2100 Bioanalyser (Agilent). All samples had an RNA integrity number >=8. Total RNA was prepared for microarray analysis using the Illumina TotalPrep RNA Amplification kit (Ambion)

treatment_protocol: Mammary glands were dissociated in collagenase and hyaluronidase for 14-16 h; treated with ammonium chloride, trypsin, dispase and DNase; then filtered to obtain a single cell suspension. Mammary cells were stained with fluorochrome-conjugated antibodies and the viability dye DAPI and were then passed through a cell sorter. Cultured basal cells were grown on Matrigel-coated cell culture plastic in keratinocyte stem cell media supplemented with 10µM Y-27632 for 1-7 days at 37°C in a 5% (vol/vol) CO2, 5% (vol/vol) O2 atmosphere.

tag: experimental factor

value: mouse mammary basal cells pre-culture

tag: growth protocol

value: mammary basal cells pre-culture

value: mammary basal cell

value: female

tag: age


title: PBMC_placebo_visit3_rep21

value: placebo

value: Day 4

value: Peripheral blood mononuclear cells


title: im 13 dpa vs. TM-1 13 dpa rep1

description: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and immature fiber mutant at 13 dpa, replicate 1

value: 13 dpa (days post anthesis)


title: 1-day-cultured mammary basal cells25.02.2010_1d FAD

description:
5282035042_D
RNA extracted from sorted mouse mammary basal cells cultured for 1 day. 1-day-cultured basal cells contain mammary stem cells at a frequency of 1 in every ~30 cells.

value: 1-day-cultured mouse mammary basal cells

value: 1-day-cultured mammary basal cells


title: mammary basal cells pre-culture10.02.2010_Basal cells

description:
5282035042_C
RNA extracted from mouse mammary basal cells sorted at high purity (~95%) by flow cytometry. Basal cells consist predominantly of myoepithelial cells intermixed with rare mammary stem cells which occur at a frequency of 1 in every ~300 basal cells.


title: 7-day-cultured mammary basal cells21.01.2010_7d FAD

description:
5282035042_E
RNA extracted from sorted mouse mammary basal cells cultured for 7 days. 7-day-cultured basal cells contain mammary stem cells at a frequency of 1 in every ~70 cells

value: 7-day-cultured mouse mammary basal cells

value: 7-day-cultured mammary basal cells


title: PBMC_placebo_visit2_rep21

value: Day 1

value: Stratagene Universal Human Reference RNA


title: GP EWS-FLI1 at 8h, rep1

source_name: Mouse GP cells, 8h after transduced with EWS-FLI1 virus

value: embryo joint

value: growth place (GP)-derived cells

value: EWS-FLI1 virus

value: BALB/cAJcl


title: FZ empty at 48h, rep1

value: osteochondrogenic progenitors derived from the facial zone (FZ) of murine long bone

value: empty virus


title: PBMC_placebo_visit4_rep20

value: Day 7


title: 7015mycelia_CHA77treated_rep3

city: Newark

first: Carla

last: Spence

state: Delaware

address: 15 Innovation Way

institute: University of Delaware

hyb_protocol: 1650 ng of Cy-3 labeled cRNA was hybridized to an Agilent Magnaporthe (v2) Gene Expression Microarray 4X44K.  Hybridized arrays were washed.

scan_protocol: Washed, hybrized arrays were scanned.

data_processing: The scanned images were processed using Feature Extraction Software version 10.7 (agilent)

organism: Pyricularia oryzae 70-15

source_name: M.oryzae 7015 mycelia, treated with bacterium CHA77

label_protocol: Samples were labeled using the Low Input Quick Amp labeling kit (Agilent)

growth_protocol: Grown on solid complete medium plates at 25 degrees C for 72 hours

extract_protocol: Samples were ground in liquid nitrogen and RNA was extracted using the Qiagen Rneasy Plant Mini Kit.

treatment_protocol: Plates were co-inculated with a 5 mm fungal plug and a 5 uL droplet of bacteria (10 ^ 6 cells per mL)

value: mycelia

tag: treatment


title: PBMC_placebo_visit3_rep20

tag: agent

value: placebo

value: Day 4


title: 7015mycelia_CHA77treated_rep2


title: GP EWS-FLI1 at 8h, rep2


title: 7015mycelia_CHA77treated_rep1


title: PBMC_placebo_visit2_rep20

tag: timepoint

value: Peripheral blood mononuclear cells


title: FZ EWS-FLI1 at 8h, rep2

source_name: Mouse FZ cells, 8h after transduced with EWS-FLI1 virus

tag: cell type


title: 1-day-cultured mammary basal cells18.02.2010_1d FAD

description:
5282035042_B
RNA extracted from sorted mouse mammary basal cells cultured for 1 day. 1-day-cultured basal cells contain mammary stem cells at a frequency of 1 in every ~30 cells.

value: 1-day-cultured mouse mammary basal cells

value: mammary basal cell

value: female


title: 7-day-cultured mammary basal cells04.03.2010_7d FAD

description:
5282035042_A
RNA extracted from sorted mouse mammary basal cells cultured for 7 days. 7-day-cultured basal cells contain mammary stem cells at a frequency of 1 in every ~70 cells

value: 7-day-cultured mouse mammary basal cells

value: 7-day-cultured mammary basal cells


title: 7015mycelia_CHAOtreated_rep3

source_name: M.oryzae 7015 mycelia, treated with bacterium CHAO

value: CHAO


title: PBMC_placebo_visit4_rep21

source_name: Stratagene Universal Human Reference RNA

tag: reference


title: FZ EWS-FLI1 at 8h, rep1

value: embryo joint


title: 7015mycelia_CHAOtreated_rep2

tag: tissue


title: GP EWS-FLI1 at 8h, rep3

value: growth place (GP)-derived cells


title: FZ EWS-FLI1 at 8h, rep3

value: EWS-FLI1 virus


title: PBMC_placebo_visit4_rep19

value: Stratagene Universal Human Reference RNA


title: 7015mycelia_CHAOtreated_rep1


title: PBMC_placebo_visit3_rep19


title: GP empty at 8h, rep3

source_name: Mouse GP cells, 8h after transduced with empty virus

value: BALB/cAJcl


title: mammary basal cells pre-culture24.02.2010_Basal cells

description:
5282035041_E
RNA extracted from mouse mammary basal cells sorted at high purity (~95%) by flow cytometry. Basal cells consist predominantly of myoepithelial cells intermixed with rare mammary stem cells which occur at a frequency of 1 in every ~300 basal cells.

value: mouse mammary basal cells pre-culture

value: mammary basal cells pre-culture


title: 1-day-cultured mammary basal cells15.01.2010_1d FAD

description:
5282035041_F
RNA extracted from sorted mouse mammary basal cells cultured for 1 day. 1-day-cultured basal cells contain mammary stem cells at a frequency of 1 in every ~30 cells.

value: 1-day-cultured mammary basal cells


title: 7015mycelia_EA105treated_rep3

source_name: M.oryzae 7015 mycelia, treated with bacterium EA105

value: mycelia


title: 7-day-cultured mammary basal cells18.02.2010_7d FAD

description:
5282035041_D
RNA extracted from sorted mouse mammary basal cells cultured for 7 days. 7-day-cultured basal cells contain mammary stem cells at a frequency of 1 in every ~70 cells


title: GP empty at 8h, rep2

value: empty virus


title: 7015mycelia_EA105treated_rep2


title: 7-day-cultured mammary basal cells28.02.2010_7d FAD

description:
5282035041_C
RNA extracted from sorted mouse mammary basal cells cultured for 7 days. 7-day-cultured basal cells contain mammary stem cells at a frequency of 1 in every ~70 cells


title: 1-day-cultured mammary basal cells11.02.2010_1d FAD

description:
5282035041_B
RNA extracted from sorted mouse mammary basal cells cultured for 1 day. 1-day-cultured basal cells contain mammary stem cells at a frequency of 1 in every ~30 cells.


title: PBMC_placebo_visit4_rep17

value: placebo

value: Day 7

value: Peripheral blood mononuclear cells


title: FZ empty at 8h, rep3

source_name: Mouse FZ cells, 8h after transduced with empty virus

value: osteochondrogenic progenitors derived from the facial zone (FZ) of murine long bone


title: 7015mycelia_EA105treated_rep1


title: mammary basal cells pre-culture14.01.2010_Basal cells

description:
5282035041_A
RNA extracted from mouse mammary basal cells sorted at high purity (~95%) by flow cytometry. Basal cells consist predominantly of myoepithelial cells intermixed with rare mammary stem cells which occur at a frequency of 1 in every ~300 basal cells.

value: mammary basal cell

value: female


title: GP empty at 8h, rep1


title: 7015mycelia_Control_rep3

source_name: M.oryzae 7015 mycelia, control

value: control


title: PBMC_placebo_visit2_rep19

value: Day 1


title: PBMC_placebo_visit3_rep17

value: Day 4


title: 7015mycelia_Control_rep2


title: 7015mycelia_Control_rep1


title: GP at 0, rep2

source_name: Mouse GP cells, no treatment

value: embryo joint

value: growth place (GP)-derived cells


title: PBMC_placebo_visit4_rep16

value: Stratagene Universal Human Reference RNA


title: PBMC_placebo_visit2_rep17


title: GP at 0, rep3

value: BALB/cAJcl


title: FZ empty at 8h, rep2


title: BxPC3_JMJD3KD_rep2

city: New York

first: Keisuke

last: Yamamoto

state: NY

address: 550 First Avenue

department: Radiation Oncology

institute: NYU School of Medicine

description: Gene expression after transfection of vector expressing shJMJD3 in BxPC3 cells.

hyb_protocol: Labeled cRNA was incubated with Blocking agent and Fragmentation buffer (Agilent Gene Expression Hybridization Kit) for 30min at 60°C. GE Hybridization Buffer HI-RPM was then added to the mixture. Samples were applied to microarrays using hybridization chambers and hybridized at 65°C for 16h. After hybridization, slides were washed sequentially with Agilent Gene Expression Wash Buffer.

scan_protocol: The hybridized array slides were scanned on an Agilent Microarray Scanner. Scanned images were quantified using Agilent Feature Extraction software (ver. 10.5.1.1).

data_processing: Microarray signal and background information were retrieved using Agilent Feature Extraction software (ver. 10.5.1.1). Extracted intensities were background-corrected and normalized by the quantile normalization method using statistical software R (http://www.R-project.org) and the Bioconductor package “Agi4x44PreProcess” (Pedro Lopez-Romero) (http://www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.html). Probes were filtered based on the Quality Flags provided by Agilent FE using the function "filter.probes" in the "Agi4x44PreProcess" package. Replicated probes were summarized using the function "summarize.probe".

source_name: human pancreatic cancer cell line BxPC3 transfected with vector expressing shJMJD3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500ng RNA using the Quick Amp Labeling Kit (One colour, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: Cells were grown in RPMI with 10% fetal bovine serum, and maintained at 37C in 5% CO2 in a humidified environment.

extract_protocol: Total RNA was extracted from cells with the RNeasy mini kit (Qiagen) following the manufacturer’s instructions, and was quantified by Nanodrop.

treatment_protocol: BxPC3 cells were transfected with either control vector or vector expressing shJMJD3.

tag: cell line

value: pancreatic cancer

tag: transfected vector


title: BxPC3_JMJD3KD_rep1


title: FZ empty at 8h, rep1


title: GP at 0, rep1


title: PBMC_placebo_visit4_rep15


title: BxPC3_JMJD3KD_rep3


title: BxPC3_Ctrl_rep3

description: Gene expression after transfection of control vector in BxPC3 cells.

source_name: human pancreatic cancer cell line BxPC3 transfected with control vector


title: PBMC_placebo_visit3_rep15

source_name: Peripheral blood mononuclear cells, placebo


title: BxPC3_Ctrl_rep2


title: PBMC_placebo_visit2_rep15


title: BxPC3_Ctrl_rep1


title: FZ at 0, rep2

source_name: Mouse FZ cells, no treatment


title: FZ at 0, rep1


title: PBMC_placebo_visit2_rep16


title: PBMC_placebo_visit2_rep14


title: FZ at 0, rep3


title: Ewing's sarcoma 16

source_name: mouse Ewing's sarcoma #4

growth_protocol: Tumors were grown in the subcutaneous space of nude mice

value: Ewing's sarcoma tumor

tag: strain

value: BALB/cAJcl-nu/nu nude mice


title: Ewing's sarcoma 7


title: PBMC_placebo_visit3_rep12


title: PBMC_placebo_visit2_rep11


title: Ewing's sarcoma 23


title: PBMC_placebo_visit4_rep11


title: Ewing's sarcoma 28


title: Ewing's sarcoma 17


title: GR3KR_dex_WITH_15d-PGJ2_6h_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: stably expressing GR3KR

hyb_protocol: Standart Illumina hybridization protocol

scan_protocol: Standart Illumina scanning protocol

data_processing: Obtained data was normalized using VST transformation and RSN normalization  used as standard approach for Illumina arrays with the R/lumi package

source_name: Isogenic HEK293 Cells, dex with 15d-PGJ2 treated, 6 h

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

growth_protocol: Isogenic HEK293 cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B,  and kept at 37 °C in a humidified 95% air/ 5% CO2

extract_protocol: Total RNA was extracted using TriPure (Roche Diagnostics GmbH, Mannheim, Germany) according to manufacture's instructions

treatment_protocol: 3x105x of Isogenic HEK293 cells were seeded at 6-well plates and allowed to grow in steroid-depleted medium (2.5 %  charcoal stripped FBS in DMEM) 36 h and the cells were subsequently treated with 100 nM of dexamethasone in the presence or absence of 5 µM 15d-PGJ2 for 6 h prior extraction of RNA

value: Isogenic Human Embryonal Kidney (HEK293) Cells

value: dexamethasone with 15d-PGJ2

value: 6 h

tag: genotype/variation


title: GR3KR_dex_WITH_15d-PGJ2_6h_rep3

description: stably expressing GR3KR


title: Ewing's sarcoma 15


title: PBMC_placebo_visit3_rep10

value: placebo

value: Peripheral blood mononuclear cells


title: PBMC_placebo_visit4_rep12

value: Day 7


title: PBMC_placebo_visit4_rep10


title: PBMC_placebo_visit2_rep12


title: C16 - Zn-inducible p53 without vs. with constitutive IMPDH II

city: clayton

first: Dave

last: Winkler

address: bayview ave

country: Australia

institute: CSIRO

hyb_protocol: MIT BioMicro Centre

scan_protocol: Arrayworx Biochip Reader

data_processing:
A gene was selected for data analyses only if the mean value of foreground pixels of the spot was greater than the sum of the mean and two standard deviations of the background pixels. For individual gene probe spots, the expression intensities of Cy5 and Cy3 channels were estimated by subtracting mean backgrounds from mean foregrounds.
The ratios of the final gene expression intensities for the asymmetrically self-renewing states to the respective symmetrically self-renewing states were calculated (log10 ratio of [asym/sym]). These ratio values were used for sparse feature selection.
DigitalGenome software (v.1.0)

source_name: tC-2: Asymmetrically self-renewing

label_protocol: MIT BioMicro Centre

extract_protocol: Trizol reagent

treatment_protocol: With 65 micromolar ZnCl2

value: Vector-transfected Ind-8 Zn-inducible p53 MEFs

source_name: tI-3: Symmetrically self-renewing (with p53 expression)

value: IMPDH II-transfected Ind-8 Zn-inducible p53 MEFs


title: PBMC_placebo_visit4_rep14


title: GR3KR_dexamethasone_6h_rep3

description: stably expressing GR3KR

source_name: Isogenic HEK293 Cells, dex treated, 6 h

value: dexamethasone


title: Ewing's sarcoma 14


title: C14 - Zn-inducible p53 without vs. with constitutive IMPDH II


title: Ewing's sarcoma 8


title: PBMC_placebo_visit3_rep9

value: Day 4


title: GR3KR_dexamethasone_6h_rep2

description: stably expressing GR3KR


title: GR3KR_dex_WITH_15d-PGJ2_6h_rep1

description: stably expressing GR3KR


title: C15 - Zn-inducible p53 without vs. with constitutive IMPDH II


title: Ewing's sarcoma 12


title: PBMC_placebo_visit2_rep10

value: Day 1


title: Ewing's sarcoma 4


title: PBMC_placebo_visit4_rep9


title: PBMC_placebo_visit4_rep8


title: PBMC_placebo_visit2_rep9


title: C11 - 32oC-inducible p53 vs. low p53 mouse mammary epithelial cells (MMECs)

hyb_protocol: MIT BIoMicro Centre

scan_protocol: Arrayworx Biochip reader

source_name: 1h-3: Asymmetrically self-renewing

value: 32oC-inducible p53 MMECs

source_name: 1g-1: Symmetrically self-renewing

value: Vector control, low p53-expressing MMECs


title: wtGR_dex_WITH_15d-PGJ2_6h_rep3

description: stably expressing wtGR

value: wtGR


title: GR3KR_dexamethasone_6h_rep1

description: stably expressing GR3KR


title: wtGR_dex_WITH_15d-PGJ2_6h_rep2

description: stably expressing wtGR


title: C13 - Zn-inducible p53 without vs. with constitutive IMPDH II

value: Vector-transfected, Ind-8 Zn-inducible p53 MEFs


title: C12 - 32oC-inducible p53 vs. low p53 mouse mammary epithelial cells (MMECs)


title: C10 - 32oC-inducible p53 vs. low p53 mouse mammary epithelial cells (MMECs)


title: PBMC_placebo_visit2_rep8

source_name: Stratagene Universal Human Reference RNA


title: PBMC_placebo_visit3_rep8

value: Stratagene Universal Human Reference RNA


title: wtGR_dex_WITH_15d-PGJ2_6h_rep1

description: stably expressing wtGR


title: C9 - 32oC-inducible p53 vs. low p53 mouse mammary epithelial cells (MMECs)


title: wtGR_dexamethasone_6h_rep3

description: stably expressing wtGR


title: PBMC_placebo_visit3_rep7


title: wtGR_dexamethasone_6h_rep1

description: stably expressing wtGR

treatment_protocol: 300 000 of Isogenic HEK293 cells were seeded at 6-well plates and allowed to grow in steroid-depleted medium (2.5 %  charcoal stripped FBS in DMEM) 36 h and the cells were subsequently treated with 100 nM of dexamethasone in the presence or absence of 5 µM 15d-PGJ2 for 6 h prior extraction of RNA


title: PBMC_placebo_visit2_rep7


title: C5 - Zn-inducible p53 MEFs with vs. without Zn

source_name: Ind-8: Asymmetrically self-renewing

value: Zn-inducible p53 MEFs

tag: medium

value: Zn-supplemented

source_name: Ind-8: Symmetrically self-renewing

treatment_protocol: Without ZnCl2

value: Zn-free


title: wtGR_dexamethasone_6h_rep2

description: stably expressing wtGR

value: Isogenic Human Embryonal Kidney (HEK293) Cells

tag: time

value: 6 h


title: C6 - Zn-inducible p53 MEFs with vs. without Zn

value: Zn-inducible MEFs

treatment_protocol: Without Zn


title: PBMC_placebo_visit4_rep7

value: placebo

value: Day 7

value: Peripheral blood mononuclear cells


title: LEPRDB/DB6_hindlimb_d1_rep3

city: Boston

first: Stephan

last: Schiekofer

state: MA

address: 700 Albany Street, W611

department: Molecular Cardiology

institute: Boston University School of Medicine

description: hindlimb muscle tissue 1 day after ischemia from male LEPRDB/DB mouse

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: hindlimb muscle tissue

label_protocol: standard Affymetrix procedures

extract_protocol: Ultraspec(TM)-II RNA Isolation System

tag: LEPRDB/DB, male, 8 weeks + 1 day, hindlimb muscle tissue 1 day after ischemia


title: LEPRDB/DB12_hindlimb_d14_rep3

description: hindlimb muscle tissue 7 days after ischemia from male LEPRDB/DB mouse

tag: LEPRDB/DB, male, 8 weeks + 14 days, hindlimb muscle tissue 14 days after ischemia


title: LEPRDB/DB10_hindlimb_d14_rep1


title: LEPRDB/DB8_hindlimb_d7_rep2

tag: LEPRDB/DB, male, 8 weeks + 7 days, hindlimb muscle tissue 7 days after ischemia


title: C7 - Zn-inducible p53 MEFs with vs. without Zn


title: LEPRDB/DB9_hindlimb_d7_rep3


title: LEPRDB/DB5_hindlimb_d1_rep2


title: C4 - Zn-inducible p53 vs. p53-null MEFs

hyb_protocol: MIT BioMicro

label_protocol: MIT BioMicro

source_name: Con-3: Symmetrically self-renewing

value: p53-null control MEFs


title: PBMC_placebo_visit4_rep6

hyb_protocol: The 8 pack format mastermixes were followed (Two color microarray-based gene expression analysis: Low input quick amp labeling (v 6.5, May 2010))

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C US84300231 using protocol GE2_107_Sep09.

label_protocol: Followed the protocol described in Two color microarray-based gene expression analysis: Low input quick amp labeling (v 6.5, May 2010) using 200ng of total RNA


title: PBMC_placebo_visit2_rep6


title: LEPRDB/DB3_hindlimb_d0_rep3

description: hindlimb muscle tissue before ischemia from male LEPRDB/DB mouse

tag: LEPRDB/DB, male, 8 weeks, hindlimb muscle tissue before ischemia


title: LEPRDB/DB7_hindlimb_d7_rep1


title: LEPRDB/DB11_hindlimb_d14_rep2


title: PBMC_placebo_visit3_rep6

value: Day 4


title: C3 - Zn-inducible p53 vs. p53-null MEFs

value: p53-null MEFS


title: C2 - Zn-inducible p53 vs. p53-null MEFs


title: LEPRDB/DB4_hindlimb_d1_rep1


title: PBMC_placebo_visit4_rep5


title: Inoculated_and_control_14dpi_Replicate 5

city: Panama

first: Luis

last: Mejia

address: Roosvelt Ave. Tupper Building – 401

department: Smithsonian Tropical Research Institute

country: Panama

institute: Smithsonian Institution

hyb_protocol: Hybridizations were performed by the Pennsylvania State University Core Genomics Faciliy, according to published facility protocols (http://www.huck.psu.edu/facilities/genomics-up/protocols/nimblegen-protocols).

scan_protocol: Arrays were scanned with an Axon 4000A scanner.

data_processing: Background correction and normalization were performed using the Normexp and print-tip loess methods respectively Ritchie et al 23(20):2700). The avedups function of limma was employed for averaging log2 scale intensity values for duplicate spots from the normalized data.

organism: Theobroma cacao

source_name: Control un-inoculated Theobroma cacao leaves

label_protocol: One µg of total RNA was amplified using mRNA amplification kit (Amino Allyl MessageAmp II™, Ambion, Austin, TX) prior to labeling and hybridization. aRNA was dye coupled with Cy3 or Cy5 (GE Health Care #RPN5661) and subsequently purified according to manufacturer’s instructions.

growth_protocol: Theobroma cacao seedlings used in this experiment were grown in Percival growth chambers (model I35LL, 115 volts, 1/4 Hp, series: 8503122.16, Percival Scientific, Inc., Perry IA) with 12/12 h light/dark photoperiod and temperatures of 30ºC and 26ºC respectively.

extract_protocol: Total RNA was extracted as in Verica et al. Plant Cell Rep. 23(6):404)

treatment_protocol: Seedlings were inoculated four times by spraying conidia (asexual spores) suspended in water (>1X10^6 spore/ml) of endophytic fungus Colletotrichum tropicale as in Mejia et al. Biological Control 46(1):4) to treated seedlings. Leaves from inoculated and un-inoculated seedlings were harvested 14 days post last inoculation (dpi) and placed in RNA stabilizing solution RNAlater until RNA was extracted.

tag: genotype

value: leaf

value: control

source_name: Theobroma cacao leaves inoculated with fungal endophyte Colletotrichum tropicale


title: LEPRDB/DB1_hindlimb_d0_rep1


title: C1 - Zn-inducible p53 vs. p53-null MEFs


title: LEPRDB/DB2_hindlimb_d0_rep2


title: Inoculated_and_control_14dpi_Replicate 4

tag: treatment

value: inoculated with fungal endophyte Colletotrichum tropicale


title: Inoculated_and_control_14dpi_Replicate 3


title: PBMC_placebo_visit3_rep5

first: Phillip

last: Monk

address: Tremona Road

institute: Synairgen Research Ltd

extract_protocol: Total RNA extracted using Qiagen PAXgene RNA extraction kit following manufacturer's instructions

tag: agent


title: Inoculated_and_control_14dpi_Replicate 6


title: WT11_hindlimb_d14_rep2

description: hindlimb muscle tissue 7 days after ischemia from male C57Bl/6 WT mouse

tag: C57Bl/6, male, 8 weeks + 14 days, hindlimb muscle tissue 14 days after ischemia


title: PBMC_placebo_visit4_rep4

tag: timepoint

tag: cell type


title: PBMC_placebo_visit3_rep4

tag: reference


title: Inoculated_and_control_14dpi_Replicate 2

tag: tissue


title: WT12_hindlimb_d14_rep3


title: PBMC_placebo_visit4_rep3


title: PBMC_placebo_visit2_rep5

value: Day 1


title: PBMC_placebo_visit2_rep4

value: Stratagene Universal Human Reference RNA


title: Inoculated_and_control_14dpi_Replicate 1


title: WT9_hindlimb_d7_rep3

tag: C57Bl/6, male, 8 weeks + 7 days, hindlimb muscle tissue 7 days after ischemia


title: WT10_hindlimb_d14_rep1


title: WT8_hindlimb_d7_rep2


title: PBMC_placebo_visit2_rep3


title: PBMC_placebo_visit3_rep3


title: WT6_hindlimb_d1_rep3

description: hindlimb muscle tissue 1 day after ischemia from male C57Bl/6 WT mouse

tag: C57Bl/6, male, 8 weeks + 1 day, hindlimb muscle tissue 1 day after ischemia


title: WT7_hindlimb_d7_rep1


title: RPI_24h_3 (gene)

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were log2 transformed and normalized using RSN normalization from lumi package in R.

source_name: TPC1 cell line, RPI-1 treated

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

extract_protocol: Total RNA with miRNA fraction was extracted from cell lines with miRNeasy mini kit (Qiagen) according to manufacturer's instructions. Subsequently, for gene expression analysis, RNA was purified using the RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer's instruction.

tag: cell line

value: papillary thyroid carcinoma-derived cell line

value: RTK inhibitor RPI-1


title: WT4_hindlimb_d1_rep1


title: WT5_hindlimb_d1_rep2


title: RPI_24h_1 (gene)


title: RPI_24h_2 (gene)


title: WT2_hindlimb_d0_rep2

description: hindlimb muscle tissue before ischemia from male C57Bl/6 WT mouse

tag: C57Bl/6, male, 8 weeks, hindlimb muscle tissue before ischemia


title: PBMC_placebo_visit3_rep2

city: Southampton

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

source_name: Peripheral blood mononuclear cells, placebo


title: PBMC_placebo_visit4_rep1


title: PBMC_placebo_visit4_rep2


title: PBMC_placebo_visit3_rep1


title: WT3_hindlimb_d0_rep3


title: DMSO_24h_1 (gene)

source_name: TPC1 cell line, control

value: DMSO control


title: PBMC_placebo_visit2_rep1


title: DMSO_24h_2 (gene)


title: PBMC_placebo_visit2_rep2


title: DMSO_24h_3 (gene)


title: EA1109_04: WT Lis

status: Public on Jun 29 2014

city: Meguro-ku, Tokyo

first: hideo

last: negishi

address: Komaba 4-6-1

department: Molecular Immunology

institute: University of Tokyo

hyb_protocol: Fragmented and biotinylated cDNA were hybridized for 18hrs at 45˚C on GeneChip Mouse Genome 430 2.0 Array.  Arrays were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method.  The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: infected WT macrophage

label_protocol: Fragmented and biotinylated cDNA were synthesized by Encore® Biotin Module（NuGEN Technologies) from 5ug cDNA according to the manufacturer's instructions.

growth_protocol: Mice were maintaind under specific pathogen-free condition in the animal facility of the University of Tokyo.

extract_protocol:
Total RNA was extruced by using NucleoSpin RNA (TaKaRa)  according to the manufacturer's instructions.
amplification protocol: cDNA were amplified  by Ovation® Pico WTA System V2（NuGEN Technologies) from 20ng total RNA according to the manufacturer's instructions.  Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

treatment_protocol: Mice were injected I.p. with 3ml of 4% thioglycolate (Difco), and peritoneal macrophages were harvested from the peritoneal cavity 3 days after by lavage with cold PBS. Cells were then cultured for 2 hours and infected with Listeria monocytogenes (0.2 moi) for 6 hous in 10% FBS RPMI without antibiotics, and then subjected to microarray analysis.

value: C57B6J :WT

value: peritoneal macrophage

tag: infection

value: infected with Listeria monocytogenes for 6 hours


title: PC-3 L+G, biological rep2 [mRNA]

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description:
PC-3 L+G_2
PC-3 cells treated for 24h with 60μM luteolin (Lut) and 60μM gefitinib (Gef).

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations to Agilent-014850 arrays were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: Scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies). The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: The Subio Platform and Subio Basic Plug-in (v1.15; Subio Inc., Aichi, Japan) was then used to calculate the between-sample fold change analyzed by one-sample t-test, Student T-test.

source_name: PC-3 cells, 60μM luteolin (Lut) and 60μM gefitinib (Gef), 24h

label_protocol: 100 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

growth_protocol: The PC-3 cells were provided by the Japanese Cancer Research Resources Bank (JCRB). The cells were maintained in 5% CO2 at 35°C in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (Hyclone Laboratory), penicillin (100U/mL), and streptomycin (100μg/mL).

extract_protocol: Total RNA was extracted from PC-3 cells 24h following treatment with DMSO, 60μM luteolin (Lut), 60μM gefitinib (Gef) or their co-administration (Lut+Gef) using an miRNeasy Mini kit according to the manufacturer's instructions (Qiagen). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).

treatment_protocol: About 1.0x10^3 PC-3 cells plated in a petri dish (diameter, 3.5 cm) were incubated at 35°C overnight, then gefitinib (iressa), luteolin and/or resveratrol dissolved in DMSO were added into the medium.

value: luteolin+gefitinib

tag: treatment duration


title: EA1109_05: MyD88KO Lis

source_name: infected MyD88-/- macrophage


title: PC-3 Gefitinib, biological rep2 [mRNA]

description:
PC-3 Gefitinib_2
PC-3 cells treated for 24h with 60μM gefitinib (Gef).

source_name: PC-3 cells, 60μM gefitinib (Gef), 24h

value: gefitinib


title: EA1109_01: WT(-)

source_name: uninfected WT macrophage

value: uninfected


title: WT1_hindlimb_d0_rep1


title: PC-3 Luteolin, biological rep2 [mRNA]

description:
PC-3 Luteolin_2
PC-3 cells treated for 24h with 60μM luteolin (Lut).

source_name: PC-3 cells, 60μM luteolin (Lut), 24h

value: luteolin


title: PC-3 L+G, biological rep2 [miRNA]

hyb_protocol: Probes were hybridized to Agilent-041686 arrays using miRNA Hybridization Kit at 55°C for 20 hours with rotation. Then, the slides were washed by Gene Expression Wash Buffer 1 at room temperature for 5 minutes and by Gene Expression Wash Buffer 2 at 37°C for 5 minutes.

scan_protocol: After hybridization and washing, the slides were scanned using an Agilent scanner (G2505C). Images were extracted using Agilent Feature Extraction software (ver. 10.7.3).

data_processing: Data were processed by the Agilent GeneSpring GX software (ver. 12.6). Total gene signal from GeneView data files extracted with default settings in Agilent Feature Extraction was used as signal for miRNAs. Differences in miRNA expressions were normalized using the PC-3 treated DMSO sample as a control and determined as if the fold change of expression values was >2.0 and the p value was <0.05 using Student's t test for further analysis.

label_protocol: 100 ng of aliquots of total RNA was used for making miRNA probes according to the Agilent protocol (ver. 2.4). Briefly, total RNA was dephosphorylated with calf intestine alkaline phosphatase, denatured with dimethyl sulfoxide and labeled with Cyanine 3-pCp using T4 RNA ligase using the miRNA Labeling Kit.


title: PC-3 Ctrl, biological rep2 [mRNA]

description:
PC-3 Ctrl_2
PC-3 cells before treatment (0h).

source_name: PC-3 cells, before treatment (0h)


title: PC-3 DMSO, biological rep2 [mRNA]

description:
PC-3 DMSO_2
PC-3 cells treated for 24h with DMSO.

source_name: PC-3 cells, DMSO, 24h

value: DMSO


title: PC-3 Gefitinib, biological rep2 [miRNA]


title: PC-3 L+G, biological rep1 [mRNA]

description:
PC-3 L+G_1
PC-3 cells treated for 24h with 60μM luteolin (Lut) and 60μM gefitinib (Gef).


title: PC-3 Luteolin, biological rep2 [miRNA]


title: JH response at 48 hours after treatment

city: Chongqing

first: Daojun

last: Cheng

address: No 2, Tiansheng, Beibei

institute: Southwest University

description: JH response at 48 Hat

hyb_protocol: Cy5-dCTP-labeled (Test samples) and Cy3-dCTP-labeled (Control samples) double-stranded cDNA were dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from images using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing: Lowess-normalized, background-subtracted data obtained from processed Red signal (Test) and processed Green signal (Control). The software from CapitalBio Crop was used. Cluster 3.0 and Mev software (version 4.2.01) were also used in further data processing. Probes with signal intensity lower than 400 after subtracting the background were considered as unexpressed genes.

organism: Bombyx mori

source_name: JHA treatment

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: The silkworm strain Dazao (p50) with a characteristic of tetramolter (four molting times during the larval stage) was used in our experiments. The larvae were reared on fresh mulberry leaves at 25°C under a 12 hour light/12 hour dark photoperiod.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: The JHA methoprene were applied to newly molted fourth instar larvae 24 hours after molting. Silkworm larvae treated with the same dose of pure acetone were used as a control. Integument samples were respectively collected from 20 silkworm larvae at different time points after JHA treatment and acetone treatment, including 12 Hat, 24 Hat, 36 Hat, and 48 Hat.

tag: treament

value: 48 hours after JHA treatment

value: integument

tag: strain

value: Dazao (p50)

tag: developmental stage

source_name: Acetone  treatment

value: 48 hours after acetone treatment


title: PC-3 Luteolin, biological rep1 [mRNA]

description:
PC-3 Luteolin_1
PC-3 cells treated for 24h with 60μM luteolin (Lut).


title: C8 - Zn-inducible p53 MEFs with vs. without Zn

source_name: Ind-8: Asymmetrically self-renewing

value: Zn-inducible p53 MEFs

tag: medium

value: Zn-supplemented

source_name: Ind-8: Symmetrically self-renewing

value: Zn-free


title: JH response at 36 hours after treatment

description: JH response at 36 Hat

value: 36 hours after JHA treatment

value: fourth instar larvae 24 hours after molting.

tag: treatment

value: 36 hours after acetone treatment


title: JH response at 24 hours after treatment

description: JH response at 24 Hat

value: 24 hours after JHA treatment

value: 24 hours after acetone treatment


title: PC-3 L+G, biological rep1 [miRNA]

value: luteolin+gefitinib


title: PC-3 DMSO, biological rep1 [mRNA]

description:
PC-3 DMSO_1
PC-3 cells treated for 24h with DMSO.


title: PC-3 Gefitinib, biological rep1 [miRNA]

description:
PC-3 Gefitinib 1
PC-3 cells treated for 24h with 60μM gefitinib (Gef).

value: gefitinib


title: PC-3 Ctrl, biological rep1 [mRNA]

description:
PC-3 Ctrl_1
PC-3 cells before treatment (0h).


title: PC-3 DMSO, biological rep2 [miRNA]


title: JH response at 12 hours after treatment

description: JH response at 12 Hat

value: 12 hours after JHA treatment

value: 12 hours after acetone treatment


title: PC-3 Luteolin, biological rep1 [miRNA]

value: luteolin


title: CD99 transfected U-2 cells (U-2/CD99wt 136) vs U-2OS parental cell lines

city: Bologna

first: Katia

last: Scotlandi

address: Via di Barbiano 1/10

institute: Istituto Ortopedico Rizzoli

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Hybridized slides were scanned using GenePix 4000B microarray scanner (Axon Instruments) that acquires data at two wavelengths simultaneously  [532nm (green) and 635nm (red)]. Signal and background intensities for both channels were calculated with GenePix 3.0 (Axon Instruments).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. (BRB-ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools.html).

source_name: Osteosarcoma CD99 transfected U-2 cell line wt136

label_protocol: Total RNA was used to obtain labelled cRNA, according to the manufacturer's instructions (Low RNA Input Fluorescent Linear Amplification Kit-Agilent Technologies).

growth_protocol: Parental cell lines were maintained in IMDM containing 10% FBS, whereas 500 g/ml neomycin was added to tranfectant cell lines medium.

extract_protocol: Total RNA was extracted using the TRIzol extraction kit (Invitrogen Life Technologies, Paisley, UK).

tag: transfection

value: Transfected with CD99 wild-type

source_name: U-2OS parental cells

value: Osteosarcoma U-2OS parental cell line [control]


title: PC-3 DMSO, biological rep1 [miRNA]

value: DMSO


title: D20- vs. D20+

status: Public on Jun 28 2014

city: Langen

first: Sunitha

last: Joseph Myladoor

state: Hessen

department: Divison of Medical Biotechnology

institute: Paul-Ehrlich-Institut

hyb_protocol: Corresponding Cy3- and Cy5-labeled cRNAs were combined in hybridization buffer and samples were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarray (4x44K) using Agilent's recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT, followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System G2505C US22502695 (Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.5.1.1) was used to read out and process the microarray image files.

label_protocol: 100 ng of each RNA was used as template to produce Cy3- and Cy5-labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol.

growth_protocol: Monocytes were cultured overnight in VLE-RPMI 1640 medium supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), L-glutamine (200 mM), non-essential amino acids (100x), 10 ml/L OPI (oxaloacetate, pyruvate and insulin) and 10% human AB serum.

extract_protocol: RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

treatment_protocol: 1x10e6 cells per well were treated with VLP or VLP+Vpx at MOI equivalents of 1 for 6 hours.

value: monocytes

value: VLP

tag: donor

value: VLP+Vpx


title: D14- vs. D14+


title: D16- vs. D16+


title: CD99 transfected U-2 cells (U-2/CD99wt 57) vs U-2OS parental cell lines_biological replicate

source_name: Osteosarcoma CD99 transfected U-2 cell line wt57


title: Sus_scrofa_CB_expr_HX12_PR39_1

city: Hangzhou

first: Xi

last: Xia

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Feed Science

institute: Zhejiang University

description: The IPEC-J2 cell line is a non-transformed intestinal cell line originally derived from jejunal epithelia isolated from a neonatal, unsuckled piglet

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

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

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

organism: Sus scrofa

source_name: intestinal epithelial cell line

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

growth_protocol: IPEC-J2 cells were grown in Hams F-12 medium supplemented with 5% fetal bovine serum and maintained in an atmosphere of 5% CO2 at 37

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol:
Cells grown to confluence , and then 12.5g/ml PR-39 were added into wells and cultured with cells for 4 hours.
Cells grown to confluence , and then 12.5g/ml PR-39 were added into wells and cultured with cells for 4 hours.


title: Sus_scrofa_CB_expr_HX12_PR39_2


title: CD99 transfected U-2 cells (U-2/CD99wt 57) vs U-2OS parental cell lines

value: Osteosarcoma CD99 transfected U-2 cell line wt57


title: Sus_scrofa_CB_expr_HX12_CTL1

treatment_protocol:
No treatment
Cells grown to confluence , and then 12.5g/ml PR-39 were added into wells and cultured with cells for 4 hours.


title: D11- vs. D11+


title: Sus_scrofa_CB_expr_HX12_CTL3


title: Sus_scrofa_CB_expr_HX12_PR39_3


title: KO 2A

city: Saint Louis

first: David

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

hyb_protocol: Performed using standard Illumina protocol on Illumina MouseWG-6 v2.0 bead arrays by the Genome Technology Access Center (GTAC) at Washington University.

scan_protocol: Standard Illumina protocol for bead arrays.

data_processing: Background subtraction and cubic spline normalization and differential expression in the fornical conjunctival epithelium performed using Illumina Genome Studio software.

source_name: Ffr2 KO conjunctival epithelium

label_protocol: The resulting cDNA was biotin labeled using the Illumina biotinylation kit.

growth_protocol: Pregnant mice were euthanized and embryos were removed at E14.5.

extract_protocol: Total RNA was extracted and purified from the prospective lens tissue obtained from one embryo using a Qiagen RNeasy Microkit (Qiagen# 74004). 15 ng of total RNA was amplified to produce 3-5 μg of cDNA using Nugen WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies Inc, #3300-12).

treatment_protocol: Embryos were frozen in OCT and sectioned at 10 microns. Laser microdissection of the fornical region of the conjunctival epithelium on a Leica LMD-6000 system after slides were dipped in 70% ethanol at 4 °C for 1 min, washed in RNase-free water twice for 30 s, rinsed in 95% ethanol, and stained in Eosin Y. Stained samples were washed in 95% ethanol and dehydrated in 100% ethanol and xylene.

tag: strain/background

value: mixed background (FVB; 129)

tag: genotype/variation

value: Fgfr2 fx/fx; Le-Cre-positive (Fgfr2-/-)

value: fornical conjunctival epithelium


title: D9- vs. D9+

tag: cell type


title: WT 1A

source_name: WT conjunctival epithelium

value: wild type

tag: tissue


title: WT 1C


title: D7- vs. D7+


title: Sus_scrofa_CB_expr_HX12_CTL2


title: D8- vs. D8+


title: Skin_WT_mouse4

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

description: Gene expression after 2 months tamoxifen treatment, normal skin control wild type mice

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

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

source_name: Skin, wild type, mouse 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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: Mice carrying a tamoxifen inducible Cre-mediated recombination system driven by the human keratin 14 promoter (K14CreER mice) from The Jackson Laboratory [Stock Number 005107, STOCK Tg(KRT14-cre/ERT)20Efu/JK14Cre] were crossed with mice carrying loxP sites surrounding Gnas exon 1 (Chen, M. et al; J Clin Invest, 2005, 115:3217-32275).

extract_protocol: Total skin RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instruction.

treatment_protocol: Mice were treated with tamoxifen (1mg per mouse, per day, in corn oil) applied by gavage to one month old mice for 5 consecutive days to induce deletion. Mice positive for K14CreER and homozygous for loxP Gnas were knockout for epidermal Gnas (Gnas eKO) wile mice positive for K14CreER but not carrying any copy of loxP Gnas were considered as control wild type mice (WT).

value: skin

tag: disease status

value: Normal

tag: genotype

value: wildtype


title: Skin_BCC_mouse2

description: Gene expression after 2 months tamoxifen treatment, basal cell carcinoma Gnas eKO mice

source_name: Skin, knockout, mouse 2

value: Basal cell carcinoma

value: Gnas knockout


title: Skin_BCC_mouse4

source_name: Skin, knockout, mouse 4


title: KO 2B


title: Skin_BCC_mouse1

source_name: Skin, knockout, mouse 1


title: KO 2C


title: Skin_BCC_mouse3

source_name: Skin, knockout, mouse 3


title: WT 1B


title: WT dorsal

data_processing: Background subtraction and cubic spline normalization and differential expression in the combined dorsal, temporal and nasal epithelium performed using Illumina Genome Studio software.

source_name: WT dorsal conjunctival epithelium

treatment_protocol: Embryos were frozen in OCT and sectioned at 10 microns. Laser microdissection of the conjunctival epithelium on a Leica LMD-6000 system after slides were dipped in 70% ethanol at 4 °C for 1 min, washed in RNase-free water twice for 30 s, rinsed in 95% ethanol, and stained in Eosin Y. Stained samples were washed in 95% ethanol and dehydrated in 100% ethanol and xylene.

value: dorsal conjunctival epithelium


title: Skin_WT_mouse3

source_name: Skin, wild type, mouse 3


title: WT nasal

source_name: WT nasal conjunctival epithelium

value: nasal conjunctival epithelium


title: Skin_WT_mouse2

source_name: Skin, wild type, mouse 2


title: WT temporal

source_name: WT temporal conjunctivalepithelium

value: temporal conjunctival epithelium


title: Caco-2 sample 3 = sample treated with IL-8

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

hyb_protocol: The labelled RNA was hybridised to a GeneChip Hu133 Plus2 array (Affymetrix, Santa Clara, CA), washed, and stained. Detailed methods for the labelling and subsequent hybridisations to the arrays are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix.

scan_protocol: The GeneChip Hu133 Plus2 array was scanned on an Affymetrix GeneChip 3000 7G scanner. Detailed methods are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix

data_processing: Packages from the Bioconductor project, integrated in an in-house developed on-line management and analysis database for multiplatform microarray experiments, were used for analysing the scanned Affymetrix arrays (Gentleman et al., 2004; Gavai et al, submitted).

source_name: epithelial cell line Caco-2 BBE (CRL 2102), treated with 100 pg/ml IL-8 for 6 hours

label_protocol: Total RNA (500 ng) extracted fromCaco-2 cells was labelled using the GeneChip 3’ IVT Express kit (cat. no. 901229).

growth_protocol: Caco-2 cells were grown in DMEM (Invitrogen) containing Glutamax and supplemented with 10% heat-inactivated fetal bovine serum (PAA laboratories, Colbe, Germany), 100 U/ml penicillin and 100 µg/ml streptomycin (Sigma, St. Louis, MO) in 6-wells microtiter plates (Costar) until polarised (14 days), maintained at 37°C in a humidified 5% CO2/95% O2 atmosphere.

extract_protocol: Total RNA was extracted from Caco-2 cell line samples with TRIzol reagent, purified and DNAse treated using the RNeasy mini kit (Qiagen, Venlo, the Netherlands) and DNase (Qiagen, Venlo, the Netherlands) following the manufacturer’s instructions. RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only if samples showed intact bands corresponding to the 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RIN (RNA integrity number) above 8.0.

treatment_protocol: Cell monolayers were treated with 100 pg/ml CXCL8, added to the cells diluted in culture medium. After 6 hours of incubation, Caco-2 cells were incubated with TriZol reagens until lysis was complete, then RNA extraction and purification were performed

value: epithelial

tag: cell line

value: Caco-2 BBE (CRL 2102)


title: KO dorsal

source_name: Sox9 KO dorsal conjunctival epithelium

value: Sox9 fx/fx; Le-Cre-positive (Sox9-/-)


title: KO temporal

source_name: Sox9 KO temporal conjunctival epithelium


title: ER-MXD3 - Time 0 - dye swap

city: Davis

first: Elva

last: Diaz

state: CA

address: 451 Health Sciences Drive GBSF 3409A

department: Pharmacology

institute: UC Davis

hyb_protocol: Hybridization was done with Ambion's SlideHyb buffers according to manufacturer's instructions. Subsequently, slides were washed according to manufacturer's instructions.

scan_protocol: Microarrays were scanned using an Axon GenePix 4000B microarray scanner (Molecular Devices) and feature extraction was conducted using GenePix Pro 6.0

data_processing: Data analysis was done in Excel. The data in the table represents each test condition normalized to reference.

label_protocol: Subsequent reverse transcription and labeling reactions were conducted with Amino Allyl MessageAmp II aRNA Kit (Ambion)

growth_protocol: DAOY cells (ATCC) were cultured in a standard humidified incubator (5% CO2, 37°C). Culture media for DAOY (DAOY media) consisted of minimum essential media (Invitrogen) supplemented with 10% Fetal Bovine Serum (Invitrogen), 1 mM Sodium Pyruvate (Invitrogen), 100 µg/ml Penicillin/Streptomycin (Invitrogen). Stable cell lines were maintained with DAOY media supplemented with 800 µg/ml of G418 Sulfate (Cellgro).

extract_protocol: Total RNA was extracted using Qiagen's RNeasy kit

treatment_protocol: Cells were treated with either ethanol vehicle control or 1µM 4-OHT

value: DAOY

value: brain/cerebellum

value: medulloblastoma

tag: expression construct

value: Ethanol

source_name: pool of all RNA


title: Caco-2 sample 1 = sample treated with IL-8


title: ER-MXD3 - 12 hours 4-OHT - dye swap

source_name: DAOY_ER-MXD3_12 hours of 1µM 4-OHT

value: 12 hours of 1µM 4-OHT


title: ER-MXD3.E66D - Time 0 - dye swap


title: ER-MXD3 - 72 hours 4-OHT - dye swap

source_name: DAOY_ER-MXD3_72 hours of 1µM 4-OHT

value: 72 hours of 1µM 4-OHT


title: Caco-2 sample 2 = sample treated with IL-8


title: ER-MXD3.E66D - 72 hours 4-OHT - dye swap

source_name: DAOY_ER-MXD3.E66D_72 hours of 1µM 4-OHT


title: ER-MXD3.E66D - 12 hours 4-OHT - dye swap

source_name: DAOY_ER-MXD3.E66D_12 hours of 1µM 4-OHT


title: BmSoxE Knockdown Replicate 3

first: Ling

last: Wei

address: No 2, Tiansheng street, Beibei district

description: Biological replicate 3 of 3

hyb_protocol: Cy5-dCTP-labeled and Cy3-dCTP-labeled double-stranded cDNA were dissolved in 80μl hybridization solution containing 3xSSC, 0.2%SDS, 5xDenhart's, and 25% formamide. The slides were covered with a LifterSlip coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42C for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42C for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

data_processing: Lowess-normalized, background-subtracted data obtained from processed signals in both test (knockdown of BmSoxE gene) and control (knockdown of EGFP gene). The software from CapitalBio Crop was used. Cluster 3.0 and Mev software (version 4.2.01) were also used in further data processing. Probes with signal intensity lower than 400 after subtracting the background were considered as unexpressed genes.

source_name: Knockdown of BmSoxE gene in silkworm BmN4-SID1 cells

growth_protocol: BmN4-SID1 cells was cultured at 27 ºC in IPL-41 medium (Sigma) supplemented with 10% fetal bovine serum (FBS) (Gibco).

treatment_protocol: An RNA interference (RNAi) experiment was performed by adding dsRNA specific for the BmSCE gene into the cultured medium. BmN4-SID1 cells were harvested at 7 days post-incubation.

value: knockdown of BmSoxE gene

source_name: Knockdown of EGFP gene in silkworm BmN4-SID1 cells

value: knockdown of EGFP gene


title: Skin_WT_mouse1

source_name: Skin, wild type, mouse 1

value: skin

value: Normal

value: wildtype


title: Caco-2 sample 3 = control sample

source_name: epithelial cell line Caco-2 BBE (CRL 2102), treated with medium control for 6 hours


title: ASP261-1

status: Public on Jun 27 2014

city: Hamamatsu

first: Mahesh

last: Mundalil Vasu

state: Shizuoka

address: 1-20-1 Handayama, Higashi Ward

department: Department of Psychiatry

institute: Hamamatsu University School of Medicine

description: Test

data_processing: Data Analysis: ΔΔCt method for the relative quantification of miRNAs. Normalization: A randomly chosen control sample was amplified in each plate and used as an inter-plate calibrator to correct for the experimental differences among consecutive PCR runs. The qPCR data was first subjected to inter-plate calibration, followed by C.elegans miR-39 (detection of the spike-in control) calibration. The expression of miR-16, an miRNA highly abundant in the red blood cells, was analyzed in each sample to examine the extent of hemolysis in the serum. Any sample that showed significant hemolysis (the value of Ct invariant miRNA – Ct miR16 was greater than 5) was omitted from further analyses. Finally, the qPCR data was normalized to the average of three invariantly expressed miRNAs, let-7a, miR-191-5p and miR-103a-3p. Among these, miR-191-5p and miR-103a-3p were selected on the basis of their performance as invariant miRNAs in the neurological array and custom array, respectively, while let-7a has been widely reported as an invariant miRNA in blood. The fold change in gene expression between the control and autism groups was determined by the Ct method of relative quantification.

label: SYBR Green

source_name: Serum, Autism

label_protocol: Two microliters of each RNA sample was used for cDNA synthesis using the miScript ІІ RT kit (QIAGEN). The reverse transcription reaction mix (20 μl) was prepared using Hispec buffer (for selective conversion of mature miRNAs into cDNA), nucleics mix, RT mix and RNase free water. The reaction mixture was incubated for 60 min at 37ºC, followed by denaturation for 5 min at 95ºC. Ten microliters of qPCR reaction mixture was prepared with a universal primer, primer assay, Template cDNA and RNase free water. All the qPCR reactions were performed in triplicate with the following cycling conditions: 95ºC →15 min, followed by 40 cycles of 94ºC →15 sec, 55ºC →30 sec and 70ºC → 30 sec.

extract_protocol: Total RNA was extracted from serum samples using MiRNeasy Serum/Plasma Kit (QIAGEN GmbH, Hilden, Germany)

tag: diagnosis

value: Autism

tag: age (yrs)


title: ASP269-1a

description: Test


title: ASP263-1

description: Test


title: ASP264-1

description: Test


title: ASP262-1

description: Test


title: ASP267-1

description: Test


title: ASP256-1

description: Test


title: ASP252-1a

description: Test


title: BmSoxE Knockdown Replicate 2

description: Biological replicate 2 of 3


title: ASP250-1

description: Test


title: ASP248-1b

description: Test


title: ER-MXD3 - 12 hours 4-OHT


title: ASP260-1

description: Test


title: KO nasal

source_name: Sox9 KO nasal conjunctival epithelium

value: mixed background (FVB; 129)

value: nasal conjunctival epithelium


title: ER-MXD3.E66D - 12 hours 4-OHT


title: ASP252-1b

description: Test


title: ASP252-1c

description: Test


title: ASP245-1a

description: Test


title: ASP224-1

description: Test


title: ASP229-1

description: Test


title: ASP233-1

description: Test


title: ASP242-1

description: Test


title: Caco-2 sample 2 = control sample

value: epithelial


title: ASP223-1

description: Test


title: ER-MXD3 - 72 hours 4-OHT


title: ER-MXD3.E66D - 72 hours 4-OHT


title: BmSoxE Knockdown Replicate 1

description: Biological replicate 1 of 3


title: ASP219-1b

description: Test


title: PC-3 Gefitinib, biological rep1 [mRNA]

source_name: PC-3 cells, 60μM gefitinib (Gef), 24h

value: gefitinib

tag: treatment duration


title: ASP219-1a

description: Test


title: ASP218-1

description: Test


title: ASP248-1a

description: Test


title: ASP239-1

description: Test


title: ASP213-1

description: Test


title: Caco-2 sample 1 = control sample

value: Caco-2 BBE (CRL 2102)


title: ER-MXD3 - Time 0

value: DAOY


title: ASP175-1a

description: Test


title: ASP174-1

description: Test


title: ASP166-1

description: Test


title: ASP222-1

description: Test


title: ASP168-1

description: Test


title: ASP155-1

description: Test


title: ASP111-1

description: Test


title: ASP150-1

description: Test


title: ASP109-1a

description: Test


title: ASP107-1

description: Test


title: ASP102-1

description: Test


title: ASP215-1

description: Test


title: ASP100-1

description: Test


title: ER-MXD3.E66D - Time 0

value: brain/cerebellum


title: ASP091-1

description: Test


title: ASP079-1

description: Test


title: ASP078-1b

description: Test


title: ASP078-1a

description: Test


title: ASP058-1

description: Test


title: ASP072-1

description: Test


title: Healthy control c2

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol. Samples were hybridized on Human U133 Plus 2.0 Arrays (using GeneTitan platform).

scan_protocol: Scanning was performed on a 7th generation GeneChip Scanner 3000, and the Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.

data_processing: RMA normalization was performed using Expression Console software.

source_name: Whole Blood of healthy control

label_protocol: Total RNA sample quality was evaluated by spectrophotometer to determine quantity, protein contamination and organic solvent contamination, and an Agilent 2100 Bioanalyzer was used to check for RNA degradation. Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol.

extract_protocol: RNA was isolated using the RiboPure-Blood kit (Ambion) and alpha and beta globin mRNA was depleted by GLOBINclear™ Kit (Ambion) according to the manufacturer’s protocol. All RNA samples were checked for purity using a ND-1000 spectrophotometer (NanoDrop Technologies) and for integrity by electrophoresis on a 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: Blood was collected on CPT tubes (Vacutainer® with Sodium Citrate; BD). Whole blood specimens were preserved on RNALater buffer (Ambion) and stored in -80oC

tag: subject id

tag: infection

value: control

tag: status

value: whole blood


title: ASP057-1

description: Test


title: Healthy control c9


title: ASP056-1

description: Test


title: ASP055-1b

description: Test


title: Healthy control c6


title: ASP050-1

description: Test


title: Healthy control c4


title: Healthy control c5


title: Healthy control c1


title: Healthy control c3


title: Convalescent Patient 55

source_name: Whole Blood of Dengue infected patient at convalescent time point

value: DENV

value: convalescent


title: Convalescent Patient 49


title: Convalescent Patient 80


title: Convalescent Patient 54


title: Healthy control c7


title: Healthy control c8


title: ASP039-1

description: Test


title: ASP020-1

description: Test


title: ASP019-1

description: Test


title: ASP010-1

description: Test


title: Convalescent Patient 44


title: Convalescent Patient 45


title: ASP006-1

description: Test


title: Convalescent Patient 48


title: Convalescent Patient 41


title: Convalescent Patient 47


title: HHCC028

description: Control

source_name: Serum, Control


title: HHCC027

description: Control


title: ASP011-1

description: Test


title: HHCC022

description: Control


title: HHCC164

description: Control


title: Convalescent Patient 39


title: Convalescent Patient 34


title: Convalescent Patient 38


title: HHCC163

description: Control


title: Convalescent Patient 33


title: Convalescent Patient 36


title: HHCC156

description: Control


title: HHCC159

description: Control


title: Convalescent Patient 3


title: Convalescent Patient 37


title: HHCC152

description: Control


title: Convalescent Patient 35


title: Convalescent Patient 6


title: HHCC150

description: Control


title: HHCC148

description: Control


title: HHCC140

description: Control


title: HHCC131

description: Control


title: Convalescent Patient 4


title: HHCC129

description: Control


title: Dengue Fever Patient 68

source_name: Whole Blood of Dengue infected patient at acute infection time point

value: DF


title: Dengue Fever Patient 80


title: Dengue Hemorrhagic Fever Patient 60

value: DHF


title: Dengue Fever Patient 66


title: Dengue Fever Patient 47


title: Dengue Fever Patient 44


title: Dengue Fever Patient 54


title: Dengue Hemorrhagic Fever Patient 48


title: HHCC125

description: Control


title: Dengue Hemorrhagic Fever Patient 49


title: HHCC126

description: Control


title: Dengue Fever Patient 55


title: HHCC124

description: Control


title: HHCC123

description: Control


title: HHCC121

description: Control


title: HHCC119

description: Control


title: HHCC128

description: Control


title: HHCC112

description: Control


title: HHCC114

description: Control


title: HHCC109

description: Control


title: HHCC110

description: Control


title: Dengue Fever Patient 43


title: Dengue Hemorrhagic Fever Patient 45


title: Dengue Hemorrhagic Fever Patient 40


title: HHCC105

description: Control


title: Dengue Fever Patient 42


title: Dengue Fever Patient 37